diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 9ef5896ca98fbc9c4af419abaf623dd727eb9423..f3190afa4fc2bcab9b4c67b09c1e55e73f2c4bd5 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -400,7 +400,7 @@ build_jar:
- DEBIAN_FRONTEND=noninteractive apt-get install -y nodejs
- mvn clean compile install -DskipTests=true
- echo "logger.minerva.level = info" >> web/src/test/resources/log4j2.properties
- - mvn install -pl web
+ - mvn install -pl web -Dtest="*Test#testDocs*"
- cp web/target/*exec.jar minerva.jar
test:dependency_conflict:
diff --git a/model/src/main/java/lcsb/mapviewer/model/plugin/Plugin.java b/model/src/main/java/lcsb/mapviewer/model/plugin/Plugin.java
index e5c0336ed10ea7082864d593990aabac769ed244..a7854a0958b4018a502d410ddcf22d183510bc51 100644
--- a/model/src/main/java/lcsb/mapviewer/model/plugin/Plugin.java
+++ b/model/src/main/java/lcsb/mapviewer/model/plugin/Plugin.java
@@ -12,6 +12,7 @@ import javax.persistence.CollectionTable;
import javax.persistence.Column;
import javax.persistence.ElementCollection;
import javax.persistence.Entity;
+import javax.persistence.FetchType;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;
@@ -76,7 +77,7 @@ public class Plugin implements MinervaEntity {
/**
* List of urls from which plugin can be downloaded.
*/
- @ElementCollection
+ @ElementCollection(fetch = FetchType.EAGER)
@CollectionTable(name = "plugin_urls", joinColumns = @JoinColumn(name = "plugin_id"))
@Column(name = "url")
@OrderBy("idx")
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/plugin/PluginDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/plugin/PluginDao.java
index 0369e9f960c7d9c62229b358de6dc7ca0a6d9d7e..4d147a64e5ba9370e83f3ea5e119a61a6c6b3f8c 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/plugin/PluginDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/plugin/PluginDao.java
@@ -37,6 +37,9 @@ public class PluginDao extends BaseDao<Plugin, PluginProperty> {
if (key.equals(PluginProperty.DEFAULT_VALUE)) {
final Predicate predicate = builder.and(root.get("isDefault").in(filterOptions.get(key)));
predicates.add(predicate);
+ } else if (key.equals(PluginProperty.PUBLIC_VALUE)) {
+ final Predicate predicate = builder.and(root.get("isPublic").in(filterOptions.get(key)));
+ predicates.add(predicate);
} else {
throw new InvalidArgumentException("Unknown property: " + key);
}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/plugin/PluginProperty.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/plugin/PluginProperty.java
index 79b1ba0c9d544774d50d40003259f446092dec8e..84a1ab28c9c1c757c693832b3c3dd2b6d74b1294 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/plugin/PluginProperty.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/plugin/PluginProperty.java
@@ -5,4 +5,5 @@ import lcsb.mapviewer.persist.dao.MinervaEntityProperty;
public enum PluginProperty implements MinervaEntityProperty<Plugin> {
DEFAULT_VALUE,
+ PUBLIC_VALUE,
}
diff --git a/web/src/main/asciidoc/converter.adoc b/web/src/main/asciidoc/converter.adoc
index 0c357e2f0e46f87bfe70aee2a8b06ab4097d8608..dadf64aa48e1ff4ef9e0d5822c51fef0563ac1b3 100644
--- a/web/src/main/asciidoc/converter.adoc
+++ b/web/src/main/asciidoc/converter.adoc
@@ -6,60 +6,80 @@ v{project-version} {build-time}
Conversion API provides access to MINERVA’s ability convert between different systems biology network formats and to export of layouts to different graphical formats.
-
== Conversion to systems biology formats
=== List available formats
+
==== CURL sample
+
include::{snippets}/converter/list_formats/curl-request.adoc[]
==== Response Fields
+
include::{snippets}/converter/list_formats/response-fields.adoc[]
==== Sample Response
-include::{snippets}/converter/list_formats/response-body.adoc[]
+include::{snippets}/converter/list_formats/response-body.adoc[]
=== Convert network from an input format to an output format
+
==== CURL sample
+
include::{snippets}/converter/format_conversion/curl-request.adoc[]
==== Path Parameters
+
include::{snippets}/converter/format_conversion/path-parameters.adoc[]
== Convert network from an input format to an output image
=== List available formats
+
==== CURL sample
+
include::{snippets}/converter/list_image_formats/curl-request.adoc[]
==== Response Fields
+
include::{snippets}/converter/list_image_formats/response-fields.adoc[]
==== Sample Response
-include::{snippets}/converter/list_image_formats/response-body.adoc[]
+include::{snippets}/converter/list_image_formats/response-body.adoc[]
=== Convert network from an input format to an output image
+
==== CURL sample
+
include::{snippets}/converter/image_conversion/curl-request.adoc[]
==== Path Parameters
+
include::{snippets}/converter/image_conversion/path-parameters.adoc[]
== Merging of maps
=== Merge
-This API call allows to merge few files into one. Layout of merged map files will be a simple matrix. By default all notes are removed from maps (it's impossible to merge them properly in formats like SBML/CellDesigner because there is one Species with the notes and alias to it in the whole diagram). Minerva can be asked to keep the notes by providing custom header "X-MINERVA-KEEP-NOTES: true", but the notes in output files might not be properly defined.
+
+This API call allows to merge few files into one.
+Layout of merged map files will be a simple matrix.
+By default, all notes are removed from maps (it's impossible to merge them properly in formats like SBML/CellDesigner because there is one Species with the notes and alias to it in the whole diagram).
+Minerva can be asked to keep the notes by providing custom header "X-MINERVA-KEEP-NOTES: true", but the notes in output files might not be properly defined.
==== CURL sample
+
include::{snippets}/converter/merge_maps/curl-request.adoc[]
==== CURL sample 2
+
include::{snippets}/converter/merge_maps_keep_notes/curl-request.adoc[]
==== Path Parameters
+
include::{snippets}/converter/merge_maps/path-parameters.adoc[]
==== Input file structure
-Input file should be a zip file with single zip folder called "maps". All map files to merge should be located in this folder.
+
+Input file should be a zip file with single zip folder called "maps".
+All map files to merge should be located in this folder.
diff --git a/web/src/main/asciidoc/index.adoc b/web/src/main/asciidoc/index.adoc
index d238420c938968fd2fa4dc8318212b048334e556..7faa4973747678316179274ef9273760c63f2cde 100644
--- a/web/src/main/asciidoc/index.adoc
+++ b/web/src/main/asciidoc/index.adoc
@@ -7,57 +7,71 @@ v{project-version} {build-time}
== Introduction
-Rest API is located in /api/ path of the deployed application. For instance, Rest API of pdmap project that can be browsed using https://pdmap.uni.lu/minerva/ will be located here: https://pdmap.uni.lu/minerva/api/
+Rest API is located in /api/ path of the deployed application.
+For instance, Rest API of Parkinson's Disease Map project that can be browsed using https://pdmap.uni.lu/minerva/ will be located here: https://pdmap.uni.lu/minerva/api/
Rest API tries to follow link:https://cloud.google.com/apis/design/[API Design Guide] by Google.
For API calls that require authentication MINERVA_AUTH_TOKEN obtained during login process must be included.
-
== QuickStart guide
+
Here is sample example that shows information about all projects accessible by guest account (anonymous user):
include::{snippets}/projects/project_data/list_guest/curl-request.adoc[]
-If we are interested in the API calls that require more privileges than anonymous user we need to login first:
+If we are interested in the API calls that require more privileges than anonymous user we need to log in first:
include::{snippets}/authentication/login/curl-request.adoc[]
include::{snippets}/authentication/login/response-body.adoc[]
-The response creates an authentication token and puts it into a cookie MINERVA_AUTH_TOKEN=xxxxxxxx. When using console curl command this cookie must be attached to every query that follows. When we have authentication token we can access information about specific user on the server:
+The response creates an authentication token and puts it into a cookie MINERVA_AUTH_TOKEN=xxxxxxxx.
+When using console curl command this cookie must be attached to every query that follows.
+When we have authentication token we can access information about specific user on the server:
include::{snippets}/user/get_user/curl-request.adoc[]
== Categories
=== <<authentication.adoc#,Authentication>>
+
=== <<configuration.adoc#,Configuration>>
+
Methods allowing to obtain configuration information from server and updating it with proper privileges
=== <<converter.adoc#,Converter>>
+
Conversion API provides access to MINERVA’s ability to convert between different systems biology network formats and to export of layouts to different graphical formats
=== <<file.adoc#,Files>>
+
Methods that allow to upload files into the system
=== <<genomics.adoc#,Genomics>>
+
Methods allowing to access genome data
=== <<license.adoc#,License>>
+
Methods allowing to access information about available licenses
=== <<mesh.adoc#,Mesh>>
+
Methods allowing to access info about mesh data
=== <<plugin.adoc#,Plugins>>
+
Methods allowing to store some data for plugin infrastructure
=== <<project.adoc#,Project>>
+
Set of methods allowing to obtain information about projects and allowing to create new project and modifying existing ones
=== <<taxonomy.adoc#,Taxonomy>>
+
Methods allowing to access info about taxonomy data
=== <<user.adoc#,Users>>
+
Set of methods allowing to obtain and manage users and their access control
diff --git a/web/src/main/asciidoc/new_api/new_api.adoc b/web/src/main/asciidoc/new_api/new_api.adoc
index e8b9c7da4e680a0c56c4b2485a971b29451f1e0b..e2bed6f0f4d601d56576012da897a86763cde4fe 100644
--- a/web/src/main/asciidoc/new_api/new_api.adoc
+++ b/web/src/main/asciidoc/new_api/new_api.adoc
@@ -6,152 +6,15 @@ v{project-version} {build-time}
== Introduction
-Here will be a list of endpoints in the new format. This is a development unstable version and might change. At some point the whole API will be rewritten.
-== Search for bio entities
-Returns list of bio entities matching the query.
+Here will be a list of endpoints in the new format.
+This is a development unstable version and might change.
+At some point the whole API will be rewritten.
-=== Path Parameters
-include::{snippets}/new_api/projects/maps/bioEntites/search/path-parameters.adoc[]
+== Categories
-=== Request Parameters
-include::{snippets}/new_api/projects/maps/bioEntites/search/request-parameters.adoc[]
+=== <<new_api_project.adoc#,Project>>
-=== Response Fields
-include::{snippets}/new_api/projects/maps/bioEntites/search/response-fields.adoc[]
+=== <<new_api_user.adoc#,Users>>
-=== CURL sample
-include::{snippets}/new_api/projects/maps/bioEntites/search/curl-request.adoc[]
-
-=== Sample Response
-include::{snippets}/new_api/projects/maps/bioEntites/search/response-body.adoc[]
-
-== Get element by id
-Returns list of bio entities matching the query.
-
-=== Path Parameters
-include::{snippets}/new_api/projects/maps/bioEntites/elements/get_by_id/path-parameters.adoc[]
-
-=== Response Fields
-include::{snippets}/new_api/projects/maps/bioEntites/elements/get_by_id/response-fields.adoc[]
-
-=== CURL sample
-include::{snippets}/new_api/projects/maps/bioEntites/elements/get_by_id/curl-request.adoc[]
-
-=== Sample Response
-include::{snippets}/new_api/projects/maps/bioEntites/elements/get_by_id/response-body.adoc[]
-
-== Download element list as csv file
-Returns csv file with list of elements.
-
-=== Path Parameters
-include::{snippets}/new_api/projects/maps/bioEntites/elements/export_to_csv/path-parameters.adoc[]
-
-=== Request Fields
-include::{snippets}/new_api/projects/maps/bioEntites/elements/export_to_csv/request-fields.adoc[]
-
-=== CURL sample
-include::{snippets}/new_api/projects/maps/bioEntites/elements/export_to_csv/curl-request.adoc[]
-
-=== Sample Response
-include::{snippets}/new_api/projects/maps/bioEntites/elements/export_to_csv/response-body.adoc[]
-
-
-
-== Get reaction by id
-Returns list of bio entities matching the query.
-
-=== Path Parameters
-include::{snippets}/new_api/projects/maps/bioEntites/reactions/get_by_id/path-parameters.adoc[]
-
-=== Response Fields
-include::{snippets}/new_api/projects/maps/bioEntites/reactions/get_by_id/response-fields.adoc[]
-
-=== CURL sample
-include::{snippets}/new_api/projects/maps/bioEntites/reactions/get_by_id/curl-request.adoc[]
-
-=== Sample Response
-include::{snippets}/new_api/projects/maps/bioEntites/reactions/get_by_id/response-body.adoc[]
-
-== Download reaction list as csv file
-Returns csv file with list of reactions.
-
-=== Path Parameters
-include::{snippets}/new_api/projects/maps/bioEntites/reactions/export_to_csv/path-parameters.adoc[]
-
-=== Request Fields
-include::{snippets}/new_api/projects/maps/bioEntites/reactions/export_to_csv/request-fields.adoc[]
-
-=== CURL sample
-include::{snippets}/new_api/projects/maps/bioEntites/reactions/export_to_csv/curl-request.adoc[]
-
-=== Sample Response
-include::{snippets}/new_api/projects/maps/bioEntites/reactions/export_to_csv/response-body.adoc[]
-
-
-
-== Chemical search
-Search chemical database.
-
-=== Path Parameters
-include::{snippets}/new_api/projects/project_chemicals/search_by_query/path-parameters.adoc[]
-
-=== Request Parameters
-include::{snippets}/new_api/projects/project_chemicals/search_by_query/request-parameters.adoc[]
-
-=== Response Fields
-include::{snippets}/new_api/projects/project_chemicals/search_by_query/response-fields.adoc[]
-
-=== CURL sample
-include::{snippets}/new_api/projects/project_chemicals/search_by_query/curl-request.adoc[]
-
-=== Sample Response
-include::{snippets}/new_api/projects/project_chemicals/search_by_query/response-body.adoc[]
-
-== Drug search
-Search drug database.
-
-=== Path Parameters
-include::{snippets}/new_api/projects/project_drugs/search_by_query/path-parameters.adoc[]
-
-=== Request Parameters
-include::{snippets}/new_api/projects/project_drugs/search_by_query/request-parameters.adoc[]
-
-=== Response Fields
-include::{snippets}/new_api/projects/project_drugs/search_by_query/response-fields.adoc[]
-
-=== CURL sample
-include::{snippets}/new_api/projects/project_drugs/search_by_query/curl-request.adoc[]
-
-=== Sample Response
-include::{snippets}/new_api/projects/project_drugs/search_by_query/response-body.adoc[]
-
-== Get list of associated bioEntities in the overlay
-Returns list of bioEntities that match entries in the overlay.
-
-=== Path Parameters
-include::{snippets}/new_api/projects/overlays/get_bioEntities/path-parameters.adoc[]
-
-=== Response Fields
-include::{snippets}/new_api/projects/overlays/get_bioEntities/response-fields.adoc[]
-
-=== CURL sample
-include::{snippets}/new_api/projects/overlays/get_bioEntities/curl-request.adoc[]
-
-=== Sample Response
-include::{snippets}/new_api/projects/overlays/get_bioEntities/response-body.adoc[]
-
-== Get project
-Returns info about project.
-
-=== Path Parameters
-include::{snippets}/new_api/projects/get_by_project_id/path-parameters.adoc[]
-
-=== Response Fields
-include::{snippets}/new_api/projects/get_by_project_id/response-fields.adoc[]
-
-=== CURL sample
-include::{snippets}/new_api/projects/get_by_project_id/curl-request.adoc[]
-
-=== Sample Response
-include::{snippets}/new_api/projects/get_by_project_id/response-body.adoc[]
+=== <<new_api_plugin.adoc#,Plugins>>
diff --git a/web/src/main/asciidoc/new_api/plugins/new_api_plugin.adoc b/web/src/main/asciidoc/new_api/plugins/new_api_plugin.adoc
new file mode 100644
index 0000000000000000000000000000000000000000..b09f837b2b5dc6450b36e7befafd9e0c44fe39e5
--- /dev/null
+++ b/web/src/main/asciidoc/new_api/plugins/new_api_plugin.adoc
@@ -0,0 +1,60 @@
+= Rest New API Documentation - Plugin
+minerva
+v{project-version} {build-time}
+:toc: left
+:sectnums:
+
+
+== List registered plugins on the server
+
+=== CURL sample
+
+include::{snippets}/new_api/plugins/list_plugins/curl-request.adoc[]
+
+=== Response Fields
+
+include::{snippets}/new_api/plugins/list_plugins/response-fields.adoc[]
+
+=== Sample Response
+
+include::{snippets}/new_api/plugins/list_plugins/response-body.adoc[]
+
+== Register new plugin on the server
+
+=== CURL sample
+
+include::{snippets}/new_api/plugins/create_plugin/curl-request.adoc[]
+
+=== Path Parameters
+
+include::{snippets}/new_api/plugins/create_plugin/path-parameters.adoc[]
+
+=== Request Fields
+
+include::{snippets}/new_api/plugins/create_plugin/request-fields.adoc[]
+
+=== Response Fields
+
+include::{snippets}/new_api/plugins/create_plugin/response-fields.adoc[]
+
+=== Sample Response
+
+include::{snippets}/new_api/plugins/create_plugin/response-body.adoc[]
+
+== Access information about plugin
+
+=== CURL sample
+
+include::{snippets}/new_api/plugins/get_by_hash/curl-request.adoc[]
+
+=== Path Parameters
+
+include::{snippets}/new_api/plugins/get_by_hash/path-parameters.adoc[]
+
+=== Response Fields
+
+include::{snippets}/new_api/plugins/get_by_hash/response-fields.adoc[]
+
+=== Sample Response
+
+include::{snippets}/new_api/plugins/get_by_hash/response-body.adoc[]
\ No newline at end of file
diff --git a/web/src/main/asciidoc/new_api/projects/chemicals/new_api_chemicals.adoc b/web/src/main/asciidoc/new_api/projects/chemicals/new_api_chemicals.adoc
new file mode 100644
index 0000000000000000000000000000000000000000..7ab0126d22f94e7d2fdb00225224c6a17b241cba
--- /dev/null
+++ b/web/src/main/asciidoc/new_api/projects/chemicals/new_api_chemicals.adoc
@@ -0,0 +1,24 @@
+= Rest New API Documentation
+minerva
+v{project-version} {build-time}
+:toc: left
+:sectnums:
+
+
+== Chemical search
+Search chemical database.
+
+=== Path Parameters
+include::{snippets}/new_api/projects/project_chemicals/search_by_query/path-parameters.adoc[]
+
+=== Request Parameters
+include::{snippets}/new_api/projects/project_chemicals/search_by_query/request-parameters.adoc[]
+
+=== Response Fields
+include::{snippets}/new_api/projects/project_chemicals/search_by_query/response-fields.adoc[]
+
+=== CURL sample
+include::{snippets}/new_api/projects/project_chemicals/search_by_query/curl-request.adoc[]
+
+=== Sample Response
+include::{snippets}/new_api/projects/project_chemicals/search_by_query/response-body.adoc[]
diff --git a/web/src/main/asciidoc/new_api/projects/drugs/new_api_drugs.adoc b/web/src/main/asciidoc/new_api/projects/drugs/new_api_drugs.adoc
new file mode 100644
index 0000000000000000000000000000000000000000..337d3bdc2612ad43424668503a0de9bca1cae445
--- /dev/null
+++ b/web/src/main/asciidoc/new_api/projects/drugs/new_api_drugs.adoc
@@ -0,0 +1,23 @@
+= Rest New API Documentation
+minerva
+v{project-version} {build-time}
+:toc: left
+:sectnums:
+
+== Drug search
+Search drug database.
+
+=== Path Parameters
+include::{snippets}/new_api/projects/project_drugs/search_by_query/path-parameters.adoc[]
+
+=== Request Parameters
+include::{snippets}/new_api/projects/project_drugs/search_by_query/request-parameters.adoc[]
+
+=== Response Fields
+include::{snippets}/new_api/projects/project_drugs/search_by_query/response-fields.adoc[]
+
+=== CURL sample
+include::{snippets}/new_api/projects/project_drugs/search_by_query/curl-request.adoc[]
+
+=== Sample Response
+include::{snippets}/new_api/projects/project_drugs/search_by_query/response-body.adoc[]
diff --git a/web/src/main/asciidoc/new_api/projects/maps/bioEntities/elements/new_api_elements.adoc b/web/src/main/asciidoc/new_api/projects/maps/bioEntities/elements/new_api_elements.adoc
new file mode 100644
index 0000000000000000000000000000000000000000..873ab1212235b28afefbb624854dc948f73e3592
--- /dev/null
+++ b/web/src/main/asciidoc/new_api/projects/maps/bioEntities/elements/new_api_elements.adoc
@@ -0,0 +1,36 @@
+= Rest New API Documentation
+minerva
+v{project-version} {build-time}
+:toc: left
+:sectnums:
+
+
+== Get element by id
+Returns list of bio entities matching the query.
+
+=== Path Parameters
+include::{snippets}/new_api/projects/maps/bioEntities/elements/get_by_id/path-parameters.adoc[]
+
+=== Response Fields
+include::{snippets}/new_api/projects/maps/bioEntities/elements/get_by_id/response-fields.adoc[]
+
+=== CURL sample
+include::{snippets}/new_api/projects/maps/bioEntities/elements/get_by_id/curl-request.adoc[]
+
+=== Sample Response
+include::{snippets}/new_api/projects/maps/bioEntities/elements/get_by_id/response-body.adoc[]
+
+== Download element list as csv file
+Returns csv file with list of elements.
+
+=== Path Parameters
+include::{snippets}/new_api/projects/maps/bioEntities/elements/export_to_csv/path-parameters.adoc[]
+
+=== Request Fields
+include::{snippets}/new_api/projects/maps/bioEntities/elements/export_to_csv/request-fields.adoc[]
+
+=== CURL sample
+include::{snippets}/new_api/projects/maps/bioEntities/elements/export_to_csv/curl-request.adoc[]
+
+=== Sample Response
+include::{snippets}/new_api/projects/maps/bioEntities/elements/export_to_csv/response-body.adoc[]
diff --git a/web/src/main/asciidoc/new_api/projects/maps/bioEntities/new_api_bioEntities.adoc b/web/src/main/asciidoc/new_api/projects/maps/bioEntities/new_api_bioEntities.adoc
new file mode 100644
index 0000000000000000000000000000000000000000..c3918332f8eeb82c079691042d13a30c619f7973
--- /dev/null
+++ b/web/src/main/asciidoc/new_api/projects/maps/bioEntities/new_api_bioEntities.adoc
@@ -0,0 +1,28 @@
+= Rest New API Documentation
+minerva
+v{project-version} {build-time}
+:toc: left
+:sectnums:
+
+
+== <<new_api_elements.adoc#,Elements>>
+
+== <<new_api_reactions.adoc#,Reactions>>
+
+== Search for bio entities
+Returns list of bio entities matching the query.
+
+=== Path Parameters
+include::{snippets}/new_api/projects/maps/bioEntities/search/path-parameters.adoc[]
+
+=== Request Parameters
+include::{snippets}/new_api/projects/maps/bioEntities/search/request-parameters.adoc[]
+
+=== Response Fields
+include::{snippets}/new_api/projects/maps/bioEntities/search/response-fields.adoc[]
+
+=== CURL sample
+include::{snippets}/new_api/projects/maps/bioEntities/search/curl-request.adoc[]
+
+=== Sample Response
+include::{snippets}/new_api/projects/maps/bioEntities/search/response-body.adoc[]
diff --git a/web/src/main/asciidoc/new_api/projects/maps/bioEntities/reactions/new_api_reactions.adoc b/web/src/main/asciidoc/new_api/projects/maps/bioEntities/reactions/new_api_reactions.adoc
new file mode 100644
index 0000000000000000000000000000000000000000..048f029a50193d424d6ba0a2b876f542cf591cda
--- /dev/null
+++ b/web/src/main/asciidoc/new_api/projects/maps/bioEntities/reactions/new_api_reactions.adoc
@@ -0,0 +1,36 @@
+= Rest New API Documentation
+minerva
+v{project-version} {build-time}
+:toc: left
+:sectnums:
+
+
+== Get reaction by id
+Returns list of bio entities matching the query.
+
+=== Path Parameters
+include::{snippets}/new_api/projects/maps/bioEntities/reactions/get_by_id/path-parameters.adoc[]
+
+=== Response Fields
+include::{snippets}/new_api/projects/maps/bioEntities/reactions/get_by_id/response-fields.adoc[]
+
+=== CURL sample
+include::{snippets}/new_api/projects/maps/bioEntities/reactions/get_by_id/curl-request.adoc[]
+
+=== Sample Response
+include::{snippets}/new_api/projects/maps/bioEntities/reactions/get_by_id/response-body.adoc[]
+
+== Download reaction list as csv file
+Returns csv file with list of reactions.
