diff --git a/datastore_server/build.gradle b/datastore_server/build.gradle
index e217f508800e5c51b2afbd9ccee16a2048234788..99154a6a60835857df79055a69bb6ce703e10004 100644
--- a/datastore_server/build.gradle
+++ b/datastore_server/build.gradle
@@ -33,7 +33,7 @@ dependencies {
'apache:commons-fileupload:+',
'lyncode:xoai-data-provider:+'
- runtime 'bioformats:bioformats:+'
+ runtime 'bioformats:bioformats:5.9.2'
testCompile (project(path: ':openbis', configuration: 'tests')) {
exclude group: 'google', module: 'gwt-user'
diff --git a/image_readers/build.gradle b/image_readers/build.gradle
index cbe3e1354466a3ef8c02d3e63538abcd29eb0f6e..50400c005e252dda519e812ac9a1cb2a08ff4258 100644
--- a/image_readers/build.gradle
+++ b/image_readers/build.gradle
@@ -7,7 +7,7 @@ dependencies {
compile project(':common'),
'imagej:ij:+',
'sun:jai:+',
- 'bioformats:bioformats:+',
+ 'bioformats:bioformats:5.9.2',
'slf4j:slf4j:+',
'slf4j:slf4j-log4j12:+'
diff --git a/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/common.js b/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/common.js
index 5819a298be25716525e5f83b98f0b06c8d86b5af..56bf7882d6194095a63ea6f39ba9a5a7d22bcdbd 100644
--- a/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/common.js
+++ b/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/common.js
@@ -1111,6 +1111,7 @@ define([ 'jquery', 'openbis', 'underscore', 'test/dtos' ], function($, defaultOp
var fo = new dtos.ExperimentTypeFetchOptions();
fo.withPropertyAssignments().withPropertyType();
fo.withPropertyAssignments().withRegistrator();
+ fo.withPropertyAssignments().withPlugin();
return fo;
};
@@ -1139,6 +1140,7 @@ define([ 'jquery', 'openbis', 'underscore', 'test/dtos' ], function($, defaultOp
var fo = new dtos.SampleTypeFetchOptions();
fo.withPropertyAssignments().withPropertyType();
fo.withPropertyAssignments().withRegistrator();
+ fo.withPropertyAssignments().withPlugin();
return fo;
};
@@ -1168,6 +1170,7 @@ define([ 'jquery', 'openbis', 'underscore', 'test/dtos' ], function($, defaultOp
var fo = new dtos.DataSetTypeFetchOptions();
fo.withPropertyAssignments().withPropertyType();
fo.withPropertyAssignments().withRegistrator();
+ fo.withPropertyAssignments().withPlugin();
return fo;
};
@@ -1186,6 +1189,7 @@ define([ 'jquery', 'openbis', 'underscore', 'test/dtos' ], function($, defaultOp
var fo = new dtos.MaterialTypeFetchOptions();
fo.withPropertyAssignments().withPropertyType();
fo.withPropertyAssignments().withRegistrator();
+ fo.withPropertyAssignments().withPlugin();
return fo;
};
@@ -1293,6 +1297,7 @@ define([ 'jquery', 'openbis', 'underscore', 'test/dtos' ], function($, defaultOp
fo.withPropertyType();
fo.withPropertyAssignment().withEntityType();
fo.withPropertyAssignment().withPropertyType();
+ fo.withPropertyAssignment().withPlugin();
return fo;
};
diff --git a/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/test-create.js b/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/test-create.js
index 20b7b5c2e4c81bf09f295394a4f931952f44a930..9b5fcef22d6d4fd6b0ab7b002fce030fa71c5907 100644
--- a/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/test-create.js
+++ b/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/test-create.js
@@ -191,6 +191,7 @@ define(
c.assertEqual(assignment.isMandatory(), true, "Assignment mandatory");
c.assertEqual(assignment.isShowInEditView(), true, "Assignment ShowInEditView");
c.assertEqual(assignment.isShowRawValueInForms(), true, "Assignment ShowRawValueInForms");
+ c.assertEqual(assignment.getPlugin().getName(), "Diff_time", "Assignment Plugin");
}
testCreate(c, fCreate, c.findExperimentType, fCheck);
@@ -272,6 +273,7 @@ define(
c.assertEqual(assignment.isMandatory(), true, "Assignment mandatory");
c.assertEqual(assignment.isShowInEditView(), true, "Assignment ShowInEditView");
c.assertEqual(assignment.isShowRawValueInForms(), true, "Assignment ShowRawValueInForms");
+ c.assertEqual(assignment.getPlugin().getName(), "Diff_time", "Assignment Plugin");
}
testCreate(c, fCreate, c.findSampleType, fCheck);
@@ -397,6 +399,7 @@ define(
c.assertEqual(assignment.isMandatory(), true, "Assignment mandatory");
c.assertEqual(assignment.isShowInEditView(), true, "Assignment ShowInEditView");
c.assertEqual(assignment.isShowRawValueInForms(), true, "Assignment ShowRawValueInForms");
+ c.assertEqual(assignment.getPlugin().getName(), "Diff_time", "Assignment Plugin");
}
testCreate(c, fCreate, c.findDataSetType, fCheck);
@@ -463,6 +466,7 @@ define(
c.assertEqual(assignment.isMandatory(), true, "Assignment mandatory");
c.assertEqual(assignment.isShowInEditView(), true, "Assignment ShowInEditView");
c.assertEqual(assignment.isShowRawValueInForms(), true, "Assignment ShowRawValueInForms");
+ c.assertEqual(assignment.getPlugin().getName(), "Diff_time", "Assignment Plugin");
}
testCreate(c, fCreate, c.findMaterialType, fCheck);
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/property/SearchPropertyAssignmentsOperationExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/property/SearchPropertyAssignmentsOperationExecutor.java
index d9eb6f2390e812a1899a68b1f48f5577988f02f0..4bb9c297dca4a67f039a0abadce7f20545279c16 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/property/SearchPropertyAssignmentsOperationExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/property/SearchPropertyAssignmentsOperationExecutor.java
@@ -40,6 +40,7 @@ import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.property.IProperty
import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.property.PropertyAssignmentKey;
import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.property.PropertyAssignmentRecord;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePropertyTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ScriptPE;
/**
* @author pkupczyk
@@ -97,6 +98,11 @@ public class SearchPropertyAssignmentsOperationExecutor extends
assignmentRecord.show_raw_value = assignment.getShowRawValue();
assignmentRecord.type_code = assignment.getEntityType().getCode();
assignmentRecord.type_id = assignment.getEntityType().getId();
+ ScriptPE script = assignment.getScript();
+ if (script != null)
+ {
+ assignmentRecord.script_id = script.getId();
+ }
assignmentRecords.add(assignmentRecord);
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/property/PropertyAssignmentRecord.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/property/PropertyAssignmentRecord.java
index b2e972d356dd65ad39cd4a6e4b305b0d03740568..7fe9fac082a1cf622d0ac389c0d147e333a6e927 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/property/PropertyAssignmentRecord.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/property/PropertyAssignmentRecord.java
@@ -52,4 +52,5 @@ public class PropertyAssignmentRecord extends ObjectBaseRecord
public Date registration_timestamp;
+ public Long script_id;
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/property/PropertyAssignmentTranslator.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/property/PropertyAssignmentTranslator.java
index 1fa9a3b5a9ed08f9c9360f655e678426dc0c6859..031ad2da473ba7b4a8a25e188bb14508e6e12a1b 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/property/PropertyAssignmentTranslator.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/property/PropertyAssignmentTranslator.java
@@ -22,6 +22,7 @@ import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
+import java.util.function.Function;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
@@ -34,6 +35,7 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.id.IEntityTypeId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.fetchoptions.ExperimentTypeFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.material.fetchoptions.MaterialTypeFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.person.Person;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.plugin.Plugin;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.PropertyAssignment;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.PropertyType;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.fetchoptions.PropertyAssignmentFetchOptions;
@@ -49,11 +51,11 @@ import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.dataset.IDataSetTy
import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.experiment.IExperimentTypeTranslator;
import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.material.IMaterialTypeTranslator;
import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.person.IPersonTranslator;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.plugin.IPluginTranslator;
import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.sample.ISampleTypeTranslator;
import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.sample.SampleQuery;
import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.semanticannotation.ISemanticAnnotationTranslator;
import ch.systemsx.cisd.openbis.generic.shared.basic.CodeConverter;
-
import it.unimi.dsi.fastutil.longs.LongOpenHashSet;
import net.lemnik.eodsql.QueryTool;
@@ -85,6 +87,9 @@ public class PropertyAssignmentTranslator implements IPropertyAssignmentTranslat
@Autowired
private IPersonTranslator personTranslator;
+ @Autowired
+ private IPluginTranslator pluginTranslator;
+
@Override
public Map<Long, PropertyAssignment> getIdToAssignmentMap(TranslationContext context, Collection<PropertyAssignmentRecord> assignmentRecords,
PropertyAssignmentFetchOptions assignmentFetchOptions)
@@ -145,7 +150,7 @@ public class PropertyAssignmentTranslator implements IPropertyAssignmentTranslat
if (assignmentFetchOptions.hasPropertyType())
{
- Map<Long, List<PropertyAssignment>> assignmentsByPropertyTypeId = getAssignmentsByPropertyTypeId(assignments, assignmentRecords);
+ Map<Long, List<PropertyAssignment>> assignmentsByPropertyTypeId = getAssignments(assignments, assignmentRecords, r -> r.prty_id);
Map<Long, PropertyType> propertyTypeMap =
propertyTypeTranslator.translate(context, assignmentsByPropertyTypeId.keySet(), assignmentFetchOptions.withPropertyType());
@@ -167,7 +172,7 @@ public class PropertyAssignmentTranslator implements IPropertyAssignmentTranslat
if (assignmentFetchOptions.hasRegistrator())
{
- Map<Long, List<PropertyAssignment>> assignmentsByRegistatorId = getAssignmentsByRegistratorId(assignments, assignmentRecords);
+ Map<Long, List<PropertyAssignment>> assignmentsByRegistatorId = getAssignments(assignments, assignmentRecords, r -> r.pers_id_registerer);
Map<Long, Person> registratorMap =
personTranslator.translate(context, assignmentsByRegistatorId.keySet(), assignmentFetchOptions.withRegistrator());
@@ -180,36 +185,28 @@ public class PropertyAssignmentTranslator implements IPropertyAssignmentTranslat
}
}
}
-
- return assignments;
- }
-
- private Map<Long, List<PropertyAssignment>> getAssignmentsByPropertyTypeId(Map<PropertyAssignmentKey, PropertyAssignment> assignments,
- Collection<PropertyAssignmentRecord> assignmentRecords)
- {
- Map<Long, List<PropertyAssignment>> map = new HashMap<Long, List<PropertyAssignment>>();
-
- for (PropertyAssignmentRecord assignmentRecord : assignmentRecords)
+
+ if (assignmentFetchOptions.hasPlugin())
{
- EntityKind entityKind = EntityKind.valueOf(assignmentRecord.kind_code);
- PropertyAssignmentKey key = new PropertyAssignmentKey(assignmentRecord.id, entityKind);
- PropertyAssignment assignment = assignments.get(key);
- List<PropertyAssignment> list = map.get(assignmentRecord.prty_id);
+ Map<Long, List<PropertyAssignment>> assignmentsByPluginId = getAssignments(assignments, assignmentRecords, r -> r.script_id);
+ Map<Long, Plugin> registratorMap =
+ pluginTranslator.translate(context, assignmentsByPluginId.keySet(), assignmentFetchOptions.withPlugin());
- if (list == null)
+ for (Map.Entry<Long, List<PropertyAssignment>> entry : assignmentsByPluginId.entrySet())
{
- list = new ArrayList<PropertyAssignment>();
- map.put(assignmentRecord.prty_id, list);
+ Plugin plugin = registratorMap.get(entry.getKey());
+ for (PropertyAssignment assignment : entry.getValue())
+ {
+ assignment.setPlugin(plugin);
+ }
}
-
- list.add(assignment);
}
- return map;
+ return assignments;
}
- private Map<Long, List<PropertyAssignment>> getAssignmentsByRegistratorId(Map<PropertyAssignmentKey, PropertyAssignment> assignments,
- Collection<PropertyAssignmentRecord> assignmentRecords)
+ private Map<Long, List<PropertyAssignment>> getAssignments(Map<PropertyAssignmentKey, PropertyAssignment> assignments,
+ Collection<PropertyAssignmentRecord> assignmentRecords, Function<PropertyAssignmentRecord, Long> extractor)
{
Map<Long, List<PropertyAssignment>> map = new HashMap<Long, List<PropertyAssignment>>();
@@ -218,15 +215,19 @@ public class PropertyAssignmentTranslator implements IPropertyAssignmentTranslat
EntityKind entityKind = EntityKind.valueOf(assignmentRecord.kind_code);
PropertyAssignmentKey key = new PropertyAssignmentKey(assignmentRecord.id, entityKind);
PropertyAssignment assignment = assignments.get(key);
- List<PropertyAssignment> list = map.get(assignmentRecord.pers_id_registerer);
-
- if (list == null)
+ Long id = extractor.apply(assignmentRecord);
+ if (id != null)
{
- list = new ArrayList<PropertyAssignment>();
- map.put(assignmentRecord.pers_id_registerer, list);
+ List<PropertyAssignment> list = map.get(id);
+
+ if (list == null)
+ {
+ list = new ArrayList<PropertyAssignment>();
+ map.put(id, list);
+ }
+
+ list.add(assignment);
}
-
- list.add(assignment);
}
return map;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/as/dto/property/PropertyAssignment.js b/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/as/dto/property/PropertyAssignment.js
index d08e89ec4ff01af84b84fff235f4c23d53dbf2dc..423964ac9cca3e91390981989765b0085f7701f8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/as/dto/property/PropertyAssignment.js
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/as/dto/property/PropertyAssignment.js
@@ -17,6 +17,7 @@ define([ "stjs", "util/Exceptions" ], function(stjs, exceptions) {
prototype.semanticAnnotationsInherited = null;
prototype.registrator = null;
prototype.registrationDate = null;
+ prototype.plugin = null;
prototype.getFetchOptions = function() {
return this.fetchOptions;
@@ -116,6 +117,16 @@ define([ "stjs", "util/Exceptions" ], function(stjs, exceptions) {
prototype.setRegistrationDate = function(registrationDate) {
this.registrationDate = registrationDate;
};
+ prototype.getPlugin = function() {
+ if (this.getFetchOptions() && this.getFetchOptions().hasPlugin()) {
+ return this.plugin;
+ } else {
+ throw new exceptions.NotFetchedException("Plugin has not been fetched.");
+ }
+ };
+ prototype.setPlugin = function(plugin) {
+ this.plugin = plugin;
+ };
}, {
fetchOptions : "PropertyAssignmentFetchOptions",
entityType : "IEntityType",
@@ -126,7 +137,8 @@ define([ "stjs", "util/Exceptions" ], function(stjs, exceptions) {
},
semanticAnnotationsInherited : "Boolean",
registrator : "Person",
- registrationDate : "Date"
+ registrationDate : "Date",
+ plugin : "Plugin"
});
return PropertyAssignment;
})
