Use constant.GDC_RELEASE_API

ucscXena · Jun 2, 2019 · f61bbc0 · f61bbc0
1 parent a90a8ee
commit f61bbc0
Showing 1 changed file with 17 additions and 17 deletions.
diff --git a/xena_gdc_etl/xena_dataset.py b/xena_gdc_etl/xena_dataset.py
@@ -30,7 +30,12 @@
 
 from xena_gdc_etl import gdc
 from .utils import mkdir_p
-from .constants import GDC_XENA_COHORT, METADATA_TEMPLATE, METADATA_VARIABLES
+from .constants import (
+ GDC_XENA_COHORT,
+ METADATA_TEMPLATE,
+ METADATA_VARIABLES,
+ GDC_RELEASE_URL,
+)
 
 
 def read_by_ext(filename, mode='r'):
@@ -780,19 +785,23 @@ class GDCOmicset(XenaDataset):
  '60', '61', '99'])},
  'muse_snv': {
  'data_type': 'Masked Somatic Mutation',
- 'analysis.workflow_type': 'MuSE Variant Aggregation and Masking' # noqa
+ 'analysis.workflow_type':
+ 'MuSE Variant Aggregation and Masking'
  },
  'mutect2_snv': {
  'data_type': 'Masked Somatic Mutation',
- 'analysis.workflow_type': 'MuTect2 Variant Aggregation and Masking' # noqa
+ 'analysis.workflow_type': 
+ 'MuTect2 Variant Aggregation and Masking'
  },
  'somaticsniper_snv': {
  'data_type': 'Masked Somatic Mutation',
- 'analysis.workflow_type': 'SomaticSniper Variant Aggregation and Masking' # noqa
+ 'analysis.workflow_type':
+ 'SomaticSniper Variant Aggregation and Masking'
  },
  'varscan2_snv': {
  'data_type': 'Masked Somatic Mutation',
- 'analysis.workflow_type': 'VarScan2 Variant Aggregation and Masking' # noqa
+ 'analysis.workflow_type':
+ 'VarScan2 Variant Aggregation and Masking'
  },
  'methylation27': {'data_type': 'Methylation Beta Value',
  'platform': 'Illumina Human Methylation 27'},
@@ -871,10 +880,7 @@ def gdc_release(self):
  anchor = re.match(
  r'(Data Release [^\s]+)\s', data_release
  ).group(1).replace(' ', '-').replace('.', '').lower()
- self.__gdc_release = (
- 'https://docs.gdc.cancer.gov/Data/Release_Notes/Data_Release_Notes/#' # noqa
- + anchor
- )
+ self.__gdc_release = GDC_RELEASE_URL + anchor
  return self.__gdc_release
 
  @gdc_release.setter
@@ -1204,10 +1210,7 @@ def gdc_release(self):
  anchor = re.match(
  r'(Data Release [^\s]+)\s', data_release
  ).group(1).replace(' ', '-').replace('.', '').lower()
- self.__gdc_release = (
- 'https://docs.gdc.cancer.gov/Data/Release_Notes/Data_Release_Notes/#' # noqa
- + anchor
- )
+ self.__gdc_release = GDC_RELEASE_URL + anchor
  return self.__gdc_release
 
  @gdc_release.setter
@@ -1507,10 +1510,7 @@ def gdc_release(self):
  anchor = re.match(
  r'(Data Release [^\s]+)\s', data_release
  ).group(1).replace(' ', '-').replace('.', '').lower()
- self.__gdc_release = (
- 'https://docs.gdc.cancer.gov/Data/Release_Notes/Data_Release_Notes/#' # noqa
- + anchor
- )
+ self.__gdc_release = GDC_RELEASE_URL + anchor
  return self.__gdc_release
 
  @gdc_release.setter