Mica without Opal (#4393)

* #4376 WIP. StudyTableSource interface added. New property sourceURN replaces opal project/table in dataset's study tables and variables. Requires ES index config update.

* sourceURN property/getter/setter renamed to source

* source package added, with unit tests

* Excel table source added, reads excel from Mica's file system

* Edit/create study tables with opal or file source. WIP.

* File path can be copied. Study table's file source can be relative to the dataset's folder

* Study table context added. Opal dtos (aggregations) are not exposed in the source plugin interface.

* Deferred init of excel datasource. Less verbose log messages when study table source operation is not supported

* SPI mica-source testing

* Deferred attachment stream extraction

* Handle disposable table sources

* Mica source plugin could be an Initialisable

* #4381 Variable taxonomies service added to support other taxonomies providers, in addition to the opal one

* mica-source plugin type renamed to mica-tables. Ne plugin type: mica-taxonomies for loading taxonomies provider services.

* Taxonomy of taxonomies is configurable. Added attribute to have a taxonomy declared but not visible.

* Variable taxonomies can be read from local folder: MICA_HOME/conf/taxonomies/variable

* AbstractTaxonomiesProviderService added

* Caching of taxonomies refactored, not functional yet

* Variable taxonomies are cached

* Fix dataset taxonomy init

* Opal taxonomies cache replaced by generic variable taxonomies cache. Variable taxonomies are decorated with variable attributes

* Code cleaning: Opal service helper merged into opal service

* classifications administration

* make sure variable taxo title/description in the meta taxo matches the one of the original taxo

* hide instead of remove a target vocabulary if type is disabled

* Plugins REST API added

* Plugin REST API added

* Service Plugin REST API added

* Update the search plugin in the upgrade procedure

* ng-obiba-mica version

* No server error when opal projects cannot be retrieved

* Fix some wording and showVariableStatistics template setting added

* Fix some wording and showVariableStatistics template setting added

* Fix harmonized variable id encoding for url

* Fix harmonized variable id encoding for url for reverse proxy

* NoSuchTableSourceException added with their web service mapper

* ng-obiba-mica latest release

* prepare for upgrade to 5.2

* StudyTableSource does not need to return the table name, this is implementation specific

* Modifying the meta txonomy requires admin role

* Plugin management requires admin role

* Clean Opal projects web services

* Helper class to read a taxonomy in YAML format from a stream

* Other study table source handled in the admin

Author: ymarcon

mica-core/pom.xml

@@ -34,6 +34,10 @@
       <groupId>org.obiba.mica</groupId>
       <artifactId>mica-web-model</artifactId>
     </dependency>
+    <dependency>
+      <groupId>org.obiba.magma</groupId>
+      <artifactId>magma-datasource-excel</artifactId>
+    </dependency>
     <dependency>
       <groupId>com.codahale.metrics</groupId>
       <artifactId>metrics-core</artifactId>

mica-core/src/main/java/org/obiba/mica/access/service/DataAccessEntityService.java

@@ -47,7 +47,7 @@
 import org.obiba.mica.core.service.MailService;
 import org.obiba.mica.core.service.SchemaFormContentFileService;
 import org.obiba.mica.core.support.IdentifierGenerator;
-import org.obiba.mica.core.support.YamlClassPathResourceReader;
+import org.obiba.mica.core.support.YamlResourceReader;
 import org.obiba.mica.dataset.service.VariableSetService;
 import org.obiba.mica.micaConfig.domain.DataAccessConfig;
 import org.obiba.mica.micaConfig.service.DataAccessConfigService;
@@ -396,7 +396,7 @@ protected void setAndLogStatus(T request, DataAccessEntityStatus to) {
   protected String generateId() {
     DataAccessConfig dataAccessConfig = dataAccessConfigService.getOrCreateConfig();
 
-    Object exclusions = YamlClassPathResourceReader.read(EXCLUSION_IDS_YAML_RESOURCE_PATH, Map.class).get("exclusions");
+    Object exclusions = YamlResourceReader.readClassPath(EXCLUSION_IDS_YAML_RESOURCE_PATH, Map.class).get("exclusions");
 