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/as/dto/property/fetchoptions/PropertyAssignmentFetchOptions.js b/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/as/dto/property/fetchoptions/PropertyAssignmentFetchOptions.js
index 169205d9021ec08a549e7cc114026e3976987343..1d47470c070bda54dcf7d44dec4349754d269f19 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/as/dto/property/fetchoptions/PropertyAssignmentFetchOptions.js
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/as/dto/property/fetchoptions/PropertyAssignmentFetchOptions.js
@@ -1,5 +1,5 @@
define([ "stjs", "as/dto/common/fetchoptions/FetchOptions", "as/dto/property/fetchoptions/PropertyTypeFetchOptions", "as/dto/person/fetchoptions/PersonFetchOptions",
- "as/dto/property/fetchoptions/PropertyAssignmentSortOptions", "as/dto/semanticannotation/fetchoptions/SemanticAnnotationFetchOptions" ], function(stjs, FetchOptions) {
+ "as/dto/plugin/fetchoptions/PluginFetchOptions", "as/dto/property/fetchoptions/PropertyAssignmentSortOptions", "as/dto/semanticannotation/fetchoptions/SemanticAnnotationFetchOptions" ], function(stjs, FetchOptions) {
var PropertyAssignmentFetchOptions = function() {
};
stjs.extend(PropertyAssignmentFetchOptions, FetchOptions, [ FetchOptions ], function(constructor, prototype) {
@@ -9,6 +9,7 @@ define([ "stjs", "as/dto/common/fetchoptions/FetchOptions", "as/dto/property/fet
prototype.propertyType = null;
prototype.semanticAnnotations = null;
prototype.registrator = null;
+ prototype.plugin = null;
prototype.sort = null;
prototype.withEntityType = function() {
@@ -63,6 +64,19 @@ define([ "stjs", "as/dto/common/fetchoptions/FetchOptions", "as/dto/property/fet
prototype.hasRegistrator = function() {
return this.registrator != null;
};
+ prototype.withPlugin = function() {
+ if (this.plugin == null) {
+ var PluginFetchOptions = require("as/dto/plugin/fetchoptions/PluginFetchOptions");
+ this.plugin = new PluginFetchOptions();
+ }
+ return this.plugin;
+ };
+ prototype.withPluginUsing = function(fetchOptions) {
+ return this.plugin = fetchOptions;
+ };
+ prototype.hasPlugin = function() {
+ return this.plugin != null;
+ };
prototype.sortBy = function() {
if (this.sort == null) {
var PropertyAssignmentSortOptions = require("as/dto/property/fetchoptions/PropertyAssignmentSortOptions");
@@ -78,6 +92,7 @@ define([ "stjs", "as/dto/common/fetchoptions/FetchOptions", "as/dto/property/fet
propertyType : "PropertyTypeFetchOptions",
semanticAnnotations : "SemanticAnnotationFetchOptions",
registrator : "PersonFetchOptions",
+ plugin : "PluginFetchOptions",
sort : "PropertyAssignmentSortOptions"
});
return PropertyAssignmentFetchOptions;
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/AbstractGetEntityTypeTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/AbstractGetEntityTypeTest.java
index 0a49f1e18e04f76b450fa3688e0f0dd527436f86..e831dbd430f097ba7e00b268c12e6b2695da09fa 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/AbstractGetEntityTypeTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/AbstractGetEntityTypeTest.java
@@ -239,6 +239,7 @@ public abstract class AbstractGetEntityTypeTest extends AbstractTest
PropertyAssignmentCreation assignmentCreation = new PropertyAssignmentCreation();
assignmentCreation.setPropertyTypeId(new PropertyTypePermId("DESCRIPTION"));
+ assignmentCreation.setPluginId(new PluginPermId("properties"));
EntityTypePermId permId = createEntityType(sessionToken, "ENTITY_TEST_TYPE", Arrays.asList(assignmentCreation), null);
@@ -248,7 +249,7 @@ public abstract class AbstractGetEntityTypeTest extends AbstractTest
assertEquals(((EntityTypePermId) type.getPermId()).getPermId(), permId.getPermId());
assertEquals(type.getCode(), permId.getPermId());
- assertPropertyAssignments(type.getPropertyAssignments(), "ENTITY_TEST_TYPE.DESCRIPTION");
+ assertPropertyAssignments(type.getPropertyAssignments(), "properties", "ENTITY_TEST_TYPE.DESCRIPTION");
assertValidationPluginNotFetched(type);
}
@@ -263,6 +264,7 @@ public abstract class AbstractGetEntityTypeTest extends AbstractTest
PropertyAssignmentCreation assignmentCreation = new PropertyAssignmentCreation();
assignmentCreation.setPropertyTypeId(new PropertyTypePermId(propertyTypeCodeWithDolar));
+ assignmentCreation.setPluginId(new PluginPermId("properties"));
EntityTypePermId permId = createEntityType(sessionToken, entityTypeCode, Arrays.asList(assignmentCreation), null);
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/AbstractTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/AbstractTest.java
index e2cb01c07a992b5fd7e4ede2379c7ec983e4fc9e..7ce17ff5f91d54b0fb0375be807d2f3b07d543ec 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/AbstractTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/AbstractTest.java
@@ -1120,13 +1120,17 @@ public class AbstractTest extends SystemTestCase
assertCollectionContainsOnly(actualSet, expectedCodes);
}
- protected static void assertPropertyAssignments(Collection<PropertyAssignment> propertyAssignments,
+ protected static void assertPropertyAssignments(Collection<PropertyAssignment> propertyAssignments, String pluginNameOrNull,
String... expectedEntityTypeAndPropertyTypeCodes)
{
Set<String> actualSet = new HashSet<String>();
for (PropertyAssignment propertyAssignment : propertyAssignments)
{
actualSet.add(propertyAssignment.getEntityType().getCode() + "." + propertyAssignment.getPropertyType().getCode());
+ if (pluginNameOrNull != null)
+ {
+ assertEquals(propertyAssignment.getPlugin().getName(), pluginNameOrNull);
+ }
}
assertCollectionContainsOnly(actualSet, expectedEntityTypeAndPropertyTypeCodes);
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/ConfirmDeletionTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/ConfirmDeletionTest.java
index f1335efd86aaa7ed371d84914db6da8687ab0e07..0f59020ff3fb1bd64c9bfa3be7e19224fe029fbe 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/ConfirmDeletionTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/ConfirmDeletionTest.java
@@ -331,13 +331,21 @@ public class ConfirmDeletionTest extends AbstractDeletionTest
@Test
public void testLogging()
{
+ // given
String sessionToken = v3api.login(TEST_USER, PASSWORD);
-
- v3api.confirmDeletions(sessionToken, Arrays.asList(new DeletionTechId(1L), new DeletionTechId(2L)));
-
- assertAccessLog("confirm-deletions DELETION_IDS('[1, 2]')");
+ ExperimentPermId experimentId = createCisdExperiment();
+ ExperimentDeletionOptions deletionOptions = new ExperimentDeletionOptions();
+ deletionOptions.setReason("It is just a test");
+ assertExperimentExists(experimentId);
+ IDeletionId deletionId = v3api.deleteExperiments(sessionToken, Collections.singletonList(experimentId), deletionOptions);
+ assertDeletionExists(deletionId);
+ // when
+ v3api.confirmDeletions(sessionToken, Collections.singletonList(deletionId));
+ // then
+ assertAccessLog("confirm-deletions DELETION_IDS('[" + deletionId + "]')");
}
+
private DataSetCreation dataSetCreation(String typeCode, String dataSetCode)
{
PhysicalDataCreation physicalCreation = new PhysicalDataCreation();
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/GetDataSetTypeTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/GetDataSetTypeTest.java
index d1a92118fbce38cc8a6a7afbd20974361b220654..98d873b208c0b71991e390564eefde4f21b79db1 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/GetDataSetTypeTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/GetDataSetTypeTest.java
@@ -68,6 +68,7 @@ public class GetDataSetTypeTest extends AbstractGetEntityTypeTest
{
fo.withPropertyAssignments().withEntityType();
fo.withPropertyAssignments().withPropertyType();
+ fo.withPropertyAssignments().withPlugin();
}
if (withValidationPlugin)
{
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/GetExperimentTypeTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/GetExperimentTypeTest.java
index 4f41ecd9faa41a7970524a3a4bb0003e265cfc1f..59cf285f23daf87966dc603748c37dc593c37b07 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/GetExperimentTypeTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/GetExperimentTypeTest.java
@@ -68,6 +68,7 @@ public class GetExperimentTypeTest extends AbstractGetEntityTypeTest
{
fo.withPropertyAssignments().withEntityType();
fo.withPropertyAssignments().withPropertyType();
+ fo.withPropertyAssignments().withPlugin();
}
if (withValidationPlugin)
{
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/GetMaterialTypeTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/GetMaterialTypeTest.java
index 2833e8078b827f4f3aa92c74d2fbb312d748751f..aa84b1ff7d136025fca5b442bb75158fa75c8197 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/GetMaterialTypeTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/GetMaterialTypeTest.java
@@ -68,6 +68,7 @@ public class GetMaterialTypeTest extends AbstractGetEntityTypeTest
{
fo.withPropertyAssignments().withEntityType();
fo.withPropertyAssignments().withPropertyType();
+ fo.withPropertyAssignments().withPlugin();
}
if (withValidationPlugin)
{
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/GetSampleTypeTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/GetSampleTypeTest.java
index 1d904181fc24d81cea207d8497cefd131c1d377f..354dfce5455fc42822774363eb9a0888bcc4e16b 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/GetSampleTypeTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/GetSampleTypeTest.java
@@ -69,6 +69,7 @@ public class GetSampleTypeTest extends AbstractGetEntityTypeTest
{
fo.withPropertyAssignments().withEntityType();
fo.withPropertyAssignments().withPropertyType();
+ fo.withPropertyAssignments().withPlugin();
}
if (withValidationPlugin)
{
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchPropertyAssignmentTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchPropertyAssignmentTest.java
index bc3be6513eeb28ccfdeb3a0ba03d375f3a0e040a..286e6010596d96d5286c1454cdf58da0e415825f 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchPropertyAssignmentTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchPropertyAssignmentTest.java
@@ -149,9 +149,9 @@ public class SearchPropertyAssignmentTest extends AbstractTest
}
}
- assertPropertyAssignments(withOwnSemanticAnnotations, "MASTER_PLATE.$PLATE_GEOMETRY", "CONTROL_LAYOUT.$PLATE_GEOMETRY",
+ assertPropertyAssignments(withOwnSemanticAnnotations, null, "MASTER_PLATE.$PLATE_GEOMETRY", "CONTROL_LAYOUT.$PLATE_GEOMETRY",
"CELL_PLATE.ORGANISM");
- assertPropertyAssignments(withInheritedSemanticAnnotations, "MASTER_PLATE.DESCRIPTION", "CONTROL_LAYOUT.DESCRIPTION", "NORMAL.ORGANISM",
+ assertPropertyAssignments(withInheritedSemanticAnnotations, null, "MASTER_PLATE.DESCRIPTION", "CONTROL_LAYOUT.DESCRIPTION", "NORMAL.ORGANISM",
"DELETION_TEST.ORGANISM", "DELETION_TEST.DESCRIPTION");
v3api.logout(sessionToken);
@@ -234,12 +234,13 @@ public class SearchPropertyAssignmentTest extends AbstractTest
PropertyAssignmentFetchOptions fo = new PropertyAssignmentFetchOptions();
fo.withEntityType();
fo.withPropertyType();
+ fo.withPlugin();
SearchResult<PropertyAssignment> searchResult =
v3api.searchPropertyAssignments(sessionToken, criteria, fo);
List<PropertyAssignment> propertyAssignments = searchResult.getObjects();
- assertPropertyAssignments(propertyAssignments, expectedEntityTypeAndPropertyTypeCodes);
+ assertPropertyAssignments(propertyAssignments, null, expectedEntityTypeAndPropertyTypeCodes);
v3api.logout(sessionToken);
}
diff --git a/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/property/PropertyAssignment.java b/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/property/PropertyAssignment.java
index 32d69393b62e38d39fb7b84d5db895034105638c..92fd9e2a24fe58df0a8743cfa2b75a42691e1fdb 100644
--- a/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/property/PropertyAssignment.java
+++ b/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/property/PropertyAssignment.java
@@ -22,6 +22,8 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.IRegistrationD
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.IRegistratorHolder;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.ISemanticAnnotationsHolder;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.person.Person;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.plugin.Plugin;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.plugin.id.IPluginId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.PropertyType;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.fetchoptions.PropertyAssignmentFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.id.PropertyAssignmentPermId;
@@ -38,7 +40,8 @@ import java.util.List;
* Class automatically generated with DtoGenerator
*/
@JsonObject("as.dto.property.PropertyAssignment")
-public class PropertyAssignment implements Serializable, IPermIdHolder, IPropertyTypeHolder, IRegistrationDateHolder, IRegistratorHolder, ISemanticAnnotationsHolder
+public class PropertyAssignment
+ implements Serializable, IPermIdHolder, IPropertyTypeHolder, IRegistrationDateHolder, IRegistratorHolder, ISemanticAnnotationsHolder
{
private static final long serialVersionUID = 1L;
@@ -81,6 +84,9 @@ public class PropertyAssignment implements Serializable, IPermIdHolder, IPropert
@JsonProperty
private Date registrationDate;
+ @JsonProperty
+ private Plugin plugin;
+
// Method automatically generated with DtoGenerator
@JsonIgnore
public PropertyAssignmentFetchOptions getFetchOptions()
@@ -141,8 +147,7 @@ public class PropertyAssignment implements Serializable, IPermIdHolder, IPropert
if (getFetchOptions() != null && getFetchOptions().hasEntityType())
{
return entityType;
- }
- else
+ } else
{
throw new NotFetchedException("Entity type has not been fetched.");
}
@@ -162,8 +167,7 @@ public class PropertyAssignment implements Serializable, IPermIdHolder, IPropert
if (getFetchOptions() != null && getFetchOptions().hasPropertyType())
{
return propertyType;
- }
- else
+ } else
{
throw new NotFetchedException("Property type has not been fetched.");
}
@@ -222,8 +226,7 @@ public class PropertyAssignment implements Serializable, IPermIdHolder, IPropert
if (getFetchOptions() != null && getFetchOptions().hasSemanticAnnotations())
{
return semanticAnnotations;
- }
- else
+ } else
{
throw new NotFetchedException("Semantic annotations have not been fetched.");
}
@@ -242,8 +245,7 @@ public class PropertyAssignment implements Serializable, IPermIdHolder, IPropert
if (getFetchOptions() != null && getFetchOptions().hasSemanticAnnotations())
{
return semanticAnnotationsInherited;
- }
- else
+ } else
{
throw new NotFetchedException("Semantic annotations have not been fetched.");
}
@@ -263,8 +265,7 @@ public class PropertyAssignment implements Serializable, IPermIdHolder, IPropert
if (getFetchOptions() != null && getFetchOptions().hasRegistrator())
{
return registrator;
- }
- else
+ } else
{
throw new NotFetchedException("Registrator has not been fetched.");
}
@@ -290,11 +291,29 @@ public class PropertyAssignment implements Serializable, IPermIdHolder, IPropert
this.registrationDate = registrationDate;
}
