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Develop branch modifications #68

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@msierk msierk commented Jan 23, 2024

Various updates to factories.

pnrobinson and others added 30 commits November 29, 2023 16:03
@pnrobinson
updating disease mapper
71e0c48
Fix bug when checking disease_stage_term_list for emptiness
7f9f9ae
Run pytest when pushing to develop
582feda
Fix (my) bug when checking disease_stage_term_list
c08bce6
Ignore phenopackets/ dir
4d04459
Add missing test data file
69672ca
Tiny refactor to simplify code
1984924
Add test data file with all unique stages
021d7a0
Remove index col from text fixture file
5acf5da
Remove index_col arg when reading in text fixture file
e6cd614
Lint
42c57b4
Remove deprecated call to assertEquals (in favor of assertEqual)
95c2c59
Fix text fixture
d2c99a1
Fix text fixture with unique stage values
99093ce
Test for parsing of stage info
73b8d52
Code to parse stage info
600c378
Add test for disease stage == ontology class
e18d377
Change test to parameterized
a7aa720
Add failing tests for sub-stages (IA, IB, IIA, etc)
ff66c16
Replace repeated hard-coded NCIT terms with global variables up top
8aa3b97
Add code to parse staging subtypes
d6ae809
@pnrobinson
Merge pull request #53 from monarch-initiative/get_stage_info
5e75975 
Get stage info
@msierk
Converted days_to_iso to use the pandas conversion
b410070 
Moved days_to_iso method to cda_factory
Added days_to_iso conversion to onset in disease factory
@msierk
merging
afdfb84
@msierk
Merge branch 'develop' of https://github.com/monarch-initiative/oncoe…
1e25c4a 
…xporter into develop
@msierk
fixed OpMutation import error
16e7e43
Add helper function to download ICD/O to NCIT mappings
b361b78
Fix broken calls to to_ga4gh()
0622b1c
Fix calls to to_ga4gh()
26d64bb
Add (broken) helper function for ICD/O -> NCIT
b7b291e
ielis and others added 30 commits February 27, 2024 16:45
@ielis
Make it a module.
0aa7cbf
@ielis
Include the mapping tables in MANIFEST.in.
8c58eae
@ielis
Add the __init__.py back.
9076d26
@rajdeepmondaldotcom
Merge pull request #79 from monarch-initiative/el-ncit-mappings
ab658ed 
Expand CDA to NCIT Mappings for 12 tissues & Enhance OpUberonMapper
@ielis
Draft GdcMutationService.
3d9f4b8
@ielis
Store id in VariationDescriptor.
4d8b58d
@sujaypatil96
use GdcMutationService in cda_table_importer
538512a
@sujaypatil96
plug in VariantInterpretation objects into phenopackets
38ff8f7
@sujaypatil96
Merge pull request #83 from monarch-initiative/gdc-mutations-modifica…
0c807e9 
…tion

Start using `GdcMutationService` and associated methods in `CdaTableImporter`
@ielis
Put GDC timeout to init.
029a544
@ielis
GDC mutation service is a private field.
c48f0a7
@ielis
Clip the maximum allowed ipython version to 8.22.2.
ed8c90c
@ielis
Merge pull request #81 from monarch-initiative/fetch-mutations-from-gdc
53b0539 
Pull mutation data from GDC
@sujaypatil96
pull in phenopacket VitalStatus metadata from GDC
cdf3400
@sujaypatil96
remove mutation_df logic from CDA
e60ec52
@msierk
Modified cda_table_importer.py to conform to the updated CDA API.
dc49ae1
@msierk
added subject_id to specimen and treatment data frames
8c7b2ca
@msierk
fixed getting variants from GDC
ac183ca
@msierk
edited comments
bc0ec02
Update cdapython dependency
2027715
@justaddcoffee
Merge pull request #86 from monarch-initiative/update_cda
4a8df16 
Update cdapython dependency
@sujaypatil96
Merge branch 'develop' into issue-82
b6b0500
@sujaypatil96
missed merge conflict resolution
6f58d49
@sujaypatil96
make call to fetch_vital_status() in _gdc API
ab86d3b
@sujaypatil96
Merge pull request #85 from monarch-initiative/issue-82
0894f71 
Pull in survival time and vital status metadata from GDC
Fix scripts to use new CDA API
fa83fea
@msierk
Merge pull request #92 from monarch-initiative/fix_scripts
5b64b16 
Fix scripts to use new CDA API
Add gene context while retrieving mutation data from GDC
93c367e
Undelete deleted files
5cabdf1
@justaddcoffee
Merge pull request #93 from monarch-initiative/add_gene_context_from_gdc
17413a3 
Add gene context while retrieving mutation data from GDC
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6 participants
@msierk @pnrobinson @ielis @justaddcoffee @rajdeepmondaldotcom @sujaypatil96