Release 1.1.0

OpenSILEX · Sep 4, 2023 · 58a123c · 58a123c
1 parent 95c8ce9
commit 58a123c
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diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -33,7 +33,7 @@ variables:
   MAVEN_OPTS_SCHUEDULES: "-Dhttps.protocols=TLSv1.2 -Dmaven.repo.local=$CI_PROJECT_DIR/.m2/repository -Dorg.slf4j.simpleLogger.log.org.apache.maven.cli.transfer.Slf4jMavenTransferListener=ERROR -Dorg.slf4j.simpleLogger.defaultLogLevel=error -Dorg.slf4j.simpleLogger.showDateTime=true -Djava.awt.headless=true"
   MAVEN_SKIP_TESTS: "false"
   # DEFAULT SERVER MAVEN VERSION
-  MVN_VERSION: 3.6.3
+  MVN_VERSION: 3.8.6
   # DEFAULT SERVER JAVA VERSION
   JAVA_VERSION: 11
   ## DEPLOY CONFIGS ##
@@ -561,6 +561,8 @@ demo:build:
 
 maximilian:build:
   <<: *build_template_with_opensilex
+  variables:
+    MAVEN_SKIP_TESTS: "true"
   rules:
     - if: $CI_COMMIT_BRANCH == "maximilian2"
 
@@ -588,6 +590,8 @@ test:maximilian:deploy:
 
 arnaud:build:
   <<: *build_template_with_opensilex
+  variables:
+    MAVEN_SKIP_TESTS: "true"
   rules:
     - if: $CI_COMMIT_BRANCH == "arnaud"
 
@@ -615,6 +619,8 @@ test:arnaud:deploy:
 
 yvan:build:
   <<: *build_template_with_opensilex
+  variables:
+    MAVEN_SKIP_TESTS: "true"
   rules:
     - if: $CI_COMMIT_BRANCH == "yvan"
   tags:
@@ -646,6 +652,8 @@ test:yvan:deploy:
 
 valentin:build:
   <<: *build_template_with_opensilex
+  variables:
+    MAVEN_SKIP_TESTS: "true"
   rules:
     - if: $CI_COMMIT_BRANCH == "test/valentin"
 
@@ -673,6 +681,8 @@ test:valentin:deploy:
 
 bernhard:build:
   <<: *build_template_with_opensilex
+  variables:
+    MAVEN_SKIP_TESTS: "true"
   rules:
     - if: $CI_COMMIT_BRANCH == "bernhard"
 
@@ -700,6 +710,8 @@ test:bernhard:deploy:
 
 gabriel:build:
   <<: *build_template_with_opensilex
+  variables:
+    MAVEN_SKIP_TESTS: "true"
   rules:
     - if: $CI_COMMIT_BRANCH == "gabriel"
 
@@ -729,6 +741,8 @@ test:gabriel:deploy:
 
 optimization:build:
   <<: *build_template_with_opensilex
+  variables:
+    MAVEN_SKIP_TESTS: "true"
   rules:
     - if: $CI_COMMIT_BRANCH == "optimization"
 
@@ -756,6 +770,8 @@ test:optimization:deploy:
 
 sebastien:build:
   <<: *build_template_with_opensilex
+  variables:
+    MAVEN_SKIP_TESTS: "true"
   rules:
     - if: $CI_COMMIT_BRANCH == "sebastien"
 
@@ -783,6 +799,8 @@ test:sebastien:deploy:
 
 bendy:build:
   <<: *build_template_with_opensilex
+  variables:
+    MAVEN_SKIP_TESTS: "true"
   rules:
     - if: $CI_COMMIT_BRANCH == "bendy"
 
@@ -810,6 +828,8 @@ test:bendy:deploy:
 
 alexiaChiavarino:build:
   <<: *build_template_with_opensilex
+  variables:
+    MAVEN_SKIP_TESTS: "true"
   rules:
     - if: $CI_COMMIT_BRANCH == "alexiaChiavarino"
   tags:
@@ -841,6 +861,8 @@ test:alexiaChiavarino:deploy:
 
 renaud:build:
   <<: *build_template_with_opensilex
+  variables:
+    MAVEN_SKIP_TESTS: "true"
   rules:
     - if: $CI_COMMIT_BRANCH == "renaud"
 
@@ -868,6 +890,8 @@ test:renaud:deploy:
 
 temporary1:build:
   <<: *build_template_with_opensilex
+  variables:
+    MAVEN_SKIP_TESTS: "true"
   rules:
     - if: $CI_COMMIT_BRANCH == "temporary1"
 