+ @JsonIgnore
+ public Plugin getPlugin()
+ {
+ if (getFetchOptions() != null && getFetchOptions().hasPlugin())
+ {
+ return plugin;
+ } else
+ {
+ throw new NotFetchedException("Plugin has not been fetched.");
+ }
+ }
+
+ public void setPlugin(Plugin plugin)
+ {
+ this.plugin = plugin;
+ }
+
// Method automatically generated with DtoGenerator
@Override
public String toString()
{
- return "PropertyAssignment entity type: " + (entityType != null ? entityType.getCode() : null) + ", property type: " + (propertyType != null ? propertyType.getCode() : null) + ", mandatory: " + mandatory;
+ return "PropertyAssignment entity type: " + (entityType != null ? entityType.getCode() : null) + ", property type: "
+ + (propertyType != null ? propertyType.getCode() : null) + ", mandatory: " + mandatory;
}
}
diff --git a/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/property/fetchoptions/PropertyAssignmentFetchOptions.java b/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/property/fetchoptions/PropertyAssignmentFetchOptions.java
index c296fc1511d61208449b7251b26a5d88242693b1..f0a962d1d9b3e085089552f27f4383405de45744 100644
--- a/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/property/fetchoptions/PropertyAssignmentFetchOptions.java
+++ b/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/property/fetchoptions/PropertyAssignmentFetchOptions.java
@@ -19,6 +19,7 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.fetchoptions.FetchOptions
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.fetchoptions.FetchOptionsToStringBuilder;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.fetchoptions.EntityTypeFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.person.fetchoptions.PersonFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.plugin.fetchoptions.PluginFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.PropertyAssignment;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.fetchoptions.PropertyTypeFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.semanticannotation.fetchoptions.SemanticAnnotationFetchOptions;
@@ -48,6 +49,9 @@ public class PropertyAssignmentFetchOptions extends FetchOptions<PropertyAssignm
@JsonProperty
private PropertyAssignmentSortOptions sort;
+
+ @JsonProperty
+ private PluginFetchOptions plugin;
// Method automatically generated with DtoGenerator
public EntityTypeFetchOptions withEntityType()
@@ -136,6 +140,25 @@ public class PropertyAssignmentFetchOptions extends FetchOptions<PropertyAssignm
{
return registrator != null;
}
+
+ public PluginFetchOptions withPlugin()
+ {
+ if (plugin == null)
+ {
+ plugin = new PluginFetchOptions();
+ }
+ return plugin;
+ }
+
+ public PluginFetchOptions withPluginUsing(PluginFetchOptions fetchOptions)
+ {
+ return plugin = fetchOptions;
+ }
+
+ public boolean hasPlugin()
+ {
+ return plugin != null;
+ }
// Method automatically generated with DtoGenerator
@Override
diff --git a/openbis_api/sourceTest/java/ch/ethz/sis/openbis/generic/sharedapi/v3/dictionary.txt b/openbis_api/sourceTest/java/ch/ethz/sis/openbis/generic/sharedapi/v3/dictionary.txt
index 5267a108c147d3d71c6a5dabb9dbb6057ae8cc92..7fd792f5b5086483b2b17fafbb4dfd58005a4f35 100644
--- a/openbis_api/sourceTest/java/ch/ethz/sis/openbis/generic/sharedapi/v3/dictionary.txt
+++ b/openbis_api/sourceTest/java/ch/ethz/sis/openbis/generic/sharedapi/v3/dictionary.txt
@@ -2231,3 +2231,10 @@ Archiving Requested Search Criteria
with Archiving Requested
with Option
+
+get Plugin
+has Plugin
+set Plugin
+with Plugin
+with Plugin Using
+
diff --git a/openbis_standard_technologies/build.gradle b/openbis_standard_technologies/build.gradle
index 52b6d0428f651371d3971bad5d8e86aa6cc1b2d9..79b276ae7afa40327b54bbda3ee9551d5bd01454 100644
--- a/openbis_standard_technologies/build.gradle
+++ b/openbis_standard_technologies/build.gradle
@@ -84,7 +84,7 @@ dependencies {
project(':screening'),
project(':rtd_phosphonetx'),
project(':plasmid'),
- 'bioformats:bioformats:+',
+ 'bioformats:bioformats:5.9.2',
'imagej:ij:+',
'cisd:cisd-openbis-knime-server:+',
'apache:xml-apis:+',
diff --git a/openbis_standard_technologies/dist/core-plugins/dropbox-monitor/2/dss/reporting-plugins/dropboxReporter/SimpleInfoObject.pyc b/openbis_standard_technologies/dist/core-plugins/dropbox-monitor/2/dss/reporting-plugins/dropboxReporter/SimpleInfoObject.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..183ac1b78d803a0a85229ae2b28e035ac42c5f96
Binary files /dev/null and b/openbis_standard_technologies/dist/core-plugins/dropbox-monitor/2/dss/reporting-plugins/dropboxReporter/SimpleInfoObject.pyc differ
diff --git a/openbis_standard_technologies/dist/core-plugins/dropbox-monitor/2/dss/reporting-plugins/dropboxReporter/Util.pyc b/openbis_standard_technologies/dist/core-plugins/dropbox-monitor/2/dss/reporting-plugins/dropboxReporter/Util.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..7862ab27e20c12749825a15c2d4502ebb6eab295
Binary files /dev/null and b/openbis_standard_technologies/dist/core-plugins/dropbox-monitor/2/dss/reporting-plugins/dropboxReporter/Util.pyc differ
diff --git a/openbis_standard_technologies/dist/core-plugins/dropbox-monitor/2/dss/reporting-plugins/dropboxReporter/test_simpleInfoTest.pyc b/openbis_standard_technologies/dist/core-plugins/dropbox-monitor/2/dss/reporting-plugins/dropboxReporter/test_simpleInfoTest.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..dc7ee0604fd06ea1cc94806217f62c6cf15b67c6
Binary files /dev/null and b/openbis_standard_technologies/dist/core-plugins/dropbox-monitor/2/dss/reporting-plugins/dropboxReporter/test_simpleInfoTest.pyc differ
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/initialize-master-data.py b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/initialize-master-data.py
index f57c0264f63f1f5a15992e412df6d7fe7b2eaf5a..ead04e46d97b8ee25bba52a26b321f5b06f4f7c1 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/initialize-master-data.py
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/initialize-master-data.py
@@ -16,12 +16,14 @@
# MasterDataRegistrationTransaction Class
import os
import sys
-from ch.systemsx.cisd.openbis.generic.server import CommonServiceProvider
-from ch.ethz.sis.openbis.generic.server.asapi.v3 import ApplicationServerApi
+
from ch.ethz.sis.openbis.generic.asapi.v3.dto.operation import SynchronousOperationExecutionOptions
-from parsers import ExcelToPoiParser, PoiToDefinitionParser, DefinitionToCreationParser, CreationToOperationParser, DuplicatesHandler
-from openbis_logic import ServerDuplicatesCreationHandler
+from ch.ethz.sis.openbis.generic.server.asapi.v3 import ApplicationServerApi
+from ch.systemsx.cisd.openbis.generic.server import CommonServiceProvider
from file_handling import list_xls_files
+from openbis_logic import OpenbisLogicHandler
+from parsers import ExcelToPoiParser, PoiToDefinitionParser, DefinitionToCreationParser, DuplicatesHandler, CreationToOperationParser
+from search_engines import SearchEngine
api = CommonServiceProvider.getApplicationContext().getBean(ApplicationServerApi.INTERNAL_SERVICE_NAME)
@@ -30,16 +32,21 @@ for excel_file_path in list_xls_files():
poi_definitions = ExcelToPoiParser.parse(excel_file_path)
definitions = PoiToDefinitionParser.parse(poi_definitions)
partial_creations = DefinitionToCreationParser.parse(definitions)
- print(partial_creations)
for creation_type, partial_creation in partial_creations.items():
if creation_type not in creations:
creations[creation_type] = partial_creation
else:
creations[creation_type].extend(partial_creation)
distinct_creations = DuplicatesHandler.get_distinct_creations(creations)
+
sessionToken = api.loginAsSystem()
-server_duplicates_handler = ServerDuplicatesCreationHandler(api, sessionToken, distinct_creations)
-creations = server_duplicates_handler.remove_already_existing_elements()
+search_engine = SearchEngine(api, sessionToken)
+existing_elements = search_engine.find_all_existing_elements(distinct_creations)
+server_duplicates_handler = OpenbisLogicHandler(distinct_creations, existing_elements)
+creations = server_duplicates_handler.remove_existing_elements_from_creations()
+creations = server_duplicates_handler.rewrite_parentchild_creationid_to_permid()
+# creations = server_duplicates_handler.rewrite_vocabulary_labels()
+
operations = CreationToOperationParser.parse(creations)
result = api.executeOperations(sessionToken, operations, SynchronousOperationExecutionOptions())
print("========================eln-life-sciences-types xls ingestion result========================")
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/life-sciences-types/scripts/valid.py b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/life-sciences-types/scripts/valid.py
index 14afec52e04849fdb34de83bdadb5a5793868218..d87950f600d11b50b96dcedef36fe8f36971140c 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/life-sciences-types/scripts/valid.py
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/life-sciences-types/scripts/valid.py
@@ -1,4 +1,3 @@
def validate(entity, isNew):
if isNew:
- if not entity.properties() is None:
- return "It is not allowed to attach properties to new sample."
\ No newline at end of file
+ return
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/life-sciences-types/types.xls b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/life-sciences-types/types.xls
index 3cdae5a2d0b77a23eaf1d1878982744bb55b51a1..473cc33398b77fb5980ba414df0437cd2cc91825 100644
Binary files a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/life-sciences-types/types.xls and b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/life-sciences-types/types.xls differ
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/life-sciences-types/types2.xls b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/life-sciences-types/types2.xls
new file mode 100644
index 0000000000000000000000000000000000000000..52bd9cc8dd6c1020b5d9b9624b4a53c092557beb
Binary files /dev/null and b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/life-sciences-types/types2.xls differ
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/openbis_logic.py b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/openbis_logic.py
index eb4006b87e254ac46b1ae55f9b78583d76c46fda..2e6c63b0bdd118e7bcb872c00ddf8a8756934101 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/openbis_logic.py
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/openbis_logic.py
@@ -1,130 +1,111 @@
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.id import ExperimentPermId
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.project.id import ProjectPermId
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id import SamplePermId, SampleIdentifier
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.space.id import SpacePermId
from parsers import VocabularyDefinitionToCreationParser, PropertyTypeDefinitionToCreationParser, SampleTypeDefinitionToCreationParser, \
ExperimentTypeDefinitionToCreationParser, DatasetTypeDefinitionToCreationParser, SpaceDefinitionToCreationParser, \
- ProjectDefinitionToCreationParser, ScriptDefinitionToCreationParser
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.search import VocabularySearchCriteria, \
- SearchVocabulariesOperation
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.property.search import PropertyTypeSearchCriteria, \
- SearchPropertyTypesOperation
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.search import SampleTypeSearchCriteria, \
- SearchSampleTypesOperation, SampleSearchCriteria, SearchSamplesOperation
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.search import ExperimentTypeSearchCriteria, \
- SearchExperimentTypesOperation
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.search import DataSetTypeSearchCriteria, \
- SearchDataSetTypesOperation
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.fetchoptions import VocabularyFetchOptions
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.property.fetchoptions import PropertyTypeFetchOptions
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.fetchoptions import SampleTypeFetchOptions, \
- SampleFetchOptions
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.fetchoptions import ExperimentTypeFetchOptions
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions import DataSetTypeFetchOptions
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.operation import SynchronousOperationExecutionOptions
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.common.search import SearchOperator
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.space.search import SpaceSearchCriteria, \
- SearchSpacesOperation
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.space.fetchoptions import SpaceFetchOptions
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.project.search import ProjectSearchCriteria, \
- SearchProjectsOperation
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.project.fetchoptions import ProjectFetchOptions
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.plugin.search import PluginSearchCriteria, \
- SearchPluginsOperation
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.plugin.fetchoptions import PluginFetchOptions
+ ProjectDefinitionToCreationParser, ExperimentDefinitionToCreationParser, ScriptDefinitionToCreationParser, SampleDefinitionToCreationParser
-class ServerDuplicatesCreationHandler(object):
-
- def __init__(self, api, sesstion_token, creations):
- self.api = api
- self.session_token = sesstion_token
+class OpenbisLogicHandler(object):
+
+ def __init__(self, creations, existing_elements):
self.creations = creations
-
- def remove_already_existing_elements(self):
- duplicates_removal_strategies = [
- {
- 'creations_type': VocabularyDefinitionToCreationParser.type,
- 'search_criteria_object' : VocabularySearchCriteria,
- 'search_operation':SearchVocabulariesOperation,
- 'fetch_options':VocabularyFetchOptions,
- 'distinct_property_name': 'code'
- },
- {
- 'creations_type': PropertyTypeDefinitionToCreationParser.type,
- 'search_criteria_object' : PropertyTypeSearchCriteria,
- 'search_operation': SearchPropertyTypesOperation,
- 'fetch_options': PropertyTypeFetchOptions,
- 'distinct_property_name': 'code'
- },
- {
- 'creations_type': SampleTypeDefinitionToCreationParser.type,
- 'search_criteria_object' : SampleTypeSearchCriteria,
- 'search_operation': SearchSampleTypesOperation,
- 'fetch_options': SampleTypeFetchOptions,
- 'distinct_property_name': 'code'
- },
- {
- 'creations_type': ExperimentTypeDefinitionToCreationParser.type,
- 'search_criteria_object' : ExperimentTypeSearchCriteria,
- 'search_operation': SearchExperimentTypesOperation,
- 'fetch_options': ExperimentTypeFetchOptions,
- 'distinct_property_name': 'code'
- },
- {
- 'creations_type': DatasetTypeDefinitionToCreationParser.type,
- 'search_criteria_object' : DataSetTypeSearchCriteria,
- 'search_operation': SearchDataSetTypesOperation,
- 'fetch_options': DataSetTypeFetchOptions,
- 'distinct_property_name': 'code'
- },
- {
- 'creations_type': SpaceDefinitionToCreationParser.type,
