From b1cd71a4978c83e4447671b6d94807a598481ad8 Mon Sep 17 00:00:00 2001 From: Gijs Kant Date: Wed, 16 Oct 2019 11:19:09 +0200 Subject: [PATCH 01/10] Reorganise test data. --- README.md | 2 +- luigi.cfg-sample | 4 ++-- test_data/{ => E2E_TEST_DATA}/config/logging.cfg | 0 .../{ => E2E_TEST_DATA}/config/ontology_config.json | 0 .../{ => E2E_TEST_DATA}/config/sources_config.json | 0 .../dropzone}/NGS/pmc_test.maf | 0 .../dropzone}/NGS/pmc_test.maf.gz | Bin .../dropzone}/NGS/pmc_test.maf.gz.sha1 | 0 .../dropzone}/NGS/pmc_test.maf.sha1 | 0 .../dropzone}/NGS/pmc_test.seg | 0 .../dropzone}/NGS/pmc_test.seg.sha1 | 0 .../dropzone}/NGS/pmc_test_all_data_by_genes.txt | 0 .../NGS/pmc_test_all_data_by_genes.txt.sha1 | 0 .../NGS/pmc_test_all_thresholded.by_genes.txt | 0 .../NGS/pmc_test_all_thresholded.by_genes.txt.sha1 | 0 .../dropzone}/biomaterial.tsv | 0 .../dropzone}/biomaterial.tsv.sha1 | 0 .../dropzone}/biosource.tsv | 0 .../dropzone}/biosource.tsv.sha1 | 0 .../dropzone}/codebook.txt | 0 .../dropzone}/codebook.txt.sha1 | 0 .../dropzone}/diagnosis.tsv | 0 .../dropzone}/diagnosis.tsv.sha1 | 0 .../dropzone}/individual.tsv | 0 .../dropzone}/individual.tsv.sha1 | 0 .../dropzone}/individual_study.tsv | 0 .../dropzone}/individual_study.tsv.sha1 | 0 .../dropzone}/study.tsv | 0 .../dropzone}/study.tsv.sha1 | 0 29 files changed, 3 insertions(+), 3 deletions(-) rename test_data/{ => E2E_TEST_DATA}/config/logging.cfg (100%) rename test_data/{ => E2E_TEST_DATA}/config/ontology_config.json (100%) rename test_data/{ => E2E_TEST_DATA}/config/sources_config.json (100%) rename test_data/{dropzone/E2E_TEST_DATA => E2E_TEST_DATA/dropzone}/NGS/pmc_test.maf (100%) rename test_data/{dropzone/E2E_TEST_DATA => E2E_TEST_DATA/dropzone}/NGS/pmc_test.maf.gz (100%) rename test_data/{dropzone/E2E_TEST_DATA => E2E_TEST_DATA/dropzone}/NGS/pmc_test.maf.gz.sha1 (100%) rename test_data/{dropzone/E2E_TEST_DATA => E2E_TEST_DATA/dropzone}/NGS/pmc_test.maf.sha1 (100%) rename test_data/{dropzone/E2E_TEST_DATA => E2E_TEST_DATA/dropzone}/NGS/pmc_test.seg (100%) rename test_data/{dropzone/E2E_TEST_DATA => E2E_TEST_DATA/dropzone}/NGS/pmc_test.seg.sha1 (100%) rename test_data/{dropzone/E2E_TEST_DATA => E2E_TEST_DATA/dropzone}/NGS/pmc_test_all_data_by_genes.txt (100%) rename test_data/{dropzone/E2E_TEST_DATA => E2E_TEST_DATA/dropzone}/NGS/pmc_test_all_data_by_genes.txt.sha1 (100%) rename test_data/{dropzone/E2E_TEST_DATA => E2E_TEST_DATA/dropzone}/NGS/pmc_test_all_thresholded.by_genes.txt (100%) rename test_data/{dropzone/E2E_TEST_DATA => E2E_TEST_DATA/dropzone}/NGS/pmc_test_all_thresholded.by_genes.txt.sha1 (100%) rename test_data/{dropzone/E2E_TEST_DATA => E2E_TEST_DATA/dropzone}/biomaterial.tsv (100%) rename test_data/{dropzone/E2E_TEST_DATA => E2E_TEST_DATA/dropzone}/biomaterial.tsv.sha1 (100%) rename test_data/{dropzone/E2E_TEST_DATA => E2E_TEST_DATA/dropzone}/biosource.tsv (100%) rename test_data/{dropzone/E2E_TEST_DATA => E2E_TEST_DATA/dropzone}/biosource.tsv.sha1 (100%) rename test_data/{dropzone/E2E_TEST_DATA => E2E_TEST_DATA/dropzone}/codebook.txt (100%) rename test_data/{dropzone/E2E_TEST_DATA => E2E_TEST_DATA/dropzone}/codebook.txt.sha1 (100%) rename test_data/{dropzone/E2E_TEST_DATA => E2E_TEST_DATA/dropzone}/diagnosis.tsv (100%) rename test_data/{dropzone/E2E_TEST_DATA => E2E_TEST_DATA/dropzone}/diagnosis.tsv.sha1 (100%) rename test_data/{dropzone/E2E_TEST_DATA => E2E_TEST_DATA/dropzone}/individual.tsv (100%) rename test_data/{dropzone/E2E_TEST_DATA => E2E_TEST_DATA/dropzone}/individual.tsv.sha1 (100%) rename test_data/{dropzone/E2E_TEST_DATA => E2E_TEST_DATA/dropzone}/individual_study.tsv (100%) rename test_data/{dropzone/E2E_TEST_DATA => E2E_TEST_DATA/dropzone}/individual_study.tsv.sha1 (100%) rename test_data/{dropzone/E2E_TEST_DATA => E2E_TEST_DATA/dropzone}/study.tsv (100%) rename test_data/{dropzone/E2E_TEST_DATA => E2E_TEST_DATA/dropzone}/study.tsv.sha1 (100%) diff --git a/README.md b/README.md index db16a3c..6c67041 100644 --- a/README.md +++ b/README.md @@ -118,7 +118,7 @@ As sha1 hashes 40 characters long the rest of the file gets ignored: `1625be750dab24057c4c82d62d27298236ebb04c diagnosis.txt` For more information, see the [CSR data model](https://github.com/thehyve/python_csr2transmart#data-model) description -and an example of [input data files](./test_data/dropzone/E2E_TEST_DATA). +and an example of [input data files](test_data/E2E_TEST_DATA/dropzone). ## Usage diff --git a/luigi.cfg-sample b/luigi.cfg-sample index 9d09624..8089162 100644 --- a/luigi.cfg-sample +++ b/luigi.cfg-sample @@ -26,7 +26,7 @@ transformation_config_dir= /config load_logs_dir_name=load_logs # TranSMART study settings -transmart_copy_jar = /transmart-core/transmart-copy/build/libs/transmart-copy-17.2.jar +transmart_copy_jar = /transmart-core/transmart-copy/build/libs/transmart-copy-17.2.5.jar study_id = CSR_STUDY top_node = \Central Subject Registry\ @@ -74,4 +74,4 @@ server_name = pmc-cbioportal-test [E2eTest] PGADMINUSER = postgres PGADMINPASSWORD = password -parent_drop_dir = /pmc-conversion/test_data/dropzone/E2E_TEST_DATA \ No newline at end of file +parent_drop_dir = /pmc-conversion/test_data/E2E_TEST_DATA/dropzone diff --git a/test_data/config/logging.cfg b/test_data/E2E_TEST_DATA/config/logging.cfg similarity index 100% rename from test_data/config/logging.cfg rename to test_data/E2E_TEST_DATA/config/logging.cfg diff --git a/test_data/config/ontology_config.json b/test_data/E2E_TEST_DATA/config/ontology_config.json similarity index 100% rename from test_data/config/ontology_config.json rename to test_data/E2E_TEST_DATA/config/ontology_config.json diff --git a/test_data/config/sources_config.json b/test_data/E2E_TEST_DATA/config/sources_config.json similarity index 100% rename from test_data/config/sources_config.json rename to test_data/E2E_TEST_DATA/config/sources_config.json diff --git a/test_data/dropzone/E2E_TEST_DATA/NGS/pmc_test.maf b/test_data/E2E_TEST_DATA/dropzone/NGS/pmc_test.maf similarity index 100% rename from test_data/dropzone/E2E_TEST_DATA/NGS/pmc_test.maf rename to test_data/E2E_TEST_DATA/dropzone/NGS/pmc_test.maf diff --git a/test_data/dropzone/E2E_TEST_DATA/NGS/pmc_test.maf.gz b/test_data/E2E_TEST_DATA/dropzone/NGS/pmc_test.maf.gz similarity index 100% rename from test_data/dropzone/E2E_TEST_DATA/NGS/pmc_test.maf.gz rename to test_data/E2E_TEST_DATA/dropzone/NGS/pmc_test.maf.gz diff --git a/test_data/dropzone/E2E_TEST_DATA/NGS/pmc_test.maf.gz.sha1 b/test_data/E2E_TEST_DATA/dropzone/NGS/pmc_test.maf.gz.sha1 similarity index 100% rename from test_data/dropzone/E2E_TEST_DATA/NGS/pmc_test.maf.gz.sha1 rename to test_data/E2E_TEST_DATA/dropzone/NGS/pmc_test.maf.gz.sha1 diff --git a/test_data/dropzone/E2E_TEST_DATA/NGS/pmc_test.maf.sha1 b/test_data/E2E_TEST_DATA/dropzone/NGS/pmc_test.maf.sha1 similarity index 100% rename from test_data/dropzone/E2E_TEST_DATA/NGS/pmc_test.maf.sha1 rename to test_data/E2E_TEST_DATA/dropzone/NGS/pmc_test.maf.sha1 diff --git a/test_data/dropzone/E2E_TEST_DATA/NGS/pmc_test.seg b/test_data/E2E_TEST_DATA/dropzone/NGS/pmc_test.seg similarity index 100% rename from test_data/dropzone/E2E_TEST_DATA/NGS/pmc_test.seg rename to test_data/E2E_TEST_DATA/dropzone/NGS/pmc_test.seg diff --git a/test_data/dropzone/E2E_TEST_DATA/NGS/pmc_test.seg.sha1 b/test_data/E2E_TEST_DATA/dropzone/NGS/pmc_test.seg.sha1 similarity index 100% rename from test_data/dropzone/E2E_TEST_DATA/NGS/pmc_test.seg.sha1 rename to test_data/E2E_TEST_DATA/dropzone/NGS/pmc_test.seg.sha1 diff --git a/test_data/dropzone/E2E_TEST_DATA/NGS/pmc_test_all_data_by_genes.txt b/test_data/E2E_TEST_DATA/dropzone/NGS/pmc_test_all_data_by_genes.txt similarity index 100% rename from test_data/dropzone/E2E_TEST_DATA/NGS/pmc_test_all_data_by_genes.txt rename to test_data/E2E_TEST_DATA/dropzone/NGS/pmc_test_all_data_by_genes.txt diff --git a/test_data/dropzone/E2E_TEST_DATA/NGS/pmc_test_all_data_by_genes.txt.sha1 b/test_data/E2E_TEST_DATA/dropzone/NGS/pmc_test_all_data_by_genes.txt.sha1 similarity index 100% rename from test_data/dropzone/E2E_TEST_DATA/NGS/pmc_test_all_data_by_genes.txt.sha1 rename to test_data/E2E_TEST_DATA/dropzone/NGS/pmc_test_all_data_by_genes.txt.sha1 diff --git