     IdentifierGenerator.Builder builder = IdentifierGenerator.newBuilder().prefix(dataAccessConfig.getIdPrefix())
       .size(dataAccessConfig.getIdLength());

mica-core/src/main/java/org/obiba/mica/config/UpgradeConfiguration.java

@@ -16,7 +16,7 @@
 
 import org.obiba.mica.core.upgrade.Mica460Upgrade;
 import org.obiba.mica.core.upgrade.Mica500Upgrade;
-import org.obiba.mica.core.upgrade.Mica510upgrade;
+import org.obiba.mica.core.upgrade.Mica520upgrade;
 import org.obiba.mica.core.upgrade.MicaVersionModifier;
 import org.obiba.mica.core.upgrade.RuntimeVersionProvider;
 import org.obiba.runtime.upgrade.UpgradeManager;
@@ -31,8 +31,8 @@ public class UpgradeConfiguration {
 
   private List<UpgradeStep> upgradeSteps;
 
-  public UpgradeConfiguration(Mica460Upgrade mica460Upgrade, Mica500Upgrade mica500Upgrade, Mica510upgrade mica510upgrade) {
-    upgradeSteps = Arrays.asList(mica460Upgrade, mica500Upgrade, mica510upgrade);
+  public UpgradeConfiguration(Mica460Upgrade mica460Upgrade, Mica500Upgrade mica500Upgrade, Mica520upgrade mica520upgrade) {
+    upgradeSteps = Arrays.asList(mica460Upgrade, mica500Upgrade, mica520upgrade);
   }
 
   @Bean

mica-core/src/main/java/org/obiba/mica/core/domain/BaseStudyTable.java

@@ -12,17 +12,32 @@
 
 import com.google.common.base.MoreObjects;
 import com.google.common.base.Strings;
+import org.obiba.mica.core.source.OpalTableSource;
 
-import java.io.Serializable;
-
-public class BaseStudyTable extends OpalTable {
+public class BaseStudyTable {
 
   protected String studyId;
 
   protected String populationId;
 
   protected int populationWeight;
 
+  private LocalizedString name;
+
+  private LocalizedString description;
+
+  private LocalizedString additionalInformation;
+
+  private int weight;
+
+  private String source;
+
+  // legacy
+  private String project;
+
+  // legacy
+  private String table;
+
   public String getStudyId() {
     return studyId;
   }
@@ -72,13 +87,66 @@ public void setPopulationWeight(int populationWeight) {
 
   @Override
   public String toString() {
-    return MoreObjects.toStringHelper(this).add("project", getProject()).add("table", getTable())
+    return MoreObjects.toStringHelper(this).add("source", getSource())
       .add("studyId", getStudyId()).add("populationId", getPopulationId())
       .toString();
   }
 
-  @Override
-  protected String getEntityId() {
-    return studyId;
+  public void setName(LocalizedString name) {
+    this.name = name;
+  }
+
+  public LocalizedString getName() {
+    return name;
+  }
+
+  public void setDescription(LocalizedString description) {
+    this.description = description;
+  }
+
+  public LocalizedString getDescription() {
+    return description;
+  }
+
+  public LocalizedString getAdditionalInformation() {
+    return additionalInformation;
+  }
+
+  public void setAdditionalInformation(LocalizedString additionalInformation) {
+    this.additionalInformation = additionalInformation;
+  }
+
+  public int getWeight() {
+    return weight;
+  }
+
+  public void setWeight(int weight) {
+    this.weight = weight;
+  }
+
+  public boolean isFor(String studyId, String source) {
+    return this.studyId.equals(studyId) && getSource().equals(source);
+  }
+
+  public void setSource(String source) {
+    this.source = source;
+  }
+
+  public String getSource() {
+    // legacy
+    if (Strings.isNullOrEmpty(source)) {
+      this.source = OpalTableSource.newSource(project, table).getURN();
+    }
+    return source;
+  }
+
+  @Deprecated
+  public void setProject(String project) {
+    this.project = project;
+  }
+
+  @Deprecated
+  public void setTable(String table) {
+    this.table = table;
   }
 }

mica-core/src/main/java/org/obiba/mica/core/domain/OpalTable.java

@@ -10,10 +10,10 @@
 
 package org.obiba.mica.core.domain;
 
-import java.io.Serializable;
-
 import com.google.common.base.MoreObjects;
 
+import java.io.Serializable;
+
 /**
  * Represents a opal table that is associated to a {@link org.obiba.mica.study.domain.Study}
  * {@link org.obiba.mica.study.domain.Population} {@link org.obiba.mica.study.domain.DataCollectionEvent}.
@@ -63,7 +63,7 @@ public boolean appliesTo(String studyId, String populationId, String dataCollect
 
   @Override
   public String toString() {
-    return MoreObjects.toStringHelper(this).add("project", getProject()).add("table", getTable())
+    return MoreObjects.toStringHelper(this).add("source", getSource())
       .add("dceId", getDataCollectionEventUId()).toString();
   }