- 'search_criteria_object' : SpaceSearchCriteria,
- 'search_operation': SearchSpacesOperation,
- 'fetch_options': SpaceFetchOptions,
- 'distinct_property_name': 'code'
- },
- {
- 'creations_type': ProjectDefinitionToCreationParser.type,
- 'search_criteria_object' : ProjectSearchCriteria,
- 'search_operation': SearchProjectsOperation,
- 'fetch_options': ProjectFetchOptions,
- 'distinct_property_name': 'code'
- },
- {
- 'creations_type': ScriptDefinitionToCreationParser.type,
- 'search_criteria_object' : PluginSearchCriteria,
- 'search_operation': SearchPluginsOperation,
- 'fetch_options': PluginFetchOptions,
- 'distinct_property_name': 'name'
- }
- ]
- for strategy in duplicates_removal_strategies:
- if strategy['creations_type'] in self.creations:
- self.creations[strategy['creations_type']] = self.remove_specific_existing_elements(**strategy)
+ self.existing_elements = existing_elements
+
+ def rewrite_parentchild_creationid_to_permid(self):
+ if ProjectDefinitionToCreationParser.type in self.creations:
+ for creation in self.creations[ProjectDefinitionToCreationParser.type]:
+ for existing_element in self.existing_elements[SpaceDefinitionToCreationParser.type]:
+ if existing_element.code == creation.spaceId.creationId:
+ creation.spaceId = SpacePermId(str(existing_element.permId))
+ break
+ if ExperimentDefinitionToCreationParser.type in self.creations:
+ for creation in self.creations[ExperimentDefinitionToCreationParser.type]:
+ for existing_element in self.existing_elements[ProjectDefinitionToCreationParser.type]:
+ if existing_element.code == creation.projectId.creationId:
+ creation.projectId = ProjectPermId(str(existing_element.permId))
+ break
+ if SampleDefinitionToCreationParser.type in self.creations:
+ for creation in self.creations[SampleDefinitionToCreationParser.type]:
+ if creation.spaceId is not None:
+ for existing_element in self.existing_elements[SpaceDefinitionToCreationParser.type]:
+ if existing_element.code == creation.spaceId.creationId:
+ creation.spaceId = SpacePermId(str(existing_element.permId))
+ break
+ if creation.projectId is not None:
+ for existing_element in self.existing_elements[ProjectDefinitionToCreationParser.type]:
+ if existing_element.code == creation.projectId.creationId:
+ creation.projectId = ProjectPermId(str(existing_element.permId))
+ break
+ if creation.experimentId is not None:
+ for existing_element in self.existing_elements[ExperimentDefinitionToCreationParser.type]:
+ if existing_element.code == creation.experimentId.creationId:
+ creation.experimentId = ExperimentPermId(str(existing_element.permId))
+ break
+
+ rewritten_children = []
+ if creation.childIds is not None:
+ for child in creation.childIds:
+ new_id = None
+ for existing_element in self.existing_elements[SampleDefinitionToCreationParser.type]:
+ if existing_element.permId.permId == child.creationId:
+ new_id = existing_element.permId
+ break
+ elif existing_element.identifier.identifier == child.creationId:
+ new_id = existing_element.identifier
+ break
+
+ if new_id is None:
+ rewritten_children.append(child)
+ else:
+ rewritten_children.append(new_id)
+
+ rewritten_parents = []
+ if creation.parentIds is not None:
+ for parent in creation.parentIds:
+ new_id = None
+ for existing_element in self.existing_elements[SampleDefinitionToCreationParser.type]:
+ if existing_element.permId.permId == parent.creationId:
+ new_id = existing_element.permId
+ break
+ elif existing_element.identifier.identifier == parent.creationId:
+ new_id = existing_element.identifier
+ break
+
+ if new_id is None:
+ rewritten_parents.append(parent)
+ else:
+ rewritten_parents.append(new_id)
+ creation.setChildIds(rewritten_children)
+ creation.setParentIds(rewritten_parents)
+
return self.creations
- def remove_specific_existing_elements(self, creations_type, search_criteria_object, search_operation, fetch_options, distinct_property_name):
- if creations_type in self.creations:
- search_criteria = self.get_search_criteria(creations_type, search_criteria_object())
- result = self.execute_search_operation(search_operation(search_criteria, fetch_options()))
- return self.filter_creations_from_existing_objects(creations_type, result.getObjects(), distinct_property_name)
+ def remove_existing_elements_from_creations(self):
+ for creations_type, existing_elements in self.existing_elements.items():
+ if creations_type == SampleDefinitionToCreationParser.type:
+ existing_object_codes = [object.identifier.identifier for object in existing_elements]
+ self.creations[creations_type] = list(filter(lambda creation: creation.code is None or self._create_sample_identifier_string(creation) not in existing_object_codes, self.creations[creations_type]))
+ else:
+ distinct_property_name = self._get_distinct_property_name(creations_type)
+ self.creations[creations_type] = self._filter_creations_from_existing_objects(creations_type, existing_elements, distinct_property_name)
+ return self.creations
- def get_search_criteria(self, creations_type, search_criteria):
- specific_creations = self.creations[creations_type]
-
- if 'withCodes' in dir(search_criteria):
- search_criteria.withCodes().thatIn([creation.code for creation in specific_creations])
- elif 'withName' in dir(search_criteria):
- for creation in specific_creations:
- search_criteria.withName().thatEquals(creation.name)
- search_criteria.withOrOperator()
+ def _get_distinct_property_name(self, creation_type):
+ if creation_type == ScriptDefinitionToCreationParser.type:
+ return 'name'
else:
- for creation in specific_creations:
- search_criteria.withCode().thatEquals(creation.code)
- search_criteria.withOrOperator()
- return search_criteria
+ return 'code'
- def execute_search_operation(self, operation):
- return self.api.executeOperations(self.session_token, [operation], SynchronousOperationExecutionOptions()).getResults().get(0).getSearchResult()
+ def _create_sample_identifier_string(self, creation):
+ spaceId = creation.spaceId.creationId if creation.spaceId is not None else None
+ projectId = creation.projectId.creationId if creation.projectId is not None else None
+# experimentId = creation.experimentId.creationId if creation.experimentId is not None else None
+ code = creation.code
+ sample_identifier = SampleIdentifier(spaceId, projectId, None, code)
+ return sample_identifier.identifier
- def filter_creations_from_existing_objects(self, creations_type, existing_objects, attr):
+ def _filter_creations_from_existing_objects(self, creations_type, existing_objects, attr):
existing_object_codes = [getattr(object, attr) for object in existing_objects]
return list(filter(lambda creation: getattr(creation, attr) not in existing_object_codes, self.creations[creations_type]))
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers.py b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers.py
deleted file mode 100644
index 0660d40d33ad535797d0bf1127c8dc520f20f2c2..0000000000000000000000000000000000000000
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers.py
+++ /dev/null
@@ -1,682 +0,0 @@
-from copy import deepcopy
-from org.python.core.io import FileIO
-from org.apache.poi.ss.usermodel import WorkbookFactory
-from org.apache.poi.ss.usermodel import CellType
-from org.apache.commons.lang import StringUtils
-from org.apache.poi.ss.util import NumberToTextConverter
-from java.lang import UnsupportedOperationException
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.create import VocabularyCreation
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.create import CreateVocabulariesOperation
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.create import VocabularyTermCreation
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.create import SampleTypeCreation, CreateSampleTypesOperation, \
- SampleCreation, CreateSamplesOperation
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.property.create import PropertyAssignmentCreation, PropertyTypeCreation, CreatePropertyTypesOperation
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.id import VocabularyPermId
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.id import EntityTypePermId
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype import EntityKind
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.create import ExperimentTypeCreation, CreateExperimentTypesOperation, \
- ExperimentCreation, CreateExperimentsOperation
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.create import DataSetTypeCreation, CreateDataSetTypesOperation
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.property.id import PropertyTypePermId
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.property import DataType
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.space.create import SpaceCreation, \
- CreateSpacesOperation
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.project.create import ProjectCreation, \
- CreateProjectsOperation
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.common.id import CreationId
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.plugin.create import PluginCreation, \
- CreatePluginsOperation
-from file_handling import get_script, get_filename_from_path
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.plugin.id import PluginPermId
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.plugin import PluginType
-
-
-class ExcelToPoiParser(object):
-
- @staticmethod
- def parse(excel_file_path):
- workbook = WorkbookFactory.create(FileIO(excel_file_path, 'r').asInputStream())
-
- data_colection = []
- for sheet in workbook.sheetIterator():
- # get whole one definition
- definitions = []
- i = 0
- sheet_done = False
- while not sheet_done:
- definition_rows = []
- while not ExcelToPoiParser.is_row_empty(sheet.getRow(i)):
- row = sheet.getRow(i)
- first_cell = row.getCell(0)
- if first_cell is None or first_cell == CellType.BLANK:
- continue
- else:
- definition_rows.append(row)
- i += 1
- i += 1 # skip empty row
-
- if not definition_rows:
- sheet_done = True
- else:
- definitions.append(definition_rows)
-
- workbook.close()
-
- definitions_stripped = []
- for definition in definitions:
- definition_stripped = []
- for row in definition:
- row_stripped = {}
- for cell in row.cellIterator():
- cell_value = ExcelToPoiParser.extract_string_value_from(cell)
- cell_value = cell_value if cell_value != '' else None
- cell_col = cell.getColumnIndex()
- row_stripped[cell_col] = cell_value
- definition_stripped.append(row_stripped)
- definitions_stripped.append(definition_stripped)
-
- return definitions_stripped
-
- @staticmethod
- def extract_string_value_from(cell):
- cell_type = cell.getCellTypeEnum()
- if cell_type == CellType.BLANK:
- return "";
- elif cell_type == CellType.BOOLEAN:
- return str(cell.getBooleanCellValue());
- elif cell_type == CellType.NUMERIC:
- return NumberToTextConverter.toText(cell.getNumericCellValue());
- elif cell_type == CellType.STRING:
- return cell.getStringCellValue();
- elif cell_type == CellType.FORMULA:
- raise SyntaxError("Excel formulas are not supported but one was found in cell " + extractCellPosition(cell));
- elif cell_type == CellType.ERROR:
- raise SyntaxError("There is an error in cell " + extractCellPosition(cell));
- else:
- raise SyntaxError("Unknown data type of cell " + extractCellPosition(cell));
-
- @staticmethod
- def is_row_empty(row):
- if row is None:
- return True
- if row.getLastCellNum <= 0:
- return True
-
- return all(ExcelToPoiParser.is_cell_empty(cell) for cell in row.cellIterator())
-
- @staticmethod
- def is_cell_empty(cell):
- if cell is not None and cell.getCellType() != CellType.BLANK and StringUtils.isNotBlank(cell.toString()):
- return False;
- return True
-
-
-class Definition(object):
- '''
- Used to hold values for object(Vocabulary, SampleType etc.) creation.
- '''
-
- def __init__(self):
- self.type = None
- self.attributes = {}
- self.properties = []
-
- def __str__(self):
- return "\n".join([
- "Definition type:",
- str(self.type),
- "Attributes:",
- str(self.attributes),
- "Properties:",
- str(self.properties),
- "==================" * 3])
-
- __repr__ = __str__
-
-
-class DefinitionParserFactory(object):
-
- @staticmethod
- def get_parser(definition_type):
- if definition_type in ['VOCABULARY_TYPE', 'SAMPLE_TYPE', 'EXPERIMENT_TYPE', 'DATASET_TYPE', 'SPACE', 'PROJECT', 'EXPERIMENT', 'SAMPLE']:
- return GeneralDefinitionParser
- else:
- raise UnsupportedOperationException("Definition of " + str(definition_type) + " is not supported (probably yet).")
-
-
-class GeneralDefinitionParser(object):
-
- @staticmethod
- def parse(poi_definition):
- DEFINITION_TYPE_ROW = 0
- DEFINITION_TYPE_CELL = 0
- ATTRIBUTES_HEADER_ROW = 1
- ATTRIBUTES_VALUES_ROW = 2
- PROPERTIES_HEADER_ROW = 3
- PROPERTIES_VALUES_ROW_START = 4
-
- definition = Definition()
- definition.type = poi_definition[DEFINITION_TYPE_ROW][DEFINITION_TYPE_CELL]
-
- for col, header in poi_definition[ATTRIBUTES_HEADER_ROW].items():
- cell_value = poi_definition[ATTRIBUTES_VALUES_ROW][col]
- definition.attributes[header] = cell_value
-
- if GeneralDefinitionParser.hasProperties(poi_definition):
- properties_headers = poi_definition[PROPERTIES_HEADER_ROW]
-
- for property_definitions in poi_definition[PROPERTIES_VALUES_ROW_START:]:
- property = {}
- for col, header in properties_headers.items():
- property[header] = property_definitions[col]
- definition.properties.append(property)
-
- return definition
-
- @staticmethod
- def hasProperties(poi_definition):
- PROPERTIES_HEADER_ROW = 3
- return len(poi_definition) > PROPERTIES_HEADER_ROW
-
-
-class PoiCleaner(object):
-
- @staticmethod
- def hasProperties(poi_definition):
- PROPERTIES_HEADER_ROW = 3
- return len(poi_definition) > PROPERTIES_HEADER_ROW
-
- @staticmethod
- def clean_data(xls_definitions):
- DEFINITION_TYPE_ROW = 0
- DEFINITION_TYPE_CELL = 0
- ATTRIBUTES_HEADER_ROW = 1
- ATTRIBUTES_VALUES_ROW = 2
- PROPERTIES_HEADER_ROW = 3
- PROPERTIES_VALUES_ROW_START = 4
-
- xls_def = deepcopy(xls_definitions)
- '''
- First row can only have definition type, rest is trimmed
- '''
- for definition in xls_def:
- definition[DEFINITION_TYPE_ROW] = {0:definition[DEFINITION_TYPE_ROW][DEFINITION_TYPE_CELL]}
- '''
- Header rows cannot have empty cells
- '''
- PoiCleaner.delete_empty_cells_from(definition, ATTRIBUTES_HEADER_ROW)
- if PoiCleaner.hasProperties(definition):
- PoiCleaner.delete_empty_cells_from(definition, PROPERTIES_HEADER_ROW)
- '''
- Values that do not have corresponding headers are removed.
- '''
- PoiCleaner.delete_cells_if_no_header(definition, ATTRIBUTES_HEADER_ROW, ATTRIBUTES_VALUES_ROW)
- if PoiCleaner.hasProperties(definition):
- for property_value_row_num in range(PROPERTIES_VALUES_ROW_START, len(definition)):
- PoiCleaner.delete_cells_if_no_header(definition, PROPERTIES_HEADER_ROW, property_value_row_num)
- '''
- All attributes and properties should have corresponding value in values row when header exists.
- If there's no corresponding value, None is inserted.