a/test_data/dropzone/E2E_TEST_DATA/NGS/pmc_test_all_thresholded.by_genes.txt b/test_data/E2E_TEST_DATA/dropzone/NGS/pmc_test_all_thresholded.by_genes.txt similarity index 100% rename from test_data/dropzone/E2E_TEST_DATA/NGS/pmc_test_all_thresholded.by_genes.txt rename to test_data/E2E_TEST_DATA/dropzone/NGS/pmc_test_all_thresholded.by_genes.txt diff --git a/test_data/dropzone/E2E_TEST_DATA/NGS/pmc_test_all_thresholded.by_genes.txt.sha1 b/test_data/E2E_TEST_DATA/dropzone/NGS/pmc_test_all_thresholded.by_genes.txt.sha1 similarity index 100% rename from test_data/dropzone/E2E_TEST_DATA/NGS/pmc_test_all_thresholded.by_genes.txt.sha1 rename to test_data/E2E_TEST_DATA/dropzone/NGS/pmc_test_all_thresholded.by_genes.txt.sha1 diff --git a/test_data/dropzone/E2E_TEST_DATA/biomaterial.tsv b/test_data/E2E_TEST_DATA/dropzone/biomaterial.tsv similarity index 100% rename from test_data/dropzone/E2E_TEST_DATA/biomaterial.tsv rename to test_data/E2E_TEST_DATA/dropzone/biomaterial.tsv diff --git a/test_data/dropzone/E2E_TEST_DATA/biomaterial.tsv.sha1 b/test_data/E2E_TEST_DATA/dropzone/biomaterial.tsv.sha1 similarity index 100% rename from test_data/dropzone/E2E_TEST_DATA/biomaterial.tsv.sha1 rename to test_data/E2E_TEST_DATA/dropzone/biomaterial.tsv.sha1 diff --git a/test_data/dropzone/E2E_TEST_DATA/biosource.tsv b/test_data/E2E_TEST_DATA/dropzone/biosource.tsv similarity index 100% rename from test_data/dropzone/E2E_TEST_DATA/biosource.tsv rename to test_data/E2E_TEST_DATA/dropzone/biosource.tsv diff --git a/test_data/dropzone/E2E_TEST_DATA/biosource.tsv.sha1 b/test_data/E2E_TEST_DATA/dropzone/biosource.tsv.sha1 similarity index 100% rename from test_data/dropzone/E2E_TEST_DATA/biosource.tsv.sha1 rename to test_data/E2E_TEST_DATA/dropzone/biosource.tsv.sha1 diff --git a/test_data/dropzone/E2E_TEST_DATA/codebook.txt b/test_data/E2E_TEST_DATA/dropzone/codebook.txt similarity index 100% rename from test_data/dropzone/E2E_TEST_DATA/codebook.txt rename to test_data/E2E_TEST_DATA/dropzone/codebook.txt diff --git a/test_data/dropzone/E2E_TEST_DATA/codebook.txt.sha1 b/test_data/E2E_TEST_DATA/dropzone/codebook.txt.sha1 similarity index 100% rename from test_data/dropzone/E2E_TEST_DATA/codebook.txt.sha1 rename to test_data/E2E_TEST_DATA/dropzone/codebook.txt.sha1 diff --git a/test_data/dropzone/E2E_TEST_DATA/diagnosis.tsv b/test_data/E2E_TEST_DATA/dropzone/diagnosis.tsv similarity index 100% rename from test_data/dropzone/E2E_TEST_DATA/diagnosis.tsv rename to test_data/E2E_TEST_DATA/dropzone/diagnosis.tsv diff --git a/test_data/dropzone/E2E_TEST_DATA/diagnosis.tsv.sha1 b/test_data/E2E_TEST_DATA/dropzone/diagnosis.tsv.sha1 similarity index 100% rename from test_data/dropzone/E2E_TEST_DATA/diagnosis.tsv.sha1 rename to test_data/E2E_TEST_DATA/dropzone/diagnosis.tsv.sha1 diff --git a/test_data/dropzone/E2E_TEST_DATA/individual.tsv b/test_data/E2E_TEST_DATA/dropzone/individual.tsv similarity index 100% rename from test_data/dropzone/E2E_TEST_DATA/individual.tsv rename to test_data/E2E_TEST_DATA/dropzone/individual.tsv diff --git a/test_data/dropzone/E2E_TEST_DATA/individual.tsv.sha1 b/test_data/E2E_TEST_DATA/dropzone/individual.tsv.sha1 similarity index 100% rename from test_data/dropzone/E2E_TEST_DATA/individual.tsv.sha1 rename to test_data/E2E_TEST_DATA/dropzone/individual.tsv.sha1 diff --git a/test_data/dropzone/E2E_TEST_DATA/individual_study.tsv b/test_data/E2E_TEST_DATA/dropzone/individual_study.tsv similarity index 100% rename from test_data/dropzone/E2E_TEST_DATA/individual_study.tsv rename to test_data/E2E_TEST_DATA/dropzone/individual_study.tsv diff --git a/test_data/dropzone/E2E_TEST_DATA/individual_study.tsv.sha1 b/test_data/E2E_TEST_DATA/dropzone/individual_study.tsv.sha1 similarity index 100% rename from test_data/dropzone/E2E_TEST_DATA/individual_study.tsv.sha1 rename to test_data/E2E_TEST_DATA/dropzone/individual_study.tsv.sha1 diff --git a/test_data/dropzone/E2E_TEST_DATA/study.tsv b/test_data/E2E_TEST_DATA/dropzone/study.tsv similarity index 100% rename from test_data/dropzone/E2E_TEST_DATA/study.tsv rename to