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Fix text fixture with unique stage values
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Justin Reese
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Nov 30, 2023
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33 changes: 16 additions & 17 deletions
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tests/data/merged_diagnosis_researchsubject_unique_stages_lung_cervix.tsv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,17 +1,16 @@ | ||
| diagnosis_id diagnosis_identifier primary_diagnosis age_at_diagnosis morphology stage grade method_of_diagnosis subject_id researchsubject_id | ||
| CDDP_EAGLE-1.CDDP-ABK3.CDDP-ABK3_diagnosis [{'system': 'GDC', 'field_name': 'case.diagnoses.diagnosis_id', 'value': '4d75dd99-1c6d-5793-a187-952e1c97dd8d'}, {'system': 'GDC', 'field_name': 'case.diagnoses.submitter_id', 'value': 'CDDP-ABK3_diagnosis'}] Adenocarcinoma, NOS 73 8140/3 not reported Surgical Resection CDDP_EAGLE.CDDP-ABK3 CDDP_EAGLE-1.CDDP-ABK3 | ||
| PDC000219.P035.P035-DX [{'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_id', 'value': '24b6c874-8beb-11ea-b1fd-0aad30af8a83'}, {'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_submitter_id', 'value': 'P035-DX'}] Squamous Cell Carcinoma 30090 IA Academia Sinica LUAD-100.P035 PDC000219.P035 | ||
| PDC000219.P067.P067-DX [{'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_id', 'value': '24b7062b-8beb-11ea-b1fd-0aad30af8a83'}, {'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_submitter_id', 'value': 'P067-DX'}] Adenocarcinoma 15288 IB Academia Sinica LUAD-100.P067 PDC000219.P067 | ||
| PDC000220.P081.P081-DX [{'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_id', 'value': '24b7217a-8beb-11ea-b1fd-0aad30af8a83'}, {'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_submitter_id', 'value': 'P081-DX'}] Adenocarcinoma 22182 IIA Academia Sinica LUAD-100.P081 PDC000220.P081 | ||
| PDC000219.P081.P081-DX [{'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_id', 'value': '24b7217a-8beb-11ea-b1fd-0aad30af8a83'}, {'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_submitter_id', 'value': 'P081-DX'}] Adenocarcinoma 22182 IIA Academia Sinica LUAD-100.P081 PDC000219.P081 | ||
| PDC000219.P020.P020-DX [{'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_id', 'value': '24b6abc1-8beb-11ea-b1fd-0aad30af8a83'}, {'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_submitter_id', 'value': 'P020-DX'}] Adenocarcinoma 24255 IIB Academia Sinica LUAD-100.P020 PDC000219.P020 | ||
| PDC000220.P085.P085-DX [{'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_id', 'value': '24b728e1-8beb-11ea-b1fd-0aad30af8a83'}, {'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_submitter_id', 'value': 'P085-DX'}] Adenocarcinoma 23206 IIIA Academia Sinica LUAD-100.P085 PDC000220.P085 | ||
| PDC000219.P102.P102-DX [{'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_id', 'value': '24b74904-8beb-11ea-b1fd-0aad30af8a83'}, {'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_submitter_id', 'value': 'P102-DX'}] Adenocarcinoma 18556 IIIB Academia Sinica LUAD-100.P102 PDC000219.P102 | ||
| PDC000219.P096.P096-DX [{'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_id', 'value': '24b73dce-8beb-11ea-b1fd-0aad30af8a83'}, {'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_submitter_id', 'value': 'P096-DX'}] Squamous Cell Carcinoma 25215 IV Academia Sinica LUAD-100.P096 PDC000219.P096 | ||