- '''
- PoiCleaner.create_cells_if_no_value_but_header_exists(definition, ATTRIBUTES_HEADER_ROW, ATTRIBUTES_VALUES_ROW)
- if PoiCleaner.hasProperties(definition):
- for property_value_row_num in range(PROPERTIES_VALUES_ROW_START, len(definition)):
- PoiCleaner.create_cells_if_no_value_but_header_exists(definition, PROPERTIES_HEADER_ROW, property_value_row_num)
- '''
- Headers to lowercase
- '''
- definition[ATTRIBUTES_HEADER_ROW] = PoiCleaner.dict_values_to_lowercase(definition[ATTRIBUTES_HEADER_ROW])
- if PoiCleaner.hasProperties(definition):
- definition[PROPERTIES_HEADER_ROW] = PoiCleaner.dict_values_to_lowercase(definition[PROPERTIES_HEADER_ROW])
-
- return xls_def
-
- @staticmethod
- def delete_empty_cells_from(definition, row_number):
- header_cell_cols_to_pop = []
- for cell_col, cell in definition[row_number].items():
- if cell is None or cell == '':
- header_cell_cols_to_pop.append(cell_col)
-
- for cell_col in header_cell_cols_to_pop:
- del definition[row_number][cell_col]
-
- return definition
-
- @staticmethod
- def delete_cells_if_no_header(definition, header_row_number, value_row_number):
- values_cell_cols_to_pop = []
- for cell_col in definition[value_row_number]:
- if cell_col not in definition[header_row_number]:
- values_cell_cols_to_pop.append(cell_col)
-
- for cell_col in values_cell_cols_to_pop:
- del definition[value_row_number][cell_col]
-
- return definition
-
- @staticmethod
- def create_cells_if_no_value_but_header_exists(definition, header_row_number, value_row_number):
- values_cell_cols_to_insert = []
- for cell_col in definition[header_row_number]:
- if cell_col not in definition[value_row_number]:
- values_cell_cols_to_insert.append(cell_col)
-
- for cell_col in values_cell_cols_to_insert:
- definition[value_row_number][cell_col] = None
-
- return definition
-
- @staticmethod
- def dict_values_to_lowercase(row):
- return dict((k, v.lower()) for (k, v) in row.items())
-
-
-class PoiToDefinitionParser(object):
-
- @staticmethod
- def parse(uncleaned_poi_definitions):
- '''
- Expecting definitions to be in such layout:
- [
- `DEFINITIONS_LIST`
- [
- `DEFINITION`
- {
- `ROWS`
- (column, row) : string_value,
- .
- .
- .
- }
- ],
- .
- .
- .
- ]
- '''
- poi_definitions = PoiCleaner.clean_data(uncleaned_poi_definitions)
- definitons = []
- for poi_definition in poi_definitions:
- FIRST_ROW = 0
- FIRST_CELL = 0
- definition_type = poi_definition[FIRST_ROW][FIRST_CELL]
- definition_parser = DefinitionParserFactory.get_parser(definition_type)
- definition = definition_parser.parse(poi_definition)
- definitons.append(definition)
-
- return definitons
-
-
-class DefinitionToCreationParser(object):
-
- @staticmethod
- def parse(definitions):
- creations = {}
-
- for definition in definitions:
- # One definition may contain more than one creation
- parsers = DefinitionToCreationParserFactory.getParsers(definition)
- for parser in parsers:
- creation = parser.parse(definition)
- if creation is None or creation == []:
- continue
- creation_type = parser.get_type()
- if creation_type not in creations:
- creations[creation_type] = []
- creations[creation_type].extend(creation if type(creation) == list else [creation])
-
- return creations
-
- @staticmethod
- def get_boolean_from_string(text):
- return True if text.lower() == u'true' else False
-
-
-class PropertyTypeDefinitionToCreationParser(object):
-
- type = "PropertyTypeCreation"
-
- @staticmethod
- def parse(definition):
- property_creations = []
- for property in definition.properties:
- property_type_creation = PropertyTypeCreation()
- property_type_creation.code = property[u'code']
- if property[u'code'].startswith(u'$'):
- property_type_creation.setInternalNameSpace(True)
- property_type_creation.setLabel(property[u'property label'])
- property_type_creation.setDataType(DataType.valueOf(property[u'property type']))
- property_type_creation.setVocabularyId(VocabularyPermId(property[u'vocabulary code']) if property[u'vocabulary code'] is not None else None)
- property_type_creation.setDescription(property[u'description'])
- property_creations.append(property_type_creation)
-
- return property_creations
-
- @staticmethod
- def get_type():
- return PropertyTypeDefinitionToCreationParser.type
-
-
-class VocabularyDefinitionToCreationParser(object):
-
- type = "VocabularyCreation"
-
- @staticmethod
- def parse(definition):
- vocabulary_creation = VocabularyCreation()
- vocabulary_creation.setCode(definition.attributes[u'code'])
- vocabulary_creation.setDescription(definition.attributes[u'description'])
-
- vocabulary_creations_terms = []
- for property in definition.properties:
- vocabulary_creation_term = VocabularyTermCreation()
- vocabulary_creation_term.setCode(property[u'code'])
- vocabulary_creation_term.setLabel(property[u'label'])
- vocabulary_creation_term.setDescription(property[u'description'])
- vocabulary_creations_terms.append(vocabulary_creation_term)
-
- vocabulary_creation.setTerms(vocabulary_creations_terms)
-
- return vocabulary_creation
-
- @staticmethod
- def get_type():
- return VocabularyDefinitionToCreationParser.type
-
-
-class PropertyAssignmentDefinitionToCreationParser(object):
-
- type = "PropertyAssignmentCreation"
-
- @staticmethod
- def parse(property):
- property_assingment_creation = PropertyAssignmentCreation()
- is_mandatory = DefinitionToCreationParser.get_boolean_from_string(property[u'mandatory'])
- property_assingment_creation.setMandatory(is_mandatory)
- should_show_in_edit_view = DefinitionToCreationParser.get_boolean_from_string(property[u'show in edit views'])
- property_assingment_creation.setShowInEditView(should_show_in_edit_view)
- property_assingment_creation.setSection(property[u'section'])
- property_assingment_creation.setPropertyTypeId(PropertyTypePermId(property[u'code']))
-
- return property_assingment_creation
-
- @staticmethod
- def get_type():
- return PropertyAssignmentDefinitionToCreationParser.type
-
-
-class SampleTypeDefinitionToCreationParser(object):
-
- type = "SampleTypeCreation"
-
- @staticmethod
- def parse(definition):
- sample_creation = SampleTypeCreation()
- sample_creation.setCode(definition.attributes[u'code'])
- should_auto_generate_codes = DefinitionToCreationParser.get_boolean_from_string(definition.attributes[u'auto generate codes'])
- sample_creation.setAutoGeneratedCode(should_auto_generate_codes)
- validation_script_path = definition.attributes[u'validation script']
-# if validation_script_path is not None:
-# sample_creation.setValidationPluginId(PluginPermId(get_filename_from_path(validation_script_path)))
-
- property_assingment_creations = []
- for property in definition.properties:
- property_assingment_creation = PropertyAssignmentDefinitionToCreationParser.parse(property)
- property_assingment_creations.append(property_assingment_creation)
-
- sample_creation.setPropertyAssignments(property_assingment_creations)
- return sample_creation
-
- @staticmethod
- def get_type():
- return SampleTypeDefinitionToCreationParser.type
-
-
-class ExperimentTypeDefinitionToCreationParser(object):
-
- type = "ExperimentTypeCreation"
-
- @staticmethod
- def parse(definition):
- experiment_type_creation = ExperimentTypeCreation()
- experiment_type_creation.setCode(definition.attributes[u'code'])
-
- property_assingment_creations = []
- for property in definition.properties:
- property_assingment_creation = PropertyAssignmentDefinitionToCreationParser.parse(property)
- property_assingment_creations.append(property_assingment_creation)
-
- experiment_type_creation.setPropertyAssignments(property_assingment_creations)
- return experiment_type_creation
-
- @staticmethod
- def get_type():
- return ExperimentTypeDefinitionToCreationParser.type
-
-
-class DatasetTypeDefinitionToCreationParser(object):
-
- type = "DatasetTypeCreation"
-
- @staticmethod
- def parse(definition):
- dataset_type_creation = DataSetTypeCreation()
- dataset_type_creation.setCode(definition.attributes[u'code'])
-
- property_assingment_creations = []
- for property in definition.properties:
- property_assingment_creation = PropertyAssignmentDefinitionToCreationParser.parse(property)
- property_assingment_creations.append(property_assingment_creation)
-
- dataset_type_creation.setPropertyAssignments(property_assingment_creations)
- return dataset_type_creation
-
- @staticmethod
- def get_type():
- return DatasetTypeDefinitionToCreationParser.type
-
-
-class SpaceDefinitionToCreationParser(object):
-
- type = "SpaceCreation"
-
- @staticmethod
- def parse(definition):
- space_creation = SpaceCreation()
- space_creation.setCode(definition.attributes[u'code'])
- space_creation.setDescription(definition.attributes[u'description'])
- creation_id = definition.attributes[u'code']
- space_creation.setCreationId(CreationId(creation_id))
- return space_creation
-
- @staticmethod
- def get_type():
- return SpaceDefinitionToCreationParser.type
-
-
-class ProjectDefinitionToCreationParser(object):
-
- type = "ProjectCreation"
-
- @staticmethod
- def parse(definition):
- project_creation = ProjectCreation()
- project_creation.setCode(definition.attributes[u'code'])
- project_creation.setDescription(definition.attributes[u'description'])
- project_creation.setSpaceId(CreationId(definition.attributes[u'space']))
- creation_id = definition.attributes[u'code']
- project_creation.setCreationId(CreationId(creation_id))
- return project_creation
-
- @staticmethod
- def get_type():
- return ProjectDefinitionToCreationParser.type
-
-
-class ExperimentDefinitionToCreationParser(object):
-
- type = "ExperimentCreation"
-
- @staticmethod
- def parse(definition):
- experiments = []
- mandatory_attributes = [u'code', u'project']
- for experiment_properties in definition.properties:
- experiment_creation = ExperimentCreation()
- experiment_creation.setTypeId(EntityTypePermId(definition.attributes[u'experiment type']))
- experiment_creation.setCode(experiment_properties[u'code'])
- experiment_creation.setProjectId(CreationId(experiment_properties[u'project']))
- creation_id = experiment_properties[u'code']
- experiment_creation.setCreationId(CreationId(creation_id))
- for property, value in experiment_properties.items():
- if property not in mandatory_attributes:
- experiment_creation.setProperty(property, value)
- experiments.append(experiment_creation)
- return experiments
-
- @staticmethod
- def get_type():
- return ExperimentDefinitionToCreationParser.type
-
-
-class SampleDefinitionToCreationParser(object):
-
- type = "SampleCreation"
-
- @staticmethod
- def parse(definition):
- samples = []
- mandatory_attributes = [u'code', u'space', u'project', u'experiment', u'auto generate code', u'parents', u'children']
- for sample_properties in definition.properties:
- sample_creation = SampleCreation()
- sample_creation.setTypeId(EntityTypePermId(definition.attributes[u'sample type']))
- if u'code' in sample_properties and sample_properties[u'code'] is not None and sample_properties[u'code'] != '':
- sample_creation.setCode(sample_properties[u'code'])
- creation_id = sample_properties[u'code']
- sample_creation.setCreationId(CreationId(creation_id))
- if u'auto generate code' in sample_properties and sample_properties[u'auto generate code'] is not None and sample_properties[u'auto generate code'] != '':
- sample_creation.setAutoGeneratedCode(DefinitionToCreationParser.get_boolean_from_string(sample_properties[u'auto generate code']))
- if u'space' in sample_properties and sample_properties[u'space'] is not None:
- sample_creation.setSpaceId(CreationId(sample_properties[u'space']))
- if u'project' in sample_properties and sample_properties[u'project'] is not None:
- sample_creation.setProjectId(CreationId(sample_properties[u'project']))
- if u'experiment' in sample_properties and sample_properties[u'experiment'] is not None:
- sample_creation.setExperimentId(CreationId(sample_properties[u'experiment']))
- for property, value in sample_properties.items():
- if property not in mandatory_attributes:
- sample_creation.setProperty(property, value)
- samples.append(sample_creation)
- return samples
-
- @staticmethod
- def get_type():
- return SampleDefinitionToCreationParser.type
-
-
-class ScriptDefinitionToCreationParser(object):
-
- type = "ScriptCreation"
-
- @staticmethod
- def parse(definition):
- scripts = []
- validation_script_path = definition.attributes[u'validation script']
- if validation_script_path is not None:
- validation_script_creation = PluginCreation()
- script_file = open(get_script(validation_script_path))
- script = script_file.read()
- script_file.close()
- validation_script_creation.setName(get_filename_from_path(validation_script_path))
- validation_script_creation.setScript(script)
- validation_script_creation.setPluginType(PluginType.ENTITY_VALIDATION)
- scripts.append(validation_script_creation)
-
- for property in definition.properties:
- dynamic_prop_script_path = property[u'dynamic script']
- if dynamic_prop_script_path is not None:
- validation_script_creation = PluginCreation()
- script_file = open(get_script(dynamic_prop_script_path))
- script = script_file.read()
- script_file.close()
- validation_script_creation.setName(get_filename_from_path(dynamic_prop_script_path))
- validation_script_creation.setScript(script)
- validation_script_creation.setPluginType(PluginType.DYNAMIC_PROPERTY)
- scripts.append(validation_script_creation)
-
- return scripts
-
- @staticmethod
- def parse_script():
- pass
-
- @staticmethod
- def get_type():
- return ScriptDefinitionToCreationParser.type
-
-
-class DefinitionToCreationParserFactory(object):
-
- @staticmethod
- def getParsers(definition):
- if definition.type == u'VOCABULARY_TYPE':
- return [VocabularyDefinitionToCreationParser]
- elif definition.type == u'SAMPLE_TYPE':
- return [SampleTypeDefinitionToCreationParser, PropertyTypeDefinitionToCreationParser, ScriptDefinitionToCreationParser]
- elif definition.type == u'EXPERIMENT_TYPE':
- return [ExperimentTypeDefinitionToCreationParser, PropertyTypeDefinitionToCreationParser]
- elif definition.type == u'DATASET_TYPE':
- return [DatasetTypeDefinitionToCreationParser, PropertyTypeDefinitionToCreationParser]
- elif definition.type == u'SPACE':
- return [SpaceDefinitionToCreationParser]
- elif definition.type == u'PROJECT':
- return [ProjectDefinitionToCreationParser]
- elif definition.type == u'EXPERIMENT':
- return [ExperimentDefinitionToCreationParser]
- elif definition.type == u'SAMPLE':
- return [SampleDefinitionToCreationParser]
- else:
- raise UnsupportedOperationException("Definition of " + str(definition.type) + " is not supported (probably yet).")
