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Commit 4aec49bc authored by felmer's avatar felmer
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SP-326, BIS-217: Extracted optional proteomics master data into module proteomics-optional 

SVN: 27233
parent 266c8a3c
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rtd_phosphonetx/source/core-plugins/proteomics-optional/1/as/initialize-master-data.py 0 → 100644
+ 81
− 0
View file @ 4aec49bc
import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.DataType as DataType
tr = service.transaction()
file_type_HTML = tr.getOrCreateNewFileFormatType('HTML')
file_type_HTML.setDescription('HTML File')
file_type_MZDATA = tr.getOrCreateNewFileFormatType('MZDATA')
file_type_MZDATA.setDescription('Mass spectrometry data format.')
file_type_MZML = tr.getOrCreateNewFileFormatType('MZML')
file_type_MZML.setDescription('Mass spectrometry data format. \
Unifiying mzXML and mzData formats, as released at the \
2008 American Society for Mass Spectrometry Meeting.')
file_type_MZXML = tr.getOrCreateNewFileFormatType('MZXML')
file_type_MZXML.setDescription('Mass spectrometry data format.')
file_type_RAW = tr.getOrCreateNewFileFormatType('RAW')
file_type_RAW.setDescription('Proprietary file format for Thermo mass sepectrometry data.')
file_type_TGZ = tr.getOrCreateNewFileFormatType('TGZ')
file_type_TGZ.setDescription('gzipped tar')
file_type_WIFF = tr.getOrCreateNewFileFormatType('WIFF')
file_type_WIFF.setDescription('Proprieatry file format for Sciex and Agilent mass spectrometry data.')
file_type_ZIP = tr.getOrCreateNewFileFormatType('ZIP')
file_type_ZIP.setDescription('A zipped package')
vocabulary_term_TREATMENT_TYPE_PH = tr.createNewVocabularyTerm('PH')
vocabulary_term_TREATMENT_TYPE_PH.setDescription(None)
vocabulary_term_TREATMENT_TYPE_PH.setUrl(None)
vocabulary_term_TREATMENT_TYPE_PH.setLabel('ph')
vocabulary_term_TREATMENT_TYPE_PH.setOrdinal(1)
vocabulary_TREATMENT_TYPE.addTerm(vocabulary_term_TREATMENT_TYPE_PH)
exp_type_BIOLOGICAL_EXPERIMENT = tr.getOrCreateNewExperimentType('BIOLOGICAL_EXPERIMENT')
exp_type_BIOLOGICAL_EXPERIMENT.setDescription('A biological experiment')
exp_type_MS_INJECT = tr.getOrCreateNewExperimentType('MS_INJECT')
exp_type_MS_INJECT.setDescription('MS injection experiment')
exp_type_MS_QUANTIFICATION = tr.getOrCreateNewExperimentType('MS_QUANTIFICATION')
exp_type_MS_QUANTIFICATION.setDescription('Quantification of LC-MS data')
data_set_type_MZXML_DATA = tr.getOrCreateNewDataSetType('MZXML_DATA')
data_set_type_MZXML_DATA.setDescription('standardized format for ms data')
data_set_type_MZXML_DATA.setContainerType(False)
data_set_type_RAW_DATA = tr.getOrCreateNewDataSetType('RAW_DATA')
data_set_type_RAW_DATA.setDescription(None)
data_set_type_RAW_DATA.setContainerType(False)
prop_type_PARENTDATASETCODES = tr.getOrCreateNewPropertyType('PARENT-DATA-SET-CODES', DataType.VARCHAR)
prop_type_PARENTDATASETCODES.setLabel('Parent Dataset Codes')
prop_type_PARENTDATASETCODES.setManagedInternally(False)
prop_type_PARENTDATASETCODES.setInternalNamespace(False)
prop_type_TREATMENT_TYPE1 = tr.getOrCreateNewPropertyType('TREATMENT_TYPE1', DataType.CONTROLLEDVOCABULARY)
prop_type_TREATMENT_TYPE1.setLabel('Treatment Type 1')
prop_type_TREATMENT_TYPE1.setManagedInternally(False)
prop_type_TREATMENT_TYPE1.setInternalNamespace(False)
prop_type_TREATMENT_TYPE1.setVocabulary(vocabulary_TREATMENT_TYPE)