| PDC000434.AP-YTZ8.AP-YTZ8-DX [{'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_id', 'value': '27d75ec5-1bb9-4f95-a796-3e5f3ff6d7e8'}, {'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_submitter_id', 'value': 'AP-YTZ8-DX'}] Lepidic adenocarcinoma 21914 8250/3 Stage IA G2 APOLLO.AP-YTZ8 PDC000434.AP-YTZ8 | ||
| PDC000435.AP-KXUT.AP-KXUT-DX [{'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_id', 'value': '1a1b0c74-5b60-4f99-b38c-a94d37d65ba5'}, {'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_submitter_id', 'value': 'AP-KXUT-DX'}] Acinar cell carcinoma 28854 8550/3 Stage IB G2 APOLLO.AP-KXUT PDC000435.AP-KXUT | ||
| PDC000435.AP-JBET.AP-JBET-DX [{'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_id', 'value': '6322317d-f35a-4de6-81ee-131d8cd39242'}, {'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_submitter_id', 'value': 'AP-JBET-DX'}] Acinar cell carcinoma 29949 8550/3 Stage IIA G2 APOLLO.AP-JBET PDC000435.AP-JBET | ||
| PDC000435.AP-MGNN.AP-MGNN-DX [{'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_id', 'value': 'ead70efa-6046-490b-92e2-63a6805cf3ca'}, {'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_submitter_id', 'value': 'AP-MGNN-DX'}] Solid carcinoma, NOS 17531 8230/3 Stage IIB G3 APOLLO.AP-MGNN PDC000435.AP-MGNN | ||
| PDC000435.AP-JKPX.AP-JKPX-DX [{'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_id', 'value': 'afa7143d-e43d-4950-b2a8-23b0a8b18d66'}, {'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_submitter_id', 'value': 'AP-JKPX-DX'}] Papillary adenocarcinoma, NOS 22279 8260/3 Stage IIIA G2 APOLLO.AP-JKPX PDC000435.AP-JKPX | ||
| PDC000435.AP-MGNN.AP-MGNN-DX [{'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_id', 'value': 'ead70efa-6046-490b-92e2-63a6805cf3ca'}, {'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_submitter_id', 'value': 'AP-MGNN-DX'}] Solid carcinoma, NOS 17531 8230/3 Stage II G3 CPTAC3 Discovery and Confirmatory.C3N-01001 PDC000125.C3N-01001 | ||
| PDC000435.AP-JKPX.AP-JKPX-DX [{'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_id', 'value': 'afa7143d-e43d-4950-b2a8-23b0a8b18d66'}, {'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_submitter_id', 'value': 'AP-JKPX-DX'}] Papillary adenocarcinoma, NOS 22279 8260/3 Stage I G2 CPTAC3 Discovery and Confirmatory.C3L-01284 PDC000125.C3L-01284 | ||
| diagnosis_id diagnosis_identifier primary_diagnosis age_at_diagnosis morphology stage grade method_of_diagnosis subject_id_di researchsubject_id researchsubject_identifier member_of_research_project primary_diagnosis_condition primary_diagnosis_site subject_id_rs | ||
| PDC000219.P090.P090-DX [{'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_id', 'value': '24b732b0-8beb-11ea-b1fd-0aad30af8a83'}, {'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_submitter_id', 'value': 'P090-DX'}] Adenocarcinoma 23827.0 IA Academia Sinica LUAD-100.P090 PDC000219.P090 [{'system': 'PDC', 'field_name': 'Case.case_id', 'value': '24b3cf5e-8beb-11ea-b1fd-0aad30af8a83'}, {'system': 'PDC', 'field_name': 'Case.case_submitter_id', 'value': 'P090'}] PDC000219 Lung Adenocarcinoma Lung Academia Sinica LUAD-100.P090 | ||
| PDC000219.P059.P059-DX [{'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_id', 'value': '24b6f6fa-8beb-11ea-b1fd-0aad30af8a83'}, {'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_submitter_id', 'value': 'P059-DX'}] Adenocarcinoma 20967.0 IB Academia Sinica LUAD-100.P059 PDC000219.P059 [{'system': 'PDC', 'field_name': 'Case.case_id', 'value': '24b3a683-8beb-11ea-b1fd-0aad30af8a83'}, {'system': 'PDC', 'field_name': 'Case.case_submitter_id', 'value': 'P059'}] PDC000219 Lung Adenocarcinoma Lung Academia Sinica LUAD-100.P059 | ||