-
-
-class DuplicatesHandler(object):
-
- @staticmethod
- def get_distinct_creations(creations):
- distinct_creations = {}
- for creation_type, creations in creations.items():
- if creation_type == ScriptDefinitionToCreationParser.type:
- distinct_creations[creation_type] = dict((creation.name, creation) for creation in creations).values()
- elif creation_type not in [SampleDefinitionToCreationParser.type]:
- distinct_creations[creation_type] = dict((creation.code, creation) for creation in creations).values()
- else:
- distinct_creations[creation_type] = list(creations)
- return distinct_creations
-
-
-class CreationToOperationParser(object):
-
- @staticmethod
- def parse(creations):
- creation_operations = []
- if VocabularyDefinitionToCreationParser.type in creations:
- creation_operations.append(CreateVocabulariesOperation(creations[VocabularyDefinitionToCreationParser.type]))
- if PropertyTypeDefinitionToCreationParser.type in creations:
- creation_operations.append(CreatePropertyTypesOperation(creations[PropertyTypeDefinitionToCreationParser.type]))
- if SampleTypeDefinitionToCreationParser.type in creations:
- creation_operations.append(CreateSampleTypesOperation(creations[SampleTypeDefinitionToCreationParser.type]))
- if ExperimentTypeDefinitionToCreationParser.type in creations:
- creation_operations.append(CreateExperimentTypesOperation(creations[ExperimentTypeDefinitionToCreationParser.type]))
- if DatasetTypeDefinitionToCreationParser.type in creations:
- creation_operations.append(CreateDataSetTypesOperation(creations[DatasetTypeDefinitionToCreationParser.type]))
- if SpaceDefinitionToCreationParser.type in creations:
- creation_operations.append(CreateSpacesOperation(creations[SpaceDefinitionToCreationParser.type]))
- if ProjectDefinitionToCreationParser.type in creations:
- creation_operations.append(CreateProjectsOperation(creations[ProjectDefinitionToCreationParser.type]))
- if ExperimentDefinitionToCreationParser.type in creations:
- creation_operations.append(CreateExperimentsOperation(creations[ExperimentDefinitionToCreationParser.type]))
- if SampleDefinitionToCreationParser.type in creations:
- creation_operations.append(CreateSamplesOperation(creations[SampleDefinitionToCreationParser.type]))
- if ScriptDefinitionToCreationParser.type in creations:
- creation_operations.append(CreatePluginsOperation(creations[ScriptDefinitionToCreationParser.type]))
- return creation_operations
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/__init__.py b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..0f3c10c3c3690bb834a59df53111873ffac988d8
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/__init__.py
@@ -0,0 +1,9 @@
+from .creation_to_operation import CreationToOperationParser
+from .definition_to_creation import DefinitionToCreationParser
+from .definition_to_creation import DuplicatesHandler, VocabularyDefinitionToCreationParser, \
+ PropertyTypeDefinitionToCreationParser, SampleTypeDefinitionToCreationParser, ExperimentTypeDefinitionToCreationParser, \
+ DatasetTypeDefinitionToCreationParser, SpaceDefinitionToCreationParser, ProjectDefinitionToCreationParser, \
+ ExperimentDefinitionToCreationParser, ScriptDefinitionToCreationParser, SampleDefinitionToCreationParser
+from .excel_to_poi import ExcelToPoiParser
+from .poi_to_definition import PoiToDefinitionParser
+
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/creation_to_operation/__init__.py b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/creation_to_operation/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..da17c96a5342705fbffea8a907ef83535f0c39a5
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/creation_to_operation/__init__.py
@@ -0,0 +1 @@
+from .creation_to_operation import CreationToOperationParser
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/creation_to_operation/creation_to_operation.py b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/creation_to_operation/creation_to_operation.py
new file mode 100644
index 0000000000000000000000000000000000000000..3baf8f307b88656295af994c4f37d6f1933f62c6
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/creation_to_operation/creation_to_operation.py
@@ -0,0 +1,39 @@
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.create import CreateDataSetTypesOperation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.create import CreateExperimentTypesOperation, CreateExperimentsOperation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.plugin.create import CreatePluginsOperation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.project.create import CreateProjectsOperation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.property.create import CreatePropertyTypesOperation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.create import CreateSampleTypesOperation, CreateSamplesOperation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.space.create import CreateSpacesOperation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.create import CreateVocabulariesOperation
+from ..definition_to_creation import VocabularyDefinitionToCreationParser, PropertyTypeDefinitionToCreationParser, SampleTypeDefinitionToCreationParser, \
+ ExperimentTypeDefinitionToCreationParser, DatasetTypeDefinitionToCreationParser, SpaceDefinitionToCreationParser, \
+ ProjectDefinitionToCreationParser, ExperimentDefinitionToCreationParser, ScriptDefinitionToCreationParser, SampleDefinitionToCreationParser
+
+
+class CreationToOperationParser(object):
+
+ @staticmethod
+ def parse(creations):
+ creation_operations = []
+ if VocabularyDefinitionToCreationParser.type in creations:
+ creation_operations.append(CreateVocabulariesOperation(creations[VocabularyDefinitionToCreationParser.type]))
+ if PropertyTypeDefinitionToCreationParser.type in creations:
+ creation_operations.append(CreatePropertyTypesOperation(creations[PropertyTypeDefinitionToCreationParser.type]))
+ if SampleTypeDefinitionToCreationParser.type in creations:
+ creation_operations.append(CreateSampleTypesOperation(creations[SampleTypeDefinitionToCreationParser.type]))
+ if ExperimentTypeDefinitionToCreationParser.type in creations:
+ creation_operations.append(CreateExperimentTypesOperation(creations[ExperimentTypeDefinitionToCreationParser.type]))
+ if DatasetTypeDefinitionToCreationParser.type in creations:
+ creation_operations.append(CreateDataSetTypesOperation(creations[DatasetTypeDefinitionToCreationParser.type]))
+ if SpaceDefinitionToCreationParser.type in creations:
+ creation_operations.append(CreateSpacesOperation(creations[SpaceDefinitionToCreationParser.type]))
+ if ProjectDefinitionToCreationParser.type in creations:
+ creation_operations.append(CreateProjectsOperation(creations[ProjectDefinitionToCreationParser.type]))
+ if ExperimentDefinitionToCreationParser.type in creations:
+ creation_operations.append(CreateExperimentsOperation(creations[ExperimentDefinitionToCreationParser.type]))
+ if SampleDefinitionToCreationParser.type in creations:
+ creation_operations.append(CreateSamplesOperation(creations[SampleDefinitionToCreationParser.type]))
+ if ScriptDefinitionToCreationParser.type in creations:
+ creation_operations.append(CreatePluginsOperation(creations[ScriptDefinitionToCreationParser.type]))
+ return creation_operations
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/definition_to_creation/__init__.py b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/definition_to_creation/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..b57ceeb03d8999dc5b928dfa8a374095b465e963
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/definition_to_creation/__init__.py
@@ -0,0 +1,6 @@
+from .creation_parsers import VocabularyDefinitionToCreationParser, PropertyTypeDefinitionToCreationParser, SampleTypeDefinitionToCreationParser, \
+ ExperimentTypeDefinitionToCreationParser, DatasetTypeDefinitionToCreationParser, SpaceDefinitionToCreationParser, \
+ ProjectDefinitionToCreationParser, ExperimentDefinitionToCreationParser, ScriptDefinitionToCreationParser, SampleDefinitionToCreationParser
+from .definition_to_creation import DefinitionToCreationParser
+from .duplicates_handler import DuplicatesHandler
+
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/definition_to_creation/creation_parsers.py b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/definition_to_creation/creation_parsers.py
new file mode 100644
index 0000000000000000000000000000000000000000..86e26673774e25b68cb5b047c7b992c77a34a168
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/definition_to_creation/creation_parsers.py
@@ -0,0 +1,358 @@
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.common.id import CreationId
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.create import DataSetTypeCreation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.id import EntityTypePermId
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.create import ExperimentTypeCreation, ExperimentCreation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.plugin import PluginType
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.plugin.create import PluginCreation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.plugin.id import PluginPermId
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.project.create import ProjectCreation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.property import DataType
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.property.create import PropertyAssignmentCreation, PropertyTypeCreation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.property.id import PropertyTypePermId
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.create import SampleTypeCreation, SampleCreation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.space.create import SpaceCreation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.create import VocabularyCreation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.create import VocabularyTermCreation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.id import VocabularyPermId
+from file_handling import get_script, get_filename_from_path
+from java.lang import UnsupportedOperationException
+
+
+def get_boolean_from_string(text):
+ return True if text.lower() == u'true' else False
+
+
+class DefinitionToCreationParserFactory(object):
+
+ @staticmethod
+ def getParsers(definition):
+ if definition.type == u'VOCABULARY_TYPE':
+ return [VocabularyDefinitionToCreationParser]
+ elif definition.type == u'SAMPLE_TYPE':
+ return [SampleTypeDefinitionToCreationParser, PropertyTypeDefinitionToCreationParser, ScriptDefinitionToCreationParser]
+ elif definition.type == u'EXPERIMENT_TYPE':
+ return [ExperimentTypeDefinitionToCreationParser, PropertyTypeDefinitionToCreationParser, ScriptDefinitionToCreationParser]
+ elif definition.type == u'DATASET_TYPE':
+ return [DatasetTypeDefinitionToCreationParser, PropertyTypeDefinitionToCreationParser, ScriptDefinitionToCreationParser]
+ elif definition.type == u'SPACE':
+ return [SpaceDefinitionToCreationParser]
+ elif definition.type == u'PROJECT':
+ return [ProjectDefinitionToCreationParser]
+ elif definition.type == u'EXPERIMENT':
+ return [ExperimentDefinitionToCreationParser]
+ elif definition.type == u'SAMPLE':
+ return [SampleDefinitionToCreationParser]
+ elif definition.type == u'PROPERTY_TYPE':
+ return [PropertyTypeDefinitionToCreationParser]
+ else:
+ raise UnsupportedOperationException("Definition of " + str(definition.type) + " is not supported (probably yet).")
+
+
+class PropertyTypeDefinitionToCreationParser(object):
+
+ type = "PropertyTypeCreation"
+
+ @staticmethod
+ def parse(definition):
+ property_creations = []
+ for property in definition.properties:
+ property_type_creation = PropertyTypeCreation()
+ property_type_creation.code = property[u'code']
+ if property[u'code'].startswith(u'$'):
+ property_type_creation.internalNameSpace = True
+ property_type_creation.label = property[u'property label']
+ property_type_creation.dataType = DataType.valueOf(property[u'property type'])
+ property_type_creation.vocabularyId = VocabularyPermId(property[u'vocabulary code']) if property[u'vocabulary code'] is not None else None
+ property_type_creation.description = property[u'description']
+ property_creations.append(property_type_creation)
+
+ return property_creations
+
+ @staticmethod
+ def get_type():
+ return PropertyTypeDefinitionToCreationParser.type
+
+
+class VocabularyDefinitionToCreationParser(object):
+
+ type = "VocabularyCreation"
+
+ @staticmethod
+ def parse(definition):
+ code = definition.attributes[u'code']
+ vocabulary_creation = VocabularyCreation()
+ vocabulary_creation.code = code
+ if code.startswith(u'$'):
+ vocabulary_creation.internalNameSpace = True
+ vocabulary_creation.description = definition.attributes[u'description']
+
+ vocabulary_creations_terms = []
+ for property in definition.properties:
+ vocabulary_creation_term = VocabularyTermCreation()
+ vocabulary_creation_term.code = property[u'code']
+ vocabulary_creation_term.label = property[u'label']
+ vocabulary_creation_term.description = property[u'description']
+ vocabulary_creations_terms.append(vocabulary_creation_term)
+
+ vocabulary_creation.terms = vocabulary_creations_terms
+
+ return vocabulary_creation
+
+ @staticmethod
+ def get_type():
+ return VocabularyDefinitionToCreationParser.type
+
+
+class PropertyAssignmentDefinitionToCreationParser(object):
+
+ type = "PropertyAssignmentCreation"
+
+ @staticmethod
+ def parse(property):
+ code = property[u'code']
+ property_assingment_creation = PropertyAssignmentCreation()
+ is_mandatory = get_boolean_from_string(property[u'mandatory'])
+ property_assingment_creation.mandatory = is_mandatory
+ should_show_in_edit_view = get_boolean_from_string(property[u'show in edit views'])
+ property_assingment_creation.showInEditView = should_show_in_edit_view
+ property_assingment_creation.section = property[u'section']
+ property_assingment_creation.propertyTypeId = PropertyTypePermId(code)
+ if u'dynamic script' in property and property[u'dynamic script'] is not None:
+ dynamic_script_path = property[u'dynamic script']
+ property_assingment_creation.pluginId = PluginPermId(ScriptDefinitionToCreationParser.get_name_for(code, dynamic_script_path))
+
+ return property_assingment_creation
+
+ @staticmethod
+ def get_type():
+ return PropertyAssignmentDefinitionToCreationParser.type
+
+
+class SampleTypeDefinitionToCreationParser(object):
+
+ type = "SampleTypeCreation"
+
+ @staticmethod
+ def parse(definition):
+ code = definition.attributes[u'code']
+ sample_creation = SampleTypeCreation()
+ sample_creation.code = code
+ should_auto_generate_codes = get_boolean_from_string(definition.attributes[u'auto generate codes'])
+ sample_creation.autoGeneratedCode = should_auto_generate_codes
+ if u'validation script' in definition.attributes and definition.attributes[u'validation script'] is not None:
+ validation_script_path = definition.attributes[u'validation script']
+ sample_creation.validationPluginId = PluginPermId(ScriptDefinitionToCreationParser.get_name_for(code, validation_script_path))
+
+ property_assingment_creations = []
+ for property in definition.properties:
+ property_assingment_creation = PropertyAssignmentDefinitionToCreationParser.parse(property)
+ property_assingment_creations.append(property_assingment_creation)
+
+ sample_creation.propertyAssignments = property_assingment_creations
+ return sample_creation
+
+ @staticmethod
+ def get_type():
+ return SampleTypeDefinitionToCreationParser.type
+
+
+class ExperimentTypeDefinitionToCreationParser(object):
+
+ type = "ExperimentTypeCreation"
+
+ @staticmethod
+ def parse(definition):
+ experiment_type_creation = ExperimentTypeCreation()
+ experiment_type_creation.code = definition.attributes[u'code']
+
+ property_assingment_creations = []
+ for property in definition.properties:
+ property_assingment_creation = PropertyAssignmentDefinitionToCreationParser.parse(property)
+ property_assingment_creations.append(property_assingment_creation)
+
+ experiment_type_creation.propertyAssignments = property_assingment_creations
+ return experiment_type_creation
+
+ @staticmethod
+ def get_type():
+ return ExperimentTypeDefinitionToCreationParser.type
+
+
+class DatasetTypeDefinitionToCreationParser(object):
+
+ type = "DatasetTypeCreation"
+
+ @staticmethod
+ def parse(definition):
+ dataset_type_creation = DataSetTypeCreation()
+ dataset_type_creation.code = definition.attributes[u'code']
+
+ property_assingment_creations = []
+ for property in definition.properties:
+ property_assingment_creation = PropertyAssignmentDefinitionToCreationParser.parse(property)
+ property_assingment_creations.append(property_assingment_creation)
+
+ dataset_type_creation.propertyAssignments = property_assingment_creations
+ return dataset_type_creation
+
+ @staticmethod
+ def get_type():
+ return DatasetTypeDefinitionToCreationParser.type
+
+
+class SpaceDefinitionToCreationParser(object):
+
+ type = "SpaceCreation"
+
+ @staticmethod
+ def parse(definition):
+ space_creation = SpaceCreation()
+ space_creation.code = definition.attributes[u'code']
+ space_creation.description = definition.attributes[u'description']
+ creation_id = definition.attributes[u'code']