prop_type_TREATMENT_TYPE2 = tr.getOrCreateNewPropertyType('TREATMENT_TYPE2', DataType.CONTROLLEDVOCABULARY)
prop_type_TREATMENT_TYPE2.setLabel('Treatment Type 2')
prop_type_TREATMENT_TYPE2.setManagedInternally(False)
prop_type_TREATMENT_TYPE2.setInternalNamespace(False)
prop_type_TREATMENT_TYPE2.setVocabulary(vocabulary_TREATMENT_TYPE)
prop_type_TREATMENT_TYPE3 = tr.getOrCreateNewPropertyType('TREATMENT_TYPE3', DataType.CONTROLLEDVOCABULARY)
prop_type_TREATMENT_TYPE3.setLabel('Treatment Type 3')
prop_type_TREATMENT_TYPE3.setManagedInternally(False)
prop_type_TREATMENT_TYPE3.setInternalNamespace(False)
prop_type_TREATMENT_TYPE3.setVocabulary(vocabulary_TREATMENT_TYPE)
rtd_phosphonetx/source/core-plugins/proteomics-optional/package-to-dist 0 → 100644
+ 0
− 0
View file @ 4aec49bc
rtd_phosphonetx/source/core-plugins/proteomics/1/as/initialize-master-data.py
+ 0
− 77
View file @ 4aec49bc
...@@ -2,32 +2,6 @@ import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.DataType as DataTyp ...@@ -2,32 +2,6 @@ import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.DataType as DataTyp
tr = service.transaction() tr = service.transaction()
file_type_HTML = tr.getOrCreateNewFileFormatType('HTML')
file_type_HTML.setDescription('HTML File')
file_type_MZDATA = tr.getOrCreateNewFileFormatType('MZDATA')
file_type_MZDATA.setDescription('Mass spectrometry data format.')
file_type_MZML = tr.getOrCreateNewFileFormatType('MZML')
file_type_MZML.setDescription('Mass spectrometry data format. \
Unifiying mzXML and mzData formats, as released at the \
2008 American Society for Mass Spectrometry Meeting.')
file_type_MZXML = tr.getOrCreateNewFileFormatType('MZXML')
file_type_MZXML.setDescription('Mass spectrometry data format.')
file_type_RAW = tr.getOrCreateNewFileFormatType('RAW')
file_type_RAW.setDescription('Proprietary file format for Thermo mass sepectrometry data.')
file_type_TGZ = tr.getOrCreateNewFileFormatType('TGZ')
file_type_TGZ.setDescription('gzipped tar')
file_type_WIFF = tr.getOrCreateNewFileFormatType('WIFF')
file_type_WIFF.setDescription('Proprieatry file format for Sciex and Agilent mass spectrometry data.')
file_type_ZIP = tr.getOrCreateNewFileFormatType('ZIP')
file_type_ZIP.setDescription('A zipped package')
vocabulary_TREATMENT_TYPE = tr.getOrCreateNewVocabulary('TREATMENT_TYPE') vocabulary_TREATMENT_TYPE = tr.getOrCreateNewVocabulary('TREATMENT_TYPE')
vocabulary_TREATMENT_TYPE.setDescription('Type of treatment of a biological sample.') vocabulary_TREATMENT_TYPE.setDescription('Type of treatment of a biological sample.')
vocabulary_TREATMENT_TYPE.setUrlTemplate(None) vocabulary_TREATMENT_TYPE.setUrlTemplate(None)
...@@ -35,25 +9,9 @@ vocabulary_TREATMENT_TYPE.setManagedInternally(False) ...@@ -35,25 +9,9 @@ vocabulary_TREATMENT_TYPE.setManagedInternally(False)
vocabulary_TREATMENT_TYPE.setInternalNamespace(False) vocabulary_TREATMENT_TYPE.setInternalNamespace(False)
vocabulary_TREATMENT_TYPE.setChosenFromList(True) vocabulary_TREATMENT_TYPE.setChosenFromList(True)
vocabulary_term_TREATMENT_TYPE_PH = tr.createNewVocabularyTerm('PH')
vocabulary_term_TREATMENT_TYPE_PH.setDescription(None)
vocabulary_term_TREATMENT_TYPE_PH.setUrl(None)
vocabulary_term_TREATMENT_TYPE_PH.setLabel('ph')
vocabulary_term_TREATMENT_TYPE_PH.setOrdinal(1)
vocabulary_TREATMENT_TYPE.addTerm(vocabulary_term_TREATMENT_TYPE_PH)