test_data/E2E_TEST_DATA/dropzone/study.tsv diff --git a/test_data/dropzone/E2E_TEST_DATA/study.tsv.sha1 b/test_data/E2E_TEST_DATA/dropzone/study.tsv.sha1 similarity index 100% rename from test_data/dropzone/E2E_TEST_DATA/study.tsv.sha1 rename to test_data/E2E_TEST_DATA/dropzone/study.tsv.sha1 From 0d48379867a344958898cce3e6a6a3bd9b38be95 Mon Sep 17 00:00:00 2001 From: Gijs Kant Date: Wed, 16 Oct 2019 11:35:09 +0200 Subject: [PATCH 02/10] Add test_logic data set. --- .../cbioportal_db_info/cancertypes.json | 1 + .../config/cbioportal_db_info/genes.json | 1 + .../cbioportal_db_info/genesaliases.json | 1 + .../test_logic/config/ontology_config.json | 162 +++++++ .../test_logic/config/sources_config.json | 422 ++++++++++++++++++ .../test_logic/dropzone/clinic/RDP-IC.tab | 7 + .../dropzone/clinic/RDP-IC.tab.sha1 | 1 + .../dropzone/clinic/RDP-Patient.tab | 7 + .../dropzone/clinic/RDP-Patient.tab.sha1 | 1 + .../dropzone/laboratory/biomaterial.txt | 22 + .../dropzone/laboratory/biomaterial.txt.sha1 | 1 + .../dropzone/laboratory/biosource.txt | 20 + .../dropzone/laboratory/biosource.txt.sha1 | 1 + .../dropzone/studies/PMCST000AAA_death.txt | 4 + .../studies/PMCST000AAA_death.txt.sha1 | 1 + .../studies/PMCST000AAA_death_codebook.txt | 1 + .../PMCST000AAA_death_codebook.txt.sha1 | 1 + .../studies/PMCST000AAA_diagnosis.txt | 20 + .../studies/PMCST000AAA_diagnosis.txt.sha1 | 1 + .../PMCST000AAA_diagnosis_codebook.txt | 1 + .../PMCST000AAA_diagnosis_codebook.txt.sha1 | 1 + .../studies/PMCST000AAA_individual.txt | 18 + .../studies/PMCST000AAA_individual.txt.sha1 | 1 + .../PMCST000AAA_individual_codebook.txt | 1 + .../PMCST000AAA_individual_codebook.txt.sha1 | 1 + .../dropzone/studies/individual_study.txt | 18 + .../studies/individual_study.txt.sha1 | 1 + .../test_logic/dropzone/studies/study.txt | 3 + .../dropzone/studies/study.txt.sha1 | 1 + 29 files changed, 721 insertions(+) create mode 100644 test_data/test_logic/config/cbioportal_db_info/cancertypes.json create mode 100644 test_data/test_logic/config/cbioportal_db_info/genes.json create mode 100644 test_data/test_logic/config/cbioportal_db_info/genesaliases.json create mode 100644 test_data/test_logic/config/ontology_config.json create mode 100644 test_data/test_logic/config/sources_config.json create mode 100644 test_data/test_logic/dropzone/clinic/RDP-IC.tab create mode 100644 test_data/test_logic/dropzone/clinic/RDP-IC.tab.sha1 create mode 100644 test_data/test_logic/dropzone/clinic/RDP-Patient.tab create mode 100644 test_data/test_logic/dropzone/clinic/RDP-Patient.tab.sha1 create mode 100644 test_data/test_logic/dropzone/laboratory/biomaterial.txt create mode 100644 test_data/test_logic/dropzone/laboratory/biomaterial.txt.sha1 create mode 100644 test_data/test_logic/dropzone/laboratory/biosource.txt create mode 100644 test_data/test_logic/dropzone/laboratory/biosource.txt.sha1 create mode 100644 test_data/test_logic/dropzone/studies/PMCST000AAA_death.txt create mode 100644 test_data/test_logic/dropzone/studies/PMCST000AAA_death.txt.sha1 create mode 100644 test_data/test_logic/dropzone/studies/PMCST000AAA_death_codebook.txt create mode 100644 test_data/test_logic/dropzone/studies/PMCST000AAA_death_codebook.txt.sha1 create mode 100644 test_data/test_logic/dropzone/studies/PMCST000AAA_diagnosis.txt create mode 100644 test_data/test_logic/dropzone/studies/PMCST000AAA_diagnosis.txt.sha1 create mode 100644 test_data/test_logic/dropzone/studies/PMCST000AAA_diagnosis_codebook.txt create mode 100644 test_data/test_logic/dropzone/studies/PMCST000AAA_diagnosis_codebook.txt.sha1 create mode 100644 test_data/test_logic/dropzone/studies/PMCST000AAA_individual.txt create mode 100644 test_data/test_logic/dropzone/studies/PMCST000AAA_individual.txt.sha1 create mode 100644 test_data/test_logic/dropzone/studies/PMCST000AAA_individual_codebook.txt create mode 100644 test_data/test_logic/dropzone/studies/PMCST000AAA_individual_codebook.txt.sha1 create mode 100644 test_data/test_logic/dropzone/studies/individual_study.txt create mode 100644 test_data/test_logic/dropzone/studies/individual_study.txt.sha1 