+ space_creation.creationId = CreationId(creation_id)
+ return space_creation
+
+ @staticmethod
+ def get_type():
+ return SpaceDefinitionToCreationParser.type
+
+
+class ProjectDefinitionToCreationParser(object):
+
+ type = "ProjectCreation"
+
+ @staticmethod
+ def parse(definition):
+ project_creation = ProjectCreation()
+ project_creation.code = definition.attributes[u'code']
+ project_creation.description = definition.attributes[u'description']
+ project_creation.spaceId = CreationId(definition.attributes[u'space'])
+ creation_id = definition.attributes[u'code']
+ project_creation.creationId = CreationId(creation_id)
+ return project_creation
+
+ @staticmethod
+ def get_type():
+ return ProjectDefinitionToCreationParser.type
+
+
+class ExperimentDefinitionToCreationParser(object):
+
+ type = "ExperimentCreation"
+
+ @staticmethod
+ def parse(definition):
+ experiments = []
+ mandatory_attributes = [u'code', u'project']
+ for experiment_properties in definition.properties:
+ experiment_creation = ExperimentCreation()
+ experiment_creation.typeId = EntityTypePermId(definition.attributes[u'experiment type'])
+ experiment_creation.code = experiment_properties[u'code']
+ experiment_creation.projectId = CreationId(experiment_properties[u'project'])
+ creation_id = experiment_properties[u'code']
+ experiment_creation.creationId = CreationId(creation_id)
+ for property, value in experiment_properties.items():
+ if property not in mandatory_attributes:
+ experiment_creation.setProperty(property, value)
+ experiments.append(experiment_creation)
+ return experiments
+
+ @staticmethod
+ def get_type():
+ return ExperimentDefinitionToCreationParser.type
+
+
+class SampleDefinitionToCreationParser(object):
+
+ type = "SampleCreation"
+
+ @staticmethod
+ def parse(definition):
+ samples = []
+ mandatory_attributes = [u'$', u'code', u'space', u'project', u'experiment', u'auto generate code', u'parents', u'children']
+ for sample_properties in definition.properties:
+ sample_creation = SampleCreation()
+ sample_creation.typeId = EntityTypePermId(definition.attributes[u'sample type'])
+ if u'code' in sample_properties and sample_properties[u'code'] is not None:
+ sample_creation.code = sample_properties[u'code']
+ creation_id = sample_properties[u'code']
+ sample_creation.creationId = CreationId(creation_id)
+ if u'$' in sample_properties and sample_properties[u'$'] is not None:
+ # may overwrite creationId from code, which is intended
+ sample_creation.creationId = CreationId(sample_properties[u'$'])
+ if u'auto generate code' in sample_properties and sample_properties[u'auto generate code'] is not None and sample_properties[u'auto generate code'] != '':
+ sample_creation.autoGeneratedCode = get_boolean_from_string(sample_properties[u'auto generate code'])
+ if u'space' in sample_properties and sample_properties[u'space'] is not None:
+ sample_creation.spaceId = CreationId(sample_properties[u'space'])
+ if u'project' in sample_properties and sample_properties[u'project'] is not None:
+ sample_creation.projectId = CreationId(sample_properties[u'project'])
+ if u'experiment' in sample_properties and sample_properties[u'experiment'] is not None:
+ sample_creation.experimentId = CreationId(sample_properties[u'experiment'])
+ if u'parents' in sample_properties and sample_properties[u'parents'] is not None:
+ parent_creationids = []
+ parents = sample_properties[u'parents'].split('\n')
+ for parent in parents:
+ parent_creationids.append(CreationId(parent))
+ sample_creation.parentIds = parent_creationids
+ if u'children' in sample_properties and sample_properties[u'children'] is not None:
+ child_creationids = []
+ children = sample_properties[u'children'].split('\n')
+ for child in children:
+ child_creationids.append(CreationId(child))
+ sample_creation.childIds = child_creationids
+
+ for property, value in sample_properties.items():
+ if property not in mandatory_attributes:
+ sample_creation.setProperty(property, value)
+ samples.append(sample_creation)
+ return samples
+
+ @staticmethod
+ def get_type():
+ return SampleDefinitionToCreationParser.type
+
+
+class ScriptDefinitionToCreationParser(object):
+
+ type = "ScriptCreation"
+
+ @staticmethod
+ def parse(definition):
+ scripts = []
+ if u'validation script' in definition.attributes:
+ validation_script_path = definition.attributes[u'validation script']
+ if validation_script_path is not None:
+ code = definition.attributes[u'code']
+ validation_script_creation = PluginCreation()
+ script_file = open(get_script(validation_script_path))
+ script = script_file.read()
+ script_file.close()
+ validation_script_creation.name = ScriptDefinitionToCreationParser.get_name_for(code, validation_script_path)
+ validation_script_creation.script = script
+ validation_script_creation.pluginType = PluginType.ENTITY_VALIDATION
+ scripts.append(validation_script_creation)
+
+ for property in definition.properties:
+ if u'dynamic script' in property:
+ dynamic_prop_script_path = property[u'dynamic script']
+ code = property[u'code']
+ if dynamic_prop_script_path is not None:
+ validation_script_creation = PluginCreation()
+ script_file = open(get_script(dynamic_prop_script_path))
+ script = script_file.read()
+ script_file.close()
+ validation_script_creation.name = ScriptDefinitionToCreationParser.get_name_for(code, dynamic_prop_script_path)
+ validation_script_creation.script = script
+ validation_script_creation.pluginType = PluginType.DYNAMIC_PROPERTY
+ scripts.append(validation_script_creation)
+
+ return scripts
+
+ @staticmethod
+ def get_name_for(owner_code, script_path):
+ return owner_code + '.' + get_filename_from_path(script_path)
+
+ @staticmethod
+ def get_type():
+ return ScriptDefinitionToCreationParser.type
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/definition_to_creation/definition_to_creation.py b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/definition_to_creation/definition_to_creation.py
new file mode 100644
index 0000000000000000000000000000000000000000..bd9e0857114abb6ad2eb9b94489465ea7e18932e
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/definition_to_creation/definition_to_creation.py
@@ -0,0 +1,23 @@
+from .creation_parsers import DefinitionToCreationParserFactory
+
+
+class DefinitionToCreationParser(object):
+
+ @staticmethod
+ def parse(definitions):
+ creations = {}
+
+ for definition in definitions:
+ # One definition may contain more than one creation
+ parsers = DefinitionToCreationParserFactory.getParsers(definition)
+ for parser in parsers:
+ creation = parser.parse(definition)
+ if creation is None or creation == []:
+ continue
+ creation_type = parser.get_type()
+ if creation_type not in creations:
+ creations[creation_type] = []
+ creations[creation_type].extend(creation if type(creation) == list else [creation])
+
+ return creations
+
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/definition_to_creation/duplicates_handler.py b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/definition_to_creation/duplicates_handler.py
new file mode 100644
index 0000000000000000000000000000000000000000..6ec8c34b7d7193fbd193c81e07dd43ec49fa6d8b
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/definition_to_creation/duplicates_handler.py
@@ -0,0 +1,16 @@
+from .creation_parsers import ScriptDefinitionToCreationParser, SampleDefinitionToCreationParser
+
+
+class DuplicatesHandler(object):
+
+ @staticmethod
+ def get_distinct_creations(creations):
+ distinct_creations = {}
+ for creation_type, creations in creations.items():
+ if creation_type == ScriptDefinitionToCreationParser.type:
+ distinct_creations[creation_type] = dict((creation.name, creation) for creation in creations).values()
+ elif creation_type not in [SampleDefinitionToCreationParser.type]:
+ distinct_creations[creation_type] = dict((creation.code, creation) for creation in creations).values()
+ else:
+ distinct_creations[creation_type] = list(creations)
+ return distinct_creations
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/excel_to_poi/__init__.py b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/excel_to_poi/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..a77a879d5aca68360c1e66b9f8637e7986077929
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/excel_to_poi/__init__.py
@@ -0,0 +1 @@
+from .excel_to_poi import ExcelToPoiParser
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/excel_to_poi/excel_to_poi.py b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/excel_to_poi/excel_to_poi.py
new file mode 100644
index 0000000000000000000000000000000000000000..ca1d8032bc8d07d366d2cd0492a4d512cd43c1cc
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/excel_to_poi/excel_to_poi.py
@@ -0,0 +1,80 @@
+from org.apache.commons.lang import StringUtils
+from org.apache.poi.ss.usermodel import CellType
+from org.apache.poi.ss.usermodel import WorkbookFactory
+from org.apache.poi.ss.util import NumberToTextConverter
+from org.python.core.io import FileIO
+
+
+class ExcelToPoiParser(object):
+
+ @staticmethod
+ def parse(excel_file_path):
+ workbook = WorkbookFactory.create(FileIO(excel_file_path, 'r').asInputStream())
+
+ data_colection = []
+ definitions = []
+ for sheet in workbook.sheetIterator():
+ i = 0
+ sheet_done = False
+ while not sheet_done:
+ definition_rows = []
+ while not ExcelToPoiParser.is_row_empty(sheet.getRow(i)):
+ row = sheet.getRow(i)
+ definition_rows.append(row)
+ i += 1
+ i += 1 # skip empty row
+
+ if not definition_rows:
+ sheet_done = True
+ else:
+ definitions.append(definition_rows)
+
+ workbook.close()
+
+ definitions_stripped = []
+ for definition in definitions:
+ definition_stripped = []
+ for row in definition:
+ row_stripped = {}
+ for cell in row.cellIterator():
+ cell_value = ExcelToPoiParser.extract_string_value_from(cell)
+ cell_value = cell_value if cell_value != '' else None
+ cell_col = cell.getColumnIndex()
+ row_stripped[cell_col] = cell_value
+ definition_stripped.append(row_stripped)
+ definitions_stripped.append(definition_stripped)
+
+ return definitions_stripped
+
+ @staticmethod
+ def extract_string_value_from(cell):
+ cell_type = cell.getCellTypeEnum()
+ if cell_type == CellType.BLANK:
+ return "";
+ elif cell_type == CellType.BOOLEAN:
+ return str(cell.getBooleanCellValue());
+ elif cell_type == CellType.NUMERIC:
+ return NumberToTextConverter.toText(cell.getNumericCellValue());
+ elif cell_type == CellType.STRING:
+ return cell.getStringCellValue();
+ elif cell_type == CellType.FORMULA:
+ raise SyntaxError("Excel formulas are not supported but one was found in cell " + extractCellPosition(cell));
+ elif cell_type == CellType.ERROR:
+ raise SyntaxError("There is an error in cell " + extractCellPosition(cell));
+ else:
+ raise SyntaxError("Unknown data type of cell " + extractCellPosition(cell));
+
+ @staticmethod
+ def is_row_empty(row):
+ if row is None:
+ return True
+ if row.getLastCellNum <= 0:
+ return True
+
+ return all(ExcelToPoiParser.is_cell_empty(cell) for cell in row.cellIterator())
+
+ @staticmethod
+ def is_cell_empty(cell):
+ if cell is not None and cell.getCellType() != CellType.BLANK and StringUtils.isNotBlank(cell.toString()):
+ return False;
+ return True
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/poi_to_definition/__init__.py b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/poi_to_definition/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..1260cc7bc899990fb6e8191ff457d841aa64b3d4
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/poi_to_definition/__init__.py
@@ -0,0 +1,2 @@
+from .poi_to_definition import PoiToDefinitionParser
+
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/poi_to_definition/definition.py b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/poi_to_definition/definition.py
new file mode 100644
index 0000000000000000000000000000000000000000..b9dce04066f511d2129170478af1e19d4df6cb8c
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/poi_to_definition/definition.py
@@ -0,0 +1,21 @@
+class Definition(object):
+ '''
+ Used to hold values for object(Vocabulary, SampleType etc.) creation.
+ '''
+
+ def __init__(self):
+ self.type = None
+ self.attributes = {}
+ self.properties = []
+
+ def __str__(self):
+ return "\n".join([
+ "Definition type:",
+ str(self.type),
+ "Attributes:",
+ str(self.attributes),
+ "Properties:",
+ str(self.properties),
+ "==================" * 3])
+
+ __repr__ = __str__
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/poi_to_definition/definition_parsers.py b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/poi_to_definition/definition_parsers.py
new file mode 100644
index 0000000000000000000000000000000000000000..2990cc1345df82b4fc01806a0bc4a67c197149d8
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/poi_to_definition/definition_parsers.py
@@ -0,0 +1,98 @@
+from .definition import Definition
+from .poi_cleaner import PoiCleaner
+
+
+class DefinitionParserFactory(object):
+
+ @staticmethod
+ def get_parser(definition_type):
+ if definition_type in ['VOCABULARY_TYPE', 'SAMPLE_TYPE', 'EXPERIMENT_TYPE', 'DATASET_TYPE', 'SPACE', 'PROJECT', 'EXPERIMENT', 'SAMPLE']:
+ return GeneralDefinitionParser
+ elif definition_type == 'PROPERTY_TYPE':
+ return PropertyTypeDefinitionParser
+ else:
+ raise UnsupportedOperationException("Definition of " + str(definition_type) + " is not supported (probably yet).")
+
+
+class PropertyTypeDefinitionParser(object):
+
+ @staticmethod
+ def parse(poi_definition):
+ DEFINITION_TYPE_ROW = 0
+ DEFINITION_TYPE_CELL = 0
+ PROPERTIES_HEADER_ROW = 1
+ PROPERTIES_VALUES_ROW_START = 2
+
+ row_numbers = {
+ 'DEFINITION_TYPE_ROW' : DEFINITION_TYPE_ROW,
+ 'DEFINITION_TYPE_CELL' : DEFINITION_TYPE_CELL,
+ 'ATTRIBUTES_HEADER_ROW' : None,
+ 'ATTRIBUTES_VALUES_ROW' : None,
+ 'PROPERTIES_HEADER_ROW' : PROPERTIES_HEADER_ROW,
+ 'PROPERTIES_VALUES_ROW_START' : PROPERTIES_VALUES_ROW_START
+ }
+
+ poi_definition = PoiCleaner.clean_data(poi_definition, row_numbers)
+
+ definition = Definition()
+ definition.type = poi_definition[DEFINITION_TYPE_ROW][DEFINITION_TYPE_CELL]
+ if GeneralDefinitionParser.hasProperties(poi_definition):
+ properties_headers = poi_definition[PROPERTIES_HEADER_ROW]
+
+ for property_definitions in poi_definition[PROPERTIES_VALUES_ROW_START:]:
+ property = {}
+ for col, header in properties_headers.items():
+ property[header] = property_definitions[col]
+ definition.properties.append(property)
+
+ return definition
+
+ @staticmethod
+ def hasProperties(poi_definition):
+ PROPERTIES_HEADER_ROW = 1
+ return len(poi_definition) > PROPERTIES_HEADER_ROW
+
+
+class GeneralDefinitionParser(object):
+
+ @staticmethod
+ def parse(poi_definition):
+ DEFINITION_TYPE_ROW = 0
+ DEFINITION_TYPE_CELL = 0
+ ATTRIBUTES_HEADER_ROW = 1
+ ATTRIBUTES_VALUES_ROW = 2
+ PROPERTIES_HEADER_ROW = 3
+ PROPERTIES_VALUES_ROW_START = 4
+
+ row_numbers = {
+ 'DEFINITION_TYPE_ROW' : DEFINITION_TYPE_ROW,
+ 'DEFINITION_TYPE_CELL' : DEFINITION_TYPE_CELL,
+ 'ATTRIBUTES_HEADER_ROW' : ATTRIBUTES_HEADER_ROW,
+ 'ATTRIBUTES_VALUES_ROW' : ATTRIBUTES_VALUES_ROW,
+ 'PROPERTIES_HEADER_ROW' : PROPERTIES_HEADER_ROW,
+ 'PROPERTIES_VALUES_ROW_START' : PROPERTIES_VALUES_ROW_START
+ }
+
+ poi_definition = PoiCleaner.clean_data(poi_definition, row_numbers)
+
+ definition = Definition()
+ definition.type = poi_definition[DEFINITION_TYPE_ROW][DEFINITION_TYPE_CELL]
+ for col, header in poi_definition[ATTRIBUTES_HEADER_ROW].items():
+ cell_value = poi_definition[ATTRIBUTES_VALUES_ROW][col]
+ definition.attributes[header] = cell_value
+
+ if GeneralDefinitionParser.hasProperties(poi_definition):
+ properties_headers = poi_definition[PROPERTIES_HEADER_ROW]
+
+ for property_definitions in poi_definition[PROPERTIES_VALUES_ROW_START:]:
+ property = {}
+ for col, header in properties_headers.items():
+ property[header] = property_definitions[col]
+ definition.properties.append(property)
+
+ return definition
+
+ @staticmethod
+ def hasProperties(poi_definition):
+ PROPERTIES_HEADER_ROW = 3
+ return len(poi_definition) > PROPERTIES_HEADER_ROW
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/poi_to_definition/poi_cleaner.py b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/poi_to_definition/poi_cleaner.py
new file mode 100644
index 0000000000000000000000000000000000000000..64845fd0884b45d05711f520dcb9517c8429c4ef
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/poi_to_definition/poi_cleaner.py
@@ -0,0 +1,86 @@
+from copy import deepcopy
+
+
+class PoiCleaner(object):
+
+ @staticmethod
+ def hasProperties(poi_definition):
+ PROPERTIES_HEADER_ROW = 3
+ return len(poi_definition) > PROPERTIES_HEADER_ROW
+
+ @staticmethod
+ def clean_data(xls_definition, row_numbers):
+ DEFINITION_TYPE_ROW = row_numbers['DEFINITION_TYPE_ROW']
+ DEFINITION_TYPE_CELL = row_numbers['DEFINITION_TYPE_CELL']
+ ATTRIBUTES_HEADER_ROW = row_numbers['ATTRIBUTES_HEADER_ROW']
+ ATTRIBUTES_VALUES_ROW = row_numbers['ATTRIBUTES_VALUES_ROW']
+ PROPERTIES_HEADER_ROW = row_numbers['PROPERTIES_HEADER_ROW']
+ PROPERTIES_VALUES_ROW_START = row_numbers['PROPERTIES_VALUES_ROW_START']
+
+ definition = deepcopy(xls_definition)
+ '''
+ First row can only have definition type, rest is trimmed. Rules for cleaning are the following:
+ 1. Header rows cannot have empty cells
+ 2. Values that do not have corresponding headers are removed.