+
+=== Path Parameters
+include::{snippets}/new_api/projects/maps/bioEntities/reactions/export_to_csv/path-parameters.adoc[]
+
+=== Request Fields
+include::{snippets}/new_api/projects/maps/bioEntities/reactions/export_to_csv/request-fields.adoc[]
+
+=== CURL sample
+include::{snippets}/new_api/projects/maps/bioEntities/reactions/export_to_csv/curl-request.adoc[]
+
+=== Sample Response
+include::{snippets}/new_api/projects/maps/bioEntities/reactions/export_to_csv/response-body.adoc[]
diff --git a/web/src/main/asciidoc/new_api/projects/maps/layers/images/new_api_images.adoc b/web/src/main/asciidoc/new_api/projects/maps/layers/images/new_api_images.adoc
index d2389bf453040c1c277530686459906f54607c3a..5a3048ddac490ef293142b1697d20d6cfc926c17 100644
--- a/web/src/main/asciidoc/new_api/projects/maps/layers/images/new_api_images.adoc
+++ b/web/src/main/asciidoc/new_api/projects/maps/layers/images/new_api_images.adoc
@@ -23,8 +23,7 @@ include::{snippets}/new_api/projects/maps/layers/images/get_image/curl-request.a
=== Sample Response
include::{snippets}/new_api/projects/maps/layers/images/get_image/response-body.adoc[]
-== Add layer
-Returns info about layer.
+== Add layer image
=== Path Parameters
include::{snippets}/new_api/projects/maps/layers/images/add_image/path-parameters.adoc[]
@@ -41,8 +40,8 @@ include::{snippets}/new_api/projects/maps/layers/images/add_image/curl-request.a
=== Sample Response
include::{snippets}/new_api/projects/maps/layers/images/add_image/response-body.adoc[]
-== Update layer
-Update layer.
+== Update layer image
+Update layer image.
=== Path Parameters
include::{snippets}/new_api/projects/maps/layers/images/update_image/path-parameters.adoc[]
@@ -59,8 +58,8 @@ include::{snippets}/new_api/projects/maps/layers/images/update_image/curl-reques
=== Sample Response
include::{snippets}/new_api/projects/maps/layers/images/update_image/response-body.adoc[]
-== Delete layer
-Delete layer.
+== Delete layer image
+Delete layer image.
=== Path Parameters
include::{snippets}/new_api/projects/maps/layers/images/delete_image/path-parameters.adoc[]
@@ -68,8 +67,8 @@ include::{snippets}/new_api/projects/maps/layers/images/delete_image/path-parame
=== CURL sample
include::{snippets}/new_api/projects/maps/layers/images/delete_image/curl-request.adoc[]
-== List layers
-List layers.
+== List layer images
+List layer images.
=== Path Parameters
include::{snippets}/new_api/projects/maps/layers/images/list_images/path-parameters.adoc[]
diff --git a/web/src/main/asciidoc/new_api/projects/maps/layers/new_api_layers.adoc b/web/src/main/asciidoc/new_api/projects/maps/layers/new_api_layers.adoc
index ac0dbf24ec0ef618765a798f7c00c1ff60daee81..92558830edc8ca5bb5cf7e866948e74eec62f55a 100644
--- a/web/src/main/asciidoc/new_api/projects/maps/layers/new_api_layers.adoc
+++ b/web/src/main/asciidoc/new_api/projects/maps/layers/new_api_layers.adoc
@@ -8,6 +8,10 @@ v{project-version} {build-time}
== Introduction
Here will be a list of endpoints in the new format. This is a development unstable version and might change. At some point the whole API will be rewritten.
+== <<new_api_images.adoc#,Images>>
+
+== <<new_api_texts.adoc#,Texts>>
+
== Get layer
Returns info about layer.
@@ -24,7 +28,6 @@ include::{snippets}/new_api/projects/maps/layers/get_layer/curl-request.adoc[]
include::{snippets}/new_api/projects/maps/layers/get_layer/response-body.adoc[]
== Add layer
-Returns info about layer.
=== Path Parameters
include::{snippets}/new_api/projects/maps/layers/add_layer/path-parameters.adoc[]
diff --git a/web/src/main/asciidoc/new_api/projects/maps/layers/texts/new_api_texts.adoc b/web/src/main/asciidoc/new_api/projects/maps/layers/texts/new_api_texts.adoc
index d1379c81a96fb857c4e17f4c70ab8060fccd2da0..5f8bb42955adb69e91c6f5c22c86ab9ffc67b28b 100644
--- a/web/src/main/asciidoc/new_api/projects/maps/layers/texts/new_api_texts.adoc
+++ b/web/src/main/asciidoc/new_api/projects/maps/layers/texts/new_api_texts.adoc
@@ -23,8 +23,7 @@ include::{snippets}/new_api/projects/maps/layers/texts/get_text/curl-request.ado
=== Sample Response
include::{snippets}/new_api/projects/maps/layers/texts/get_text/response-body.adoc[]
-== Add layer
-Returns info about layer.
+== Add layer text
=== Path Parameters
include::{snippets}/new_api/projects/maps/layers/texts/add_text/path-parameters.adoc[]
@@ -41,8 +40,8 @@ include::{snippets}/new_api/projects/maps/layers/texts/add_text/curl-request.ado
=== Sample Response
include::{snippets}/new_api/projects/maps/layers/texts/add_text/response-body.adoc[]
-== Update layer
-Update layer.
+== Update layer text
+Update layer text
=== Path Parameters
include::{snippets}/new_api/projects/maps/layers/texts/update_text/path-parameters.adoc[]
@@ -59,8 +58,8 @@ include::{snippets}/new_api/projects/maps/layers/texts/update_text/curl-request.
=== Sample Response
include::{snippets}/new_api/projects/maps/layers/texts/update_text/response-body.adoc[]
-== Delete layer
-Delete layer.
+== Delete layer text
+Delete layer text
=== Path Parameters
include::{snippets}/new_api/projects/maps/layers/texts/delete_text/path-parameters.adoc[]
@@ -68,8 +67,8 @@ include::{snippets}/new_api/projects/maps/layers/texts/delete_text/path-paramete
=== CURL sample
include::{snippets}/new_api/projects/maps/layers/texts/delete_text/curl-request.adoc[]
-== List layers
-List layers.
+== List layer texts
+List layer texts
=== Path Parameters
include::{snippets}/new_api/projects/maps/layers/texts/list_texts/path-parameters.adoc[]
diff --git a/web/src/main/asciidoc/new_api/projects/maps/new_api_maps.adoc b/web/src/main/asciidoc/new_api/projects/maps/new_api_maps.adoc
new file mode 100644
index 0000000000000000000000000000000000000000..24dfa0e96ff3bedfcda689648e000e1aea4be8c3
--- /dev/null
+++ b/web/src/main/asciidoc/new_api/projects/maps/new_api_maps.adoc
@@ -0,0 +1,9 @@
+= Rest New API Documentation - Project
+minerva
+v{project-version} {build-time}
+:toc: left
+:sectnums:
+
+== <<new_api_bioEntities.adoc#,BioEntities>>
+
+== <<new_api_layers.adoc#,Layers>>
\ No newline at end of file
diff --git a/web/src/main/asciidoc/new_api/projects/new_api_project.adoc b/web/src/main/asciidoc/new_api/projects/new_api_project.adoc
new file mode 100644
index 0000000000000000000000000000000000000000..46a2ef7a29ab3b4cf6b0bc16edefe41d36054c3b
--- /dev/null
+++ b/web/src/main/asciidoc/new_api/projects/new_api_project.adoc
@@ -0,0 +1,17 @@
+= Rest New API Documentation - Project
+minerva
+v{project-version} {build-time}
+:toc: left
+:sectnums:
+
+== <<new_api_project_data.adoc#,Project Data>>
+
+== <<new_api_chemicals.adoc#,Chemicals>>
+
+== <<new_api_drugs.adoc#,Drugs>>
+
+== <<new_api_glyphs.adoc#,Glyphs>>
+
+== <<new_api_maps.adoc#,Maps>>
+
+=== <<new_api_overlays.adoc#,Overlays>>
diff --git a/web/src/main/asciidoc/new_api/projects/new_api_project_data.adoc b/web/src/main/asciidoc/new_api/projects/new_api_project_data.adoc
new file mode 100644
index 0000000000000000000000000000000000000000..6cb8a721efc01daf1006db85ca9d44cdd98e469c
--- /dev/null
+++ b/web/src/main/asciidoc/new_api/projects/new_api_project_data.adoc
@@ -0,0 +1,128 @@
+= Rest New API Documentation - Projects
+minerva
+v{project-version} {build-time}
+:toc: left
+:sectnums:
+
+== Get project by projectId
+
+Returns metadata of the project.
+
+=== CURL sample
+
+include::{snippets}/new_api/projects/get_by_project_id/curl-request.adoc[]
+
+=== Path Parameters
+
+include::{snippets}/new_api/projects/get_by_project_id/path-parameters.adoc[]
+
+=== Response Fields
+
+include::{snippets}/new_api/projects/get_by_project_id/response-fields.adoc[]
+
+=== Sample Response
+
+include::{snippets}/new_api/projects/get_by_project_id/response-body.adoc[]
+
+== List
+
+List all projects.
+
+=== CURL sample
+
+include::{snippets}/new_api/projects/list_projects/curl-request.adoc[]
+
+=== Response Fields
+
+include::{snippets}/new_api/projects/list_projects/response-fields.adoc[]
+
+=== Sample Response
+
+include::{snippets}/new_api/projects/list_projects/response-body.adoc[]
+
+== Create project (for editor)
+
+Creates project without a diagram.
+This is not useful yet.
+
+=== Path Parameters
+
+include::{snippets}/new_api/projects/create_project_from_json/path-parameters.adoc[]
+
+=== Request Fields
+
+include::{snippets}/new_api/projects/create_project_from_json/request-fields.adoc[]
+
+=== Response Fields
+
+include::{snippets}/new_api/projects/create_project_from_json/response-fields.adoc[]
+
+=== CURL sample
+
+include::{snippets}/new_api/projects/create_project_from_json/curl-request.adoc[]
+
+=== Sample Response
+
+include::{snippets}/new_api/projects/create_project_from_json/response-body.adoc[]
+
+== Update project
+
+Updates project.
+
+=== Path Parameters
+
+include::{snippets}/new_api/projects/update_project/path-parameters.adoc[]
+
+=== Request Fields
+
+include::{snippets}/new_api/projects/update_project/request-fields.adoc[]
+
+=== Response Fields
+
+include::{snippets}/new_api/projects/update_project/response-fields.adoc[]
+
+=== CURL sample
+
+include::{snippets}/new_api/projects/update_project/curl-request.adoc[]
+
+=== Sample Response
+
+include::{snippets}/new_api/projects/update_project/response-body.adoc[]
+
+== Delete project
+
+=== Path Parameters
+
+include::{snippets}/new_api/projects/delete_project/path-parameters.adoc[]
+
+=== CURL sample
+
+include::{snippets}/new_api/projects/delete_project/curl-request.adoc[]
+
+=== Sample Response
+
+include::{snippets}/new_api/projects/delete_project/response-body.adoc[]
+
+== Get logs
+
+Gets logs generated on project upload.
+
+=== Path Parameters
+
+include::{snippets}/new_api/projects/logs/list/path-parameters.adoc[]
+
+=== Request Parameters
+
+include::{snippets}/new_api/projects/logs/list/request-parameters.adoc[]
+
+=== Response Fields
+
+include::{snippets}/new_api/projects/logs/list/response-fields.adoc[]
+
+=== CURL sample
+
+include::{snippets}/new_api/projects/logs/list/curl-request.adoc[]
+
+=== Sample Response
+
+include::{snippets}/new_api/projects/logs/list/response-body.adoc[]
\ No newline at end of file
diff --git a/web/src/main/asciidoc/new_api/projects/overlays/new_api_overlays.adoc b/web/src/main/asciidoc/new_api/projects/overlays/new_api_overlays.adoc
new file mode 100644
index 0000000000000000000000000000000000000000..e601eeabb962e77c5b341c5fa8ec0116d3b21284
--- /dev/null
+++ b/web/src/main/asciidoc/new_api/projects/overlays/new_api_overlays.adoc
@@ -0,0 +1,21 @@
+= Rest New API Documentation
+minerva
+v{project-version} {build-time}
+:toc: left
+:sectnums:
+
+
+== Get list of associated bioEntities in the overlay
+Returns list of bioEntities that match entries in the overlay.
+
+=== Path Parameters
+include::{snippets}/new_api/projects/overlays/get_bioEntities/path-parameters.adoc[]
+
+=== Response Fields
+include::{snippets}/new_api/projects/overlays/get_bioEntities/response-fields.adoc[]
+
+=== CURL sample
+include::{snippets}/new_api/projects/overlays/get_bioEntities/curl-request.adoc[]
+
+=== Sample Response
+include::{snippets}/new_api/projects/overlays/get_bioEntities/response-body.adoc[]
diff --git a/web/src/main/asciidoc/new_api/users/new_api_user.adoc b/web/src/main/asciidoc/new_api/users/new_api_user.adoc
new file mode 100644
index 0000000000000000000000000000000000000000..c1e5967451630e01c8bf8f4655efd96e45f8047c
--- /dev/null
+++ b/web/src/main/asciidoc/new_api/users/new_api_user.adoc
@@ -0,0 +1,202 @@
+= Rest New API Documentation - User
+minerva
+v{project-version} {build-time}
+:toc: left
+:sectnums:
+
+
+== Get user by id
+
+Returns user data.
+
+=== CURL sample
+
+include::{snippets}/new_api/users/get_by_id/curl-request.adoc[]
+
+=== Path Parameters
+
+include::{snippets}/new_api/users/get_by_id/path-parameters.adoc[]
+
+=== Response Fields
+
+include::{snippets}/new_api/users/get_by_id/response-fields.adoc[]
+
+=== Sample Response
+
+include::{snippets}/new_api/users/get_by_id/response-body.adoc[]
+
+== List all users
+
+=== CURL sample
+
+include::{snippets}/new_api/users/list_users/curl-request.adoc[]
+
+=== Path Parameters
+
+include::{snippets}/new_api/users/list_users/path-parameters.adoc[]
+
+=== Response Fields
+
+include::{snippets}/new_api/users/list_users/response-fields.adoc[]
+
+=== Sample Response
+
+include::{snippets}/new_api/users/list_users/response-body.adoc[]
+
+== Create user
+
+=== CURL sample
+
+include::{snippets}/new_api/users/create_user/curl-request.adoc[]
+
+=== Path Parameters
+
+include::{snippets}/new_api/users/create_user/path-parameters.adoc[]
+
+=== Request Fields
+
+include::{snippets}/new_api/users/create_user/request-fields.adoc[]
+
+=== Response Fields
+
+include::{snippets}/new_api/users/create_user/response-fields.adoc[]
+
+=== Sample Response
+
+include::{snippets}/new_api/users/create_user/response-body.adoc[]
+
+== Update user
+
+=== CURL sample
+
+include::{snippets}/new_api/users/update_user/curl-request.adoc[]
+
+=== Path Parameters
+
+include::{snippets}/new_api/users/update_user/path-parameters.adoc[]
+
+=== Request Fields
+
+include::{snippets}/new_api/users/update_user/request-fields.adoc[]
+
+=== Response Fields
+
+include::{snippets}/new_api/users/update_user/response-fields.adoc[]
+
+=== Sample Response
+
+include::{snippets}/new_api/users/update_user/response-body.adoc[]
+
+== Grant user privilege
+
+=== Path Parameters
+
+include::{snippets}/new_api/users/grant_privilege/path-parameters.adoc[]
+
+=== Request Fields
+
+include::{snippets}/new_api/users/grant_privilege/request-fields.adoc[]
+
+=== Response Fields
+
+include::{snippets}/new_api/users/grant_privilege/response-fields.adoc[]
+
+=== CURL sample
+
+include::{snippets}/new_api/users/grant_privilege/curl-request.adoc[]
+
+=== Sample Response
+
+include::{snippets}/new_api/users/grant_privilege/response-body.adoc[]
+
+== Revoke user privilege
+
+=== Path Parameters
+
+include::{snippets}/new_api/users/revoke_privilege/path-parameters.adoc[]
+
+=== Request Fields
+
+include::{snippets}/new_api/users/revoke_privilege/request-fields.adoc[]
+
+=== Response Fields
+
+include::{snippets}/new_api/users/revoke_privilege/response-fields.adoc[]
+
+=== CURL sample
+
+include::{snippets}/new_api/users/revoke_privilege/curl-request.adoc[]
+
+=== Sample Response
+
+include::{snippets}/new_api/users/revoke_privilege/response-body.adoc[]
+
+== Delete user
+
+=== CURL sample
+
+include::{snippets}/new_api/users/delete_user/curl-request.adoc[]
+
+=== Path Parameters
+
+include::{snippets}/new_api/users/delete_user/path-parameters.adoc[]
+
+== Request password reset over email
+
+=== CURL sample
+
+include::{snippets}/new_api/users/request_reset_password/curl-request.adoc[]
+
+=== Path Parameters
+
+include::{snippets}/new_api/users/request_reset_password/path-parameters.adoc[]
+
+== Reset password using token obtained over email
+
+=== CURL sample
+
+include::{snippets}/new_api/users/reset_password/curl-request.adoc[]
+
+=== Request Fields
+
+include::{snippets}/new_api/users/reset_password/request-fields.adoc[]
+
+== Register new user
+
+=== CURL sample
+
+include::{snippets}/new_api/users/register_user/curl-request.adoc[]
+
+=== Request Fields
+
+include::{snippets}/new_api/users/register_user/request-fields.adoc[]
+
+=== Response Fields
+
+include::{snippets}/new_api/users/register_user/response-fields.adoc[]
+
+=== Sample Response
+
+include::{snippets}/new_api/users/register_user/response-body.adoc[]
+
+== Confirm email
+
+=== CURL sample
+
+include::{snippets}/new_api/users/confirm_email/curl-request.adoc[]
+
+=== Request Parameters
+
+include::{snippets}/new_api/users/confirm_email/request-parameters.adoc[]
+
+=== Path Parameters
+
+include::{snippets}/new_api/users/confirm_email/path-parameters.adoc[]
+
+=== Response Fields
+
+include::{snippets}/new_api/users/confirm_email/response-fields.adoc[]
+
+=== Sample Response
+
+include::{snippets}/new_api/users/confirm_email/response-body.adoc[]
diff --git a/web/src/main/asciidoc/project.adoc b/web/src/main/asciidoc/project.adoc
index a91134a53667fa9ae62bea8d2d0032e4951007ef..26fb0c1be3734133dfbd386e1b007bf6cd1489cf 100644
--- a/web/src/main/asciidoc/project.adoc
+++ b/web/src/main/asciidoc/project.adoc
@@ -5,11 +5,18 @@ v{project-version} {build-time}
:sectnums:
-=== <<project_data.adoc#,Project Data>>
-=== <<project_backgrounds.adoc#,Project Backgrounds>>
-=== <<project_chemicals.adoc#,Project Chemicals>>
-=== <<project_comments.adoc#,Project Comments>>
-=== <<project_drugs.adoc#,Project Drugs>>
-=== <<project_maps.adoc#,Project Maps>>
-=== <<project_overlays.adoc#,Project Overlays>>
-=== <<project_privileges.adoc#,Project Privileges>>
+== <<project_data.adoc#,Project Data>>
+
+== <<project_backgrounds.adoc#,Project Backgrounds>>
+
+== <<project_chemicals.adoc#,Project Chemicals>>
+
+== <<project_comments.adoc#,Project Comments>>
+
+== <<project_drugs.adoc#,Project Drugs>>
+
+== <<project_maps.adoc#,Project Maps>>
+
+== <<project_overlays.adoc#,Project Overlays>>
+
+== <<project_privileges.adoc#,Project Privileges>>
diff --git a/web/src/main/asciidoc/projects/project_data.adoc b/web/src/main/asciidoc/projects/project_data.adoc
index 07bb0dab29712ca69e18a650bff35b468f2db656..b8302e6c9d0f7c6db5d8b3bd945ce33669874175 100644
--- a/web/src/main/asciidoc/projects/project_data.adoc
+++ b/web/src/main/asciidoc/projects/project_data.adoc
@@ -5,156 +5,198 @@ v{project-version} {build-time}
:sectnums:
== Get project
-Returns meta data of the project.
+
+Returns metadata of the project.
=== CURL sample
+
include::{snippets}/projects/project_data/get_project/curl-request.adoc[]
=== Path Parameters
+
include::{snippets}/projects/project_data/get_project/path-parameters.adoc[]
=== Response Fields
+
include::{snippets}/projects/project_data/get_project/response-fields.adoc[]
=== Sample Response
-include::{snippets}/projects/project_data/get_project/response-body.adoc[]
+include::{snippets}/projects/project_data/get_project/response-body.adoc[]
== List
+
List all projects.
=== CURL sample
+
include::{snippets}/projects/project_data/list/curl-request.adoc[]
=== Response Fields
+
include::{snippets}/projects/project_data/list/response-fields.adoc[]
=== Sample Response
-include::{snippets}/projects/project_data/list/response-body.adoc[]
+include::{snippets}/projects/project_data/list/response-body.adoc[]
== Create project
+
Creates project from file that is already uploaded to minerva.
=== Path Parameters
+
include::{snippets}/projects/project_data/create_simple/path-parameters.adoc[]
=== Request Parameters
+
include::{snippets}/projects/project_data/create_simple/request-parameters.adoc[]
//=== Response Fields
//include::{snippets}/projects/project_data/create_simple/response-fields.adoc[]
=== Example 1.
+
Upload of project from simple file
==== CURL sample
+
include::{snippets}/projects/project_data/create_simple/curl-request.adoc[]
==== Sample Response
+
include::{snippets}/projects/project_data/create_simple/response-body.adoc[]
=== Example 2.
+
Upload of project from complex zip file
==== CURL sample
+
include::{snippets}/projects/project_data/create_zip/curl-request.adoc[]
==== Sample Response
-include::{snippets}/projects/project_data/create_zip/response-body.adoc[]
+include::{snippets}/projects/project_data/create_zip/response-body.adoc[]
== Update project
+
Updates project.
=== Path Parameters
+
include::{snippets}/projects/project_data/update/path-parameters.adoc[]
=== Request Fields
+
include::{snippets}/projects/project_data/update/request-fields.adoc[]
//=== Response Fields
//include::{snippets}/projects/project_data/update/response-fields.adoc[]
=== CURL sample
+
include::{snippets}/projects/project_data/update/curl-request.adoc[]
=== Sample Response
-include::{snippets}/projects/project_data/update/response-body.adoc[]
+include::{snippets}/projects/project_data/update/response-body.adoc[]
== Delete project
=== Path Parameters
+
include::{snippets}/projects/project_data/delete/path-parameters.adoc[]
=== CURL sample
+
include::{snippets}/projects/project_data/delete/curl-request.adoc[]
=== Sample Response
-include::{snippets}/projects/project_data/delete/response-body.adoc[]
+include::{snippets}/projects/project_data/delete/response-body.adoc[]
== Get source
+
Gets source file used to create the project.
=== Path Parameters
+
include::{snippets}/projects/project_data/get_source_file/path-parameters.adoc[]
=== CURL sample
+
include::{snippets}/projects/project_data/get_source_file/curl-request.adoc[]
=== Sample Response
+
include::{snippets}/projects/project_data/get_source_file/response-body.adoc[]
== Get logs
+
Gets logs generated on project upload.
=== Path Parameters
+
include::{snippets}/projects/project_data/get_project_logs/path-parameters.adoc[]
=== Request Parameters
+
include::{snippets}/projects/project_data/get_project_logs/request-parameters.adoc[]
=== Response Fields
+
include::{snippets}/projects/project_data/get_project_logs/response-fields.adoc[]
=== CURL sample
+
include::{snippets}/projects/project_data/get_project_logs/curl-request.adoc[]
=== Sample Response
+
include::{snippets}/projects/project_data/get_project_logs/response-body.adoc[]
== Get statistics
+
Gets set of statistics about the project.
=== Path Parameters
+
include::{snippets}/projects/project_data/get_project_statistics/path-parameters.adoc[]
=== Response Fields
+
include::{snippets}/projects/project_data/get_project_statistics/response-fields.adoc[]
=== CURL sample
+
include::{snippets}/projects/project_data/get_project_statistics/curl-request.adoc[]
=== Sample Response
+
include::{snippets}/projects/project_data/get_project_statistics/response-body.adoc[]
== Get publications
+
Gets publication list used in the project.
=== Path Parameters
+
include::{snippets}/projects/project_data/get_publications/path-parameters.adoc[]
=== Request Parameters
+
include::{snippets}/projects/project_data/get_project_logs/request-parameters.adoc[]
=== Response Fields
+
include::{snippets}/projects/project_data/get_publications/response-fields.adoc[]
=== CURL sample
+
include::{snippets}/projects/project_data/get_publications/curl-request.adoc[]
=== Sample Response
+
include::{snippets}/projects/project_data/get_publications/response-body.adoc[]
diff --git a/web/src/main/asciidoc/projects/project_drugs.adoc b/web/src/main/asciidoc/projects/project_drugs.adoc
index 68f66110ef833b49343042425cf24dbdad577ca4..5ed51468b8f55283243c463b6eac332187c4c3dd 100644
--- a/web/src/main/asciidoc/projects/project_drugs.adoc
+++ b/web/src/main/asciidoc/projects/project_drugs.adoc
@@ -5,39 +5,50 @@ v{project-version} {build-time}
:sectnums:
== Get drug
-Returns drugs data with project related connections.
+
+Returns drug data with project related connections.
