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resolved issue #5 #6

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resolved issue #5 #6

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314e72f
resolved issue #2: resolved error in get_projects_info() function
Feb 20, 2019
a7d89f6
resolved issue #2: resolved error in get_projects_info() function
Feb 20, 2019
9836504
Merge branch 'master' of https://github.com/yunhailuo/xena-GDC-ETL
Feb 21, 2019
1f6e26e
resolved issue #5: resolved error in gdc.py
Feb 21, 2019
c8810a3
resolved issue #5: resolved error in gdc.py
Feb 21, 2019
0f7bba1
resolved issue #5: resolved error in gdc.py
Feb 21, 2019
5d24ab9
resolved issue #5: resolved error in gdc.py
Feb 21, 2019
23e489f
removed white space
Mar 1, 2019
de93d11
added error handling
Mar 1, 2019
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9 changes: 6 additions & 3 deletions gdc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -376,8 +376,7 @@ def get_project_info(projects=None):
project_df = search('projects', in_filter=in_filter,
fields=['name', 'primary_site', 'project_id',
'program.name'])
return project_df.set_index('id')

return project_df

def get_samples_clinical(projects=None):
"""Get info for all samples of ``projects`` and clinical info for all
Expand Down Expand Up @@ -431,7 +430,11 @@ def main():
print('A simple python module providing selected GDC API functionalities.')

# Simple test
print(get_project_info(['TCGA-THCA']).head())
df = get_project_info(['TCGA-THCA'])
if(df.empty==False):
print(df.head())
else:
print("Empty dataframe!")


if __name__ == '__main__':
Expand Down
5 changes: 4 additions & 1 deletion gdc2xena.py
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Original file line number Diff line number Diff line change
Expand Up @@ -134,7 +134,10 @@ def main():
root_dir = os.path.abspath(args.root)
projects = args.projects
if 'all' in [p.lower() for p in projects]:
projects = [str(x) for x in gdc.get_project_info().index]
projects = [str(x) for x in gdc.get_project_info()]
for project in projects:
if(project.empty==False):
project = project.index
for p in args.not_projects:
projects.remove(p)
xena_dtypes = args.datatype
Expand Down