+ 3. All attributes and properties should have corresponding value in values row when header exists.
+ If there's no corresponding value, None is inserted.
+ 4. Headers to lowercase
+ '''
+ definition[DEFINITION_TYPE_ROW] = {0:definition[DEFINITION_TYPE_ROW][DEFINITION_TYPE_CELL]}
+
+ if ATTRIBUTES_HEADER_ROW is not None:
+ PoiCleaner.delete_empty_cells_from(definition, ATTRIBUTES_HEADER_ROW)
+ if ATTRIBUTES_VALUES_ROW is not None:
+ PoiCleaner.delete_cells_if_no_header(definition, ATTRIBUTES_HEADER_ROW, ATTRIBUTES_VALUES_ROW)
+ PoiCleaner.create_cells_if_no_value_but_header_exists(definition, ATTRIBUTES_HEADER_ROW, ATTRIBUTES_VALUES_ROW)
+ definition[ATTRIBUTES_HEADER_ROW] = PoiCleaner.dict_values_to_lowercase(definition[ATTRIBUTES_HEADER_ROW])
+
+ if PoiCleaner.hasProperties(definition) and PROPERTIES_HEADER_ROW is not None:
+ PoiCleaner.delete_empty_cells_from(definition, PROPERTIES_HEADER_ROW)
+ if PROPERTIES_VALUES_ROW_START is not None:
+ for property_value_row_num in range(PROPERTIES_VALUES_ROW_START, len(definition)):
+ PoiCleaner.delete_cells_if_no_header(definition, PROPERTIES_HEADER_ROW, property_value_row_num)
+ PoiCleaner.create_cells_if_no_value_but_header_exists(definition, PROPERTIES_HEADER_ROW, property_value_row_num)
+ definition[PROPERTIES_HEADER_ROW] = PoiCleaner.dict_values_to_lowercase(definition[PROPERTIES_HEADER_ROW])
+
+ return definition
+
+ @staticmethod
+ def delete_empty_cells_from(definition, row_number):
+ header_cell_cols_to_pop = []
+ for cell_col, cell in definition[row_number].items():
+ if cell is None or cell == '':
+ header_cell_cols_to_pop.append(cell_col)
+
+ for cell_col in header_cell_cols_to_pop:
+ del definition[row_number][cell_col]
+
+ return definition
+
+ @staticmethod
+ def delete_cells_if_no_header(definition, header_row_number, value_row_number):
+ values_cell_cols_to_pop = []
+ for cell_col in definition[value_row_number]:
+ if cell_col not in definition[header_row_number]:
+ values_cell_cols_to_pop.append(cell_col)
+
+ for cell_col in values_cell_cols_to_pop:
+ del definition[value_row_number][cell_col]
+
+ return definition
+
+ @staticmethod
+ def create_cells_if_no_value_but_header_exists(definition, header_row_number, value_row_number):
+ values_cell_cols_to_insert = []
+ for cell_col in definition[header_row_number]:
+ if cell_col not in definition[value_row_number]:
+ values_cell_cols_to_insert.append(cell_col)
+
+ for cell_col in values_cell_cols_to_insert:
+ definition[value_row_number][cell_col] = None
+
+ return definition
+
+ @staticmethod
+ def dict_values_to_lowercase(row):
+ return dict((k, v.lower()) for (k, v) in row.items())
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/poi_to_definition/poi_to_definition.py b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/poi_to_definition/poi_to_definition.py
new file mode 100644
index 0000000000000000000000000000000000000000..8f921f64b412162b1bb793d0d90e23a9b35525f7
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/parsers/poi_to_definition/poi_to_definition.py
@@ -0,0 +1,36 @@
+from .definition_parsers import DefinitionParserFactory
+
+
+class PoiToDefinitionParser(object):
+
+ @staticmethod
+ def parse(poi_definitions):
+ '''
+ Expecting definitions to be in such layout:
+ [
+ `DEFINITIONS_LIST`
+ [
+ `DEFINITION`
+ {
+ `ROWS`
+ (column, row) : string_value,
+ .
+ .
+ .
+ }
+ ],
+ .
+ .
+ .
+ ]
+ '''
+ definitons = []
+ for poi_definition in poi_definitions:
+ FIRST_ROW = 0
+ FIRST_CELL = 0
+ definition_type = poi_definition[FIRST_ROW][FIRST_CELL]
+ definition_parser = DefinitionParserFactory.get_parser(definition_type)
+ definition = definition_parser.parse(poi_definition)
+ definitons.append(definition)
+
+ return definitons
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/search_engines/__init__.py b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/search_engines/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..0dc844ed16ac3a1ecf31f210f5e9430fbb72da37
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/search_engines/__init__.py
@@ -0,0 +1 @@
+from .search_engine import SearchEngine
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/search_engines/search_engine.py b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/search_engines/search_engine.py
new file mode 100644
index 0000000000000000000000000000000000000000..42634e1ef274b9b68f57a1c759bb91944a021527
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/search_engines/search_engine.py
@@ -0,0 +1,156 @@
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.common.search import SearchOperator
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions import DataSetTypeFetchOptions
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.search import DataSetTypeSearchCriteria, SearchDataSetTypesOperation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.fetchoptions import ExperimentTypeFetchOptions, ExperimentFetchOptions
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.search import ExperimentTypeSearchCriteria, \
+ SearchExperimentTypesOperation, ExperimentSearchCriteria, SearchExperimentsOperation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.operation import SynchronousOperationExecutionOptions
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.plugin.fetchoptions import PluginFetchOptions
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.plugin.search import PluginSearchCriteria, SearchPluginsOperation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.project.fetchoptions import ProjectFetchOptions
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.project.search import ProjectSearchCriteria, SearchProjectsOperation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.property.fetchoptions import PropertyTypeFetchOptions
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.property.search import PropertyTypeSearchCriteria, SearchPropertyTypesOperation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.fetchoptions import SampleTypeFetchOptions, SampleFetchOptions
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.search import SampleTypeSearchCriteria, \
+ SearchSampleTypesOperation, SampleSearchCriteria, SearchSamplesOperation, \
+ SampleSearchRelation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.space.fetchoptions import SpaceFetchOptions
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.space.search import SpaceSearchCriteria, SearchSpacesOperation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.fetchoptions import VocabularyFetchOptions
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.search import VocabularySearchCriteria, SearchVocabulariesOperation
+from parsers import VocabularyDefinitionToCreationParser, PropertyTypeDefinitionToCreationParser, SampleTypeDefinitionToCreationParser, \
+ ExperimentTypeDefinitionToCreationParser, DatasetTypeDefinitionToCreationParser, SpaceDefinitionToCreationParser, \
+ ProjectDefinitionToCreationParser, ExperimentDefinitionToCreationParser, ScriptDefinitionToCreationParser, SampleDefinitionToCreationParser
+
+
+class SearchEngine():
+
+ def __init__(self, api, sesstion_token):
+ self.api = api
+ self.session_token = sesstion_token
+
+ def find_all_existing_elements(self, creations):
+ search_strategy = [
+ {
+ 'creations_type': VocabularyDefinitionToCreationParser.type,
+ 'search_criteria_object' : VocabularySearchCriteria,
+ 'search_operation':SearchVocabulariesOperation,
+ 'fetch_options':VocabularyFetchOptions
+ },
+ {
+ 'creations_type': PropertyTypeDefinitionToCreationParser.type,
+ 'search_criteria_object' : PropertyTypeSearchCriteria,
+ 'search_operation': SearchPropertyTypesOperation,
+ 'fetch_options': PropertyTypeFetchOptions
+ },
+ {
+ 'creations_type': SampleTypeDefinitionToCreationParser.type,
+ 'search_criteria_object' : SampleTypeSearchCriteria,
+ 'search_operation': SearchSampleTypesOperation,
+ 'fetch_options': SampleTypeFetchOptions
+ },
+ {
+ 'creations_type': ExperimentTypeDefinitionToCreationParser.type,
+ 'search_criteria_object' : ExperimentTypeSearchCriteria,
+ 'search_operation': SearchExperimentTypesOperation,
+ 'fetch_options': ExperimentTypeFetchOptions
+ },
+ {
+ 'creations_type': DatasetTypeDefinitionToCreationParser.type,
+ 'search_criteria_object' : DataSetTypeSearchCriteria,
+ 'search_operation': SearchDataSetTypesOperation,
+ 'fetch_options': DataSetTypeFetchOptions
+ },
+ {
+ 'creations_type': SpaceDefinitionToCreationParser.type,
+ 'search_criteria_object' : SpaceSearchCriteria,
+ 'search_operation': SearchSpacesOperation,
+ 'fetch_options': SpaceFetchOptions
+ },
+ {
+ 'creations_type': ProjectDefinitionToCreationParser.type,
+ 'search_criteria_object' : ProjectSearchCriteria,
+ 'search_operation': SearchProjectsOperation,
+ 'fetch_options': ProjectFetchOptions
+ },
+ {
+ 'creations_type': ExperimentDefinitionToCreationParser.type,
+ 'search_criteria_object' : ExperimentSearchCriteria,
+ 'search_operation': SearchExperimentsOperation,
+ 'fetch_options': ExperimentFetchOptions
+ },
+ {
+ 'creations_type': SampleDefinitionToCreationParser.type,
+ 'search_criteria_object' : SampleSearchCriteria,
+ 'search_operation': SearchSamplesOperation,
+ 'fetch_options': SampleFetchOptions
+ },
+ {
+ 'creations_type': ScriptDefinitionToCreationParser.type,
+ 'search_criteria_object' : PluginSearchCriteria,
+ 'search_operation': SearchPluginsOperation,
+ 'fetch_options': PluginFetchOptions
+ }
+ ]
+
+ existing_elements = {}
+ for strategy in search_strategy:
+ creations_type = strategy['creations_type']
+ if creations_type in creations:
+ existing_specific_elements = self._get_existing_elements(creations=creations, **strategy)
+ if existing_specific_elements is not None:
+ existing_elements[creations_type] = existing_specific_elements
+ return existing_elements
+
+ def _get_existing_elements(self, creations, creations_type, search_criteria_object, search_operation, fetch_options):
+ search_criteria = self._get_search_criteria(creations_type, creations[creations_type], search_criteria_object)
+ if search_criteria is []:
+ return None
+ result = self._execute_search_operation(search_operation(search_criteria, fetch_options()))
+ return result.getObjects()
+
+ def _get_search_criteria(self, creations_type, specific_creations, search_criteria_class):
+ search_criteria = search_criteria_class()
+
+ if creations_type == SampleDefinitionToCreationParser.type:
+ search_criterias = []
+ for creation in specific_creations:
+ search_criteria.withOrOperator()
+ if creation.code is not None:
+ search_criteria.withCode().thatEquals(creation.code)
+ if creation.experimentId is not None:
+ search_criteria.withExperiment().withCode().thatEquals(creation.experimentId.creationId)
+ else:
+ search_criteria.withoutExperiment()
+
+ if creation.projectId is not None:
+ search_criteria.withProject().withCode().thatEquals(creation.projectId.creationId)
+ else:
+ search_criteria.withoutProject()
+
+ if creation.spaceId is not None:
+ search_criteria.withSpace().withCode().thatEquals(creation.spaceId.creationId)
+ else:
+ search_criteria.withoutSpace()
+
+ search_criterias.append(search_criteria)
+ return search_criteria
+
+ if 'withCodes' in dir(search_criteria):
+ search_criteria.withCodes().thatIn([creation.code for creation in specific_creations])
+ elif 'withName' in dir(search_criteria):
+ for creation in specific_creations:
+ search_criteria.withName().thatEquals(creation.name)
+ search_criteria.withOrOperator()
+ else:
+ for creation in specific_creations:
+ search_criteria.withCode().thatEquals(creation.code)
+ search_criteria.withOrOperator()
+ return search_criteria
+
+ def _execute_search_operation(self, operation):
+ operations = []
+ operations.extend(operation if type(operation) == list else [operation])
+ return self.api.executeOperations(self.session_token, operations, SynchronousOperationExecutionOptions()).getResults().get(0).getSearchResult()
+
diff --git a/screening/build.gradle b/screening/build.gradle
index 31394fd8925e66a4904614d8f1b1c6d718652394..e9fe8c77801eeec99367a4b167d046026dfd7f6c 100644
--- a/screening/build.gradle
+++ b/screening/build.gradle
@@ -14,7 +14,7 @@ dependencies {
project(':datastore_server'),
'openhms:jackcess:+',
'reveregroup:gwt-image-loader:+',
- 'bioformats:bioformats:+'
+ 'bioformats:bioformats:5.9.2'
testCompile project(path: ':datastore_server', configuration: 'tests')
}