create mode 100644 test_data/test_logic/dropzone/studies/study.txt create mode 100644 test_data/test_logic/dropzone/studies/study.txt.sha1 diff --git a/test_data/test_logic/config/cbioportal_db_info/cancertypes.json b/test_data/test_logic/config/cbioportal_db_info/cancertypes.json new file mode 100644 index 0000000..742e9f4 --- /dev/null +++ b/test_data/test_logic/config/cbioportal_db_info/cancertypes.json @@ -0,0 +1 @@ +[{"id":"aastr","name":"Anaplastic Astrocytoma","color":"Gray"},{"id":"aca","name":"Adrenocortical Adenoma","color":"Purple"},{"id":"acbc","name":"Adenoid Cystic Breast Cancer","color":"HotPink"},{"id":"acc","name":"Adrenocortical Carcinoma","color":"Purple"},{"id":"accc","name":"Acinic Cell Carcinoma","color":"DarkRed"},{"id":"acn","name":"Acinar Cell Carcinoma, NOS","color":"Black"},{"id":"acpg","name":"Craniopharyngioma, Adamantinomatous Type","color":"Gray"},{"id":"acpp","name":"Atypical Choroid Plexus Papilloma","color":"Gray"},{"id":"acrm","name":"Acral Melanoma","color":"Black"},{"id":"acyc","name":"Adenoid Cystic Carcinoma","color":"DarkRed"},{"id":"adnos","name":"Adenocarcinoma, NOS","color":"Black"},{"id":"adpa","name":"Aggressive Digital Papillary Adenocarcinoma","color":"Black"},{"id":"adrenal_gland","name":"Adrenal Gland","color":"Purple"},{"id":"aeca","name":"Sweat Gland Carcinoma/Apocrine Eccrine Carcinoma","color":"Black"},{"id":"afx","name":"Atypical Fibroxanthoma","color":"Black"},{"id":"agng","name":"Anaplastic Ganglioglioma","color":"Gray"},{"id":"aitl","name":"Angioimmunoblastic T-Cell Lymphoma","color":"LimeGreen"},{"id":"alcl","name":"Anaplastic Large Cell Lymphoma","color":"LimeGreen"},{"id":"all","name":"Acute Lymphoid Leukemia","color":"LightSalmon"},{"id":"aluca","name":"Atypical Lung Carcinoid","color":"Gainsboro"},{"id":"ambl","name":"Large Cell/Anaplastic Medulloblastoma","color":"Gray"},{"id":"aml","name":"Acute Myeloid Leukemia","color":"LightSalmon"},{"id":"amol","name":"Acute Monocytic Leukemia","color":"LightSalmon"},{"id":"ampca","name":"Ampullary Carcinoma","color":"Purple"},{"id":"ampulla_of_vater","name":"Ampulla of Vater","color":"Purple"},{"id":"angl","name":"Angiocentric Glioma","color":"Gray"},{"id":"angs","name":"Angiosarcoma","color":"LightYellow"},{"id":"anm","name":"Anaplastic Meningioma","color":"Gray"},{"id":"ansc","name":"Anal Squamous Cell Carcinoma","color":"SaddleBrown"},{"id":"aoast","name":"Anaplastic Oligoastrocytoma","color":"Gray"},{"id":"aodg","name":"Anaplastic Oligodendroglioma","color":"Gray"},{"id":"apad","name":"Appendiceal Adenocarcinoma","color":"SaddleBrown"},{"id":"ape","name":"Anaplastic Ependymoma","color":"Gray"},{"id":"aptad","name":"Atypical Pituitary Adenoma","color":"Gray"},{"id":"armm","name":"Anorectal Mucosal Melanoma","color":"SaddleBrown"},{"id":"arms","name":"Alveolar Rhabdomyosarcoma","color":"LightYellow"},{"id":"asps","name":"Alveolar Soft Part Sarcoma","color":"LightYellow"},{"id":"astb","name":"Astroblastoma","color":"Gray"},{"id":"astr","name":"Astrocytoma","color":"Gray"},{"id":"atm","name":"Atypical Meningioma","color":"Gray"},{"id":"atrt","name":"Atypical Teratoid/Rhabdoid Tumor","color":"Gray"},{"id":"ball","name":"B-Cell Acute Lymphoid Leukemia","color":"LightSalmon"},{"id":"bcc","name":"Basal Cell Carcinoma","color":"Black"},{"id":"bcca","name":"Choriocarcinoma","color":"Gray"},{"id":"bcl","name":"B-Cell Lymphoma","color":"LimeGreen"},{"id":"bec","name":"Embryonal Carcinoma","color":"Gray"},{"id":"bgct","name":"Germ Cell Tumor, Brain","color":"Gray"},{"id":"biliary_tract","name":"Biliary Tract","color":"Green"},{"id":"bimt","name":"Immature Teratoma","color":"Gray"},{"id":"bl","name":"Burkitt Lymphoma","color":"LimeGreen"},{"id":"blad","name":"Bladder Adenocarcinoma","color":"Yellow"},{"id":"bladder","name":"Bladder/Urinary Tract","color":"Yellow"},{"id":"blca","name":"Bladder Urothelial Carcinoma","color":"Yellow"},{"id":"blclc","name":"Basaloid Large Cell Carcinoma of the Lung","color":"Gainsboro"},{"id":"blood","name":"Blood","color":"LightSalmon"},{"id":"blpt","name":"Borderline Phyllodes Tumor of