| PDC000219.P009.P009-DX [{'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_id', 'value': '24b69730-8beb-11ea-b1fd-0aad30af8a83'}, {'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_submitter_id', 'value': 'P009-DX'}] Adenocarcinoma 19639.0 IIA Academia Sinica LUAD-100.P009 PDC000219.P009 [{'system': 'PDC', 'field_name': 'Case.case_id', 'value': '24b36177-8beb-11ea-b1fd-0aad30af8a83'}, {'system': 'PDC', 'field_name': 'Case.case_submitter_id', 'value': 'P009'}] PDC000219 Lung Adenocarcinoma Lung Academia Sinica LUAD-100.P009 | ||
| PDC000219.P020.P020-DX [{'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_id', 'value': '24b6abc1-8beb-11ea-b1fd-0aad30af8a83'}, {'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_submitter_id', 'value': 'P020-DX'}] Adenocarcinoma 24255.0 IIB Academia Sinica LUAD-100.P020 PDC000219.P020 [{'system': 'PDC', 'field_name': 'Case.case_id', 'value': '24b36fce-8beb-11ea-b1fd-0aad30af8a83'}, {'system': 'PDC', 'field_name': 'Case.case_submitter_id', 'value': 'P020'}] PDC000219 Lung Adenocarcinoma Lung Academia Sinica LUAD-100.P020 | ||
| PDC000219.P042.P042-DX [{'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_id', 'value': '24b6d647-8beb-11ea-b1fd-0aad30af8a83'}, {'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_submitter_id', 'value': 'P042-DX'}] Adenocarcinoma 22242.0 IIIA Academia Sinica LUAD-100.P042 PDC000219.P042 [{'system': 'PDC', 'field_name': 'Case.case_id', 'value': '24b38d81-8beb-11ea-b1fd-0aad30af8a83'}, {'system': 'PDC', 'field_name': 'Case.case_submitter_id', 'value': 'P042'}] PDC000219 Lung Adenocarcinoma Lung Academia Sinica LUAD-100.P042 | ||
| PDC000219.P102.P102-DX [{'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_id', 'value': '24b74904-8beb-11ea-b1fd-0aad30af8a83'}, {'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_submitter_id', 'value': 'P102-DX'}] Adenocarcinoma 18556.0 IIIB Academia Sinica LUAD-100.P102 PDC000219.P102 [{'system': 'PDC', 'field_name': 'Case.case_id', 'value': '24b3dbf9-8beb-11ea-b1fd-0aad30af8a83'}, {'system': 'PDC', 'field_name': 'Case.case_submitter_id', 'value': 'P102'}] PDC000219 Lung Adenocarcinoma Lung Academia Sinica LUAD-100.P102 | ||
| PDC000220.P096.P096-DX [{'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_id', 'value': '24b73dce-8beb-11ea-b1fd-0aad30af8a83'}, {'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_submitter_id', 'value': 'P096-DX'}] Squamous Cell Carcinoma 25215.0 IV Academia Sinica LUAD-100.P096 PDC000220.P096 [{'system': 'PDC', 'field_name': 'Case.case_id', 'value': '24b3d61f-8beb-11ea-b1fd-0aad30af8a83'}, {'system': 'PDC', 'field_name': 'Case.case_submitter_id', 'value': 'P096'}] PDC000220 Lung Squamous Cell Carcinoma Lung Academia Sinica LUAD-100.P096 | ||
| PDC000434.AP-AAFC.AP-AAFC-DX [{'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_id', 'value': '2692314d-2367-4f65-b0d4-9f6bb142a8eb'}, {'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_submitter_id', 'value': 'AP-AAFC-DX'}] Acinar cell carcinoma 27393.0 8550/3 Stage IA G2 APOLLO.AP-AAFC PDC000434.AP-AAFC [{'system': 'PDC', 'field_name': 'Case.case_id', 'value': 'be87bdee-8b47-42de-be58-c866e86e9997'}, {'system': 'PDC', 'field_name': 'Case.case_submitter_id', 'value': 'AP-AAFC'}] PDC000434 Lung Adenocarcinoma Bronchus and lung APOLLO.AP-AAFC | ||
| PDC000436.AP-RA2G.AP-RA2G-DX [{'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_id', 'value': 'bda3fd3c-9b41-4daf-9ff3-65850cd5c133'}, {'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_submitter_id', 'value': 'AP-RA2G-DX'}] Acinar cell carcinoma 30315.0 8550/3 Stage IB G3 APOLLO.AP-RA2G PDC000436.AP-RA2G [{'system': 'PDC', 'field_name': 'Case.case_id', 'value': '5629fe7e-ee5e-4e2e-bc4b-2c4a99183d61'}, {'system': 'PDC', 'field_name': 'Case.case_submitter_id', 'value': 'AP-RA2G'}] PDC000436 Lung Adenocarcinoma Bronchus and lung APOLLO.AP-RA2G | ||
