fixed metadata field issues

study_creator.py

@@ -164,7 +164,7 @@ def setup_study(content):
         if type(organization['Contact']) == list:
             print("MULTIPLE CONTACTS DETECTED... -.-")
             print(organization['Contact'])
-        study['email'] = organization['Contact']['@email']
+        study['Email address'] = organization['Contact']['@email']
         # organization['Contact']['@sec_email']
 
         if 'Name' in organization['Contact']:
@@ -189,11 +189,11 @@ def setup_study(content):
     study_object = content['STUDY']
     study['Study identifier'] = study_object['@accession']
     study['alias'] = study_object['@alias']
-    study['StudyTitle'] = study_object['DESCRIPTOR']['STUDY_TITLE']
+    study['Study title'] = study_object['DESCRIPTOR']['STUDY_TITLE']
     if 'STUDY_ABSTRACT' in study_object['DESCRIPTOR']:
-        study['StudyDescription'] = study_object['DESCRIPTOR']['STUDY_ABSTRACT']
+        study['Study description'] = study_object['DESCRIPTOR']['STUDY_ABSTRACT']
     else:
-        study['StudyDescription'] = "No study description available for " +study_object['@accession']
+        study['Study description'] = "No study description available for " +study_object['@accession']
     if 'STUDY_TYPE' in study_object['DESCRIPTOR']:
         study['type'] = study_object['DESCRIPTOR']['STUDY_TYPE']['@existing_study_type']
 
@@ -218,11 +218,11 @@ def setup_observation_unit(content):
     observation_unit['Study identifier'] = experiment['STUDY_REF']['@accession']
     
     if "TITLE" in sample:
-        observation_unit['Observational description'] = sample['TITLE']
-        observation_unit['Observational name'] = sample['TITLE']
+        observation_unit['Observational unit description'] = sample['TITLE']
+        observation_unit['Observational unit name'] = sample['TITLE']
     else:
-        observation_unit['Observational description'] = 'Automatic OU title from SRA ' + sample['@accession']
-        observation_unit['Observational name'] = 'Automatic OU title from SRA ' + sample['@accession']
+        observation_unit['Observational unit description'] = 'Automatic OU title from SRA ' + sample['@accession']
+        observation_unit['Observational unit name'] = 'Automatic OU title from SRA ' + sample['@accession']
 
     return observation_unit
 
@@ -246,10 +246,10 @@ def setup_sample(content):
     # TODO check which name is used in the end
     if "TITLE" in sample_object:
         sample['Sample title'] = sample_object['TITLE']
-        sample['Sample name'] = sample_object['TITLE']
+        sample['sample name'] = sample_object['TITLE']
     else:
         sample['Sample title'] = 'Automatic sample title from SRA ' + sample['Sample identifier']
-        sample['Sample name'] = 'Automatic sample title from SRA ' + sample['Sample identifier']
+        sample['sample name'] = 'Automatic sample title from SRA ' + sample['Sample identifier']
 
     sample['NCBI taxonomy ID'] = sample_object['SAMPLE_NAME']['TAXON_ID']
 
@@ -331,7 +331,7 @@ def setup_assay(content):
     assay['Library layout'] = list(dict(library['LIBRARY_LAYOUT']).keys())
 
     # Machine
-    assay['Instument model'] = content['EXPERIMENT']['PLATFORM']['ILLUMINA']['INSTRUMENT_MODEL']
+    assay['Instrument model'] = content['EXPERIMENT']['PLATFORM']['ILLUMINA']['INSTRUMENT_MODEL']
     
     if 'ILLUMINA' in content['EXPERIMENT']['PLATFORM']:
         assay['Platform'] = 'Illumina'