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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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12 changes: 10 additions & 2 deletions gdc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -228,6 +228,7 @@ def search(endpoint, in_filter={}, exclude_filter={}, fields=[], expand=[],
response = requests.post(url, data=payload)
else:
response = requests.get(url, params=payload)

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Prefer not to have whitespace changes if not necessary.

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sure. will change that.

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removed white space.

if response.status_code == 200:
results = response.json()['data']['hits']
if typ.lower() == 'json':
Expand Down Expand Up @@ -376,8 +377,11 @@ 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')

if(project_df.empty==False):
return project_df.set_index('id')
else:
return project_df
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I think this function should just return project_df not matter what to make things consistent. And returning empty dataframe on failed/no-hit search seems reasonable to me. Therefore, things has to be changed here accordingly. And the check here may be whether project_df is None since search can return None. So check that and make sure it returns empty dataframe properly.

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@yunhailuo so you mean to return project_df itself? I mean the other functions would get changed where we were using project_df.set_index('id') state of dataframe.

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@arp95 Exactly.

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@yunhailuo Thanks for clearing out. Working on it.

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@yunhailuo if the project_df returned is null, then should I remove that project from projects array in gdc2xena file or just leave it empty?

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@yunhailuo yunhailuo Mar 1, 2019 •
edited
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@arp95 I think an empty projects array makes more sense to me. That means you didn't get any valid projects from gdc.get_project_info(). For that line, it will be all or none, right? So there is no removing one project from projects array?


def get_samples_clinical(projects=None):
"""Get info for all samples of ``projects`` and clinical info for all
Expand Down Expand Up @@ -431,7 +435,11 @@ 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()
if(df.empty==False):
print(df.head())
else:
print("Empty dataframe!")


if __name__ == '__main__':
Expand Down