Commit b0744c88 authored by Pinar Alper's avatar Pinar Alper
Browse files

Added default terminologies users by DAISY

parent 2237adaf
......@@ -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]):
......
......@@ -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)
......
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{
"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
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......@@ -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
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/'
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