the Breast","color":"HotPink"},{"id":"blsc","name":"Bladder Squamous Cell Carcinoma","color":"Yellow"},{"id":"bmgct","name":"Mixed Germ Cell Tumor","color":"Gray"},{"id":"bmgt","name":"Malignant Teratoma","color":"Gray"},{"id":"bmt","name":"Mature Teratoma","color":"Gray"},{"id":"bone","name":"Bone","color":"White"},{"id":"bowel","name":"Bowel","color":"SaddleBrown"},{"id":"bpdcn","name":"Blastic Plasmacytoid Dendritic Cell Neoplasm","color":"LightSalmon"},{"id":"bpscc","name":"Basaloid Penile Squamous Cell Carcinoma","color":"Blue"},{"id":"bpt","name":"Benign Phyllodes Tumor of the Breast","color":"HotPink"},{"id":"brain","name":"CNS/Brain","color":"Gray"},{"id":"brame","name":"Adenomyoepithelioma of the Breast","color":"HotPink"},{"id":"brca","name":"Invasive Breast Carcinoma","color":"HotPink"},{"id":"brca-es0","name":"Breast Invasive Carcinoma","color":"HotPink"},{"id":"brcanos","name":"Breast Invasive Cancer, 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\ No newline at end of file diff --git a/test_data/test_logic/config/ontology_config.json b/test_data/test_logic/config/ontology_config.json new file mode 100644 index 0000000..f6fc60a --- /dev/null +++ b/test_data/test_logic/config/ontology_config.json @@ -0,0 +1,162 @@ +{ + "nodes": [ + { + "name": "01. Patient information", + "children": [ + { + "name": "03. Gender", + "concept_code": "Individual.gender" + }, + { + "name": "01. Date of birth", + "concept_code": "Individual.birth_date" + }, + { + "name": "02. Taxonomy", + "concept_code": "Individual.taxonomy" + }, + { + "name": "04. Date of death", + "concept_code": "Individual.death_date" + }, + { + "name": "Informed_consent", + "children": [ + { + "name": "01. Informed consent type", + "concept_code": "Individual.ic_type" + }, + { + "name": "Informed consent version", + "concept_code": "Individual.ic_version" + }, + { + "name": "02. Date informed Consent given", + "concept_code": "Individual.ic_given_date" + }, + { + "name": "03. Date informed consent withdrawn", + "concept_code": "Individual.ic_withdrawn_date" + }, + { + "name": "04. Informed consent material", + "concept_code": "Individual.ic_material" + }, + { + "name": "05. Informed consent data", + "concept_code": "Individual.ic_data" + }, + { + "name": "06. Informed consent linking external database", + "concept_code": "Individual.ic_linking_ext" + }, + { + "name": "07. Report hereditary susceptibility", + "concept_code": "Individual.report_her_susc" + } + ] + } + ] + }, + { + "name": "02. Diagnosis information", + "children": [ + { + "name": "02. Tumor type", + "concept_code": "Diagnosis.tumor_type" + }, + { + "name": "03. Topography", + "concept_code": "Diagnosis.topography" + }, + { + "name": "Treatment", + "concept_code": "Diagnosis.treatment_protocol" + }, + { + "name": "04. Tumor stage", + "concept_code": "Diagnosis.tumor_stage" + }, + { + "name": "01. Date of diagnosis", + "concept_code": "Diagnosis.diagnosis_date" + }, + { + "name": "05. Center of treatment", + "concept_code": "Diagnosis.center_treatment" + } + ] + }, + { + "name": "03. Biosource information", + "children": [ + { + "name": "06. Biosource dedicated for specific study", + "concept_code": "Biosource.biosource_dedicated" + }, + { + "name": "01. Biosource parent", + "concept_code": "Biosource.src_biosource_id" + }, + { + "name": "03. Tissue", + "concept_code": "Biosource.tissue" + }, + { + "name": "02. Date of biosource", + "concept_code": "Biosource.biosource_date" + }, + { + "name": "04. Disease status", + "concept_code": "Biosource.disease_status" + }, + { + "name": "05. Tumor percentage", + "concept_code": "Biosource.tumor_percentage" + } + ] + }, + { + "name": "04. Biomaterial information", + "children": [ + { + "name": "01. Biomaterial parent", + "concept_code": "Biomaterial.src_biomaterial_id" + }, + { + "name": "02. Date of biomaterial", + "concept_code": "Biomaterial.biomaterial_date" + }, + { + "name": "03. Biomaterial type", + "concept_code": "Biomaterial.type" + } + ] + }, + { + "name": "05. Study information", + "children": [ + { + "name": "01. Study