=== CURL sample 1
+
include::{snippets}/projects/project_drugs/search_by_query/curl-request.adoc[]
=== CURL sample 2
+
include::{snippets}/projects/project_drugs/search_by_target/curl-request.adoc[]
=== Path Parameters
+
include::{snippets}/projects/project_drugs/search_by_query/path-parameters.adoc[]
=== Request Parameters
+
include::{snippets}/projects/project_drugs/search_by_query/request-parameters.adoc[]
=== Response Fields
+
include::{snippets}/projects/project_drugs/search_by_query/response-fields.adoc[]
=== Sample Response
-include::{snippets}/projects/project_drugs/search_by_query/response-body.adoc[]
+include::{snippets}/projects/project_drugs/search_by_query/response-body.adoc[]
== Get suggested drug queries
+
Get list of suggested drug queries in the context of the project.
=== CURL sample
+
include::{snippets}/projects/project_drugs/suggested_query_list/curl-request.adoc[]
=== Path Parameters
+
include::{snippets}/projects/project_drugs/suggested_query_list/path-parameters.adoc[]
=== Response Fields
+
include::{snippets}/projects/project_drugs/suggested_query_list/response-fields.adoc[]
=== Sample Response
+
include::{snippets}/projects/project_drugs/suggested_query_list/response-body.adoc[]
diff --git a/web/src/main/asciidoc/projects/project_overlays.adoc b/web/src/main/asciidoc/projects/project_overlays.adoc
index 999c38e1be21dc0097c9ca119b74f04230ecd819..7f5e4ac8d423167dfe6d089df000ce3e2fb5b572 100644
--- a/web/src/main/asciidoc/projects/project_overlays.adoc
+++ b/web/src/main/asciidoc/projects/project_overlays.adoc
@@ -7,152 +7,184 @@ v{project-version} {build-time}
== List data overlays
=== Path Parameters
+
include::{snippets}/projects/project_overlays/get_all_by_creator/path-parameters.adoc[]
=== Response Fields
+
include::{snippets}/projects/project_overlays/get_all_by_creator/response-fields.adoc[]
=== CURL sample 1
+
include::{snippets}/projects/project_overlays/get_all/curl-request.adoc[]
=== Sample Response 1
+
include::{snippets}/projects/project_overlays/get_all/response-body.adoc[]
=== CURL sample 2
+
include::{snippets}/projects/project_overlays/get_all_by_creator/curl-request.adoc[]
=== Sample Response 2
-include::{snippets}/projects/project_overlays/get_all_by_creator/response-body.adoc[]
+include::{snippets}/projects/project_overlays/get_all_by_creator/response-body.adoc[]
-== Get data overlay
+== Get data overlay
=== Path Parameters
+
include::{snippets}/projects/project_overlays/get_by_id/path-parameters.adoc[]
=== Response Fields
+
include::{snippets}/projects/project_overlays/get_by_id/response-fields.adoc[]
=== CURL sample
+
include::{snippets}/projects/project_overlays/get_by_id/curl-request.adoc[]
=== Sample Response
-include::{snippets}/projects/project_overlays/get_by_id/response-body.adoc[]
+include::{snippets}/projects/project_overlays/get_by_id/response-body.adoc[]
== Add overlay
=== Path Parameters
+
include::{snippets}/projects/project_overlays/create_from_file/path-parameters.adoc[]
=== Request Parameters
+
include::{snippets}/projects/project_overlays/create_from_file/request-parameters.adoc[]
=== Response Fields
+
include::{snippets}/projects/project_overlays/create_from_file/response-fields.adoc[]
=== CURL sample from file
+
include::{snippets}/projects/project_overlays/create_from_file/curl-request.adoc[]
=== Sample Response from file
+
include::{snippets}/projects/project_overlays/create_from_file/response-body.adoc[]
=== CURL sample from content
+
include::{snippets}/projects/project_overlays/create_from_content/curl-request.adoc[]
=== Sample Response from content
-include::{snippets}/projects/project_overlays/create_from_content/response-body.adoc[]
+include::{snippets}/projects/project_overlays/create_from_content/response-body.adoc[]
== Update overlay
=== Path Parameters
+
include::{snippets}/projects/project_overlays/update_overlay/path-parameters.adoc[]
=== Request Fields
+
include::{snippets}/projects/project_overlays/update_overlay/request-fields.adoc[]
=== Response Fields
+
include::{snippets}/projects/project_overlays/update_overlay/response-fields.adoc[]
=== CURL sample
+
include::{snippets}/projects/project_overlays/update_overlay/curl-request.adoc[]
=== Sample Response
-include::{snippets}/projects/project_overlays/update_overlay/response-body.adoc[]
+include::{snippets}/projects/project_overlays/update_overlay/response-body.adoc[]
== Delete overlay
=== CURL sample
+
include::{snippets}/projects/project_overlays/delete_overlay/curl-request.adoc[]
=== Path Parameters
-include::{snippets}/projects/project_overlays/delete_overlay/path-parameters.adoc[]
+include::{snippets}/projects/project_overlays/delete_overlay/path-parameters.adoc[]
== Download source data
=== Path Parameters
+
include::{snippets}/projects/project_overlays/download_source/path-parameters.adoc[]
=== CURL sample
+
include::{snippets}/projects/project_overlays/download_source/curl-request.adoc[]
=== Sample Response
-include::{snippets}/projects/project_overlays/download_source/response-body.adoc[]
+include::{snippets}/projects/project_overlays/download_source/response-body.adoc[]
== Download legend
=== Path Parameters
-include::{snippets}/projects/project_legend/download_source/path-parameters.adoc[]
+
+include::{snippets}/projects/project_overlays/download_legend/path-parameters.adoc[]
=== CURL sample
-include::{snippets}/projects/project_legend/download_source/curl-request.adoc[]
+include::{snippets}/projects/project_overlays/download_legend/curl-request.adoc[]
-== Get list of associated bioEntites
+== Get list of associated bioEntities
=== Path Parameters
+
include::{snippets}/projects/project_overlays/get_bio_entities/path-parameters.adoc[]
=== Response Fields
+
include::{snippets}/projects/project_overlays/get_bio_entities/response-fields.adoc[]
=== CURL sample
+
include::{snippets}/projects/project_overlays/get_bio_entities/curl-request.adoc[]
=== Sample Response
-include::{snippets}/projects/project_overlays/get_bio_entities/response-body.adoc[]
+include::{snippets}/projects/project_overlays/get_bio_entities/response-body.adoc[]
== Get reaction data
=== Path Parameters
+
include::{snippets}/projects/project_overlays/get_reaction/path-parameters.adoc[]
=== Response Fields
+
include::{snippets}/projects/project_overlays/get_reaction/response-fields.adoc[]
=== CURL sample
+
include::{snippets}/projects/project_overlays/get_reaction/curl-request.adoc[]
=== Sample Response
-include::{snippets}/projects/project_overlays/get_reaction/response-body.adoc[]
+include::{snippets}/projects/project_overlays/get_reaction/response-body.adoc[]
== Get element data
=== Path Parameters
+
include::{snippets}/projects/project_overlays/get_element/path-parameters.adoc[]
=== Response Fields
+
include::{snippets}/projects/project_overlays/get_element/response-fields.adoc[]
=== CURL sample
+
include::{snippets}/projects/project_overlays/get_element/curl-request.adoc[]
=== Sample Response
+
include::{snippets}/projects/project_overlays/get_element/response-body.adoc[]
diff --git a/web/src/main/java/lcsb/mapviewer/web/api/plugin/NewPluginController.java b/web/src/main/java/lcsb/mapviewer/web/api/plugin/NewPluginController.java
index 1803cbd3b94cb4f6ebedc16a6563811abcaeda39..d30f236e74071654dea2cd630c1f5f78978cafce 100644
--- a/web/src/main/java/lcsb/mapviewer/web/api/plugin/NewPluginController.java
+++ b/web/src/main/java/lcsb/mapviewer/web/api/plugin/NewPluginController.java
@@ -127,7 +127,7 @@ public class NewPluginController {
@GetMapping(value = "/")
public ResponseEntity<?> listPlugins(final Pageable pageable) {
final Map<PluginProperty, Object> pluginFilter = new HashMap<>();
- pluginFilter.put(PluginProperty.DEFAULT_VALUE, true);
+ pluginFilter.put(PluginProperty.PUBLIC_VALUE, true);
final Page<Plugin> plugins = pluginService.getAll(pluginFilter, pageable);
return serializer.prepareResponse(plugins);
}
diff --git a/web/src/main/java/lcsb/mapviewer/web/api/project/NewProjectController.java b/web/src/main/java/lcsb/mapviewer/web/api/project/NewProjectController.java
index 72c72660895c9467b3134b38d604be8b85a9133f..c7bdce6b3c82fa2adf3741fdc7c3bb91c9925457 100644
--- a/web/src/main/java/lcsb/mapviewer/web/api/project/NewProjectController.java
+++ b/web/src/main/java/lcsb/mapviewer/web/api/project/NewProjectController.java
@@ -49,6 +49,7 @@ import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import java.util.UUID;
@RestController
@Validated
@@ -100,7 +101,7 @@ public class NewProjectController {
public ResponseEntity<?> addProject(
final Authentication authentication,
final @Valid @RequestBody NewProjectDTO data)
- throws QueryException, ObjectNotFoundException, ObjectExistsException {
+ throws QueryException, ObjectNotFoundException, ObjectExistsException, FailedDependencyException, IOException {
Project project = projectService.getProjectByProjectId(data.getProjectId());
if (project != null) {
@@ -109,17 +110,18 @@ public class NewProjectController {
project = new Project(data.getProjectId());
data.saveToProject(project);
project.setOwner(userService.getUserByLogin(authentication.getName()));
+ project.setDirectory(UUID.randomUUID().toString());
projectService.add(project);
project = projectService.getProjectByProjectId(data.getProjectId(), true);
- return serializer.prepareResponse(project, HttpStatus.CREATED);
+ return serializer.prepareResponse(project,
+ new ProjectResponseDecorator(minervaNetController.getSharedProjects(), meshService, taxonomyService), HttpStatus.CREATED);
}
@PreAuthorize("hasAnyAuthority('IS_ADMIN', 'IS_CURATOR')")
@PostMapping(value = "/{projectId:.+}:move")
public ResponseEntity<?> moveProject(
final @NotBlank @PathVariable(value = "projectId") String projectId,
- final Authentication authentication,
final @Valid @RequestBody NewMoveProjectDTO data)
throws ObjectNotFoundException, ObjectExistsException, UpdateConflictException {
@@ -136,7 +138,7 @@ public class NewProjectController {
throw new UpdateConflictException("Cannot move project. Project is shared in minerva net");
}
- boolean sharedProject = false;
+ boolean sharedProject;
try {
sharedProject = minervaNetController.getSharedProjects().contains(data.getProjectId());
} catch (Exception e) {
diff --git a/web/src/main/java/lcsb/mapviewer/web/api/project/map/bioentity/elements/NewElementsController.java b/web/src/main/java/lcsb/mapviewer/web/api/project/map/bioentity/elements/NewElementsController.java
index 7fca9770d4ede9a52bcb7ad285f7878da6c9d002..cd2728315c0f12246adf3c745a72667e21c81e65 100644
--- a/web/src/main/java/lcsb/mapviewer/web/api/project/map/bioentity/elements/NewElementsController.java
+++ b/web/src/main/java/lcsb/mapviewer/web/api/project/map/bioentity/elements/NewElementsController.java
@@ -100,10 +100,9 @@ public class NewElementsController extends BaseController {
}
final List<Element> elements = elementService.getElementsByFilter(properties, Pageable.unpaged(), true).getContent();
- if (elements.size() == 0) {
+ if (elements.isEmpty()) {
throw new ObjectNotFoundException("Element does not exists");
}
- logger.debug(elements.get(0).getGlyph());
return serializer.prepareResponse(elements.get(0), bioEntityResponseDecorator);
}
diff --git a/web/src/main/java/lcsb/mapviewer/web/api/user/NewUserController.java b/web/src/main/java/lcsb/mapviewer/web/api/user/NewUserController.java
index abefda97ed55655b347da82eae753d350abf9d23..3885a7cf96534a61305be090957e7252ea958d7c 100644
--- a/web/src/main/java/lcsb/mapviewer/web/api/user/NewUserController.java
+++ b/web/src/main/java/lcsb/mapviewer/web/api/user/NewUserController.java
@@ -283,7 +283,6 @@ public class NewUserController extends BaseController {
final @Valid @RequestBody ResetPasswordDTO data)
throws IOException, QueryException, ObjectNotFoundException {
try {
- logger.debug("XXX");
userService.resetPassword(data.getToken(), passwordEncoder.encode(data.getPassword()));
return okStatus();
} catch (final InvalidTokenException e) {
diff --git a/web/src/test/java/lcsb/mapviewer/web/ChemicalControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/ChemicalControllerIntegrationTest.java
index 5c8a7fb8616349af9237700dc203bf7acd3c6ba8..1fd2cf6635f209f1031adc7bf378ae871e80c04c 100644
--- a/web/src/test/java/lcsb/mapviewer/web/ChemicalControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/ChemicalControllerIntegrationTest.java
@@ -67,7 +67,7 @@ public class ChemicalControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testSearchChemicalsInProjectUrl() throws Exception {
+ public void testDocsSearchChemicalsInProjectUrl() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
final RequestBuilder request = get("/minerva/api/projects/{projectId}/chemicals:search?query=stilbene oxide", TEST_PROJECT)
@@ -98,7 +98,7 @@ public class ChemicalControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testGetSuggestedList() throws Exception {
+ public void testDocsGetSuggestedList() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
final MiriamData bloodLossDisease = new MiriamData(MiriamType.MESH_2012, "D016063");
@@ -185,7 +185,7 @@ public class ChemicalControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testSearchChemicalsByTarget() throws Exception {
+ public void testDocsSearchChemicalsByTarget() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
Element element = null;
diff --git a/web/src/test/java/lcsb/mapviewer/web/CommentControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/CommentControllerIntegrationTest.java
index de5a422215f3258dc04ec5b691264f47d55d82a5..a6af56f93f1dc9a7ebb4b6deedad5ca06edbde7a 100644
--- a/web/src/test/java/lcsb/mapviewer/web/CommentControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/CommentControllerIntegrationTest.java
@@ -102,7 +102,7 @@ public class CommentControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testAdminSeesAllComments() throws Exception {
+ public void testDocsAdminSeesAllComments() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
createComments();
@@ -358,7 +358,7 @@ public class CommentControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testRemoveAsAdmin() throws Exception {
+ public void testDocsRemoveAsAdmin() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
Comment comment = createAndPersistComment(map, null);
@@ -436,7 +436,7 @@ public class CommentControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testGetReactionCommentsAsAdmin() throws Exception {
+ public void testDocsGetReactionCommentsAsAdmin() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
createReactionComment();
@@ -508,7 +508,7 @@ public class CommentControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testGetElementCommentsAsAdmin() throws Exception {
+ public void testDocsGetElementCommentsAsAdmin() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
createElementComment();
@@ -585,7 +585,7 @@ public class CommentControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testGetPointCommentsAsAdmin() throws Exception {
+ public void testDocsGetPointCommentsAsAdmin() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
createAndPersistComment(map, null);
@@ -664,7 +664,7 @@ public class CommentControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testAddElementCommentAsUserWithAccess() throws Exception {
+ public void testDocsAddElementCommentAsUserWithAccess() throws Exception {
MockHttpSession session = createSession(TEST_USER_LOGIN, TEST_USER_PASSWORD);
String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
@@ -807,7 +807,7 @@ public class CommentControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testAddReactionCommentAsUserWithAccess() throws Exception {
+ public void testDocsAddReactionCommentAsUserWithAccess() throws Exception {
MockHttpSession session = createSession(TEST_USER_LOGIN, TEST_USER_PASSWORD);
String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
@@ -884,7 +884,7 @@ public class CommentControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testAddPointCommentAsUserWithAccess() throws Exception {
+ public void testDocsAddPointCommentAsUserWithAccess() throws Exception {
MockHttpSession session = createSession(TEST_USER_LOGIN, TEST_USER_PASSWORD);
String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
diff --git a/web/src/test/java/lcsb/mapviewer/web/ConfigurationControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/ConfigurationControllerIntegrationTest.java
index 19f32ea9daef1701a2e6291e7804c5ecdf5ef19b..2ca82ae2d5edbdbb2cc2375f2c58bd254df6d1bc 100644
--- a/web/src/test/java/lcsb/mapviewer/web/ConfigurationControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/ConfigurationControllerIntegrationTest.java
@@ -88,7 +88,7 @@ public class ConfigurationControllerIntegrationTest extends ControllerIntegratio
}
@Test
- public void accessConfigurationAsAnonymous() throws Exception {
+ public void testDocsAccessConfigurationAsAnonymous() throws Exception {
RequestBuilder request = get("/minerva/api/configuration/");
mockMvc.perform(request)
@@ -99,7 +99,7 @@ public class ConfigurationControllerIntegrationTest extends ControllerIntegratio
}
@Test
- public void accessConfigurationOptionsAsAnonymous() throws Exception {
+ public void testDocsAccessConfigurationOptionsAsAnonymous() throws Exception {
RequestBuilder request = get("/minerva/api/configuration/options/");
String response = mockMvc.perform(request)
@@ -120,7 +120,7 @@ public class ConfigurationControllerIntegrationTest extends ControllerIntegratio
}
@Test
- public void testSetSmtpPort() throws Exception {
+ public void testDocsSetSmtpPort() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
Map<String, Object> option = new HashMap<>();
diff --git a/web/src/test/java/lcsb/mapviewer/web/ConfigurationDapiControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/ConfigurationDapiControllerIntegrationTest.java
index f2d0729e9c937410afe0b56851c696f73f2a80d2..fade729d5e4ab58e275f4235565b4a6298be3a6e 100644
--- a/web/src/test/java/lcsb/mapviewer/web/ConfigurationDapiControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/ConfigurationDapiControllerIntegrationTest.java
@@ -33,7 +33,7 @@ public class ConfigurationDapiControllerIntegrationTest extends ControllerIntegr
private ObjectMapper objectMapper;
@Test
- public void getDapiConfiguration() throws Exception {
+ public void testDocsGetDapiConfiguration() throws Exception {
RequestBuilder request = get("/minerva/api/configuration/dapi/");
mockMvc.perform(request)
@@ -45,7 +45,7 @@ public class ConfigurationDapiControllerIntegrationTest extends ControllerIntegr
}
@Test
- public void getDapiDatabasesConfiguration() throws Exception {
+ public void testDocsGetDapiDatabasesConfiguration() throws Exception {
RequestBuilder request = get("/minerva/api/configuration/dapi/database/");
mockMvc.perform(request)
@@ -61,7 +61,7 @@ public class ConfigurationDapiControllerIntegrationTest extends ControllerIntegr
}
@Test
- public void getDapiDrugBankReleaseConfiguration() throws Exception {
+ public void testDocsGetDapiDrugBankReleaseConfiguration() throws Exception {
assumeTrue("DAPI credentials are not provided", isDapiConfigurationAvailable());
RequestBuilder request = get("/minerva/api/configuration/dapi/database/{database}/release/", "DrugBank");
@@ -97,7 +97,7 @@ public class ConfigurationDapiControllerIntegrationTest extends ControllerIntegr
}
@Test
- public void acceptLicenseReleaseWithAccess() throws Exception {
+ public void testDocsAcceptLicenseReleaseWithAccess() throws Exception {
assumeTrue("DAPI credentials are not provided", isDapiConfigurationAvailable());
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
@@ -125,7 +125,7 @@ public class ConfigurationDapiControllerIntegrationTest extends ControllerIntegr
}
@Test
- public void testRegisterExistingDapiUser() throws Exception {
+ public void testDocsRegisterExistingDapiUser() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
UserDto user = new UserDto();
@@ -161,11 +161,9 @@ public class ConfigurationDapiControllerIntegrationTest extends ControllerIntegr
.contentType(MediaType.APPLICATION_JSON)
.session(session);
- String content = mockMvc.perform(request)
+ mockMvc.perform(request)
.andExpect(status().isBadRequest())
.andReturn().getResponse().getContentAsString();
-
- logger.debug(content);
}
}
diff --git a/web/src/test/java/lcsb/mapviewer/web/ConvertControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/ConvertControllerIntegrationTest.java
index 2713295db5f679173bbf56c9e7b1f7e063cea14d..fffb39097a0a0936489391f91c36eabede4d6885 100644
--- a/web/src/test/java/lcsb/mapviewer/web/ConvertControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/ConvertControllerIntegrationTest.java
@@ -94,7 +94,7 @@ public class ConvertControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testMergeCellDesignerMaps() throws Exception {
+ public void testDocsMergeCellDesignerMaps() throws Exception {
byte[] body = Files.readAllBytes(new File("src/test/resources/convert/cd-maps.zip").toPath());
RequestBuilder request = post("/minerva/api/convert/merge/{inputFormat}:{outputFormat}", "CellDesigner_SBML",
"CellDesigner_SBML")
@@ -163,7 +163,7 @@ public class ConvertControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testListAvailableFormats() throws Exception {
+ public void testDocsListAvailableFormats() throws Exception {
RequestBuilder request = get("/minerva/api/convert/");
mockMvc.perform(request)
@@ -185,7 +185,7 @@ public class ConvertControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void convertCellDesignerToGpml() throws Exception {
+ public void testDocsConvertCellDesignerToGpml() throws Exception {
File file = new File("src/test/resources/convert/cd-sample.xml");
String content = FileUtils.readFileToString(file, StandardCharsets.UTF_8);
RequestBuilder request = post("/minerva/api/convert/{inputFormat}:{outputFormat}", "CellDesigner_SBML", "GPML")
@@ -204,7 +204,7 @@ public class ConvertControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testListAvailableImageFormats() throws Exception {
+ public void testDocsListAvailableImageFormats() throws Exception {
RequestBuilder request = get("/minerva/api/convert/image/");
mockMvc.perform(request)
@@ -226,7 +226,7 @@ public class ConvertControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void convertCellDesignerToSvg() throws Exception {
+ public void testDocsConvertCellDesignerToSvg() throws Exception {
File file = new File("src/test/resources/convert/cd-sample.xml");
String content = FileUtils.readFileToString(file, StandardCharsets.UTF_8);
RequestBuilder request = post("/minerva/api/convert/image/{inputFormat}:{outputFormat}", "CellDesigner_SBML", "png")
@@ -503,7 +503,7 @@ public class ConvertControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testMergeCellDesignerWithTextArea() throws Exception {
+ public void testDocsMergeCellDesignerWithTextArea() throws Exception {
Model model = new ModelFullIndexed(null);
Layer layer = createLayer();
LayerText text = new LayerText(new Rectangle2D.Double(10, 20, 30, 40), "test text");
@@ -568,7 +568,7 @@ public class ConvertControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testPreserveNotesWithCustomHeader() throws Exception {
+ public void testDocsPreserveNotesWithCustomHeader() throws Exception {
byte[] body = Files.readAllBytes(new File("src/test/resources/convert/cd-maps-with-notes.zip").toPath());
RequestBuilder request = post("/minerva/api/convert/merge/{inputFormat}:{outputFormat}", "CellDesigner_SBML",
"CellDesigner_SBML")
diff --git a/web/src/test/java/lcsb/mapviewer/web/DrugControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/DrugControllerIntegrationTest.java
index 818e5b458c26dd76c82a4c9ff52d030c307c40a2..93eb33fc1424b513a7eb41ea8fdd12eae2a88379 100644
--- a/web/src/test/java/lcsb/mapviewer/web/DrugControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/DrugControllerIntegrationTest.java
@@ -38,7 +38,7 @@ public class DrugControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void testSearchDrugsInProjectUrl() throws Exception {
+ public void testDocsSearchDrugsInProjectUrl() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
final RequestBuilder request = get("/minerva/api/projects/{projectId}/drugs:search?query=aspirin", TEST_PROJECT)
@@ -75,7 +75,7 @@ public class DrugControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void testSearchDrugsByTargetInSubmap() throws Exception {
+ public void testDocsSearchDrugsByTargetInSubmap() throws Exception {
Project project = createAndPersistProject(TEST_PROJECT_ID);
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
@@ -84,19 +84,17 @@ public class DrugControllerIntegrationTest extends ControllerIntegrationTest {
final RequestBuilder request = get("/minerva/api/projects/{projectId}/drugs:search?target=ALIAS:" + submapId, project.getProjectId())
.session(session);
- String content = mockMvc.perform(request)
+ mockMvc.perform(request)
.andDo(document("projects/project_drugs/search_by_target",
getProjectPathParameters(),
getChemicalFilter(),
listOfDrugFields()))
.andExpect(status().is2xxSuccessful())
.andReturn().getResponse().getContentAsString();
-
- logger.debug(content);
}
@Test
- public void testGetSuggestedList() throws Exception {
+ public void testDocsGetSuggestedList() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
final RequestBuilder request = get("/minerva/api/projects/{projectId}/drugs/suggestedQueryList", TEST_PROJECT)
diff --git a/web/src/test/java/lcsb/mapviewer/web/FileControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/FileControllerIntegrationTest.java
index f2772b0fff26aae6cb56b934509c2529a005ca63..caf5fb1512c9d1bcb48b846ac45aaac5ade23a55 100644
--- a/web/src/test/java/lcsb/mapviewer/web/FileControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/FileControllerIntegrationTest.java
@@ -1,21 +1,10 @@
package lcsb.mapviewer.web;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.springframework.restdocs.mockmvc.MockMvcRestDocumentation.document;
-import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.get;
-import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.post;
-import static org.springframework.restdocs.payload.PayloadDocumentation.fieldWithPath;
-import static org.springframework.restdocs.payload.PayloadDocumentation.responseFields;
-import static org.springframework.restdocs.request.RequestDocumentation.parameterWithName;
-import static org.springframework.restdocs.request.RequestDocumentation.pathParameters;
-import static org.springframework.restdocs.request.RequestDocumentation.requestParameters;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
-
-import java.util.Arrays;
-import java.util.List;
-import java.util.Map;
-
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
+import lcsb.mapviewer.services.interfaces.IFileService;
+import lcsb.mapviewer.services.interfaces.IUserService;
import org.apache.http.client.entity.UrlEncodedFormEntity;
import org.apache.http.message.BasicNameValuePair;
import org.apache.http.util.EntityUtils;
@@ -29,12 +18,21 @@ import org.springframework.restdocs.payload.FieldDescriptor;
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
import org.springframework.test.web.servlet.RequestBuilder;
-import com.fasterxml.jackson.core.type.TypeReference;
-import com.fasterxml.jackson.databind.ObjectMapper;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
-import lcsb.mapviewer.model.cache.UploadedFileEntry;
-import lcsb.mapviewer.services.interfaces.IFileService;
-import lcsb.mapviewer.services.interfaces.IUserService;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.springframework.restdocs.mockmvc.MockMvcRestDocumentation.document;
+import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.get;
+import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.post;
+import static org.springframework.restdocs.payload.PayloadDocumentation.fieldWithPath;
+import static org.springframework.restdocs.payload.PayloadDocumentation.responseFields;
+import static org.springframework.restdocs.request.RequestDocumentation.parameterWithName;
+import static org.springframework.restdocs.request.RequestDocumentation.pathParameters;
+import static org.springframework.restdocs.request.RequestDocumentation.requestParameters;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
@RunWith(SpringJUnit4ClassRunner.class)
public class FileControllerIntegrationTest extends ControllerIntegrationTest {
@@ -53,7 +51,7 @@ public class FileControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void canCreateAndUploadFile() throws Exception {
+ public void testDocsCanCreateAndUploadFile() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
@@ -107,7 +105,7 @@ public class FileControllerIntegrationTest extends ControllerIntegrationTest {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
UploadedFileEntry file = new UploadedFileEntry();
- file.setFileContent(new byte[] {});
+ file.setFileContent(new byte[]{});
file.setLength(99999);
fileService.add(file);
@@ -130,7 +128,7 @@ public class FileControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void getInfoAboutFile() throws Exception {
+ public void testDocsGetInfoAboutFile() throws Exception {
UploadedFileEntry file = createFile("Hello world",
userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN));
try {
diff --git a/web/src/test/java/lcsb/mapviewer/web/FunctionControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/FunctionControllerIntegrationTest.java
index df091300e3cf3e5a787501eec0e71e5b523fee72..15e2f7b3160bf7a4b83507e16318df7214565ea4 100644
--- a/web/src/test/java/lcsb/mapviewer/web/FunctionControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/FunctionControllerIntegrationTest.java
@@ -1,19 +1,8 @@
package lcsb.mapviewer.web;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.springframework.restdocs.mockmvc.MockMvcRestDocumentation.document;
-import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.get;
-import static org.springframework.restdocs.payload.PayloadDocumentation.fieldWithPath;
-import static org.springframework.restdocs.payload.PayloadDocumentation.responseFields;
-import static org.springframework.restdocs.request.RequestDocumentation.parameterWithName;
-import static org.springframework.restdocs.request.RequestDocumentation.pathParameters;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
-
-import java.util.Arrays;
-import java.util.List;
-import java.util.Map;
-
+import com.fasterxml.jackson.core.type.TypeReference;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.model.ModelData;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
@@ -25,10 +14,19 @@ import org.springframework.restdocs.payload.ResponseFieldsSnippet;
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
import org.springframework.test.web.servlet.RequestBuilder;
-import com.fasterxml.jackson.core.type.TypeReference;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.model.ModelData;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.springframework.restdocs.mockmvc.MockMvcRestDocumentation.document;
+import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.get;
+import static org.springframework.restdocs.payload.PayloadDocumentation.fieldWithPath;
+import static org.springframework.restdocs.payload.PayloadDocumentation.responseFields;
+import static org.springframework.restdocs.request.RequestDocumentation.parameterWithName;
+import static org.springframework.restdocs.request.RequestDocumentation.pathParameters;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
@RunWith(SpringJUnit4ClassRunner.class)
public class FunctionControllerIntegrationTest extends ControllerIntegrationTest {
@@ -76,7 +74,7 @@ public class FunctionControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testGetFunctions() throws Exception {
+ public void testDocsGetFunctions() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
RequestBuilder request = get("/minerva/api/projects/{projectId}/models/{mapId}/functions/", TEST_PROJECT, map.getId())
@@ -91,13 +89,13 @@ public class FunctionControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testGetFunction() throws Exception {
+ public void testDocsGetFunction() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
RequestBuilder request = get("/minerva/api/projects/{projectId}/models/{mapId}/functions/{functionId}", TEST_PROJECT,
map.getId(),
map.getFunctions().iterator().next().getId())
- .session(session);
+ .session(session);
String response = mockMvc.perform(request)
.andExpect(status().is2xxSuccessful())
@@ -136,7 +134,7 @@ public class FunctionControllerIntegrationTest extends ControllerIntegrationTest
private ResponseFieldsSnippet listOfFunctionFields() {
return responseFields(
fieldWithPath("[]").description("list of functions"))
- .andWithPrefix("[].", functionFields());
+ .andWithPrefix("[].", functionFields());
}
}
diff --git a/web/src/test/java/lcsb/mapviewer/web/GenomicsControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/GenomicsControllerIntegrationTest.java
index 61f7b1879a8aea8f1d1f3dc3aae87ec258bd58c5..84ae0eff669d555626acf3592777d9c0bfc05600 100644
--- a/web/src/test/java/lcsb/mapviewer/web/GenomicsControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/GenomicsControllerIntegrationTest.java
@@ -17,7 +17,6 @@ import org.apache.http.message.BasicNameValuePair;
import org.apache.http.util.EntityUtils;
import org.junit.After;
import org.junit.Before;
-import org.junit.Ignore;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.springframework.beans.factory.annotation.Autowired;
@@ -34,7 +33,7 @@ import java.util.Calendar;
import java.util.List;
import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.assertFalse;
import static org.springframework.restdocs.mockmvc.MockMvcRestDocumentation.document;
import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.delete;
import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.get;
@@ -49,8 +48,8 @@ import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.
