Merge pull request #58 from elixir-europe/dev

MIAPPE compliance improvements
elixir-europe · Oct 15, 2019 · 1108e60 · 1108e60
2 parents 2ffb326 + 9c6e4ea
commit 1108e60
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Showing 2 changed files with 7 additions and 16 deletions.
diff --git a/brapi_to_isa.py b/brapi_to_isa.py
@@ -181,7 +181,7 @@ def create_study_sample_and_assay(client, brapi_study_id, isa_study,  growth_pro
 
         phenotyping_process = Process(executes_protocol=phenotyping_protocol)
         phenotyping_process.inputs.append(this_isa_sample)
-        phenotyping_process.name = obs_unit["observationUnitDbId"] 
+        phenotyping_process.name =  att_test(obs_unit, 'observationLevel', PAR_defaultObsLvl).lower()
 
         # Adding Parameter Value[Collection Date] column
         # col_date_pp = ProtocolParameter(parameter_name=OntologyAnnotation(term="Collection Date"))

diff --git a/brapi_to_isa_converter.py b/brapi_to_isa_converter.py
@@ -191,7 +191,7 @@ def create_isa_study(self, brapi_study_id, investigation, obs_levels_in_study):
                 affiliation=att_test(brapicontact, 'institutionName', PAR_NAinData), email=att_test(brapicontact, 'email'), address=PAR_NAinBrAPI, roles=[role])
                 this_study.contacts.append(contact)
 
-        # Adding dataLinks inforamtion
+        # Adding dataLinks information
         if att_test(brapi_study,'dataLinks'):
             for brapidata in brapi_study['dataLinks']:
                 this_study.comments.append(Comment(name="Study Data File Link",value=brapidata['url']))
@@ -205,14 +205,10 @@ def create_isa_study(self, brapi_study_id, investigation, obs_levels_in_study):
                 self.logger.info("The observation level " + level + " is not supported by MIAPPE at this moment and will not be validated.")
                 self.logger.info("Following observation levels are supported: " + str(PAR_suppObsLvl) + ".")
 
-            oref_mt = OntologySource(
-                name="OBI", description=self.ontologies["obi"][0], file=self.ontologies["obi"][1])
             oa_mt = OntologyAnnotation(
-                term="phenotyping", term_accession="", term_source=oref_mt)
-            oref_tt = OntologySource(
-                name="OBI", description=self.ontologies["obi"][0], file=self.ontologies["obi"][1])
+                term="phenotyping", term_accession="", term_source="")
             oa_tt = OntologyAnnotation(
-                term=level + " level analysis", term_accession="", term_source=oref_tt)
+                term=level + " level analysis", term_accession="", term_source="")
 
             isa_assay_file = "a_" + str(brapi_study_id) + "_" + level + ".txt"
             new_assay = Assay(measurement_type=oa_mt,
@@ -221,11 +217,6 @@ def create_isa_study(self, brapi_study_id, investigation, obs_levels_in_study):
 
             this_study.assays.append(new_assay)
 
-            if oref_mt not in investigation.ontology_source_references:
-                investigation.ontology_source_references.append(oref_mt)
-            if oref_tt not in investigation.ontology_source_references:
-                investigation.ontology_source_references.append(oref_tt)
-
         self.logger.info("Number of ISA assays: " + str(len(this_study.assays)))
 
         return this_study, investigation
@@ -270,9 +261,9 @@ def create_isa_tdf_from_obsvars(self, obsvars):
 
             else:
                 if att_test(obs_var, 'synonyms'):  
-                    elements['Variable Name'].append('; '.join(obs_var['synonyms']) + ' (BrAPI variableDbId: ' + att_test(obs_var, 'observationVariableDbId', 'NA') + ')')
+                    elements['Variable Name'].append('; '.join(obs_var['synonyms']) + ' (BrAPI variableDbId: ' + att_test(obs_var, 'observationVariableDbId', PAR_NAinData) + ')')
                 else: 
-                     elements['Variable Name'].append('(BrAPI variableDbId: ' + att_test(obs_var, 'observationVariableDbId', 'NA') + ')')
+                     elements['Variable Name'].append('(BrAPI variableDbId: ' + att_test(obs_var, 'observationVariableDbId', PAR_NAinData) + ')')
 
             elements['Trait'].append(att_test(obs_var['trait'], 'name'))
 
@@ -314,7 +305,7 @@ def create_isa_obs_data_from_obsvars(self, obs_units, obs_variables, level, germ
         for obslvl in obs_levels[level]:
             obs_levels_header.append("observationLevels[{}]".format(obslvl))
         # headers belonging observation unit
-        obs_unit_header = ["observationUnitDbId", "observationUnitXref",
+        obs_unit_header = ["observationUnitName", "observationUnitXref",
                            "X", "Y", "germplasmDbId", "germplasmName"]
         # headers belonging germplasm
         germpl_header = ["accessionNumber"]