@@ -895,6 +919,8 @@ test:temporary1:deploy:
 
 emilie:build:
   <<: *build_template_with_opensilex
+  variables:
+    MAVEN_SKIP_TESTS: "true"
   rules:
     - if: $CI_COMMIT_BRANCH == "emilie"
 
@@ -926,6 +952,8 @@ test:emilie:deploy:
 
 brice:build:
   <<: *build_template_with_opensilex
+  variables:
+    MAVEN_SKIP_TESTS: "true"
   rules:
     - if: $CI_COMMIT_BRANCH == "brice"
 
@@ -953,6 +981,8 @@ test:brice:deploy:
 
 mariem:build:
   <<: *build_template_with_opensilex
+  variables:
+    MAVEN_SKIP_TESTS: "true"
   rules:
     - if: $CI_COMMIT_BRANCH == "mariem"
 

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,23 +1,30 @@
 <!-- TOC -->
 * [Changelog](#changelog)
-  * [[1.0.0]](#100)
+  * [[1.1.0] - BB](#110---bb)
     * [New features](#new-features)
     * [Fixed or optimized](#fixed-or-optimized)
+  * [[1.0.1] - Ambitious Amber](#101---ambitious-amber)
+    * [Fixed or optimized](#fixed-or-optimized-1)
       * [API](#api)
       * [Web client](#web-client)
-  * [[1.0.0-rc+7]](#100-rc7)
+  * [[1.0.0] - Ambitious Amber](#100---ambitious-amber)
     * [New features](#new-features-1)
-    * [Fixed or optimized](#fixed-or-optimized-1)
-  * [[1.0.0-rc+6]](#100-rc6)
     * [Fixed or optimized](#fixed-or-optimized-2)
+      * [API](#api-1)
+      * [Web client](#web-client-1)
+  * [[1.0.0-rc+7]](#100-rc7)
+    * [New features](#new-features-2)
+    * [Fixed or optimized](#fixed-or-optimized-3)
+  * [[1.0.0-rc+6]](#100-rc6)
+    * [Fixed or optimized](#fixed-or-optimized-4)
     * [Added or changed](#added-or-changed)
   * [[1.0.0-rc+5.2]](#100-rc52)
-    * [Fixed or optimized](#fixed-or-optimized-3)
+    * [Fixed or optimized](#fixed-or-optimized-5)
   * [[1.0.0-rc+5.1]](#100-rc51)
-    * [Fixed or optimized](#fixed-or-optimized-4)
+    * [Fixed or optimized](#fixed-or-optimized-6)
   * [[1.0.0-rc+5]](#100-rc5)
     * [Added or changed](#added-or-changed-1)
-    * [Fixed or optimized](#fixed-or-optimized-5)
+    * [Fixed or optimized](#fixed-or-optimized-7)
   * [[1.0.0-rc+4.1] - 2022-07-13](#100-rc41---2022-07-13)
     * [Fixed](#fixed)
   * [[1.0.0-rc+4] - 2022-06-13](#100-rc4---2022-06-13)
@@ -33,10 +40,10 @@
     * [Some Known Issues](#some-known-issues)
   * [[1.0.0-rc+1] - 2021-11-02](#100-rc1---2021-11-02)
     * [Added](#added-1)
-    * [Fixed or optimized](#fixed-or-optimized-6)
+    * [Fixed or optimized](#fixed-or-optimized-8)
   * [[1.0.0-rc] - 2021-10-08](#100-rc---2021-10-08)
     * [Added](#added-2)
-    * [Fixed or optimized](#fixed-or-optimized-7)
+    * [Fixed or optimized](#fixed-or-optimized-9)
     * [Changed](#changed)
     * [Major bugs identified](#major-bugs-identified)
   * [[1.0.0-beta+2.1] - 2021-07-27](#100-beta21---2021-07-27)
@@ -61,7 +68,51 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [1.0.0]
+## [1.1.0] - Blazing Basalt
+
+> WARNING : upgrading to this new version require manual operations. Please
+> see the [versioning notes](https://github.com/OpenSILEX/opensilex/blob/master/opensilex-doc/src/main/resources/release/1.1.0.md).
+> Also available [here](opensilex-doc%2Fsrc%2Fmain%2Fresources%2Frelease%2F1.1.0.md)
+
+### Changes and new features
+
+- [Map] You can now visualize data in a chart by selecting an object in the map view
+- [Person] You can now search persons by their ORCID
+- [User] The User API is now deprecated
+- [Account] The form for creating accounts has been simplified
+- [Experiment] Associated facilities are now part of the available facilities for scientific objects of the experiments
+- [Experiment] The "Visualization" tab of a scientific object in an experiment has been removed
+- [Experiment] Scientific object count is now displayed on the scientific objects tab
+- [Germplasm group] Added documentation that you can read by hovering the question mark
+
+### Fixed or optimized
+
+- [Front] Minor visual fixes
+- [Experiment] On the "Data" page of an experiment, targets are now always correctly displayed
+- [Data] Importing multiple variables in one CSV no longer duplicates devices in provenance
+- [Data] Adding annotation during data import now uses the correct date and time
+- [Map] Fixed some issues with the zoom
+- [Organization] Fixed an issue where you had to click twice on "create organization" or "create site" to perform the action
+- [Facility] Tweaked the "Monitoring" page of a facility for better ergonomy
+- [Charts] Tweaked the display of graphs with multi-scale axis for better ergonomy
+- [Charts] Fixed a bug where data with the value 0 where sometimes displayed as undefined
+- [Charts] Charts no longer aggregate data points
+- [PHIS] PHIS logo is now displayed if the dashboard chart is not configured
+
+## [1.0.1] - Ambitious Amber
+
+### Fixed or optimized
+
+#### API
+
+- [Person/User] Removed User and Person delete web services
+
+#### Web client
+
+- [Person/Account] Removed Account and Person delete buttons
+- [Profiles] Added translation for Dataverse credentials menu
+
+## [1.0.0] - Ambitious Amber
 
