diff --git a/plasmid/source/core-plugins/newbrowser/1/as/initialize-master-data.py b/plasmid/source/core-plugins/newbrowser/1/as/initialize-master-data.py
index 6364474ab586df106a7630c635d1f2e25e6a899a..343e596858ec69c18265d353ab5f489f88c3a956 100644
--- a/plasmid/source/core-plugins/newbrowser/1/as/initialize-master-data.py
+++ b/plasmid/source/core-plugins/newbrowser/1/as/initialize-master-data.py
@@ -20,12 +20,14 @@ import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.DataType as DataTyp
##
## Help Methods
##
+vocabulariesCache = {};
propertiesCache = {};
tr = service.transaction()
def createVocabularyWithTerms(vocabularyCode, terms):
vocabulary = tr.createNewVocabulary(vocabularyCode);
addTerms(vocabulary, terms);
+ vocabulariesCache[vocabularyCode] = vocabulary;
def addTerms(vocabulary, terms):
for term in terms:
@@ -35,17 +37,30 @@ def addTermWithLabel(vocabulary, termCode, termLabel):
newTerm = tr.createNewVocabularyTerm(termCode);
newTerm.setLabel(termLabel);
vocabulary.addTerm(newTerm);
-
+
+def createSampleTypeWithProperties(sampleTypeCode, description, properties):
+ newSampleType = tr.getOrCreateNewSampleType(sampleTypeCode);
+ newSampleType.setDescription(description);
+ newSampleType.setAutoGeneratedCode(True);
+ newSampleType.setGeneratedCodePrefix(sampleTypeCode[:3]);
+ addProperties(newSampleType, properties);
+
+def createDataSetTypeWithProperties(dataSetCode, kind, description, properties):
+ newDataSet = tr.getOrCreateNewDataSetType(dataSetCode);
+ newDataSet.setDataSetKind(kind);
+ newDataSet.setDescription(description);
+ addProperties(newDataSet, properties);
+
def createExperimentTypeWithProperties(experimentTypeCode, description, properties):
newExperiment = tr.getOrCreateNewExperimentType(experimentTypeCode);
newExperiment.setDescription(description);
addProperties(newExperiment, properties);
-
+
def addProperties(entity, properties):
for property in properties:
- addProperty(entity, property[0], property[1], property[2], property[3], property[4]);
-
-def addProperty(entity, propertyCode, section, propertyLabel, dataType, propertyDescription):
+ addProperty(entity, property[0], property[1], property[2], property[3], property[4], property[5]);
+
+def addProperty(entity, propertyCode, section, propertyLabel, dataType, vocabularyCode, propertyDescription):
property = None;
if propertyCode in propertiesCache:
@@ -55,6 +70,8 @@ def addProperty(entity, propertyCode, section, propertyLabel, dataType, property
property.setDescription(propertyDescription);
property.setLabel(propertyLabel);
propertiesCache[propertyCode] = property;
+ if dataType == DataType.CONTROLLEDVOCABULARY:
+ property.setVocabulary(vocabulariesCache[vocabularyCode]);
propertyAssignment = tr.assignPropertyType(entity, property);
propertyAssignment.setSection(section);
@@ -326,12 +343,20 @@ createVocabularyWithTerms("MACHINE", [
["SRX_101A", "Konica Minolta SRX-101A"],
["LIGHT_CYCLER", "LightCycler 480"]
]);
+
##
-## Property Types
+## DataSet Types
##
-NOTES = tr.getOrCreateNewPropertyType("NOTES", DataType.MULTILINE_VARCHAR);
-NOTES.setDescription("Notes regarding the dataset");
-NOTES.setLabel("Notes");
+
+createDataSetTypeWithProperties("ELN_PREVIEW", "PHYSICAL", "ELN Preview image", []);
+
+createDataSetTypeWithProperties("SEQ_FILE", "PHYSICAL", "", [
+ ["NOTES", "General information", "Notes", DataType.MULTILINE_VARCHAR, None, "Notes regarding the dataset"],
+]);
+
+createDataSetTypeWithProperties("RAW_DATA", "PHYSICAL", "", [
+ ["NOTES", "General information", "Notes", DataType.MULTILINE_VARCHAR, None, "Notes regarding the dataset"],
+]);
##
## Experiment Types
@@ -354,31 +379,32 @@ createExperimentTypeWithProperties("PCR_PROTOCOL", "BOX TO HOLD SAMPLES OF THIS
