Added default terminologies users by DAISY

metadata_tools/importxls/from_owncohort_exporter.py

@@ -98,7 +98,7 @@ class FromOwncohortXlsExporter(DatasetExporter):
             if not dataset_data['title']:
                 print('Missing dataset title ----> {}'.format(full_file_path))
             if sheet[22, 2]:
-                dataset_data['project'] = sheet[22, 2]
+                dataset_data['project'] = sheet[5, 2]
 
             share_list = []
             if process_yes_no_answer(sheet[27, 2]):

metadata_tools/importxls/projects_exporter.py

@@ -35,8 +35,8 @@ class ProjectsExporter:
                 for pp in pi.split(delimeter):
                     pp_data = {}
                     name_list = get_names_from_string(pp)
-                    pp_data['first_name'] = name_list[0]
-                    pp_data['last_name'] = name_list[1]
+                    pp_data['first_name'] = name_list[0].replace('.','').replace(',','')
+                    pp_data['last_name'] = name_list[1].replace('.','').replace(',','')
                     pp_data['role'] = 'Principal_Investigator'
                     pp_data['institution'] = 'ELU_I_77'
                     contacts_list.append(pp_data)
@@ -47,8 +47,8 @@ class ProjectsExporter:
                 for prs in personnel.split(delimeter):
                     prs_data = {}
                     name_list = get_names_from_string(prs)
-                    prs_data['first_name'] = name_list[0]
-                    prs_data['last_name'] = name_list[1]
+                    prs_data['first_name'] = name_list[0].replace('.','').replace(',','')
+                    prs_data['last_name'] = name_list[1].replace('.','').replace(',','')
                     prs_data['role'] = 'Researcher'
                     prs_data['institution'] = 'ELU_I_77'
                     contacts_list.append(prs_data)

metadata_tools/resources/ga4gh_codes.json

-{
-  "ga4gh_codes": [
-    [
-      'NRES',
-      'No restrictions',
-      'No restrictions on data use.'
-    ],
-    [
-      'GRU(CC)',
-      'General Research use and Clinical Care',
-      'For health/medical/biomedical purposes and other biological research, including the study of population origins or ancestry.'
-    ],
-    [
-      'HMB(CC)',
-      'Health/medical/biomedical Research and Clinical Care',
-      'Use of the data is limited to health/medical/biomedical purposes, does not include the study of population origins or ancestry.'
-    ],
-    [
-      'DS-[XX](CC)',
-      'Disease-specific Research and Clinical Care.',
-      'Use of the data must be related to [disease].'
-    ],
-    [
-      'POA',
-      'Population Origins/Ancestry research',
-      'Use of the data is limited to the study of population origins or ancestry.'
-    ],
-    [
-      'RS-[XX]',
-      'Other Research-specific restrictions',
-      'Use of the data is limited to studies of [research type] (e.g., pediatric research).'
-    ],
-    [
-      'RUO',
-      'Research Use Only',
-      'Use of data is limited to research purposes (e.g., does not include its use in clinical care).'
-    ],
-    [
-      'NMDS',
-      'No \"General Methods\" Research',
-      'Use of the data includes methods development research (e.g., development of software or algorithms) ONLY within the bounds of other data use limitations.'
-    ],
-    [
-      'GSO',
-      'Genetic Studies Only',
-      'Use of the data is limited to genetic studies only (i.e., no research using only the phenotype data).'
-    ],
-    [
-      'NPU',
-      'Not-for-profit Use Only',
-      'Use of the data is limited to not-for-profit organizations.'
-    ],
-    [
-      'PUB',
-      'Publication Required',
-      'Requestor agrees to make results of studies using the data available to the larger scientific community.'
-    ],
-    [
-      'COL-[XX]',
-      'Collaboration Required',
-      'Requestor must agree to collaboration with the primary study investigator(s).'
-    ],
-    [
-      'RTN',
-      'Return data to database/resource',
-      'Requestor must return derived/enriched data to the database/resource.'
-    ],
-    [
-      'IRB',
-      'Ethics Approval Required',
-      'Requestor must provide documentation of local IRB/REC approval.'
-    ],
-    [
-      'GS-[XX]',
-      'Geographical Restrictions',
-      'Use of the data is limited to within [geographic region].'
-    ],
-    [
-      'MOR-[XX]',
-      'Publication Moratorium/Embargo',
-      'Requestor agrees not to publish results of studies until [date].'
-    ],
-    [
-      'TS-[XX]',
-      'Time Limits on use',
-      'Use of data is approved for [x months].'
-    ],
-    [
-      'US',
-      'User-Specific restrictions',
-      'Use of data is limited to use by approved users.'
-    ],
-    [
-      'PS',
-      'Project-Specific restrictions',
-      'Use of data is limited to use within an approved project.'
-    ],
-    [
-      'IS',
-      'Institution-Specific restrictions',
-      'Use of data is limited to use within an approved institution.'
-    ]
-  ]
-}
\ No newline at end of file

tests/importxls/test_projects.py

@@ -83,5 +83,6 @@ class TestProjectsParser(TestCase):
                     project_dicts.extend(projects_in_file)
         with open('projects.json', 'w') as outfile:
             json.dump(project_dicts, outfile, indent=4)
+        print("Total projects--->{}".format(len(project_dicts)))
         return project_dicts
 

tests/importxls/test_utils.py

 
-SHEETS_FOLDER ='/Users/pinar_alper/ownCloud/Data Protection/RequirementAnalysis/LCSB-Inventory/internal_data_survey/ANSWERS'
+SHEETS_FOLDER ='/path.to.folder holding.xls.based.daisy.records.to.be.imported/'