exp_type_BIOLOGICAL_EXPERIMENT = tr.getOrCreateNewExperimentType('BIOLOGICAL_EXPERIMENT')
exp_type_BIOLOGICAL_EXPERIMENT.setDescription('A biological experiment')
exp_type_MS_INJECT = tr.getOrCreateNewExperimentType('MS_INJECT')
exp_type_MS_INJECT.setDescription('MS injection experiment')
exp_type_MS_SEARCH = tr.getOrCreateNewExperimentType('MS_SEARCH') exp_type_MS_SEARCH = tr.getOrCreateNewExperimentType('MS_SEARCH')
exp_type_MS_SEARCH.setDescription('MS_SEARCH experiment') exp_type_MS_SEARCH.setDescription('MS_SEARCH experiment')
exp_type_MS_QUANTIFICATION = tr.getOrCreateNewExperimentType('MS_QUANTIFICATION')
exp_type_MS_QUANTIFICATION.setDescription('Quantification of LC-MS data')
samp_type_MS_INJECTION = tr.getOrCreateNewSampleType('MS_INJECTION') samp_type_MS_INJECTION = tr.getOrCreateNewSampleType('MS_INJECTION')
samp_type_MS_INJECTION.setDescription('injection of a biological sample into a MS') samp_type_MS_INJECTION.setDescription('injection of a biological sample into a MS')
samp_type_MS_INJECTION.setListable(True) samp_type_MS_INJECTION.setListable(True)
...@@ -68,42 +26,7 @@ samp_type_SEARCH.setSubcodeUnique(False) ...@@ -68,42 +26,7 @@ samp_type_SEARCH.setSubcodeUnique(False)
samp_type_SEARCH.setAutoGeneratedCode(False) samp_type_SEARCH.setAutoGeneratedCode(False)
samp_type_SEARCH.setGeneratedCodePrefix('S') samp_type_SEARCH.setGeneratedCodePrefix('S')
data_set_type_MZXML_DATA = tr.getOrCreateNewDataSetType('MZXML_DATA')
data_set_type_MZXML_DATA.setDescription('standardized format for ms data')
data_set_type_MZXML_DATA.setContainerType(False)
data_set_type_PROT_RESULT = tr.getOrCreateNewDataSetType('PROT_RESULT') data_set_type_PROT_RESULT = tr.getOrCreateNewDataSetType('PROT_RESULT')
data_set_type_PROT_RESULT.setDescription('protXML file') data_set_type_PROT_RESULT.setDescription('protXML file')
data_set_type_PROT_RESULT.setContainerType(False) data_set_type_PROT_RESULT.setContainerType(False)
data_set_type_RAW_DATA = tr.getOrCreateNewDataSetType('RAW_DATA')
data_set_type_RAW_DATA.setDescription(None)
data_set_type_RAW_DATA.setContainerType(False)
prop_type_PARENTDATASETCODES = tr.getOrCreateNewPropertyType('PARENT-DATA-SET-CODES', DataType.VARCHAR)
prop_type_PARENTDATASETCODES.setLabel('Parent Dataset Codes')
prop_type_PARENTDATASETCODES.setManagedInternally(False)
prop_type_PARENTDATASETCODES.setInternalNamespace(False)
prop_type_TREATMENT_TYPE1 = tr.getOrCreateNewPropertyType('TREATMENT_TYPE1', DataType.CONTROLLEDVOCABULARY)
prop_type_TREATMENT_TYPE1.setLabel('Treatment Type 1')
prop_type_TREATMENT_TYPE1.setManagedInternally(False)
prop_type_TREATMENT_TYPE1.setInternalNamespace(False)
prop_type_TREATMENT_TYPE1.setVocabulary(vocabulary_TREATMENT_TYPE)
prop_type_TREATMENT_TYPE2 = tr.getOrCreateNewPropertyType('TREATMENT_TYPE2', DataType.CONTROLLEDVOCABULARY)
prop_type_TREATMENT_TYPE2.setLabel('Treatment Type 2')
prop_type_TREATMENT_TYPE2.setManagedInternally(False)
prop_type_TREATMENT_TYPE2.setInternalNamespace(False)
prop_type_TREATMENT_TYPE2.setVocabulary(vocabulary_TREATMENT_TYPE)
prop_type_TREATMENT_TYPE3 = tr.getOrCreateNewPropertyType('TREATMENT_TYPE3', DataType.CONTROLLEDVOCABULARY)
prop_type_TREATMENT_TYPE3.setLabel('Treatment Type 3')
prop_type_TREATMENT_TYPE3.setManagedInternally(False)
prop_type_TREATMENT_TYPE3.setInternalNamespace(False)
prop_type_TREATMENT_TYPE3.setVocabulary(vocabulary_TREATMENT_TYPE)
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