@RunWith(SpringJUnit4ClassRunner.class)
public class GenomicsControllerIntegrationTest extends ControllerIntegrationTest {
- private MiriamData ebolaId = new MiriamData(MiriamType.TAXONOMY, "1570291");
- private String ebolaUrl = "ftp://hgdownload.cse.ucsc.edu/goldenPath/eboVir3/bigZips/eboVir3.2bit";
+ private final MiriamData ebolaId = new MiriamData(MiriamType.TAXONOMY, "1570291");
+ private final String ebolaUrl = "ftp://hgdownload.cse.ucsc.edu/goldenPath/eboVir3/bigZips/eboVir3.2bit";
@Autowired
private ProjectSnippets snippets;
@@ -85,8 +84,7 @@ public class GenomicsControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- @Ignore("Taxonomy database issue")
- public void testGetTaxonomies() throws Exception {
+ public void testDocsGetTaxonomies() throws Exception {
RequestBuilder request = get("/minerva/api/genomics/taxonomies/");
@@ -101,7 +99,7 @@ public class GenomicsControllerIntegrationTest extends ControllerIntegrationTest
List<Object> data = objectMapper.readValue(response, new TypeReference<List<Object>>() {
});
- assertTrue("list of taxonomies shouldn't be empty", data.size() > 0);
+ assertFalse("list of taxonomies shouldn't be empty", data.isEmpty());
}
private List<FieldDescriptor> organismResponseFields() {
@@ -116,8 +114,7 @@ public class GenomicsControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- @Ignore("Taxonomy database issue")
- public void testGetGenomeTypes() throws Exception {
+ public void testDocsGetGenomeTypes() throws Exception {
RequestBuilder request = get("/minerva/api/genomics/taxonomies/{taxonomyId}/genomeTypes/", "9606");
@@ -141,8 +138,7 @@ public class GenomicsControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- @Ignore("Taxonomy database issue")
- public void testGetAllGenomeVersions() throws Exception {
+ public void testDocsGetAllGenomeVersions() throws Exception {
RequestBuilder request = get("/minerva/api/genomics/taxonomies/{taxonomyId}/genomeTypes/{genomeType}/versions/", "9606",
ReferenceGenomeType.UCSC.name());
@@ -165,11 +161,11 @@ public class GenomicsControllerIntegrationTest extends ControllerIntegrationTest
List<Object> data = objectMapper.readValue(response, new TypeReference<List<Object>>() {
});
- assertTrue(data.size() > 0);
+ assertFalse(data.isEmpty());
}
@Test
- public void testGetRemoteUrl() throws Exception {
+ public void testDocsGetRemoteUrl() throws Exception {
RequestBuilder request = get(
"/minerva/api/genomics/taxonomies/{taxonomyId}/genomeTypes/{genomeType}/versions/{version}:getAvailableRemoteUrls",
@@ -195,11 +191,11 @@ public class GenomicsControllerIntegrationTest extends ControllerIntegrationTest
List<Object> data = objectMapper.readValue(response, new TypeReference<List<Object>>() {
});
- assertTrue(data.size() > 0);
+ assertFalse(data.isEmpty());
}
@Test
- public void testDownloadGenomeDataFromRemote() throws Exception {
+ public void testDocsDownloadGenomeDataFromRemote() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
String body = EntityUtils.toString(new UrlEncodedFormEntity(
@@ -207,7 +203,7 @@ public class GenomicsControllerIntegrationTest extends ControllerIntegrationTest
new BasicNameValuePair("organismId", ebolaId.getResource()),
new BasicNameValuePair("type", ReferenceGenomeType.UCSC.name()),
new BasicNameValuePair("version", "eboVir3"),
- new BasicNameValuePair("url", "http://minerva-dev.lcsb.uni.lu/eboVir3.2bit"))));
+ new BasicNameValuePair("url", "https://minerva-dev.lcsb.uni.lu/eboVir3.2bit"))));
RequestBuilder request = post("/minerva/api/genomics/")
.contentType(MediaType.APPLICATION_FORM_URLENCODED)
@@ -228,7 +224,7 @@ public class GenomicsControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testGetDownloadedGenomes() throws Exception {
+ public void testDocsGetDownloadedGenomes() throws Exception {
createGenome();
RequestBuilder request = get("/minerva/api/genomics/");
@@ -242,7 +238,7 @@ public class GenomicsControllerIntegrationTest extends ControllerIntegrationTest
.andReturn().getResponse().getContentAsString();
}
- private ReferenceGenome createGenome() throws Exception {
+ private ReferenceGenome createGenome() {
ReferenceGenome genome = new ReferenceGenome();
genome.setOrganism(ebolaId);
genome.setSourceUrl(ebolaUrl);
@@ -260,7 +256,7 @@ public class GenomicsControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testGetGenomeInformation() throws Exception {
+ public void testDocsGetGenomeInformation() throws Exception {
createGenome();
BigFileEntry entry = new BigFileEntry();
@@ -349,7 +345,7 @@ public class GenomicsControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void deleteGenomeInformation() throws Exception {
+ public void testDocsDeleteGenomeInformation() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
ReferenceGenome genome = createGenome();
@@ -390,7 +386,7 @@ public class GenomicsControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void addGeneMappingInformation() throws Exception {
+ public void testDocsAddGeneMappingInformation() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
ReferenceGenome genome = createGenome();
@@ -416,7 +412,7 @@ public class GenomicsControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void deleteGeneMappingInformation() throws Exception {
+ public void testDocsDeleteGeneMappingInformation() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
ReferenceGenome genome = createGenome();
@@ -480,7 +476,7 @@ public class GenomicsControllerIntegrationTest extends ControllerIntegrationTest
new BasicNameValuePair("organismId", ""),
new BasicNameValuePair("type", ReferenceGenomeType.UCSC.name()),
new BasicNameValuePair("version", "eboVir3"),
- new BasicNameValuePair("url", "http://minerva-dev.lcsb.uni.lu/eboVir3.2bit"))));
+ new BasicNameValuePair("url", "https://minerva-dev.lcsb.uni.lu/eboVir3.2bit"))));
RequestBuilder request = post("/minerva/api/genomics/")
.contentType(MediaType.APPLICATION_FORM_URLENCODED)
diff --git a/web/src/test/java/lcsb/mapviewer/web/LicenseControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/LicenseControllerIntegrationTest.java
index d2ec2f366aefe41e3429e0076bdc9836a9a54ab0..d037c7046947da34b45fb0e060cff7fc618817a9 100644
--- a/web/src/test/java/lcsb/mapviewer/web/LicenseControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/LicenseControllerIntegrationTest.java
@@ -24,7 +24,7 @@ public class LicenseControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testListLicenses() throws Exception {
+ public void testDocsListLicenses() throws Exception {
final RequestBuilder request = get("/minerva/api/licenses/");
diff --git a/web/src/test/java/lcsb/mapviewer/web/MapControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/MapControllerIntegrationTest.java
index 8547b0cd899eb69073511c34f78f351ec9a4f2b2..39086ea37e9f759e52908a6ae06832c1014cb1ba 100644
--- a/web/src/test/java/lcsb/mapviewer/web/MapControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/MapControllerIntegrationTest.java
@@ -42,48 +42,6 @@ import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
import org.springframework.test.web.servlet.MvcResult;
import org.springframework.test.web.servlet.RequestBuilder;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.springframework.restdocs.mockmvc.MockMvcRestDocumentation.document;
-import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.get;
-import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.patch;
-import static org.springframework.restdocs.payload.PayloadDocumentation.fieldWithPath;
-import static org.springframework.restdocs.payload.PayloadDocumentation.requestFields;
-import static org.springframework.restdocs.payload.PayloadDocumentation.responseFields;
-import static org.springframework.restdocs.payload.PayloadDocumentation.subsectionWithPath;
-import static org.springframework.restdocs.request.RequestDocumentation.parameterWithName;
-import static org.springframework.restdocs.request.RequestDocumentation.pathParameters;
-import static org.springframework.restdocs.request.RequestDocumentation.requestParameters;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
-import org.apache.commons.lang3.StringUtils;
-import org.apache.http.client.entity.UrlEncodedFormEntity;
-import org.apache.http.message.BasicNameValuePair;
-import org.apache.http.util.EntityUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.junit.runner.RunWith;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.MediaType;
-import org.springframework.mock.web.MockHttpSession;
-import org.springframework.restdocs.payload.FieldDescriptor;
-import org.springframework.restdocs.payload.JsonFieldType;
-import org.springframework.restdocs.payload.ResponseFieldsSnippet;
-import org.springframework.restdocs.request.PathParametersSnippet;
-import org.springframework.restdocs.request.RequestParametersSnippet;
-import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
-import org.springframework.test.web.servlet.MvcResult;
-import org.springframework.test.web.servlet.RequestBuilder;
-
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
@@ -426,7 +384,7 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void testGetAllElementsFilteredByType() throws Exception {
+ public void testDocsGetAllElementsFilteredByType() throws Exception {
RequestBuilder request = get(
"/minerva/api/projects/{projectId}/models/{mapId}/bioEntities/elements/?columns=name,complexId&type=Protein",
TEST_PROJECT, "*");
@@ -487,7 +445,7 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void testGetAllReactions() throws Exception {
+ public void testDocsGetAllReactions() throws Exception {
RequestBuilder request = get("/minerva/api/projects/{projectId}/models/{mapId}/bioEntities/reactions/", TEST_PROJECT, "*");
String response = mockMvc.perform(request)
@@ -506,7 +464,7 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void testGetAllReactionsWithFilteredColumns() throws Exception {
+ public void testDocsGetAllReactionsWithFilteredColumns() throws Exception {
RequestBuilder request = get("/minerva/api/projects/{projectId}/models/{mapId}/bioEntities/reactions/?columns=id,notes",
TEST_PROJECT, "*");
@@ -529,7 +487,7 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void testSearchBioEntitiesAsAnonymous() throws Exception {
+ public void testDocsSearchBioEntitiesAsAnonymous() throws Exception {
RequestBuilder request = get("/minerva/api/projects/{projectId}/models/{mapId}/bioEntities:search?coordinates={coords}",
TEST_PROJECT, map.getId(),
"104.36,182.81");
@@ -610,7 +568,7 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void testSearchBioEntitiesOnEverySubmap() throws Exception {
+ public void testDocsSearchBioEntitiesOnEverySubmap() throws Exception {
Element element = map.getElements().iterator().next();
RequestBuilder request = get("/minerva/api/projects/{projectId}/models/{mapId}/bioEntities:search?query={query}",
@@ -683,7 +641,7 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void testSuggestedQueryList() throws Exception {
+ public void testDocsSuggestedQueryList() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
RequestBuilder request = get("/minerva/api/projects/{projectId}/models/{mapId}/bioEntities/suggestedQueryList",
@@ -763,7 +721,7 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void testUpdateMap() throws Exception {
+ public void testDocsUpdateMap() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
Double centerX = 10.0;
@@ -875,7 +833,7 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void testDownloadImage() throws Exception {
+ public void testDocsDownloadImage() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
RequestBuilder request = get("/minerva/api/projects/{projectId}/models/{mapId}:downloadImage?"
@@ -956,7 +914,7 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void testDownloadImageDataOverlay() throws Exception {
+ public void testDocsDownloadImageDataOverlay() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
DataOverlay overlay = createOverlay(TEST_PROJECT,
@@ -1010,7 +968,7 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void testDownloadImagePolygon() throws Exception {
+ public void testDocsDownloadImagePolygon() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
RequestBuilder request = get("/minerva/api/projects/{projectId}/models/{mapId}:downloadImage?"
@@ -1072,7 +1030,7 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
});
int elements = ((List<?>) result.get("data")).size();
- assertTrue(elements == 1);
+ assertEquals(1, elements);
}
@Test
diff --git a/web/src/test/java/lcsb/mapviewer/web/MapControllerIntegrationTestWithGlyph.java b/web/src/test/java/lcsb/mapviewer/web/MapWithGlyphControllerIntegrationTest.java
similarity index 94%
rename from web/src/test/java/lcsb/mapviewer/web/MapControllerIntegrationTestWithGlyph.java
rename to web/src/test/java/lcsb/mapviewer/web/MapWithGlyphControllerIntegrationTest.java
index 23ae3675e8b81b06396fefe19fb66770e1b3a44f..6c73bed9acc6981613baf1049c3b3a4ee31e2e65 100644
--- a/web/src/test/java/lcsb/mapviewer/web/MapControllerIntegrationTestWithGlyph.java
+++ b/web/src/test/java/lcsb/mapviewer/web/MapWithGlyphControllerIntegrationTest.java
@@ -1,20 +1,14 @@
package lcsb.mapviewer.web;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-import static org.springframework.restdocs.mockmvc.MockMvcRestDocumentation.document;
-import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.get;
-import static org.springframework.restdocs.payload.PayloadDocumentation.responseFields;
-import static org.springframework.restdocs.payload.PayloadDocumentation.subsectionWithPath;
-import static org.springframework.restdocs.request.RequestDocumentation.parameterWithName;
-import static org.springframework.restdocs.request.RequestDocumentation.pathParameters;
-import static org.springframework.restdocs.request.RequestDocumentation.requestParameters;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
-
-import java.util.List;
-import java.util.Map;
-
+import com.fasterxml.jackson.core.type.TypeReference;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.converter.graphics.PngImageGenerator;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.security.PrivilegeType;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.services.interfaces.IUserService;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
@@ -25,19 +19,23 @@ import org.springframework.restdocs.request.RequestParametersSnippet;
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
import org.springframework.test.web.servlet.RequestBuilder;
-import com.fasterxml.jackson.core.type.TypeReference;
+import java.util.List;
+import java.util.Map;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.converter.graphics.PngImageGenerator;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.security.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.services.interfaces.IUserService;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+import static org.springframework.restdocs.mockmvc.MockMvcRestDocumentation.document;
+import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.get;
+import static org.springframework.restdocs.payload.PayloadDocumentation.responseFields;
+import static org.springframework.restdocs.payload.PayloadDocumentation.subsectionWithPath;
+import static org.springframework.restdocs.request.RequestDocumentation.parameterWithName;
+import static org.springframework.restdocs.request.RequestDocumentation.pathParameters;
+import static org.springframework.restdocs.request.RequestDocumentation.requestParameters;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
@RunWith(SpringJUnit4ClassRunner.class)
-public class MapControllerIntegrationTestWithGlyph extends ControllerIntegrationTest {
+public class MapWithGlyphControllerIntegrationTest extends ControllerIntegrationTest {
private User anonymous;
@@ -76,14 +74,14 @@ public class MapControllerIntegrationTestWithGlyph extends ControllerIntegration
RequestBuilder request = get("/minerva/api/projects/" + TEST_PROJECT + "/models/" + map.getId() + ":downloadImage?"
+ "handlerClass=" + PngImageGenerator.class.getCanonicalName())
- .session(session);
+ .session(session);
mockMvc.perform(request)
.andExpect(status().is2xxSuccessful());
}
@Test
- public void testGetMapsWithForProject() throws Exception {
+ public void testDocsGetMapsWithForProject() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
RequestBuilder request = get("/minerva/api/projects/{projectId}/models/", BUILT_IN_PROJECT).session(session);
@@ -96,7 +94,7 @@ public class MapControllerIntegrationTestWithGlyph extends ControllerIntegration
}
@Test
- public void testGetAllElements() throws Exception {
+ public void testDocsGetAllElements() throws Exception {
userService.grantUserPrivilege(anonymous, PrivilegeType.READ_PROJECT, project.getProjectId());
RequestBuilder request = get("/minerva/api/projects/{projectId}/models/{mapId}/bioEntities/elements/", TEST_PROJECT, "*");
@@ -118,7 +116,7 @@ public class MapControllerIntegrationTestWithGlyph extends ControllerIntegration
}
@Test
- public void testGetMapById() throws Exception {
+ public void testDocsGetMapById() throws Exception {
userService.grantUserPrivilege(anonymous, PrivilegeType.READ_PROJECT, project.getProjectId());
RequestBuilder request = get("/minerva/api/projects/{projectId}/models/{mapId}", TEST_PROJECT, map.getId());
@@ -151,13 +149,13 @@ public class MapControllerIntegrationTestWithGlyph extends ControllerIntegration
}
@Test
- public void testDownloadModelByElementList() throws Exception {
+ public void testDocsDownloadModelByElementList() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
RequestBuilder request = get("/minerva/api/projects/{projectId}/models/{mapId}:downloadModel?"
+ "handlerClass=" + CellDesignerXmlParser.class.getCanonicalName()
+ "&elementIds=" + map.getElements().iterator().next().getId(), TEST_PROJECT, map.getId())
- .session(session);
+ .session(session);
mockMvc.perform(request)
.andDo(document("projects/project_maps/download_with_element_list",
@@ -168,12 +166,12 @@ public class MapControllerIntegrationTestWithGlyph extends ControllerIntegration
}
@Test
- public void testDownloadModel() throws Exception {
+ public void testDocsDownloadModel() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
RequestBuilder request = get("/minerva/api/projects/{projectId}/models/{mapId}:downloadModel?"
+ "handlerClass=" + CellDesignerXmlParser.class.getCanonicalName(), TEST_PROJECT, map.getId())
- .session(session);
+ .session(session);
mockMvc.perform(request)
.andDo(document("projects/project_maps/download_model_simple",
@@ -198,13 +196,13 @@ public class MapControllerIntegrationTestWithGlyph extends ControllerIntegration
}
@Test
- public void testDownloadModelByPolygon() throws Exception {
+ public void testDocsDownloadModelByPolygon() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
RequestBuilder request = get("/minerva/api/projects/{projectId}/models/{mapId}:downloadModel?"