 > WARNING : upgrading to this new version require manual operations. Please
 > see the [versioning notes](https://github.com/OpenSILEX/opensilex/blob/master/opensilex-doc/src/main/resources/release/1.0.0.md).

diff --git a/opensilex-core/src/main/java/org/opensilex/core/data/api/DataAPI.java b/opensilex-core/src/main/java/org/opensilex/core/data/api/DataAPI.java
@@ -1558,7 +1558,6 @@ private boolean validateCSVRow(
 
         ParsedDateTimeMongo parsedDateTimeMongo = null;
 
-        List<ProvEntityModel> agents = new ArrayList<>();
         List<URI> experiments = new ArrayList<>();
         SPARQLNamedResourceModel target = null;
 
@@ -1858,8 +1857,7 @@ else if (headerByIndex.get(colIndex).equalsIgnoreCase(annotationHeader)){
                                     URI rootType = rootDeviceTypes.get(deviceFromDeviceColumn.getType());
                                     agent.setType(rootType);
                                     agent.setUri(deviceFromDeviceColumn.getUri());
-                                    agents.add(agent);
-                                    provenanceModel.setProvWasAssociatedWith(agents);
+                                    provenanceModel.setProvWasAssociatedWith(Collections.singletonList(agent));
 
                                 } else if (sensingDeviceFoundFromProvenance) {
 
@@ -1871,8 +1869,7 @@ else if (headerByIndex.get(colIndex).equalsIgnoreCase(annotationHeader)){
                                     URI rootType = rootDeviceTypes.get(checkedDevice.getType());
                                     agent.setType(rootType);
                                     agent.setUri(checkedDevice.getUri());
-                                    agents.add(agent);
-                                    provenanceModel.setProvWasAssociatedWith(agents);
+                                    provenanceModel.setProvWasAssociatedWith(Collections.singletonList(agent));
 
                                 }
 
@@ -1934,9 +1931,13 @@ else if (headerByIndex.get(colIndex).equalsIgnoreCase(annotationHeader)){
             }else{
                 if(validRow){
                     annotationFromAnnotationColumn.setTargets(Collections.singletonList( target==null ? object.getUri() : target.getUri()));
-                    String onlyDateString = parsedDateTimeMongo.getInstant().toString().substring(0, 11);
-                    String setToMidday = onlyDateString + "12:00:00Z";
-                    annotationFromAnnotationColumn.setCreated(Instant.parse( setToMidday ).atOffset(ZoneOffset.ofTotalSeconds(0)));
+                    Instant usedInstant = parsedDateTimeMongo.getInstant();
+                    if(!parsedDateTimeMongo.getIsDateTime()){
+                        String onlyDateString = parsedDateTimeMongo.getInstant().toString().substring(0, 11);
+                        String setToMidday = onlyDateString + "12:00:00Z";
+                        usedInstant = Instant.parse( setToMidday );
+                    }
+                    annotationFromAnnotationColumn.setCreated(usedInstant.atOffset(ZoneOffset.ofTotalSeconds(0)));
                     csvValidation.addToAnnotationsOnObjects(annotationFromAnnotationColumn);
                 }
             }