| PDC000436.AP-27JZ.AP-27JZ-DX [{'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_id', 'value': '71ad488f-b314-4932-acf7-9561761c6ec2'}, {'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_submitter_id', 'value': 'AP-27JZ-DX'}] Acinar cell carcinoma 24836.0 8550/3 Stage IIA G3 APOLLO.AP-27JZ PDC000436.AP-27JZ [{'system': 'PDC', 'field_name': 'Case.case_id', 'value': 'c3d87659-d18b-4f58-8ff1-e4780d5e5a74'}, {'system': 'PDC', 'field_name': 'Case.case_submitter_id', 'value': 'AP-27JZ'}] PDC000436 Lung Adenocarcinoma Bronchus and lung APOLLO.AP-27JZ | ||
| PDC000435.AP-DT88.AP-DT88-DX [{'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_id', 'value': 'bf7617d1-2e94-4423-889b-13308ba29edf'}, {'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_submitter_id', 'value': 'AP-DT88-DX'}] Papillary adenocarcinoma, NOS 30680.0 8260/3 Stage IIB G2 APOLLO.AP-DT88 PDC000435.AP-DT88 [{'system': 'PDC', 'field_name': 'Case.case_id', 'value': '3ca2cf34-fa0c-40e8-81ea-ca353e74e4fe'}, {'system': 'PDC', 'field_name': 'Case.case_submitter_id', 'value': 'AP-DT88'}] PDC000435 Lung Adenocarcinoma Bronchus and lung APOLLO.AP-DT88 | ||
| PDC000434.AP-MAZ4.AP-MAZ4-DX [{'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_id', 'value': '182be20e-6bd1-415b-a5e5-4d35a3e1cdb8'}, {'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_submitter_id', 'value': 'AP-MAZ4-DX'}] Solid carcinoma, NOS 25566.0 8230/3 Stage IIIA G3 APOLLO.AP-MAZ4 PDC000434.AP-MAZ4 [{'system': 'PDC', 'field_name': 'Case.case_id', 'value': '11362304-fd12-4f36-8e9d-608972ae1a26'}, {'system': 'PDC', 'field_name': 'Case.case_submitter_id', 'value': 'AP-MAZ4'}] PDC000434 Lung Adenocarcinoma Bronchus and lung APOLLO.AP-MAZ4 | ||
| CDDP_EAGLE-1.CDDP-ABK3.CDDP-ABK3_diagnosis [{'system': 'GDC', 'field_name': 'case.diagnoses.diagnosis_id', 'value': '4d75dd99-1c6d-5793-a187-952e1c97dd8d'}, {'system': 'GDC', 'field_name': 'case.diagnoses.submitter_id', 'value': 'CDDP-ABK3_diagnosis'}] Adenocarcinoma, NOS 73.0 8140/3 not reported Surgical Resection CDDP_EAGLE.CDDP-ABK3 CDDP_EAGLE-1.CDDP-ABK3 [{'system': 'GDC', 'field_name': 'case.case_id', 'value': '292b1b0d-3f37-413f-ad95-e99f8afe16e0'}, {'system': 'GDC', 'field_name': 'case.submitter_id', 'value': 'CDDP-ABK3'}] CDDP_EAGLE-1 Adenomas and Adenocarcinomas Bronchus and lung CDDP_EAGLE.CDDP-ABK3 | ||
| PDC000434.AP-MAZ4.AP-MAZ4-DX [{'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_id', 'value': '182be20e-6bd1-415b-a5e5-4d35a3e1cdb8'}, {'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_submitter_id', 'value': 'AP-MAZ4-DX'}] Solid carcinoma, NOS 25566.0 8230/3 Stage I G3 APOLLO.AP-MAZ4 PDC000434.AP-MAZ4 [{'system': 'PDC', 'field_name': 'Case.case_id', 'value': '11362304-fd12-4f36-8e9d-608972ae1a26'}, {'system': 'PDC', 'field_name': 'Case.case_submitter_id', 'value': 'AP-MAZ4'}] PDC000434 Lung Adenocarcinoma Bronchus and lung APOLLO.AP-MAZ4 | ||
| PDC000434.AP-MAZ4.AP-MAZ4-DX [{'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_id', 'value': '182be20e-6bd1-415b-a5e5-4d35a3e1cdb8'}, {'system': 'PDC', 'field_name': 'Diagnosis.diagnosis_submitter_id', 'value': 'AP-MAZ4-DX'}] Solid carcinoma, NOS 25566.0 8230/3 Stage II G3 APOLLO.AP-MAZ4 PDC000434.AP-MAZ4 [{'system': 'PDC', 'field_name': 'Case.case_id', 'value': '11362304-fd12-4f36-8e9d-608972ae1a26'}, {'system': 'PDC', 'field_name': 'Case.case_submitter_id', 'value': 'AP-MAZ4'}] PDC000434 Lung Adenocarcinoma Bronchus and lung APOLLO.AP-MAZ4 |