+ "handlerClass=" + CellDesignerXmlParser.class.getCanonicalName()
+ "&polygonString=0,0;100,0;0,100&strictCutoff=false", TEST_PROJECT, map.getId())
- .session(session);
+ .session(session);
mockMvc.perform(request)
.andDo(document("projects/project_maps/download_from_polygon",
diff --git a/web/src/test/java/lcsb/mapviewer/web/MeshControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/MeshControllerIntegrationTest.java
index 5e311400d5d6fbabfb38737395fdb8aebb315e39..6c7ffe2fa4008432d3b1ebe1aa3d2ed8252701a3 100644
--- a/web/src/test/java/lcsb/mapviewer/web/MeshControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/MeshControllerIntegrationTest.java
@@ -13,18 +13,6 @@ import org.springframework.test.web.servlet.RequestBuilder;
import java.util.Map;
-import com.fasterxml.jackson.core.type.TypeReference;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.junit.runner.RunWith;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
-import org.springframework.test.web.servlet.RequestBuilder;
-
-import java.util.Map;
-
import static org.junit.Assert.assertTrue;
import static org.springframework.restdocs.mockmvc.MockMvcRestDocumentation.document;
import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.get;
@@ -49,7 +37,7 @@ public class MeshControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void testGetMesh() throws Exception {
+ public void testDocsGetMesh() throws Exception {
RequestBuilder request = get("/minerva/api/mesh/{meshId}", "D010300");
diff --git a/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java
index 95a71410de0e1850b4b74e55a5764218e8e5ae00..6dd0ad29820357f0138b691d8e6f6e553abd8593 100644
--- a/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java
@@ -102,7 +102,7 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testListOverlaysByCreator() throws Exception {
+ public void testDocsListOverlaysByCreator() throws Exception {
createOverlay(TEST_PROJECT, user);
@@ -153,7 +153,7 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testCuratorShouldSeeAllOverlays() throws Exception {
+ public void testDocsCuratorShouldSeeAllOverlays() throws Exception {
final DataOverlay layout = createOverlay(TEST_PROJECT, project.getOwner());
layout.setPublic(true);
@@ -225,7 +225,7 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testAdminCanAccessUserOverlay() throws Exception {
+ public void testDocsAdminCanAccessUserOverlay() throws Exception {
final DataOverlay overlay = createOverlay(TEST_PROJECT, user);
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
@@ -280,7 +280,7 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testGetBioEntitiesForOverlay() throws Exception {
+ public void testDocsGetBioEntitiesForOverlay() throws Exception {
final ModelData submap = map.getSubmodels().iterator().next().getSubmodel();
final String content = createOverlayContentForAllEntities(map);
final DataOverlay overlay = createOverlay(project, user, content);
@@ -456,7 +456,7 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testGetReactionForOverlay() throws Exception {
+ public void testDocsGetReactionForOverlay() throws Exception {
final DataOverlay overlay = createOverlay(user);
final MockHttpSession session = createSession(TEST_USER_LOGIN, TEST_USER_PASSWORD);
@@ -501,7 +501,7 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testGetReactionForOverlayWithColor() throws Exception {
+ public void testDocsGetReactionForOverlayWithColor() throws Exception {
final DataOverlay overlay = createOverlayWithColor(project, user);
final MockHttpSession session = createSession(TEST_USER_LOGIN, TEST_USER_PASSWORD);
@@ -550,7 +550,7 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testGetElementsForOverlay() throws Exception {
+ public void testDocsGetElementsForOverlay() throws Exception {
final User admin = userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN);
final DataOverlay overlay = createOverlay(admin);
@@ -600,7 +600,7 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testAdminCreateOverlay() throws Exception {
+ public void testDocsAdminCreateOverlay() throws Exception {
final User admin = userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN);
final UploadedFileEntry file = createFile("element_identifier\tvalue\n\t-1", admin);
@@ -630,7 +630,7 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testAdminCreateOverlayFromContent() throws Exception {
+ public void testDocsAdminCreateOverlayFromContent() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
final String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
@@ -731,7 +731,7 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testAdminCanRemoveOverlay() throws Exception {
+ public void testDocsAdminCanRemoveOverlay() throws Exception {
final DataOverlay overlay = createOverlay(user);
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
@@ -788,7 +788,7 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testAdminCanUpdateOverlay() throws Exception {
+ public void testDocsAdminCanUpdateOverlay() throws Exception {
final DataOverlay overlay = createOverlay(user);
final Map<String, Object> updateOverlay =
@@ -883,7 +883,7 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testAdminCanAccessOverlaySource() throws Exception {
+ public void testDocsAdminCanAccessOverlaySource() throws Exception {
final DataOverlay overlay = createOverlay(user);
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
@@ -1668,7 +1668,7 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testDownloadOverlayLegend() throws Exception {
+ public void testDocsDownloadOverlayLegend() throws Exception {
final DataOverlay overlay = createOverlay(user);
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
diff --git a/web/src/test/java/lcsb/mapviewer/web/ParameterControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/ParameterControllerIntegrationTest.java
index 2f2d0214d47aa9ec9e59b073f454ee3a817e0c4c..ecaaf997fd40fb9b866bacc7cee04bc52c129057 100644
--- a/web/src/test/java/lcsb/mapviewer/web/ParameterControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/ParameterControllerIntegrationTest.java
@@ -72,7 +72,7 @@ public class ParameterControllerIntegrationTest extends ControllerIntegrationTes
}
@Test
- public void testGetParameters() throws Exception {
+ public void testDocsGetParameters() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
RequestBuilder request = get("/minerva/api/projects/{projectId}/models/{mapId}/parameters/", TEST_PROJECT, "*")
@@ -87,7 +87,7 @@ public class ParameterControllerIntegrationTest extends ControllerIntegrationTes
}
@Test
- public void testGetParameter() throws Exception {
+ public void testDocsGetParameter() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
RequestBuilder request = get("/minerva/api/projects/{projectId}/models/{mapId}/parameters/{parameterId}", TEST_PROJECT, "*",
diff --git a/web/src/test/java/lcsb/mapviewer/web/PluginControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/PluginControllerIntegrationTest.java
index 6d5f2947b8baae8596740b32ed8eb2fef9f76f69..505ea66f20d15fc20fe3665672e07b310e1a41f7 100644
--- a/web/src/test/java/lcsb/mapviewer/web/PluginControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/PluginControllerIntegrationTest.java
@@ -70,7 +70,7 @@ public class PluginControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void listPlugins() throws Exception {
+ public void testDocsListPlugins() throws Exception {
createPlugin();
RequestBuilder request = get("/minerva/api/plugins/");
@@ -104,7 +104,7 @@ public class PluginControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void createPublicPluginWithPrivileges() throws Exception {
+ public void testDocsCreatePublicPluginWithPrivileges() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
@@ -146,7 +146,7 @@ public class PluginControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void getPluginInfo() throws Exception {
+ public void testDocsGetPluginInfo() throws Exception {
Plugin plugin = createPlugin();
RequestBuilder request = get("/minerva/api/plugins/{hash}", plugin.getHash());
@@ -246,7 +246,7 @@ public class PluginControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void setAndGetGlobalPluginData() throws Exception {
+ public void testDocsTestDocsSetAndGetGlobalPluginData() throws Exception {
String body = "value=xxx";
Plugin plugin = createPlugin();
@@ -279,7 +279,7 @@ public class PluginControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void setAndGetUserPluginData() throws Exception {
+ public void testDocsSetAndGetUserPluginData() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_LOGIN);
String body = "value=xxx";
diff --git a/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationForDocsTest.java b/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationForDocsTest.java
index 574fc65d93564e434735119f85a0696398a30cc5..93f54874aa2e87f61b55d36fd3135611df24ae0e 100644
--- a/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationForDocsTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationForDocsTest.java
@@ -75,7 +75,7 @@ public class ProjectControllerIntegrationForDocsTest extends ControllerIntegrati
}
@Test
- public void addComplexProjectAsCurator() throws Exception {
+ public void testDocsAddComplexProjectAsCurator() throws Exception {
User admin = userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN);
try {
UploadedFileEntry fileEntry = createFile(
@@ -144,7 +144,7 @@ public class ProjectControllerIntegrationForDocsTest extends ControllerIntegrati
}
@Test
- public void addProjectAsCurator() throws Exception {
+ public void testDocsAddProjectAsCurator() throws Exception {
User admin = userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN);
try {
UploadedFileEntry fileEntry = createFile(
diff --git a/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTest.java
index 29819fe5e649b8e86f2b6fb61ca03bc723b7571b..3b42686a9406118e880c45a247785677c0d2057b 100644
--- a/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTest.java
@@ -115,7 +115,7 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testGetAllProjectsAsAdmin() throws Exception {
+ public void testDocsGetAllProjectsAsAdmin() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
final RequestBuilder request = get("/minerva/api/projects/")
.session(session);
@@ -139,7 +139,7 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testGetSourceFile() throws Exception {
+ public void testDocsGetSourceFile() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
createAndPersistProject(TEST_PROJECT);
final RequestBuilder request = get("/minerva/api/projects/{projectId}:downloadSource", TEST_PROJECT)
@@ -176,7 +176,7 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testGetLimitedProjectsAsGuest() throws Exception {
+ public void testDocsGetLimitedProjectsAsGuest() throws Exception {
final Project project2 = new Project(TEST_PROJECT_2);
project2.setOwner(userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN));
projectService.add(project2);
@@ -198,7 +198,7 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testUserPrivilegesChangeDuringActiveSession() throws Exception {
+ public void testDocsUserPrivilegesChangeDuringActiveSession() throws Exception {
final MockHttpSession session = createSession(CURATOR_LOGIN, CURATOR_PASSWORD);
final Project project = createAndPersistProject(TEST_PROJECT);
@@ -216,7 +216,7 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testGetLogsForProject() throws Exception {
+ public void testDocsGetLogsForProject() throws Exception {
final Project project = createAndPersistProject(TEST_PROJECT);
userService.grantUserPrivilege(curator, PrivilegeType.READ_PROJECT, project.getProjectId());
@@ -258,7 +258,7 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testGetStatisticsForProject() throws Exception {
+ public void testDocsGetStatisticsForProject() throws Exception {
createAndPersistProject(TEST_PROJECT);
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
@@ -281,7 +281,7 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testGrantPrivilege() throws Exception {
+ public void testDocsGrantPrivilege() throws Exception {
createAndPersistProject(TEST_PROJECT);
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
@@ -316,7 +316,7 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testRevokePrivilege() throws Exception {
+ public void testDocsRevokePrivilege() throws Exception {
final Project project = createAndPersistProject(TEST_PROJECT);
userService.grantUserPrivilege(curator, PrivilegeType.READ_PROJECT, project.getProjectId());
@@ -362,7 +362,7 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testUpdateProject() throws Exception {
+ public void testDocsUpdateProject() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
createAndPersistProject(TEST_PROJECT);
@@ -596,7 +596,7 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testGetSubmapConnectionsForProject() throws Exception {
+ public void testDocsGetSubmapConnectionsForProject() throws Exception {
createAndPersistProject(TEST_PROJECT);
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
@@ -721,7 +721,7 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
}
@Test(timeout = 10000)
- public void removeProjectWithUsedFile() throws Exception {
+ public void testDocsRemoveProjectWithUsedFile() throws Exception {
final User admin = userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN);
try {
createFullProject(admin);
@@ -884,7 +884,7 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testGetBackgrounds() throws Exception {
+ public void testDocsGetBackgrounds() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
createAndPersistProject(TEST_PROJECT);
final RequestBuilder request = get("/minerva/api/projects/{projectId}/backgrounds/", TEST_PROJECT)
@@ -966,7 +966,7 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testGetBackgroundById() throws Exception {
+ public void testDocsGetBackgroundById() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
final Project project = createAndPersistProject(TEST_PROJECT);
final RequestBuilder request = get("/minerva/api/projects/{projectId}/backgrounds/{backgroundId}", TEST_PROJECT,
@@ -980,7 +980,7 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testUpdateBackgroundById() throws Exception {
+ public void testDocsUpdateBackgroundById() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
final Project project = createAndPersistProject(TEST_PROJECT);
final ProjectBackground background = new ProjectBackground("weird_title");
@@ -1011,7 +1011,7 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testRemoveBackgroundById() throws Exception {
+ public void testDocsRemoveBackgroundById() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
final User admin = userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN);
@@ -1343,7 +1343,7 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testArchiveProject() throws Exception {
+ public void testDocsArchiveProject() throws Exception {
final Project project = createProjectWithBackground();
final String projectHomeDir = projectService.getProjectHomeDir(project);
@@ -1397,7 +1397,7 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
- public void testReviveProject() throws Exception {
+ public void testDocsReviveProject() throws Exception {
final Project project = createAndPersistProject(TEST_PROJECT);
project.setStatus(ProjectStatus.ARCHIVED);
project.removeProjectBackground(project.getProjectBackgrounds().get(0));
diff --git a/web/src/test/java/lcsb/mapviewer/web/PublicationsControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/PublicationsControllerIntegrationTest.java
index a87d5e2b98ce883b1d1b0fc47977a20246e9ed34..0cf0805e0d59c905f53607e9e7196d7967dddaa5 100644
--- a/web/src/test/java/lcsb/mapviewer/web/PublicationsControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/PublicationsControllerIntegrationTest.java
@@ -43,7 +43,7 @@ public class PublicationsControllerIntegrationTest extends ControllerIntegration
}
@Test
- public void testGetPublicationsForMap() throws Exception {
+ public void testDocsGetPublicationsForMap() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
RequestBuilder request = get("/minerva/api/projects/{projectId}/models/{mapId}/publications/", TEST_PROJECT, map.getId())
diff --git a/web/src/test/java/lcsb/mapviewer/web/TaxonomiesControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/TaxonomiesControllerIntegrationTest.java
index 665cc216f551c53b2618b43e8dc3b75b06fc7195..e965ed0e884639e0e45713341e7c1c8a542281c3 100644
--- a/web/src/test/java/lcsb/mapviewer/web/TaxonomiesControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/TaxonomiesControllerIntegrationTest.java
@@ -1,13 +1,5 @@
package lcsb.mapviewer.web;
-import static org.springframework.restdocs.mockmvc.MockMvcRestDocumentation.document;
-import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.get;
-import static org.springframework.restdocs.payload.PayloadDocumentation.fieldWithPath;
-import static org.springframework.restdocs.payload.PayloadDocumentation.responseFields;
-import static org.springframework.restdocs.request.RequestDocumentation.parameterWithName;
-import static org.springframework.restdocs.request.RequestDocumentation.pathParameters;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
-
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
@@ -16,6 +8,14 @@ import org.springframework.restdocs.payload.JsonFieldType;
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
import org.springframework.test.web.servlet.RequestBuilder;
+import static org.springframework.restdocs.mockmvc.MockMvcRestDocumentation.document;
+import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.get;
+import static org.springframework.restdocs.payload.PayloadDocumentation.fieldWithPath;
+import static org.springframework.restdocs.payload.PayloadDocumentation.responseFields;
+import static org.springframework.restdocs.request.RequestDocumentation.parameterWithName;
+import static org.springframework.restdocs.request.RequestDocumentation.pathParameters;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
+
@RunWith(SpringJUnit4ClassRunner.class)
public class TaxonomiesControllerIntegrationTest extends ControllerIntegrationTest {
@@ -28,7 +28,7 @@ public class TaxonomiesControllerIntegrationTest extends ControllerIntegrationTe
}
@Test
- public void testGetTaxonomy() throws Exception {
+ public void testDocsGetTaxonomy() throws Exception {
RequestBuilder request = get("/minerva/api/taxonomy/{taxonomyId}/", "9606");
diff --git a/web/src/test/java/lcsb/mapviewer/web/UnitsControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/UnitsControllerIntegrationTest.java
index 4d171768d8ec278745ee0eaa832a1bd4055de22b..01eeba221cda5faff91fd3ec3c8185ac5a72de76 100644
--- a/web/src/test/java/lcsb/mapviewer/web/UnitsControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/UnitsControllerIntegrationTest.java
@@ -1,17 +1,7 @@
package lcsb.mapviewer.web;
-import static org.springframework.restdocs.mockmvc.MockMvcRestDocumentation.document;
-import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.get;
-import static org.springframework.restdocs.payload.PayloadDocumentation.fieldWithPath;
-import static org.springframework.restdocs.payload.PayloadDocumentation.responseFields;
-import static org.springframework.restdocs.payload.PayloadDocumentation.subsectionWithPath;
-import static org.springframework.restdocs.request.RequestDocumentation.parameterWithName;
-import static org.springframework.restdocs.request.RequestDocumentation.pathParameters;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
-
-import java.util.Arrays;
-import java.util.List;
-
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.model.ModelData;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
@@ -23,8 +13,17 @@ import org.springframework.restdocs.payload.ResponseFieldsSnippet;
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
import org.springframework.test.web.servlet.RequestBuilder;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.model.ModelData;
+import java.util.Arrays;
+import java.util.List;
+
+import static org.springframework.restdocs.mockmvc.MockMvcRestDocumentation.document;
+import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.get;
+import static org.springframework.restdocs.payload.PayloadDocumentation.fieldWithPath;
+import static org.springframework.restdocs.payload.PayloadDocumentation.responseFields;
+import static org.springframework.restdocs.payload.PayloadDocumentation.subsectionWithPath;
+import static org.springframework.restdocs.request.RequestDocumentation.parameterWithName;
+import static org.springframework.restdocs.request.RequestDocumentation.pathParameters;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
@RunWith(SpringJUnit4ClassRunner.class)
public class UnitsControllerIntegrationTest extends ControllerIntegrationTest {
@@ -66,7 +65,7 @@ public class UnitsControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void testGetUnits() throws Exception {
+ public void testDocsGetUnits() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
RequestBuilder request = get("/minerva/api/projects/{projectId}/models/{mapId}/units/", TEST_PROJECT, "*")
@@ -81,12 +80,12 @@ public class UnitsControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void testGetUnit() throws Exception {
+ public void testDocsGetUnit() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
RequestBuilder request = get("/minerva/api/projects/{projectId}/models/{mapId}/units/{unitId}", TEST_PROJECT, "*",
map.getUnits().iterator().next().getId())
- .session(session);
+ .session(session);
mockMvc.perform(request)
.andDo(document("projects/project_maps/get_unit",
@@ -117,7 +116,7 @@ public class UnitsControllerIntegrationTest extends ControllerIntegrationTest {
private ResponseFieldsSnippet listOfUnitsFields() {
return responseFields(
fieldWithPath("[]").description("list of units"))
- .andWithPrefix("[].", unitFields());
+ .andWithPrefix("[].", unitFields());
}
}
diff --git a/web/src/test/java/lcsb/mapviewer/web/UserControllerAnonymousIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/UserControllerAnonymousIntegrationTest.java
index b60a5c673370d2e415d9f4dfc0fe67e935140fd1..08244ac91ae8fe14053ce300892f0ca7dc5aa9cb 100644
--- a/web/src/test/java/lcsb/mapviewer/web/UserControllerAnonymousIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/UserControllerAnonymousIntegrationTest.java
@@ -97,7 +97,7 @@ public class UserControllerAnonymousIntegrationTest extends ControllerIntegratio
}
@Test
- public void checkIsAuthenticatedAdmin() throws Exception {
+ public void testDocsCheckIsAuthenticatedAdmin() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
RequestBuilder request = get("/minerva/api/users/isSessionValid")
@@ -131,7 +131,7 @@ public class UserControllerAnonymousIntegrationTest extends ControllerIntegratio
}
@Test
- public void testLogin() throws Exception {
+ public void testDocsLogin() throws Exception {
RequestBuilder request = post("/minerva/api/doLogin")
.contentType(MediaType.APPLICATION_FORM_URLENCODED)
.content("login=" + BUILT_IN_TEST_ADMIN_LOGIN + "&password=" + BUILT_IN_TEST_ADMIN_PASSWORD);
@@ -150,7 +150,7 @@ public class UserControllerAnonymousIntegrationTest extends ControllerIntegratio
}
@Test
- public void testLogout() throws Exception {
+ public void testDocsLogout() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
RequestBuilder request = post("/minerva/api/doLogout")
diff --git a/web/src/test/java/lcsb/mapviewer/web/UserControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/UserControllerIntegrationTest.java
index d8a03626b9c9ea62ab5c70a41a09f86bddc40e25..c3f2d496aeb7a4033e7c4cff10f6a5052a8a840b 100644
--- a/web/src/test/java/lcsb/mapviewer/web/UserControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/UserControllerIntegrationTest.java
@@ -115,7 +115,7 @@ public class UserControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void grantPrivilege() throws Exception {
+ public void testDocsGrantPrivilege() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
UserPrivilegesDTO data = new UserPrivilegesDTO();
@@ -184,7 +184,7 @@ public class UserControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void grantProjectPrivilege() throws Exception {
+ public void testDocsGrantProjectPrivilege() throws Exception {
Project project = new Project(TEST_PROJECT);
project.setOwner(userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN));
projectService.add(project);
@@ -296,7 +296,7 @@ public class UserControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void fetchUserPrivilege() throws Exception {
+ public void testDocsFetchUserPrivilege() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
RequestBuilder request = get("/minerva/api/users/{login}", TEST_USER_LOGIN)
@@ -407,7 +407,7 @@ public class UserControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void testAddUser() throws Exception {
+ public void testDocsAddUser() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
@@ -490,7 +490,7 @@ public class UserControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void userUpdateOwnPassword() throws Exception {
+ public void testDocsUserUpdateOwnPassword() throws Exception {
MockHttpSession session = createSession(TEST_USER_LOGIN, TEST_USER_PASSWORD);
String newPassword = "new pass";
@@ -633,7 +633,7 @@ public class UserControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void removeUserWithLayouts() throws Exception {
+ public void testDocsRemoveUserWithLayouts() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
Project project = new Project(TEST_PROJECT);
@@ -675,7 +675,7 @@ public class UserControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void testGetUsers() throws Exception {
+ public void testDocsGetUsers() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
RequestBuilder grantRequest = get("/minerva/api/users/")
@@ -846,7 +846,7 @@ public class UserControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void updateProjectUploadPreferences() throws Exception {
+ public void testDocsUpdateProjectUploadPreferences() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
UserAnnotationSchema preferences = new UserAnnotationSchema();
@@ -874,7 +874,7 @@ public class UserControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void updateElementAnnotatorsPreferences() throws Exception {
+ public void testDocsUpdateElementAnnotatorsPreferences() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
UserAnnotationSchema preferences = new UserAnnotationSchema();
@@ -912,7 +912,7 @@ public class UserControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void updateGuiPreferences() throws Exception {
+ public void testDocsUpdateGuiPreferences() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
UserAnnotationSchema preferences = new UserAnnotationSchema();
@@ -1128,7 +1128,7 @@ public class UserControllerIntegrationTest extends ControllerIntegrationTest {
}
@Test
- public void registerNewUser() throws Exception {
+ public void testDocsRegisterNewUser() throws Exception {
try {
configurationService.setConfigurationValue(ConfigurationElementType.MINERVA_ROOT,
"https://minerva-dev.lcsb.uni.lu/minerva/");
diff --git a/web/src/test/java/lcsb/mapviewer/web/UserControllerIntegrationTestWithoutTransaction.java b/web/src/test/java/lcsb/mapviewer/web/UserControllerIntegrationWithoutTransactionTest.java
similarity index 96%
rename from web/src/test/java/lcsb/mapviewer/web/UserControllerIntegrationTestWithoutTransaction.java
rename to web/src/test/java/lcsb/mapviewer/web/UserControllerIntegrationWithoutTransactionTest.java
index e8e4923cd466d15e01cdcd9df91eb30bf4503e85..1425ffe6e6da73bdca9616e46a16735637858256 100644
--- a/web/src/test/java/lcsb/mapviewer/web/UserControllerIntegrationTestWithoutTransaction.java
+++ b/web/src/test/java/lcsb/mapviewer/web/UserControllerIntegrationWithoutTransactionTest.java
@@ -48,7 +48,7 @@ import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.