createExperimentTypeWithProperties("WESTERN_BLOTTING_PROTOCOL", "BOX TO HOLD SAMPLES OF THIS TYPE FOR ORGANIZATIONAL PURPOSES", []);
createExperimentTypeWithProperties("DEFAULT_EXPERIMENT", "Default Experiment", [
- ["NAME", "General", "Name", DataType.VARCHAR, "Name"],
- ["EXPERIMENTAL_GOALS", "General", "Experimental goals", DataType.MULTILINE_VARCHAR, "Goal of the experiment"],
- ["GRANT", "General", "Grant", DataType.VARCHAR, "grant name"],
- ["START_DATE", "General", "Start Date", DataType.TIMESTAMP, "Start Date"],
- ["END_DATE", "General", "End Date", DataType.TIMESTAMP, "End Date"],
- ["EXPERIMENTAL_RESULTS", "General", "Experimental results", DataType.MULTILINE_VARCHAR, "Brief summary of the results obtained"]
+ ["NAME", "General", "Name", DataType.VARCHAR, None, "Name"],
+ ["EXPERIMENTAL_GOALS", "General", "Experimental goals", DataType.MULTILINE_VARCHAR, None, "Goal of the experiment"],
+ ["GRANT", "General", "Grant", DataType.VARCHAR, None, "grant name"],
+ ["START_DATE", "General", "Start Date", DataType.TIMESTAMP, None, "Start Date"],
+ ["END_DATE", "General", "End Date", DataType.TIMESTAMP, None, "End Date"],
+ ["EXPERIMENTAL_RESULTS","General", "Experimental results", DataType.MULTILINE_VARCHAR, None, "Brief summary of the results obtained"],
+ ["XMLCOMMENTS", "Comments","Comments List", DataType.XML, None, "Several comments can be added by different users"]
]);
##
-## Dataset
+## Sample Types
##
-ELN_PREVIEW = tr.getOrCreateNewDataSetType("ELN_PREVIEW")
-ELN_PREVIEW.setDescription("ELN Preview");
-ELN_PREVIEW.setDataSetKind("PHYSICAL");
-SEQ_FILE = tr.getOrCreateNewDataSetType("SEQ_FILE")
-SEQ_FILE.setDescription("");
-SEQ_FILE.setDataSetKind("PHYSICAL");
-
-SEQ_FILE_NOTES = tr.assignPropertyType(SEQ_FILE, NOTES);
-SEQ_FILE_NOTES.setSection("General information");
-
-RAW_DATA = tr.getOrCreateNewDataSetType("RAW_DATA")
-RAW_DATA.setDescription("");
-RAW_DATA.setDataSetKind("PHYSICAL");
-
-RAW_DATA_NOTES = tr.assignPropertyType(RAW_DATA, NOTES);
-RAW_DATA_NOTES.setSection("General information");
\ No newline at end of file
+createSampleTypeWithProperties("ANTIBODY", "", [
+ ["NAME", "General", "Name", DataType.VARCHAR, None, "Name"],
+ ["HOST", "General", "Host", DataType.CONTROLLEDVOCABULARY, "HOST", "Host used to produce the antibody"],
+ ["FOR_WHAT", "General", "For what", DataType.MULTILINE_VARCHAR, None, "For what kind of experimental application/readout this sample is used in the lab"],
+ ["DETECTION", "General", "Detection", DataType.CONTROLLEDVOCABULARY, "DETECTION","Protein detection system (fill in this information only for secondary antibodies)"],
+ ["EPITOPE", "General", "Epitope", DataType.MULTILINE_VARCHAR, None, "Epitope of the antibody"],
+ ["CLONALITY", "General", "Clonality", DataType.CONTROLLEDVOCABULARY, "CLONALITY","Clonality of the antibody"],
+ ["ISOTYPE", "General", "Isotype", DataType.MULTILINE_VARCHAR, None, "Isotype of the antibody"],
+ ["SUPPLIER", "Supplier and storage", "Supplier", DataType.MULTILINE_VARCHAR, None, "Supplier of the product"],
+ ["ARTICLE_NUMBER", "Supplier and storage", "Art. Number", DataType.MULTILINE_VARCHAR, None, "Article number of the product"],
+ ["STORAGE", "Supplier and storage", "Storage", DataType.CONTROLLEDVOCABULARY, "STORAGE", "Storage conditions of the product"],
+ ["STOCK_CONCENTRATION", "Supplier and storage", "Stock concentration", DataType.VARCHAR, None, "Stock concentration of the solution where the product is kept in the lab"],
+ ["PUBLICATION", "Comments", "Publication", DataType.MULTILINE_VARCHAR, None, "Publication from where the information was first found OR technical sheet given by the manufacturer"],
+ ["NOTES", "Comments", "Notes", DataType.MULTILINE_VARCHAR, None, "Notes"],
+ ["XMLCOMMENTS", "Comments", "Comments List", DataType.XML, None, "Several comments can be added by different users"]
+]);