@RunWith(SpringJUnit4ClassRunner.class)
@Rollback
@ActiveProfiles("EmailSenderEnabledEmailProfile")
-public class UserControllerIntegrationTestWithoutTransaction extends ControllerIntegrationTest {
+public class UserControllerIntegrationWithoutTransactionTest extends ControllerIntegrationTest {
private static final String TEST_USER_LOGIN_2 = "test_user2";
@@ -141,7 +141,7 @@ public class UserControllerIntegrationTestWithoutTransaction extends ControllerI
final int status = mockMvc.perform(request).andReturn().getResponse().getStatus();
assertNotEquals(500, status);
} catch (final Throwable e) {
- e.printStackTrace();
+ logger.error(e, e);
exceptionHappened.setTrue();
}
}
@@ -203,7 +203,7 @@ public class UserControllerIntegrationTestWithoutTransaction extends ControllerI
public void requestResetPasswordForUnknownUser() throws Exception {
configureServerForResetPasswordRequest();
- final RequestBuilder grantRequest = post("/minerva/api/users/blabla:requestResetPassword");
+ final RequestBuilder grantRequest = post("/minerva/api/users/blah:requestResetPassword");
mockMvc.perform(grantRequest)
.andExpect(status().is4xxClientError());
@@ -211,7 +211,7 @@ public class UserControllerIntegrationTestWithoutTransaction extends ControllerI
}
@Test
- public void resetPassword() throws Exception {
+ public void testDocsResetPassword() throws Exception {
configureServerForResetPasswordRequest();
final String newPassword = "pass2";
@@ -284,7 +284,7 @@ public class UserControllerIntegrationTestWithoutTransaction extends ControllerI
}
@Test
- public void confirmReigstrationOfNewUser() throws Exception {
+ public void testDocsConfirmRegistrationOfNewUser() throws Exception {
configureServerForResetPasswordRequest();
User user = userService.getUserByLogin(TEST_USER_LOGIN);
@@ -342,7 +342,7 @@ public class UserControllerIntegrationTestWithoutTransaction extends ControllerI
}
@Test
- public void confirmReigstrationOfNewUserWithNotRequiredApproval() throws Exception {
+ public void confirmRegistrationOfNewUserWithNotRequiredApproval() throws Exception {
configureServerForResetPasswordRequest();
configurationService.setConfigurationValue(ConfigurationElementType.REQUIRE_APPROVAL_FOR_AUTO_REGISTERED_USERS,
"false");
@@ -379,7 +379,7 @@ public class UserControllerIntegrationTestWithoutTransaction extends ControllerI
configurationService.setConfigurationValue(ConfigurationElementType.ALLOW_AUTO_REGISTER, "true");
final Map<String, Object> data = new HashMap<>();
data.put("email", "blah");
- data.put("password", "123qweasdzxc");
+ data.put("password", "123blah");
data.put("name", "Piotr");
data.put("surname", "Gawron");
@@ -393,7 +393,7 @@ public class UserControllerIntegrationTestWithoutTransaction extends ControllerI
}
@Test
- public void confirmReigstrationOfNewUserWithInvlaidToken() throws Exception {
+ public void confirmRegistrationOfNewUserWithInvalidToken() throws Exception {
configureServerForResetPasswordRequest();
User user = userService.getUserByLogin(TEST_USER_LOGIN);
@@ -419,7 +419,7 @@ public class UserControllerIntegrationTestWithoutTransaction extends ControllerI
}
@Test
- public void resetPasswordWithExpredToken() throws Exception {
+ public void resetPasswordWithExpiredToken() throws Exception {
configureServerForResetPasswordRequest();
final Calendar expires = Calendar.getInstance();
@@ -441,7 +441,7 @@ public class UserControllerIntegrationTestWithoutTransaction extends ControllerI
}
@Test
- public void requestResetPassword() throws Exception {
+ public void testDocsRequestResetPassword() throws Exception {
final long count = userService.getPasswordTokenCount();
configureServerForResetPasswordRequest();
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/NewApiDocs.java b/web/src/test/java/lcsb/mapviewer/web/api/NewApiDocs.java
index f09af5dd47ed71b1b883efc969018f314108b1b8..ad3c9406ca953663e2d65d5b662f2c727fe25061 100644
--- a/web/src/test/java/lcsb/mapviewer/web/api/NewApiDocs.java
+++ b/web/src/test/java/lcsb/mapviewer/web/api/NewApiDocs.java
@@ -10,6 +10,7 @@ import org.apache.logging.log4j.Logger;
import org.springframework.restdocs.payload.FieldDescriptor;
import org.springframework.restdocs.payload.JsonFieldType;
import org.springframework.restdocs.payload.RequestFieldsSnippet;
+import org.springframework.restdocs.request.ParameterDescriptor;
import org.springframework.restdocs.request.RequestParametersSnippet;
import org.springframework.restdocs.snippet.Snippet;
@@ -54,6 +55,10 @@ public class NewApiDocs {
return new NewApiDocs().getProjectFields(prefix);
}
+ public static List<FieldDescriptor> getJobResponse(final String prefix) {
+ return new NewApiDocs().getJobFields(prefix);
+ }
+
public static List<FieldDescriptor> getUserResponse(final String prefix) {
return new NewApiDocs().getUserFields(prefix);
}
@@ -118,6 +123,46 @@ public class NewApiDocs {
.optional());
}
+ public static RequestFieldsSnippet getCreateProjectFields() {
+ return requestFields(
+ fieldWithPath("projectId")
+ .type(JsonFieldType.STRING)
+ .description("project identifier"),
+ fieldWithPath("name")
+ .type(JsonFieldType.STRING)
+ .description("name"),
+ fieldWithPath("version")
+ .type(JsonFieldType.STRING)
+ .description("version"),
+ fieldWithPath("notifyEmail")
+ .type(JsonFieldType.STRING)
+ .description("email used for notifications about this project"),
+ fieldWithPath("sbgnFormat")
+ .type(JsonFieldType.BOOLEAN)
+ .description("should the project be visualized using sbgn standard")
+ );
+ }
+
+ public static RequestFieldsSnippet getUpdateProjectFields() {
+ return requestFields(
+ fieldWithPath("projectId")
+ .type(JsonFieldType.STRING)
+ .description("project identifier"),
+ fieldWithPath("name")
+ .type(JsonFieldType.STRING)
+ .description("name"),
+ fieldWithPath("version")
+ .type(JsonFieldType.STRING)
+ .description("version"),
+ fieldWithPath("notifyEmail")
+ .type(JsonFieldType.STRING)
+ .description("email used for notifications about this project"),
+ fieldWithPath("sbgnFormat")
+ .type(JsonFieldType.BOOLEAN)
+ .description("should the project be visualized using sbgn standard")
+ );
+ }
+
public static RequestFieldsSnippet getReactionCsvRequest() {
return requestFields(new NewApiDocs().getReactionCsvFields());
}
@@ -172,6 +217,112 @@ public class NewApiDocs {
);
}
+ public static RequestFieldsSnippet getAddUserRequest() {
+ return requestFields(
+ fieldWithPath("name")
+ .description("first name")
+ .type(JsonFieldType.STRING),
+ fieldWithPath("surname")
+ .description("family name")
+ .type(JsonFieldType.STRING),
+ fieldWithPath("login")
+ .description("login")
+ .type(JsonFieldType.STRING),
+ fieldWithPath("orcidId")
+ .description("orcid identifier (https://orcid.org/)")
+ .optional()
+ .type(JsonFieldType.STRING),
+ fieldWithPath("password")
+ .description("password")
+ .type(JsonFieldType.STRING),
+ fieldWithPath("email")
+ .description("email")
+ .type(JsonFieldType.STRING),
+ fieldWithPath("connectedToLdap")
+ .description("is the account connected to ldap")
+ .type(JsonFieldType.BOOLEAN),
+ fieldWithPath("active")
+ .description("is active")
+ .type(JsonFieldType.BOOLEAN),
+ fieldWithPath("termsOfUseConsent")
+ .description("did user consent to the terms of use")
+ .type(JsonFieldType.BOOLEAN)
+ );
+ }
+
+ public static RequestFieldsSnippet getAddPluginRequest() {
+ return requestFields(
+ fieldWithPath("name")
+ .description("name")
+ .type(JsonFieldType.STRING),
+ fieldWithPath("version")
+ .description("version of the plugin")
+ .type(JsonFieldType.STRING),
+ fieldWithPath("url")
+ .description("location of the javascript file")
+ .type(JsonFieldType.STRING),
+ fieldWithPath("public")
+ .description("should the plugin be listed in the browser")
+ .type(JsonFieldType.BOOLEAN),
+ fieldWithPath("default")
+ .description("should the plugin be loaded by default when opening diagram browser")
+ .optional()
+ .type(JsonFieldType.BOOLEAN),
+ fieldWithPath("hash")
+ .description("hash of plugin javascript file")
+ .type(JsonFieldType.STRING)
+ );
+ }
+
+ public static RequestFieldsSnippet getGrantUserPrivilegeRequest() {
+ return requestFields(
+ fieldWithPath("privilegeType")
+ .description("typo of privilege")
+ .type(JsonFieldType.STRING),
+ fieldWithPath("objectId")
+ .description("referenced object id (if necessary)")
+ .optional()
+ .type(JsonFieldType.STRING)
+ );
+ }
+
+ public static RequestFieldsSnippet getRegisterUserRequest() {
+ return requestFields(
+ fieldWithPath("email")
+ .description("user email (and login)")
+ .type(JsonFieldType.STRING),
+ fieldWithPath("login")
+ .ignored(),
+ fieldWithPath("orcidId")
+ .ignored(),
+ fieldWithPath("connectedToLdap")
+ .ignored(),
+ fieldWithPath("active")
+ .ignored(),
+ fieldWithPath("termsOfUseConsent")
+ .ignored(),
+ fieldWithPath("password")
+ .description("password")
+ .type(JsonFieldType.STRING),
+ fieldWithPath("name")
+ .description("given name)")
+ .type(JsonFieldType.STRING),
+ fieldWithPath("surname")
+ .description("family name")
+ .type(JsonFieldType.STRING));
+ }
+
+ public static RequestFieldsSnippet getPasswordResetRequest() {
+ return requestFields(
+ fieldWithPath("password")
+ .description("new password")
+ .type(JsonFieldType.STRING),
+ fieldWithPath("token")
+ .description("reset password token obtained using email")
+ .type(JsonFieldType.STRING)
+ );
+ }
+
public static RequestFieldsSnippet getAddDataOverlayGroupRequest() {
return requestFields(
fieldWithPath("name")
@@ -272,6 +423,26 @@ public class NewApiDocs {
);
}
+ public static List<ParameterDescriptor> getLogsSearchFilter() {
+ return Arrays.asList(
+ parameterWithName("level")
+ .description("warning level")
+ .optional(),
+ parameterWithName("sort")
+ .description("sort order")
+ .optional(),
+ parameterWithName("LEVEL.dir")
+ .ignored()
+ .description("sort order direction"),
+ parameterWithName("<SORT>.dir")
+ .optional()
+ .description("sort order direction"),
+ parameterWithName("search")
+ .optional()
+ .description("search query")
+ );
+ }
+
private List<FieldDescriptor> getOverlayBioEntityPairFields(final String prefix) {
final List<FieldDescriptor> result = new ArrayList<>();
result.addAll(Arrays.asList(
@@ -1124,6 +1295,7 @@ public class NewApiDocs {
.type(JsonFieldType.STRING),
fieldWithPath(prefix + "topMap.id")
.description("id of the top map")
+ .optional()
.type(JsonFieldType.NUMBER),
fieldWithPath(prefix + "logEntries")
.description("flag indicating that there are log entries attached to the project")
@@ -1138,6 +1310,31 @@ public class NewApiDocs {
.optional());
}
+ public List<FieldDescriptor> getJobFields(final String prefix) {
+ return Arrays.asList(
+ fieldWithPath(prefix + "id")
+ .description("job id")
+ .type(JsonFieldType.NUMBER),
+ fieldWithPath(prefix + "jobType")
+ .description("job type")
+ .type(JsonFieldType.STRING),
+ fieldWithPath(prefix + "jobStatus")
+ .description("job status")
+ .type(JsonFieldType.STRING),
+ fieldWithPath(prefix + "jobStarted")
+ .description("when the job execution started")
+ .optional()
+ .type(JsonFieldType.STRING),
+ fieldWithPath(prefix + "jobFinished")
+ .description("when the job execution finished")
+ .optional()
+ .type(JsonFieldType.STRING),
+ fieldWithPath(prefix + "priority")
+ .description("job priority (1 is the highest priority)")
+ .type(JsonFieldType.NUMBER)
+ );
+ }
+
public List<FieldDescriptor> getUserFields(final String prefix) {
return Arrays.asList(
fieldWithPath(prefix + "id")
@@ -1218,6 +1415,38 @@ public class NewApiDocs {
);
}
+ public List<FieldDescriptor> getProjectLogFields(final String prefix) {
+ return Arrays.asList(
+ subsectionWithPath(prefix + "id")
+ .description("log entry id")
+ .type(JsonFieldType.NUMBER),
+ subsectionWithPath(prefix + "content")
+ .description("log entry content")
+ .type(JsonFieldType.STRING),
+ subsectionWithPath(prefix + "severity")
+ .description("log entry level")
+ .type(JsonFieldType.STRING),
+ subsectionWithPath(prefix + "type")
+ .description("type of the entry")
+ .type(JsonFieldType.STRING),
+ subsectionWithPath(prefix + "objectIdentifier")
+ .description("element identifier related to the log entry")
+ .optional()
+ .type(JsonFieldType.STRING),
+ subsectionWithPath(prefix + "objectClass")
+ .description("element identifier type related to the log entry")
+ .optional()
+ .type(JsonFieldType.STRING),
+ subsectionWithPath(prefix + "mapName")
+ .description("map name where element is located")
+ .type(JsonFieldType.STRING),
+ subsectionWithPath(prefix + "source")
+ .description("which module reported the error")
+ .optional()
+ .type(JsonFieldType.STRING)
+ );
+ }
+
public List<FieldDescriptor> getPluginFields(final String prefix) {
return Arrays.asList(
fieldWithPath(prefix + "hash")
@@ -1509,6 +1738,65 @@ public class NewApiDocs {
return responseFields(fields);
}
+ public static Snippet getPluginsSearchResult() {
+ final String prefix = "content[].";
+ final List<FieldDescriptor> fields = new ArrayList<>();
+ fields.add(fieldWithPath("content")
+ .description("list of plugins on the page")
+ .type(JsonFieldType.ARRAY));
+ fields.addAll(getPluginResponse(prefix));
+ fields.addAll(getPageableFields());
+ return responseFields(fields);
+ }
+
+ public static Snippet getLayerImagesSearchResult() {
+ final String prefix = "content[].";
+ final List<FieldDescriptor> fields = new ArrayList<>();
+ fields.add(fieldWithPath("content")
+ .description("list of layer images on the page")
+ .type(JsonFieldType.ARRAY));
+ fields.addAll(getLayerImageResponse(prefix));
+ fields.addAll(getPageableFields());
+ return responseFields(fields);
+ }
+
+ public static Snippet getLayerTextsSearchResult() {
+ final String prefix = "content[].";
+ final List<FieldDescriptor> fields = new ArrayList<>();
+ fields.add(fieldWithPath("content")
+ .description("list of layer texts on the page")
+ .type(JsonFieldType.ARRAY));
+ fields.addAll(getLayerTextResponse(prefix));
+ fields.addAll(getPageableFields());
+ return responseFields(fields);
+ }
+
+ public static Snippet getProjectsSearchResult() {
+ final String prefix = "content[].";
+ final List<FieldDescriptor> fields = new ArrayList<>();
+ fields.add(fieldWithPath("content")
+ .description("list of projects on the page")
+ .type(JsonFieldType.ARRAY));
+ fields.addAll(getProjectResponse(prefix));
+ fields.addAll(getPageableFields());
+ return responseFields(fields);
+ }
+
+ public static Snippet getProjectLogsSearchResult() {
+ final String prefix = "content[].";
+ final List<FieldDescriptor> fields = new ArrayList<>();
+ fields.add(fieldWithPath("content")
+ .description("list of projects on the page")
+ .type(JsonFieldType.ARRAY));
+ fields.addAll(getProjectLogResponse(prefix));
+ fields.addAll(getPageableFields());
+ return responseFields(fields);
+ }
+
+ public static List<FieldDescriptor> getProjectLogResponse(final String prefix) {
+ return new NewApiDocs().getProjectLogFields(prefix);
+ }
+
public static Snippet getUserSearchResult() {
final String prefix = "content[].";
final List<FieldDescriptor> fields = new ArrayList<>();
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/plugin/NewPluginControllerTest.java b/web/src/test/java/lcsb/mapviewer/web/api/plugin/NewPluginControllerTest.java
index 2fefda636c93b71a406a9f0e01fb87d33c41fe8d..7d7ad5c1023a5872cea9b14a65a2d51559d27e36 100644
--- a/web/src/test/java/lcsb/mapviewer/web/api/plugin/NewPluginControllerTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/api/plugin/NewPluginControllerTest.java
@@ -1,5 +1,6 @@
package lcsb.mapviewer.web.api.plugin;
+import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.ObjectMapper;
import lcsb.mapviewer.model.plugin.Plugin;
import lcsb.mapviewer.services.interfaces.IPluginService;
@@ -11,6 +12,7 @@ import org.junit.Before;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.data.domain.Page;
import org.springframework.http.MediaType;
import org.springframework.mock.web.MockHttpServletResponse;
import org.springframework.mock.web.MockHttpSession;
@@ -19,6 +21,8 @@ import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
import org.springframework.test.web.servlet.RequestBuilder;
import javax.servlet.http.HttpServletResponse;
+import java.util.ArrayList;
+import java.util.List;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotEquals;
@@ -30,6 +34,7 @@ import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuild
import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.post;
import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.put;
import static org.springframework.restdocs.payload.PayloadDocumentation.responseFields;
+import static org.springframework.restdocs.request.RequestDocumentation.pathParameters;
import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
@RunWith(SpringJUnit4ClassRunner.class)
@@ -48,23 +53,27 @@ public class NewPluginControllerTest extends ControllerIntegrationTest {
private ObjectMapper objectMapper;
+ private List<String> pluginHashes = new ArrayList<>();
+
@Before
public void setUp() throws Exception {
objectMapper = newApiResponseSerializer.getObjectMapper();
+ pluginHashes = new ArrayList<>();
}
@After
public void tearDown() throws Exception {
- Plugin plugin = pluginService.getByHash(PLUGIN_HASH);
- if (plugin != null) {
- pluginService.delete(plugin);
+ for (String hash : pluginHashes) {
+ Plugin plugin = pluginService.getByHash(hash);
+ if (plugin != null) {
+ pluginService.delete(plugin);
+ }
}
}
@Test
- public void testGetPlugin() throws Exception {
- Plugin plugin = createPlugin(PLUGIN_HASH);
- pluginService.add(plugin);
+ public void testDocsGetPlugin() throws Exception {
+ Plugin plugin = createAndPersistPlugin(PLUGIN_HASH);
final RequestBuilder request = get("/minerva/new_api/plugins/{hash}", plugin.getHash());
@@ -76,11 +85,17 @@ public class NewPluginControllerTest extends ControllerIntegrationTest {
.andExpect(status().is2xxSuccessful());
}
+ private Plugin createAndPersistPlugin(final String hash) {
+ Plugin plugin = createPlugin(hash);
+ persistPlugin(plugin);
+ return plugin;
+ }
+
private static Plugin createPlugin(final String hash) {
Plugin plugin = new Plugin();
plugin.setHash(hash);
- plugin.setName("plugin");
- plugin.setVersion("1.0.0");
+ plugin.setName(faker.name().name());
+ plugin.setVersion(faker.number().digit() + "." + faker.number().digit() + "." + faker.number().digit());
return plugin;
}
@@ -93,7 +108,7 @@ public class NewPluginControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testCreatePlugin() throws Exception {
+ public void testDocsCreatePlugin() throws Exception {
final NewPluginDTO data = createPluginDTO(PLUGIN_HASH);
final RequestBuilder request = post("/minerva/new_api/plugins/")
@@ -102,6 +117,10 @@ public class NewPluginControllerTest extends ControllerIntegrationTest {
final MockHttpServletResponse response = mockMvc.perform(request)
.andExpect(status().isCreated())
+ .andDo(document("new_api/plugins/create_plugin",
+ pathParameters(),
+ NewApiDocs.getAddPluginRequest(),
+ responseFields(NewApiDocs.getPluginResponse(""))))
.andReturn().getResponse();
assertNotNull(response.getHeader("ETag"));
@@ -122,8 +141,7 @@ public class NewPluginControllerTest extends ControllerIntegrationTest {
@Test
public void testCreatePluginExisting() throws Exception {
- Plugin plugin = createPlugin(PLUGIN_HASH);
- pluginService.add(plugin);
+ createAndPersistPlugin(PLUGIN_HASH);
final NewPluginDTO data = createPluginDTO(PLUGIN_HASH);
@@ -140,8 +158,7 @@ public class NewPluginControllerTest extends ControllerIntegrationTest {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
- Plugin plugin = createPlugin(PLUGIN_HASH);
- pluginService.add(plugin);
+ createAndPersistPlugin(PLUGIN_HASH);
final NewPluginDTO data = createPluginDTO(PLUGIN_HASH);
@@ -155,7 +172,7 @@ public class NewPluginControllerTest extends ControllerIntegrationTest {
.andReturn().getResponse();
assertNotNull(response.getHeader("ETag"));
- plugin = pluginService.getByHash(PLUGIN_HASH);
+ Plugin plugin = pluginService.getByHash(PLUGIN_HASH);
assertEquals(data.getVersion(), plugin.getVersion());
}
@@ -164,8 +181,7 @@ public class NewPluginControllerTest extends ControllerIntegrationTest {
public void testUpdatePluginWithMissingData() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
- Plugin plugin = createPlugin(PLUGIN_HASH);
- pluginService.add(plugin);
+ createAndPersistPlugin(PLUGIN_HASH);
final NewPluginDTO data = createPluginDTO(PLUGIN_HASH);
data.setName(null);
@@ -183,8 +199,7 @@ public class NewPluginControllerTest extends ControllerIntegrationTest {
public void testUpdatePluginWithOldVersion() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
- Plugin plugin = createPlugin(PLUGIN_HASH);
- pluginService.add(plugin);
+ createAndPersistPlugin(PLUGIN_HASH);
final NewPluginDTO data = createPluginDTO(PLUGIN_HASH);
@@ -202,8 +217,7 @@ public class NewPluginControllerTest extends ControllerIntegrationTest {
public void testUpdatePluginWithGoodVersion() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
- Plugin plugin = createPlugin(PLUGIN_HASH);
- pluginService.add(plugin);
+ Plugin plugin = createAndPersistPlugin(PLUGIN_HASH);
String originalVersion = plugin.getEntityVersion() + "";
@@ -228,10 +242,9 @@ public class NewPluginControllerTest extends ControllerIntegrationTest {
private NewPluginDTO createPluginDTO(final String hash) {
final NewPluginDTO data = new NewPluginDTO();
- data.setName("my name");
+ data.setName(faker.name().name());
data.setHash(hash);
- data.setName("starter-kit");
- data.setVersion("0.0.1");
+ data.setVersion(faker.number().digit() + "." + faker.number().digit() + "." + faker.number().digit());
data.setUrl(PLUGIN_URL);
return data;
}
@@ -241,8 +254,7 @@ public class NewPluginControllerTest extends ControllerIntegrationTest {
public void testDeletePlugin() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
- Plugin plugin = createPlugin(PLUGIN_HASH);
- pluginService.add(plugin);
+ createAndPersistPlugin(PLUGIN_HASH);
final RequestBuilder request = delete("/minerva/new_api/plugins/{pluginId}/", PLUGIN_HASH)
.session(session);
@@ -267,8 +279,7 @@ public class NewPluginControllerTest extends ControllerIntegrationTest {
@Test
public void testDeleteNoAccessPlugin() throws Exception {
- Plugin plugin = createPlugin(PLUGIN_HASH);
- pluginService.add(plugin);
+ createAndPersistPlugin(PLUGIN_HASH);
final RequestBuilder request = delete("/minerva/new_api/plugins/{pluginId}/", PLUGIN_HASH);
@@ -280,8 +291,7 @@ public class NewPluginControllerTest extends ControllerIntegrationTest {
public void testDeletePluginWithGoodVersion() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
- Plugin plugin = createPlugin(PLUGIN_HASH);
- pluginService.add(plugin);
+ Plugin plugin = createAndPersistPlugin(PLUGIN_HASH);
final String originalVersion = plugin.getEntityVersion() + "";
@@ -297,8 +307,7 @@ public class NewPluginControllerTest extends ControllerIntegrationTest {
public void testDeletePluginWithWrongVersion() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
- Plugin plugin = createPlugin(PLUGIN_HASH);
- pluginService.add(plugin);
+ createAndPersistPlugin(PLUGIN_HASH);
final RequestBuilder request = delete("/minerva/new_api/plugins/{pluginId}/", PLUGIN_HASH)
.header("If-Match", "-1")
@@ -309,10 +318,39 @@ public class NewPluginControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testListPlugins() throws Exception {
+ public void testDocsListPlugins() throws Exception {
+ Plugin plugin = createPlugin(PLUGIN_HASH);
+ plugin.setPublic(true);
+ persistPlugin(plugin);
+
+
+ plugin = createPlugin(faker.hashing().md5());
+ plugin.addUrl(PLUGIN_URL);
+ persistPlugin(plugin);
+
+ plugin = createPlugin(faker.hashing().md5());
+ plugin.addUrl(PLUGIN_URL);
+ persistPlugin(plugin);
+
final RequestBuilder request = get("/minerva/new_api/plugins/");
- mockMvc.perform(request)
- .andExpect(status().isOk());
+ String content = mockMvc.perform(request)
+ .andExpect(status().isOk())
+ .andDo(document("new_api/plugins/list_plugins",
+ pathParameters(),
+ NewApiDocs.getPluginsSearchResult()))
+ .andReturn().getResponse().getContentAsString();
+
+ final Page<Object> page = objectMapper.readValue(content, new TypeReference<Page<Object>>() {
+ });
+ assertEquals(1, page.getTotalElements());
+ assertEquals(0, page.getNumber());
+ assertEquals(1, page.getNumberOfElements());
+
+ }
+
+ private void persistPlugin(final Plugin plugin) {
+ pluginService.add(plugin);
+ pluginHashes.add(plugin.getHash());
}
}
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/project/NewProjectControllerTest.java b/web/src/test/java/lcsb/mapviewer/web/api/project/NewProjectControllerTest.java
index 15a2de3f6a369ac1a576d5747c11e1b10a43d76e..75c4b7c2ac308f498843ed909d3eca8898bd6620 100644
--- a/web/src/test/java/lcsb/mapviewer/web/api/project/NewProjectControllerTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/api/project/NewProjectControllerTest.java
@@ -54,6 +54,8 @@ import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuild
import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.put;
import static org.springframework.restdocs.payload.PayloadDocumentation.fieldWithPath;
import static org.springframework.restdocs.payload.PayloadDocumentation.responseFields;
+import static org.springframework.restdocs.request.RequestDocumentation.pathParameters;
+import static org.springframework.restdocs.request.RequestDocumentation.requestParameters;
import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
@RunWith(SpringJUnit4ClassRunner.class)
@@ -94,7 +96,7 @@ public class NewProjectControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testGetProject() throws Exception {
+ public void testDocsGetProject() throws Exception {
createEmptyProject(TEST_PROJECT);
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
@@ -157,7 +159,7 @@ public class NewProjectControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testCreateProject() throws Exception {
+ public void testDocsCreateProject() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
final NewProjectDTO data = createProjectDTO(TEST_PROJECT);
@@ -169,6 +171,10 @@ public class NewProjectControllerTest extends ControllerIntegrationTest {
final MockHttpServletResponse response = mockMvc.perform(request)
.andExpect(status().isCreated())
+ .andDo(document("new_api/projects/create_project_from_json",
+ pathParameters(),
+ NewApiDocs.getCreateProjectFields(),
+ responseFields(NewApiDocs.getProjectResponse(""))))
.andReturn().getResponse();
assertNotNull(response.getHeader("ETag"));
@@ -191,7 +197,7 @@ public class NewProjectControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testUpdateProject() throws Exception {
+ public void testDocsUpdateProject() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
createEmptyProject(TEST_PROJECT);
@@ -205,6 +211,10 @@ public class NewProjectControllerTest extends ControllerIntegrationTest {
final HttpServletResponse response = mockMvc.perform(request)
.andExpect(status().isOk())
+ .andDo(document("new_api/projects/update_project",
+ projectPathParameters(),
+ NewApiDocs.getUpdateProjectFields(),
+ responseFields(NewApiDocs.getProjectResponse(""))))
.andReturn().getResponse();
assertNotNull(response.getHeader("ETag"));
@@ -275,16 +285,16 @@ public class NewProjectControllerTest extends ControllerIntegrationTest {
private NewProjectDTO createProjectDTO(final String projectId) {
final NewProjectDTO data = new NewProjectDTO();
- data.setName("my name");
- data.setNotifyEmail("minerva@uni.lu");
+ data.setName(faker.name().name());
+ data.setNotifyEmail(faker.internet().emailAddress());
data.setProjectId(projectId);
- data.setSbgnFormat(false);
- data.setVersion("0.0.1");
+ data.setSbgnFormat(faker.bool().bool());
+ data.setVersion(faker.number().randomDigit() + "." + faker.number().randomDigit() + "." + faker.number().randomDigit());
return data;
}
@Test
- public void testDeleteProject() throws Exception {
+ public void testDocsDeleteProject() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
createEmptyProject(TEST_PROJECT);
@@ -293,6 +303,9 @@ public class NewProjectControllerTest extends ControllerIntegrationTest {
final String response = mockMvc.perform(request)
.andExpect(status().isAccepted())
+ .andDo(document("new_api/projects/delete_project",
+ projectPathParameters(),
+ responseFields(NewApiDocs.getJobResponse(""))))
.andReturn().getResponse()
.getContentAsString();
@@ -387,11 +400,23 @@ public class NewProjectControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testListProjects() throws Exception {
- final RequestBuilder request = get("/minerva/new_api/projects/");
+ public void testDocsListProjects() throws Exception {
+ final RequestBuilder request = get("/minerva/new_api/projects/?size=10&page=0");
+
+ String response = mockMvc.perform(request)
+ .andExpect(status().isOk())
+ .andDo(document("new_api/projects/list_projects",
+ requestParameters(getPageableFilter()),
+ NewApiDocs.getProjectsSearchResult()))
+ .andReturn().getResponse().getContentAsString();
+
+ final Page<Object> page = objectMapper.readValue(response, new TypeReference<Page<Object>>() {
+ });
+ assertEquals(1, page.getTotalElements());
+ assertEquals(10, page.getSize());
+ assertEquals(0, page.getNumber());
+ assertEquals(1, page.getNumberOfElements());
- mockMvc.perform(request)
- .andExpect(status().isOk());
}
@Test
@@ -472,7 +497,7 @@ public class NewProjectControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testGetProjects() throws Exception {
+ public void testDocsGetProjects() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
final RequestBuilder request = get("/minerva/new_api/projects/")
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/project/NewProjectLogEntryControllerTest.java b/web/src/test/java/lcsb/mapviewer/web/api/project/NewProjectLogEntryControllerTest.java
index b2b1accdce7d6ab13b7a7d78cf40849385b1f43b..6484d8bf34c70d59482209ae3cc058d1ef543193 100644
--- a/web/src/test/java/lcsb/mapviewer/web/api/project/NewProjectLogEntryControllerTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/api/project/NewProjectLogEntryControllerTest.java
@@ -4,7 +4,9 @@ import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.ObjectMapper;
import lcsb.mapviewer.services.interfaces.IMinervaJobService;
import lcsb.mapviewer.web.ControllerIntegrationTest;
+import lcsb.mapviewer.web.api.NewApiDocs;
import lcsb.mapviewer.web.api.NewApiResponseSerializer;
+import org.apache.commons.collections4.ListUtils;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
@@ -16,7 +18,9 @@ import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
import org.springframework.test.web.servlet.RequestBuilder;
import static org.junit.Assert.assertEquals;
+import static org.springframework.restdocs.mockmvc.MockMvcRestDocumentation.document;
import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.get;
+import static org.springframework.restdocs.request.RequestDocumentation.requestParameters;
import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
@RunWith(SpringJUnit4ClassRunner.class)
@@ -42,17 +46,21 @@ public class NewProjectLogEntryControllerTest extends ControllerIntegrationTest
}
@Test
- public void testGetLogsForProject() throws Exception {
+ public void testDocsGetLogsForProject() throws Exception {
createAndPersistProject(TEST_PROJECT);
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
RequestBuilder request = get(
- "/minerva/new_api/projects/{projectId}/logEntry/?page=1&size=5&level=warning&sort=LEVEL&LEVEL.dir=desc&search=mess",
+ "/minerva/new_api/projects/{projectId}/logEntry/?page=0&size=5&level=warning&sort=LEVEL&LEVEL.dir=desc&search=mess",
TEST_PROJECT).session(session);
String response = mockMvc.perform(request)
.andExpect(status().is2xxSuccessful())
+ .andDo(document("new_api/projects/logs/list",
+ projectPathParameters(),
+ requestParameters(ListUtils.union(NewApiDocs.getLogsSearchFilter(), getPageableFilter())),
+ NewApiDocs.getProjectLogsSearchResult()))
.andReturn().getResponse().getContentAsString();
Page<Object> result = objectMapper.readValue(response, new TypeReference<Page<Object>>() {
});
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/project/chemicals/NewChemicalControllerTest.java b/web/src/test/java/lcsb/mapviewer/web/api/project/chemicals/NewChemicalControllerTest.java
index 766934cedf667c70a38941514421c1c8d257bbc8..0217b3908d3c7d349420d7e1a69992ad21d8155d 100644
--- a/web/src/test/java/lcsb/mapviewer/web/api/project/chemicals/NewChemicalControllerTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/api/project/chemicals/NewChemicalControllerTest.java
@@ -48,7 +48,7 @@ public class NewChemicalControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testSearchChemicalsInProjectUrl() throws Exception {
+ public void testDocsSearchChemicalsInProjectUrl() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
RequestBuilder request = get("/minerva/new_api/projects/{projectId}/chemicals:search?query=stilbene oxide", TEST_PROJECT)
@@ -64,7 +64,7 @@ public class NewChemicalControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testSuggestedQueryList() throws Exception {
+ public void testDocsSuggestedQueryList() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
final MiriamData bloodLossDisease = new MiriamData(MiriamType.MESH_2012, "D016063");
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/project/drugs/NewDrugControllerTest.java b/web/src/test/java/lcsb/mapviewer/web/api/project/drugs/NewDrugControllerTest.java
index 3ea076e86b8adfa5eeabd0492207a3b04193ab8c..e0552850dbccad19ad6af7dbb9c894875963f823 100644
--- a/web/src/test/java/lcsb/mapviewer/web/api/project/drugs/NewDrugControllerTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/api/project/drugs/NewDrugControllerTest.java
@@ -29,7 +29,7 @@ public class NewDrugControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testSearchDrugsInProjectUrl() throws Exception {
+ public void testDocsSearchDrugsInProjectUrl() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
RequestBuilder request = get("/minerva/new_api/projects/{projectId}/drugs:search?query={query}", TEST_PROJECT, "aspirin")
@@ -44,7 +44,7 @@ public class NewDrugControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testSuggestedQueryList() throws Exception {
+ public void testDocsSuggestedQueryList() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
final RequestBuilder request = get(
"/minerva/new_api/projects/{projectId}/drugs/suggestedQueryList", TEST_PROJECT)
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/project/glyph/NewProjectGlyphControllerTest.java b/web/src/test/java/lcsb/mapviewer/web/api/project/glyph/NewProjectGlyphControllerTest.java
index 02d8b3f65a392f8d53af1fe8cd5f16f08489bedd..039a1eae8e47990f46d085d2858931f8cfc8e84d 100644
--- a/web/src/test/java/lcsb/mapviewer/web/api/project/glyph/NewProjectGlyphControllerTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/api/project/glyph/NewProjectGlyphControllerTest.java
@@ -24,6 +24,7 @@ import static org.springframework.restdocs.mockmvc.MockMvcRestDocumentation.docu
import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.get;
import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.multipart;
import static org.springframework.restdocs.payload.PayloadDocumentation.responseFields;
+import static org.springframework.restdocs.request.RequestDocumentation.requestParameters;
import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
@RunWith(SpringJUnit4ClassRunner.class)
@@ -49,7 +50,7 @@ public class NewProjectGlyphControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testGetGlyphsForProject() throws Exception {
+ public void testDocsGetGlyphsForProject() throws Exception {
createProjectWithGlyph(TEST_PROJECT);
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
@@ -62,6 +63,7 @@ public class NewProjectGlyphControllerTest extends ControllerIntegrationTest {
.andExpect(status().is2xxSuccessful())
.andDo(document("new_api/projects/glyphs/list_glyphs",
getProjectPathParameters(),
+ requestParameters(getPageableFilter()),
NewApiDocs.getGlyphsSearchResult()))
.andReturn().getResponse().getContentAsString();
Page<Object> result = objectMapper.readValue(response, new TypeReference<Page<Object>>() {
@@ -70,7 +72,7 @@ public class NewProjectGlyphControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testAddGlyph() throws Exception {
+ public void testDocsAddGlyph() throws Exception {
createProjectWithGlyph(TEST_PROJECT);
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/project/map/bioentity/NewBioEntitiesControllerTest.java b/web/src/test/java/lcsb/mapviewer/web/api/project/map/bioentity/NewBioEntitiesControllerTest.java
index a6e84e78568594686ba38dc6194a7f9d1be9ce98..4064c97fcd315a7e78fe14050d05493a2e8c17dd 100644
--- a/web/src/test/java/lcsb/mapviewer/web/api/project/map/bioentity/NewBioEntitiesControllerTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/api/project/map/bioentity/NewBioEntitiesControllerTest.java
@@ -92,7 +92,7 @@ public class NewBioEntitiesControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testSearchProteinAndDocument() throws Exception {
+ public void testDocsSearchProteinAndDocument() throws Exception {
final RequestBuilder request = get(
"/minerva/new_api/projects/{projectId}/models/{mapId}/bioEntities/:search?query=GSTA&size=20&page=0&perfectMatch=false", TEST_PROJECT, "*");
@@ -111,7 +111,7 @@ public class NewBioEntitiesControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testSearchAnyType() throws Exception {
+ public void testDocsSearchAnyType() throws Exception {
final RequestBuilder request = get(
"/minerva/new_api/projects/{projectId}/models/{mapId}/bioEntities/:search?", TEST_PROJECT, "*");
@@ -156,7 +156,7 @@ public class NewBioEntitiesControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testSuggestedQueryList() throws Exception {
+ public void testDocsSuggestedQueryList() throws Exception {
final RequestBuilder request = get(
"/minerva/new_api/projects/{projectId}/models/{mapId}/bioEntities/suggestedQueryList", TEST_PROJECT, "*");
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/project/map/bioentity/element/NewElementControllerTest.java b/web/src/test/java/lcsb/mapviewer/web/api/project/map/bioentity/element/NewElementControllerTest.java
index 42b92cdcfe77ea6cba10ca53dfecf1f47d2f1155..cb4d32ecfa1c2e7d90dce0ddb1edb019b5ffebf7 100644
--- a/web/src/test/java/lcsb/mapviewer/web/api/project/map/bioentity/element/NewElementControllerTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/api/project/map/bioentity/element/NewElementControllerTest.java
@@ -465,8 +465,6 @@ public class NewElementControllerTest extends ControllerIntegrationTest {
.andReturn().getResponse();
assertNotNull(response.getHeader("ETag"));
- logger.debug(response.getContentAsString());
-
Map<String, Object> result = objectMapper.readValue(response.getContentAsString(), new TypeReference<Map<String, Object>>() {
});
assertNotNull(result.get("sboTerm"));
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/project/map/bioentity/elements/NewElementsControllerTest.java b/web/src/test/java/lcsb/mapviewer/web/api/project/map/bioentity/elements/NewElementsControllerTest.java
index 5526277776e7e1bf2e456b5438531d73e1eec33a..dd0f4a993782e48005bbbac3a45f004269a1a746 100644
--- a/web/src/test/java/lcsb/mapviewer/web/api/project/map/bioentity/elements/NewElementsControllerTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/api/project/map/bioentity/elements/NewElementsControllerTest.java
@@ -70,7 +70,7 @@ public class NewElementsControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testGetElementById() throws Exception {
+ public void testDocsGetElementById() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
Project projectWithGlyph = createProjectWithGlyph(TEST_PROJECT_ID);
try {
@@ -88,14 +88,12 @@ public class NewElementsControllerTest extends ControllerIntegrationTest {
element.getId())
.session(session);
- String response = mockMvc.perform(request)
+ mockMvc.perform(request)
.andExpect(status().is2xxSuccessful())
- .andDo(document("new_api/projects/maps/bioEntites/elements/get_by_id",
+ .andDo(document("new_api/projects/maps/bioEntities/elements/get_by_id",
getElementPathParameters(),
responseFields(NewApiDocs.getElementResponse(""))))
.andReturn().getResponse().getContentAsString();
-
- logger.debug(response);
} finally {
removeProject(projectWithGlyph);
}
@@ -367,7 +365,7 @@ public class NewElementsControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testExportToCsvAndDocument() throws Exception {
+ public void testDocsExportToCsvAndDocument() throws Exception {
Compartment compartment = null;
for (Element element : map.getElements()) {
if (element instanceof Compartment) {
@@ -395,7 +393,7 @@ public class NewElementsControllerTest extends ControllerIntegrationTest {
mockMvc.perform(request)
.andExpect(status().is2xxSuccessful())
- .andDo(document("new_api/projects/maps/bioEntites/elements/export_to_csv",
+ .andDo(document("new_api/projects/maps/bioEntities/elements/export_to_csv",
getMapPathParameters(),
NewApiDocs.getElementCsvRequest()))
.andReturn().getResponse().getContentAsString();
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/project/map/bioentity/reactions/NewReactionsControllerTest.java b/web/src/test/java/lcsb/mapviewer/web/api/project/map/bioentity/reactions/NewReactionsControllerTest.java
index b3750224bc25448fbc32c7ba87f7e6d768987dab..16ef1dc8e3fbc7a7cbbedbcaef70cedb5ff404f2 100644
--- a/web/src/test/java/lcsb/mapviewer/web/api/project/map/bioentity/reactions/NewReactionsControllerTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/api/project/map/bioentity/reactions/NewReactionsControllerTest.java
@@ -1,23 +1,5 @@
package lcsb.mapviewer.web.api.project.map.bioentity.reactions;
-import static org.junit.Assert.assertEquals;
-import static org.springframework.restdocs.mockmvc.MockMvcRestDocumentation.document;
-import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.get;
-import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.post;
-import static org.springframework.restdocs.payload.PayloadDocumentation.responseFields;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
-
-import java.util.Arrays;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.junit.runner.RunWith;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.MediaType;
-import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
-import org.springframework.test.web.servlet.RequestBuilder;
-
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.compartment.Compartment;
@@ -31,6 +13,25 @@ import lcsb.mapviewer.services.interfaces.IUserService;
import lcsb.mapviewer.web.ControllerIntegrationTest;
import lcsb.mapviewer.web.api.NewApiDocs;
import lcsb.mapviewer.web.api.NewApiResponseSerializer;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
+import org.springframework.test.web.servlet.RequestBuilder;
+
+import java.util.Arrays;
+import java.util.Collections;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.springframework.restdocs.mockmvc.MockMvcRestDocumentation.document;
+import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.get;
+import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.post;
+import static org.springframework.restdocs.payload.PayloadDocumentation.responseFields;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
@RunWith(SpringJUnit4ClassRunner.class)
public class NewReactionsControllerTest extends ControllerIntegrationTest {
@@ -41,8 +42,6 @@ public class NewReactionsControllerTest extends ControllerIntegrationTest {
@Autowired
private NewApiResponseSerializer newApiResponseSerializer;
- private User anonymous;
-
private Project project;
private ModelData map;
@@ -52,7 +51,7 @@ public class NewReactionsControllerTest extends ControllerIntegrationTest {
objectMapper = newApiResponseSerializer.getObjectMapper();
project = createAndPersistProject(TEST_PROJECT);
map = project.getTopModel().getModelData();
- anonymous = userService.getUserByLogin(Configuration.ANONYMOUS_LOGIN);
+ User anonymous = userService.getUserByLogin(Configuration.ANONYMOUS_LOGIN);
userService.grantUserPrivilege(anonymous, PrivilegeType.READ_PROJECT, project.getProjectId());
}
@@ -62,24 +61,22 @@ public class NewReactionsControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testGetReactionById() throws Exception {
+ public void testDocsGetReactionById() throws Exception {
RequestBuilder request = get(
"/minerva/new_api/projects/{projectId}/models/{mapId}/bioEntities/reactions/{reactionId}",
TEST_PROJECT, map.getId(), map.getReactions().iterator().next().getId());
- String response = mockMvc.perform(request)
+ mockMvc.perform(request)
.andExpect(status().is2xxSuccessful())
- .andDo(document("new_api/projects/maps/bioEntites/reactions/get_by_id",
+ .andDo(document("new_api/projects/maps/bioEntities/reactions/get_by_id",
getReactionPathParameters(),
responseFields(NewApiDocs.getReactionResponse(""))))
.andReturn().getResponse().getContentAsString();
- logger.debug(response);
-
}
@Test
- public void testGetNonexistingReactionById() throws Exception {
+ public void testGetNotExistingReactionById() throws Exception {
RequestBuilder request = get(
"/minerva/new_api/projects/{projectId}/models/{mapId}/bioEntities/reactions/{reactionId}",
TEST_PROJECT, map.getId(), 0);
@@ -122,8 +119,8 @@ public class NewReactionsControllerTest extends ControllerIntegrationTest {
RequestBuilder request = post(
"/minerva/new_api/projects/{projectId}/models/{mapId}/bioEntities/reactions/:downloadCsv",
TEST_PROJECT, "*")
- .content(objectMapper.writeValueAsBytes(requestBody))
- .contentType(MediaType.APPLICATION_JSON);
+ .content(objectMapper.writeValueAsBytes(requestBody))
+ .contentType(MediaType.APPLICATION_JSON);
String content = mockMvc.perform(request)
.andExpect(status().is2xxSuccessful())
@@ -146,8 +143,8 @@ public class NewReactionsControllerTest extends ControllerIntegrationTest {
RequestBuilder request = post(
"/minerva/new_api/projects/{projectId}/models/{mapId}/bioEntities/reactions/:downloadCsv",
TEST_PROJECT, "*")
- .content(objectMapper.writeValueAsBytes(requestBody))
- .contentType(MediaType.APPLICATION_JSON);
+ .content(objectMapper.writeValueAsBytes(requestBody))
+ .contentType(MediaType.APPLICATION_JSON);
String content = mockMvc.perform(request)
.andExpect(status().is2xxSuccessful())
@@ -166,14 +163,14 @@ public class NewReactionsControllerTest extends ControllerIntegrationTest {
"id",
"modelId"));
- requestBody.setAnnotations(Arrays.asList(
+ requestBody.setAnnotations(Collections.singletonList(
"PUBMED"));
RequestBuilder request = post(
"/minerva/new_api/projects/{projectId}/models/{mapId}/bioEntities/reactions/:downloadCsv",
TEST_PROJECT, "*")
- .content(objectMapper.writeValueAsBytes(requestBody))
- .contentType(MediaType.APPLICATION_JSON);
+ .content(objectMapper.writeValueAsBytes(requestBody))
+ .contentType(MediaType.APPLICATION_JSON);
String content = mockMvc.perform(request)
.andExpect(status().is2xxSuccessful())
@@ -188,123 +185,128 @@ public class NewReactionsControllerTest extends ControllerIntegrationTest {
@Test
public void testExportWithElementTypeToCsv() throws Exception {
DownloadCsvRequest requestBody = new DownloadCsvRequest();
- requestBody.setElementTypes(Arrays.asList(new Drug("").getStringType()));
+ requestBody.setElementTypes(Collections.singletonList(new Drug("").getStringType()));
requestBody.setColumns(Arrays.asList(
"id",
"modelId"));
RequestBuilder request = post(
"/minerva/new_api/projects/{projectId}/models/{mapId}/bioEntities/reactions/:downloadCsv",
TEST_PROJECT, "*")
- .content(objectMapper.writeValueAsBytes(requestBody))
- .contentType(MediaType.APPLICATION_JSON);
+ .content(objectMapper.writeValueAsBytes(requestBody))
+ .contentType(MediaType.APPLICATION_JSON);
String content = mockMvc.perform(request)
.andExpect(status().is2xxSuccessful())
.andReturn().getResponse().getContentAsString();
int lines = content.split("\n").length;
- assertEquals("Ther should be no reaction with Drug", 1, lines);
+ assertEquals("There should be no reaction with Drug", 1, lines);
}
@Test
public void testExportWithElementTypeToCsv2() throws Exception {
DownloadCsvRequest requestBody = new DownloadCsvRequest();
- requestBody.setElementTypes(Arrays.asList(new SimpleMolecule("").getStringType()));
+ requestBody.setElementTypes(Collections.singletonList(new SimpleMolecule("").getStringType()));
requestBody.setColumns(Arrays.asList(
"id",
"modelId"));
RequestBuilder request = post(
"/minerva/new_api/projects/{projectId}/models/{mapId}/bioEntities/reactions/:downloadCsv",
TEST_PROJECT, "*")
- .content(objectMapper.writeValueAsBytes(requestBody))
- .contentType(MediaType.APPLICATION_JSON);
+ .content(objectMapper.writeValueAsBytes(requestBody))
+ .contentType(MediaType.APPLICATION_JSON);
String content = mockMvc.perform(request)
.andExpect(status().is2xxSuccessful())
.andReturn().getResponse().getContentAsString();
int lines = content.split("\n").length;
- assertEquals("Ther should be one reaction with Protein", 2, lines);
+ assertEquals("There should be one reaction with Protein", 2, lines);
}
@Test
public void testExportWithReactionTypeAFToCsv() throws Exception {
DownloadCsvRequest requestBody = new DownloadCsvRequest();
- requestBody.setReactionTypes(Arrays.asList("Activity flow"));
+ requestBody.setReactionTypes(Collections.singletonList("Activity flow"));
requestBody.setColumns(Arrays.asList(
"id",
"modelId"));
RequestBuilder request = post(
"/minerva/new_api/projects/{projectId}/models/{mapId}/bioEntities/reactions/:downloadCsv",
TEST_PROJECT, "*")
- .content(objectMapper.writeValueAsBytes(requestBody))
- .contentType(MediaType.APPLICATION_JSON);
+ .content(objectMapper.writeValueAsBytes(requestBody))
+ .contentType(MediaType.APPLICATION_JSON);
String content = mockMvc.perform(request)
.andExpect(status().is2xxSuccessful())
.andReturn().getResponse().getContentAsString();
int lines = content.split("\n").length;
- assertEquals("Ther should be no AF reaction", 1, lines);
+ assertEquals("There should be no AF reaction", 1, lines);
}
@Test
public void testExportWithReactionTypePDToCsv() throws Exception {
DownloadCsvRequest requestBody = new DownloadCsvRequest();
- requestBody.setReactionTypes(Arrays.asList("Process description"));
+ requestBody.setReactionTypes(Collections.singletonList("Process description"));
requestBody.setColumns(Arrays.asList(
"id",
"modelId"));
RequestBuilder request = post(
"/minerva/new_api/projects/{projectId}/models/{mapId}/bioEntities/reactions/:downloadCsv",
TEST_PROJECT, "*")
- .content(objectMapper.writeValueAsBytes(requestBody))
- .contentType(MediaType.APPLICATION_JSON);
+ .content(objectMapper.writeValueAsBytes(requestBody))
+ .contentType(MediaType.APPLICATION_JSON);
String content = mockMvc.perform(request)
.andExpect(status().is2xxSuccessful())
.andReturn().getResponse().getContentAsString();
int lines = content.split("\n").length;
- assertEquals("Ther should be one PD reaction", 2, lines);
+ assertEquals("There should be one PD reaction", 2, lines);
}
@Test
- public void testExportToCsvAndDocument() throws Exception {
+ public void testDocsExportToCsvAndDocument() throws Exception {
Compartment compartment = null;
for (Element element : map.getElements()) {
if (element instanceof Compartment) {
compartment = (Compartment) element;
}
-
}
+ assertNotNull(compartment);
- DownloadCsvRequest requestBody = new DownloadCsvRequest();
- requestBody.setSubmaps(Arrays.asList(map.getId()));
- requestBody.setElementTypes(Arrays.asList(new SimpleMolecule("").getStringType()));
- requestBody.setIncludedCompartmentIds(Arrays.asList(compartment.getId()));
- requestBody.setReactionTypes(Arrays.asList("Process description"));
- requestBody.setColumns(Arrays.asList(
- "id",
- "modelId"));
- requestBody.setAnnotations(Arrays.asList(
- "PUBMED"));
+ DownloadCsvRequest requestBody = createDownloadCsvRequest(compartment);
RequestBuilder request = post(
"/minerva/new_api/projects/{projectId}/models/{mapId}/bioEntities/reactions/:downloadCsv",
TEST_PROJECT, "*")
- .content(objectMapper.writeValueAsBytes(requestBody))
- .contentType(MediaType.APPLICATION_JSON);
+ .content(objectMapper.writeValueAsBytes(requestBody))
+ .contentType(MediaType.APPLICATION_JSON);
String content = mockMvc.perform(request)
.andExpect(status().is2xxSuccessful())
- .andDo(document("new_api/projects/maps/bioEntites/reactions/export_to_csv",
+ .andDo(document("new_api/projects/maps/bioEntities/reactions/export_to_csv",
getMapPathParameters(),
NewApiDocs.getReactionCsvRequest()))
.andReturn().getResponse().getContentAsString();
int lines = content.split("\n").length;
- assertEquals("Ther should be one PD reaction", 2, lines);
+ assertEquals("There should be one PD reaction", 2, lines);
+ }
+
+ private DownloadCsvRequest createDownloadCsvRequest(final Compartment compartment) {
+ DownloadCsvRequest requestBody = new DownloadCsvRequest();
+ requestBody.setSubmaps(Collections.singletonList(map.getId()));
+ requestBody.setElementTypes(Collections.singletonList(new SimpleMolecule("").getStringType()));
+ requestBody.setIncludedCompartmentIds(Collections.singletonList(compartment.getId()));
+ requestBody.setReactionTypes(Collections.singletonList("Process description"));
+ requestBody.setColumns(Arrays.asList(
+ "id",
+ "modelId"));
+ requestBody.setAnnotations(Collections.singletonList(
+ "PUBMED"));
+ return requestBody;
}
@Test
@@ -319,8 +321,8 @@ public class NewReactionsControllerTest extends ControllerIntegrationTest {
RequestBuilder request = post(
"/minerva/new_api/projects/{projectId}/models/{mapId}/bioEntities/reactions/:downloadCsv",
TEST_PROJECT, "*")
- .content(objectMapper.writeValueAsBytes(requestBody))
- .contentType(MediaType.APPLICATION_JSON);
+ .content(objectMapper.writeValueAsBytes(requestBody))
+ .contentType(MediaType.APPLICATION_JSON);
String content = mockMvc.perform(request)
.andExpect(status().is2xxSuccessful())
@@ -330,7 +332,6 @@ public class NewReactionsControllerTest extends ControllerIntegrationTest {
for (String string : lines) {
assertEquals(requestBody.getColumns().size(), string.split(",").length);
}
- logger.debug(content);
}
}
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/project/map/layer/NewLayerControllerTest.java b/web/src/test/java/lcsb/mapviewer/web/api/project/map/layer/NewLayerControllerTest.java
index eb645ec0189b8ec14c51a83a7cebc1d8a7a4a1b4..e586f147555560c2198592955b02363c0075f9aa 100644
--- a/web/src/test/java/lcsb/mapviewer/web/api/project/map/layer/NewLayerControllerTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/api/project/map/layer/NewLayerControllerTest.java
@@ -38,6 +38,7 @@ import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuild
import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.post;
import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.put;
import static org.springframework.restdocs.payload.PayloadDocumentation.responseFields;
+import static org.springframework.restdocs.request.RequestDocumentation.requestParameters;
import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
@RunWith(SpringJUnit4ClassRunner.class)
@@ -78,7 +79,7 @@ public class NewLayerControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testGetLayer() throws Exception {
+ public void testDocsGetLayer() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
@@ -117,7 +118,7 @@ public class NewLayerControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testCreateLayer() throws Exception {
+ public void testDocsCreateLayer() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
final NewLayerDTO data = createLayerDTO();
@@ -157,7 +158,7 @@ public class NewLayerControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testUpdateLayer() throws Exception {
+ public void testDocsUpdateLayer() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
final NewLayerDTO data = createLayerDTO();
@@ -223,7 +224,7 @@ public class NewLayerControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testDeleteLayer() throws Exception {
+ public void testDocsDeleteLayer() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
final RequestBuilder request = delete("/minerva/new_api/projects/{projectId}/maps/{mapId}/layers/{layerId}",
@@ -289,7 +290,7 @@ public class NewLayerControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testListLayers() throws Exception {
+ public void testDocsListLayers() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
final RequestBuilder request = get("/minerva/new_api/projects/{projectId}/maps/{mapId}/layers/", TEST_PROJECT, mapId)
@@ -298,6 +299,7 @@ public class NewLayerControllerTest extends ControllerIntegrationTest {
mockMvc.perform(request)
.andDo(document("new_api/projects/maps/layers/list_layers",
getMapPathParameters(),
+ requestParameters(getPageableFilter()),
NewApiDocs.getLayersSearchResult()))
.andExpect(status().isOk());
}
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/project/map/layer/image/NewLayerImageControllerTest.java b/web/src/test/java/lcsb/mapviewer/web/api/project/map/layer/image/NewLayerImageControllerTest.java
index 7c860a626d19edeccc960960913cf056f7f53ab9..ca3b51b595cef005d6f514a7c0f087b97d857c33 100644
--- a/web/src/test/java/lcsb/mapviewer/web/api/project/map/layer/image/NewLayerImageControllerTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/api/project/map/layer/image/NewLayerImageControllerTest.java
@@ -40,6 +40,7 @@ import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuild
import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.post;
import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.put;
import static org.springframework.restdocs.payload.PayloadDocumentation.responseFields;
+import static org.springframework.restdocs.request.RequestDocumentation.requestParameters;
import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
@RunWith(SpringJUnit4ClassRunner.class)
@@ -83,7 +84,7 @@ public class NewLayerImageControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testGetLayerImage() throws Exception {
+ public void testDocsGetLayerImage() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
@@ -139,7 +140,7 @@ public class NewLayerImageControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testCreateLayerImage() throws Exception {
+ public void testDocsCreateLayerImage() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
final NewImageDTO data = createLayerImageDTO();
@@ -184,7 +185,7 @@ public class NewLayerImageControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testUpdateLayerImage() throws Exception {
+ public void testDocsUpdateLayerImage() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
final NewImageDTO data = createLayerImageDTO();
@@ -250,7 +251,7 @@ public class NewLayerImageControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testDeleteLayerImage() throws Exception {
+ public void testDocsDeleteLayerImage() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
final RequestBuilder request = delete("/minerva/new_api/projects/{projectId}/maps/{mapId}/layers/{layerId}/images/{imageId}",
@@ -316,7 +317,7 @@ public class NewLayerImageControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testListLayerImages() throws Exception {
+ public void testDocsListLayerImages() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
final RequestBuilder request = get("/minerva/new_api/projects/{projectId}/maps/{mapId}/layers/{layerId}/images/",
@@ -324,6 +325,10 @@ public class NewLayerImageControllerTest extends ControllerIntegrationTest {
.session(session);
mockMvc.perform(request)
+ .andDo(document("new_api/projects/maps/layers/images/list_images",
+ getLayerPathParameters(),
+ requestParameters(getPageableFilter()),
+ NewApiDocs.getLayerImagesSearchResult()))
.andExpect(status().isOk());
}
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/project/map/layer/oval/NewLayerOvalControllerTest.java b/web/src/test/java/lcsb/mapviewer/web/api/project/map/layer/oval/NewLayerOvalControllerTest.java
index 69d38c1da2c4ffc00438f25f9ec1273a9ecdab94..1f88bbe68ed7565079b26d547c0dafae64817a27 100644
--- a/web/src/test/java/lcsb/mapviewer/web/api/project/map/layer/oval/NewLayerOvalControllerTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/api/project/map/layer/oval/NewLayerOvalControllerTest.java
@@ -158,7 +158,6 @@ public class NewLayerOvalControllerTest extends ControllerIntegrationTest {
assertNotNull(response.getHeader("ETag"));
final Map<String, Object> result = objectMapper.readValue(response.getContentAsString(), new TypeReference<Map<String, Object>>() {
});
- logger.debug(response.getContentAsString());
final Map<LayerOvalProperty, Object> filter = new HashMap<>();
filter.put(LayerOvalProperty.PROJECT_ID, TEST_PROJECT);
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/project/map/layer/rect/NewLayerRectControllerTest.java b/web/src/test/java/lcsb/mapviewer/web/api/project/map/layer/rect/NewLayerRectControllerTest.java
index f4bafa4d49bac798f607dcd96248c6fc1534765d..ad3cf62e49cfa818d27b59ae89de12733fdf6af2 100644
--- a/web/src/test/java/lcsb/mapviewer/web/api/project/map/layer/rect/NewLayerRectControllerTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/api/project/map/layer/rect/NewLayerRectControllerTest.java
@@ -147,8 +147,6 @@ public class NewLayerRectControllerTest extends ControllerIntegrationTest {
final NewRectDTO data = createLayerRectDTO();
- logger.debug(objectMapper.writeValueAsString(data));
-
final RequestBuilder request = post("/minerva/new_api/projects/{projectId}/maps/{mapId}/layers/{layerId}/rects/",
TEST_PROJECT,
mapId, layerId)
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/project/map/layer/text/NewLayerTextControllerTest.java b/web/src/test/java/lcsb/mapviewer/web/api/project/map/layer/text/NewLayerTextControllerTest.java
index b2fd3561ce3d4ea62fa946e299dc01fc18c97042..0edd6f4687ebd98100da224dead3a5aab451c1e4 100644
--- a/web/src/test/java/lcsb/mapviewer/web/api/project/map/layer/text/NewLayerTextControllerTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/api/project/map/layer/text/NewLayerTextControllerTest.java
@@ -44,6 +44,7 @@ import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuild
import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.post;
import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.put;
import static org.springframework.restdocs.payload.PayloadDocumentation.responseFields;
+import static org.springframework.restdocs.request.RequestDocumentation.requestParameters;
import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
@RunWith(SpringJUnit4ClassRunner.class)
@@ -89,7 +90,7 @@ public class NewLayerTextControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testGetLayerText() throws Exception {
+ public void testDocsGetLayerText() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
@@ -154,7 +155,7 @@ public class NewLayerTextControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testCreateLayerText() throws Exception {
+ public void testDocsCreateLayerText() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
final NewTextDTO data = createLayerTextDTO();
@@ -204,7 +205,7 @@ public class NewLayerTextControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testUpdateLayerText() throws Exception {
+ public void testDocsUpdateLayerText() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
final NewTextDTO data = createLayerTextDTO();
@@ -270,7 +271,7 @@ public class NewLayerTextControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testDeleteLayerText() throws Exception {
+ public void testDocsDeleteLayerText() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
final RequestBuilder request = delete("/minerva/new_api/projects/{projectId}/maps/{mapId}/layers/{layerId}/texts/{textId}",
@@ -336,7 +337,7 @@ public class NewLayerTextControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testListLayerTexts() throws Exception {
+ public void testDocsListLayerTexts() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
final RequestBuilder request = get("/minerva/new_api/projects/{projectId}/maps/{mapId}/layers/{layerId}/texts/",
@@ -344,6 +345,10 @@ public class NewLayerTextControllerTest extends ControllerIntegrationTest {
.session(session);
mockMvc.perform(request)
+ .andDo(document("new_api/projects/maps/layers/texts/list_texts",
+ getLayerPathParameters(),
+ requestParameters(getPageableFilter()),
+ NewApiDocs.getLayerTextsSearchResult()))
.andExpect(status().isOk());
}
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/project/map/publication/NewPublicationControllerTest.java b/web/src/test/java/lcsb/mapviewer/web/api/project/map/publication/NewPublicationControllerTest.java
index b13e22184ef24f4aa1fc4f58a66a6bb3634fa76c..2295fe98684cebd43431ec7682b55adc50cb7542 100644
--- a/web/src/test/java/lcsb/mapviewer/web/api/project/map/publication/NewPublicationControllerTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/api/project/map/publication/NewPublicationControllerTest.java
@@ -13,7 +13,6 @@ import org.junit.Before;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.mock.web.MockHttpServletResponse;
import org.springframework.mock.web.MockHttpSession;
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
import org.springframework.test.web.servlet.RequestBuilder;
@@ -67,9 +66,8 @@ public class NewPublicationControllerTest extends ControllerIntegrationTest {
TEST_PROJECT, mapId)
.session(session);
- final MockHttpServletResponse response = mockMvc.perform(request)
+ mockMvc.perform(request)
.andExpect(status().isOk())
.andReturn().getResponse();
- logger.debug(response.getContentAsString());
}
}
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/project/overlay/NewOverlayControllerTest.java b/web/src/test/java/lcsb/mapviewer/web/api/project/overlay/NewOverlayControllerTest.java
index f59fb3bc0be2265a7bb2820049619c9e7a893fbb..0c8297e06c88bc1991975385815926e26a04222b 100644
--- a/web/src/test/java/lcsb/mapviewer/web/api/project/overlay/NewOverlayControllerTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/api/project/overlay/NewOverlayControllerTest.java
@@ -85,7 +85,7 @@ public class NewOverlayControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testGetBioEntitiesForOverlay() throws Exception {
+ public void testDocsGetBioEntitiesForOverlay() throws Exception {
final String content = createOverlayContentForAllEntities(map);
final DataOverlay overlay = createOverlay(project, userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN), content);
@@ -172,7 +172,7 @@ public class NewOverlayControllerTest extends ControllerIntegrationTest {
@Test
- public void testGetOverlay() throws Exception {
+ public void testDocsGetOverlay() throws Exception {
final User admin = userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN);
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
@@ -233,8 +233,6 @@ public class NewOverlayControllerTest extends ControllerIntegrationTest {
final Map<String, Object> result = objectMapper.readValue(response.getContentAsString(), new TypeReference<Map<String, Object>>() {
});
- logger.debug(response.getContentAsString());
-
assertNotNull(dataOverlayService.getDataOverlayById((int) result.get("id")));
}
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/project/overlay/entries/NewOverlayEntryTypesControllerTest.java b/web/src/test/java/lcsb/mapviewer/web/api/project/overlay/entries/NewOverlayEntryTypesControllerTest.java
index d10d1abb792e8d757a33f5a39c135502bb261c39..f8b4fad84c7af419b6bf6486daa09cdd5ff1d08e 100644
--- a/web/src/test/java/lcsb/mapviewer/web/api/project/overlay/entries/NewOverlayEntryTypesControllerTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/api/project/overlay/entries/NewOverlayEntryTypesControllerTest.java
@@ -172,10 +172,9 @@ public class NewOverlayEntryTypesControllerTest extends ControllerIntegrationTes
dataOverlayEntry.getId())
.session(session);
- final String content = mockMvc.perform(request)
+ mockMvc.perform(request)
.andExpect(status().isOk())
.andReturn().getResponse().getContentAsString();
- logger.debug(content);
}
@Test
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/user/NewUserControllerTest.java b/web/src/test/java/lcsb/mapviewer/web/api/user/NewUserControllerTest.java
index 3c701807eb509af54c1d8da5b38fb7583ff9266b..0f8b88a591522b7d1f828d5900b1182bdc3bd737 100644
--- a/web/src/test/java/lcsb/mapviewer/web/api/user/NewUserControllerTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/api/user/NewUserControllerTest.java
@@ -47,6 +47,7 @@ import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuild
import static org.springframework.restdocs.payload.PayloadDocumentation.fieldWithPath;
import static org.springframework.restdocs.payload.PayloadDocumentation.responseFields;
import static org.springframework.restdocs.request.RequestDocumentation.parameterWithName;
+import static org.springframework.restdocs.request.RequestDocumentation.pathParameters;
import static org.springframework.restdocs.request.RequestDocumentation.requestParameters;
import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
@@ -80,7 +81,7 @@ public class NewUserControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testGetUserAsAdmin() throws Exception {
+ public void testDocsGetUserAsAdmin() throws Exception {
User user = userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN);
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
@@ -108,17 +109,13 @@ public class NewUserControllerTest extends ControllerIntegrationTest {
final MockHttpServletResponse response = mockMvc.perform(request)
.andExpect(status().isOk())
- .andDo(document("new_api/users/get_by_id",
- getUserPathParameters(),
- responseFields(NewApiDocs.getUserResponse(""))))
- .andExpect(status().is2xxSuccessful())
.andReturn().getResponse();
assertNotNull(response.getHeader("ETag"));
}
@Test
- public void testGrantPrivilege() throws Exception {
+ public void testDocsGrantPrivilege() throws Exception {
User user = createUser(TEST_USER_LOGIN, TEST_USER_PASSWORD);
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
@@ -133,6 +130,7 @@ public class NewUserControllerTest extends ControllerIntegrationTest {
.andExpect(status().isOk())
.andDo(document("new_api/users/grant_privilege",
getUserPathParameters(),
+ NewApiDocs.getGrantUserPrivilegeRequest(),
responseFields(NewApiDocs.getUserResponse(""))))
.andExpect(status().is2xxSuccessful());
@@ -141,7 +139,7 @@ public class NewUserControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testRevokePrivilege() throws Exception {
+ public void testDocsRevokePrivilege() throws Exception {
User user = createUser(TEST_USER_LOGIN, TEST_USER_PASSWORD);
userService.grantUserPrivilege(user, PrivilegeType.IS_CURATOR);
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
@@ -157,6 +155,7 @@ public class NewUserControllerTest extends ControllerIntegrationTest {
.andExpect(status().isOk())
.andDo(document("new_api/users/revoke_privilege",
getUserPathParameters(),
+ NewApiDocs.getGrantUserPrivilegeRequest(),
responseFields(NewApiDocs.getUserResponse(""))))
.andExpect(status().is2xxSuccessful());
@@ -235,7 +234,7 @@ public class NewUserControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testCreateUser() throws Exception {
+ public void testDocsCreateUser() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
final NewUserDTO data = createUserDTO(TEST_USER_LOGIN);
@@ -247,6 +246,10 @@ public class NewUserControllerTest extends ControllerIntegrationTest {
final MockHttpServletResponse response = mockMvc.perform(request)
.andExpect(status().isCreated())
+ .andDo(document("new_api/users/create_user",
+ NewApiDocs.getAddUserRequest(),
+ pathParameters(),
+ responseFields(NewApiDocs.getUserResponse(""))))
.andReturn().getResponse();
assertNotNull(response.getHeader("ETag"));
@@ -258,9 +261,9 @@ public class NewUserControllerTest extends ControllerIntegrationTest {
data.setLogin(login);
data.setPassword(TEST_USER_PASSWORD);
data.setActive(true);
- data.setName("test name");
- data.setEmail("test@test.com");
- data.setSurname("surname");
+ data.setName(faker.name().firstName());
+ data.setEmail(faker.internet().emailAddress());
+ data.setSurname(faker.name().lastName());
data.setConnectedToLdap(false);
data.setTermsOfUseConsent(false);
return data;
@@ -282,7 +285,7 @@ public class NewUserControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testUpdateUser() throws Exception {
+ public void testDocsUpdateUser() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
User user = createUser(TEST_USER_LOGIN, TEST_USER_PASSWORD);
@@ -296,6 +299,10 @@ public class NewUserControllerTest extends ControllerIntegrationTest {
final HttpServletResponse response = mockMvc.perform(request)
.andExpect(status().isOk())
+ .andDo(document("new_api/users/update_user",
+ getUserPathParameters(),
+ NewApiDocs.getAddUserRequest(),
+ responseFields(NewApiDocs.getUserResponse(""))))
.andReturn().getResponse();
assertNotNull(response.getHeader("ETag"));
@@ -365,7 +372,7 @@ public class NewUserControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testDeleteUser() throws Exception {
+ public void testDocsDeleteUser() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
User user = createUser(TEST_USER_LOGIN, TEST_USER_PASSWORD);
@@ -373,7 +380,10 @@ public class NewUserControllerTest extends ControllerIntegrationTest {
.session(session);
mockMvc.perform(request)
- .andExpect(status().isOk());
+ .andExpect(status().isOk())
+ .andDo(document("new_api/users/delete_user",
+ getUserPathParameters()));
+
assertNull(userService.getById(user.getId()));
}
@@ -450,14 +460,15 @@ public class NewUserControllerTest extends ControllerIntegrationTest {
}
@Test
- public void testGetUsers() throws Exception {
+ public void testDocsGetUsers() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
final RequestBuilder request = get("/minerva/new_api/users/")
.session(session);
mockMvc.perform(request)
- .andDo(document("new_api/users/get_users",
+ .andDo(document("new_api/users/list_users",
+ pathParameters(),
NewApiDocs.getUserSearchResult()))
.andExpect(status().is2xxSuccessful())
.andReturn().getResponse().getContentAsString();
@@ -539,7 +550,7 @@ public class NewUserControllerTest extends ControllerIntegrationTest {
}
@Test
- public void resetPassword() throws Exception {
+ public void testDocsResetPassword() throws Exception {
configureServerForResetPasswordRequest();
User user = createUser(TEST_USER_LOGIN, TEST_USER_PASSWORD);
user.setEmail("test@test.xyz");
@@ -562,6 +573,8 @@ public class NewUserControllerTest extends ControllerIntegrationTest {
.contentType(MediaType.APPLICATION_JSON);
mockMvc.perform(resetRequest)
+ .andDo(document("new_api/users/reset_password",
+ NewApiDocs.getPasswordResetRequest()))
.andExpect(status().is2xxSuccessful());
createSession(TEST_USER_LOGIN, newPassword);
@@ -611,7 +624,7 @@ public class NewUserControllerTest extends ControllerIntegrationTest {
}
@Test
- public void confirmRegistrationOfNewUser() throws Exception {
+ public void testDocsConfirmRegistrationOfNewUser() throws Exception {
User user = createUser(TEST_USER_LOGIN, TEST_USER_PASSWORD);
user.setEmail("test@test.xyz");
user.setActive(false);
@@ -633,7 +646,7 @@ public class NewUserControllerTest extends ControllerIntegrationTest {
.content(body);
mockMvc.perform(resetRequest)
- .andDo(document("user/confirm_email",
+ .andDo(document("new_api/users/confirm_email",
userPathParameters(),
requestParameters(parameterWithName("token")
.description("token obtained in the registration email")),
@@ -724,6 +737,30 @@ public class NewUserControllerTest extends ControllerIntegrationTest {
.andExpect(status().isBadRequest());
}
+ @Test
+ public void testDocsRegisterNewUser() throws Exception {
+ configureServerForResetPasswordRequest();
+
+ configurationService.setConfigurationValue(ConfigurationElementType.ALLOW_AUTO_REGISTER, "true");
+ final NewUserDTO data = createUserDTO(TEST_USER_LOGIN);
+ data.setConnectedToLdap(false);
+ data.setActive(true);
+ data.setTermsOfUseConsent(false);
+
+ final RequestBuilder request = post("/minerva/new_api/users/:registerUser")
+ .contentType(MediaType.APPLICATION_JSON)
+ .content(objectMapper.writeValueAsString(data));
+
+ mockMvc.perform(request)
+ .andDo(document("new_api/users/register_user",
+ NewApiDocs.getRegisterUserRequest(),
+ responseFields(NewApiDocs.getUserResponse(""))))
+ .andExpect(status().isOk());
+ User user = userService.getUserByLogin(TEST_USER_LOGIN);
+ assertFalse(user.isConfirmed());
+ assertFalse(user.isActive());
+ }
+
@Test
public void confirmRegistrationOfNewUserWithInvalidToken() throws Exception {
User user = createUser(TEST_USER_LOGIN, TEST_USER_PASSWORD);
@@ -776,7 +813,7 @@ public class NewUserControllerTest extends ControllerIntegrationTest {
}
@Test
- public void requestResetPassword() throws Exception {
+ public void testDocsRequestResetPassword() throws Exception {
final long count = userService.getPasswordTokenCount();
configureServerForResetPasswordRequest();
@@ -787,7 +824,7 @@ public class NewUserControllerTest extends ControllerIntegrationTest {
final RequestBuilder grantRequest = post("/minerva/new_api/users/{login}:requestResetPassword", TEST_USER_LOGIN);
mockMvc.perform(grantRequest)
- .andDo(document("user/request_reset_password",
+ .andDo(document("new_api/users/request_reset_password",
userPathParameters()))
.andExpect(status().is2xxSuccessful());
assertEquals(count + 1, userService.getPasswordTokenCount());