ID", + "concept_code": "Study.study_id" + }, + { + "name": "02. Study acronym", + "concept_code": "Study.acronym" + }, + { + "name": "03. Study title", + "concept_code": "Study.title" + }, + { + "name": "Study datadictionary", + "concept_code": "Study.datadictionary" + }, + { + "name": "04. Individual Study ID", + "concept_code": "IndividualStudy.individual_study_id" + } + ] + } + ] +} diff --git a/test_data/test_logic/config/sources_config.json b/test_data/test_logic/config/sources_config.json new file mode 100644 index 0000000..10f4755 --- /dev/null +++ b/test_data/test_logic/config/sources_config.json @@ -0,0 +1,422 @@ +{ + "entities": { + "Individual": { + "attributes": [ + { + "name": "individual_id", + "sources": [ + { + "file": "clinic/RDP-Patient.tab", + "column": "INDIVIDUAL_ID" + }, + { + "file": "clinic/RDP-IC.tab", + "column": "INDIVIDUAL_ID" + }, + { + "file": "studies/PMCST000AAA_individual.txt", + "column": "INDIVIDUAL_ID" + }, + { + "file": "studies/PMCST000AAA_death.txt", + "column": "INDIVIDUAL_ID" + } + ] + }, + { + "name": "birth_date", + "sources": [ + { + "file": "clinic/RDP-Patient.tab", + "column": "Gebdat", + "date_format": "%d%b%Y" + }, + { + "file": "studies/PMCST000AAA_individual.txt", + "column": "DTOB", + "date_format": "%d/%m/%Y %H:%M:%S" + } + ] + }, + { + "name": "gender", + "sources": [ + { + "file": "clinic/RDP-Patient.tab", + "column": "Geslacht" + }, + { + "file": "studies/PMCST000AAA_individual.txt", + "column": "SEX" + } + ] + }, + { + "name": "death_date", + "sources": [ + { + "file": "clinic/RDP-Patient.tab", + "column": "Overldat", + "date_format": "%d%b%Y" + }, + { + "file": "studies/PMCST000AAA_death.txt", + "column": "DTDEATH", + "date_format": "%d/%m/%Y %H:%M:%S" + } + ] + }, + { + "name": "ic_type", + "sources": [ + { + "file": "clinic/RDP-IC.tab", + "column": "00004_Toestemmingsstatus" + }, + { + "file": "studies/PMCST000AAA_individual.txt", + "column": "IFCDATR" + } + ] + }, + { + "name": "ic_given_date", + "sources": [ + { + "file": "clinic/RDP-IC.tab", + "column": "00007_Datum toestemming", + "date_format": "%d/%m/%Y" + } + ] + }, + { + "name": "ic_withdrawn_date", + "sources": [ + { + "file": "clinic/RDP-IC.tab", + "column": "00010_Datum geen toestemming", + "date_format": "%d/%m/%Y" + } + ] + }, + { + "name": "report_her_susc", + "sources": [ + { + "file": "clinic/RDP-IC.tab", + "column": "00012_Datum einde deelname", + "date_format": "%d/%m/%Y" + } + ] + }, + { + "name": "ic_material", + "sources": [ + { + "file": "studies/PMCST000AAA_individual.txt", + "column": "IFCMAT" + } + ] + }, + { + "name": "ic_data", + "sources": [ + { + "file": "studies/PMCST000AAA_individual.txt", + "column": "IFCGIV" + } + ] + }, + { + "name": "ic_linking_ext", + "sources": [ + { + "file": "studies/PMCST000AAA_individual.txt", + "column": "IFCCOM" + } + ] + } + ] + }, + "Diagnosis": { + "attributes": [ + { + "name": "individual_id", + "sources": [ + { + "file": "studies/PMCST000AAA_diagnosis.txt", + "column": "INDIVIDUAL_ID" + } + ] + }, + { + "name": "diagnosis_id", + "sources": [ + { + "file": "studies/PMCST000AAA_diagnosis.txt", + "column": "CIDDIAG" + } + ] + }, + { + "name": "tumor_type", + "sources": [ + { + "file": "studies/PMCST000AAA_diagnosis.txt", + "column": "DIAGCD" + } + ] + }, + { + "name": "topography", + "sources": [ + { + "file": "studies/PMCST000AAA_diagnosis.txt", + "column": "PLOCCD" + } + ] + }, + { + "name": "tumor_stage", + "sources": [ + { + "file": "studies/PMCST000AAA_diagnosis.txt", + "column": "DIAGGRSTX" + } + ] + }, + { + "name": "diagnosis_date", + "sources": [ + { + "file": "studies/PMCST000AAA_diagnosis.txt", + "column": "IDAABA", + "date_format": "%d/%m/%Y %H:%M:%S" + } + ] + }, + { + "name": "center_treatment", + "sources": [ + { + "file": "studies/PMCST000AAA_diagnosis.txt", + "column": "HOSPDIAG" + } + ] + } + ] + }, + "Biosource": { + "attributes": [ + { + "name": "biosource_id", + "sources": [ + { + "file": "laboratory/biosource.txt" + } + ] + }, + { + "name": "individual_id", + "sources": [ + { + "file": "laboratory/biosource.txt" + } + ] + }, + { + "name": "diagnosis_id", + "sources": [ + { + "file": "laboratory/biosource.txt" + } + ] + }, + { + "name": "src_biosource_id", + "sources": [ + { + "file": "laboratory/biosource.txt" + } + ] + }, + { + "name": "biosource_dedicated", + "sources": [ + { + "file": "laboratory/biosource.txt" + } + ] + }, + { + "name": "tissue", + "sources": [ + { + "file": "laboratory/biosource.txt" + } + ] + }, + { + "name": "biosource_date", + "sources": [ + { + "file": "laboratory/biosource.txt", + "date_format": "%d/%m/%Y" + } + ] + }, + { + "name": "disease_status", + "sources": [ + { + "file": "laboratory/biosource.txt" + } + ] + }, + { + "name": "tumor_percentage", + "sources": [ + { + "file": "laboratory/biosource.txt" + } + ] + } + ] + }, + "Biomaterial": { + "attributes": [ + { + "name": "biomaterial_id", + "sources": [ + { + "file": "laboratory/biomaterial.txt" + } + ] + }, + { + "name": "src_biosource_id", + "sources": [ + { + "file": "laboratory/biomaterial.txt" + } + ] + }, + { + "name": "src_biomaterial_id", + "sources": [ + { + "file": "laboratory/biomaterial.txt" + } + ] + }, + { + "name": "biomaterial_date", + "sources": [ + { + "file": "laboratory/biomaterial.txt", + "date_format": "%d/%m/%Y" + } + ] + }, + { + "name": "type", + "sources": [ + { + "file": "laboratory/biomaterial.txt" + } + ] + } + ] + }, + "Study": { + "attributes": [ + { + "name": "study_id", + "sources": [ + { + "file": "studies/study.txt", + "column": "STUDY_ID" + } + ] + }, + { + "name": "acronym", + "sources": [ + { + "file": "studies/study.txt" + } + ] + }, + { + "name": "title", + "sources": [ + { + "file": "studies/study.txt" + } + ] + }, + { + "name": "datadictionary", + "sources": [ + { + "file": "studies/study.txt" + } + ] + } + ] + }, + "IndividualStudy": { + "attributes": [ + { + "name": "individual_study_id", + "sources": [ + { + "file": "studies/individual_study.txt", + "column": "INDIVIDUAL_STUDY_ID" + } + ] + }, + { + "name": "individual_id", + "sources": [ + { + "file": "studies/individual_study.txt", + "column": "INDIVIDUAL_ID" + } + ] + }, + { + "name": "study_id", + "sources": [ + { + "file": "studies/individual_study.txt", + "column": "STUDY_ID" + } + ] + } + ] + } + }, + "codebooks": { + "studies/PMCST000AAA_individual.txt": "studies/PMCST000AAA_individual_codebook.txt", + "studies/PMCST000AAA_diagnosis.txt": "studies/PMCST000AAA_diagnosis_codebook.txt", + "studies/PMCST000AAA_death.txt": "studies/PMCST000AAA_death_codebook.txt" + }, + "file_format": { + "studies/PMCST000AAA_individual.txt": { + "delimiter": "," + }, + "studies/PMCST000AAA_diagnosis.txt": { + "delimiter": "," + }, + "studies/PMCST000AAA_death.txt": { + "delimiter": "," + }, + "studies/study.txt": { + "delimiter": "," + }, + "studies/individual_study.txt": { + "delimiter": "," + } + } +} diff --git a/test_data/test_logic/dropzone/clinic/RDP-IC.tab b/test_data/test_logic/dropzone/clinic/RDP-IC.tab new file mode 100644 index 0000000..eac36c0 --- /dev/null +++ b/test_data/test_logic/dropzone/clinic/RDP-IC.tab @@ -0,0 +1,7 @@ +INDIVIDUAL_ID 00004_Toestemmingsstatus 00007_Datum toestemming 00010_Datum geen toestemming 00012_Datum einde deelname +PAT1 expliciete toestemming 24/04/2018 +PAT13 mogelijke kandidaat +PAT14 geen toestemming 28/11/2017 +PAT15 proefpersoon informatie uitgereikt maar nog geen toestemming ontvangen +PAT16 geïnformeerd door studieteam +PAT17 mogelijke kandidaat diff --git a/test_data/test_logic/dropzone/clinic/RDP-IC.tab.sha1 b/test_data/test_logic/dropzone/clinic/RDP-IC.tab.sha1 new file mode 100644 index 0000000..a616f62 --- /dev/null +++ b/test_data/test_logic/dropzone/clinic/RDP-IC.tab.sha1 @@ -0,0 +1 @@ +f84346dff7e4fae2e720b118d1f4cd846a4ec5d3 RDP-IC.tab diff --git a/test_data/test_logic/dropzone/clinic/RDP-Patient.tab b/test_data/test_logic/dropzone/clinic/RDP-Patient.tab new file mode 100644 index 0000000..f7893f0 --- /dev/null +++ b/test_data/test_logic/dropzone/clinic/RDP-Patient.tab @@ -0,0 +1,7 @@ +INDIVIDUAL_ID Gebdat Geslacht Overleden Overldat +PAT1 15AUG2000 M 0 +PAT2 18FEB1989 M 0 +PAT3 07NOV2001 M 0 +PAT15 08JAN1999 V 0 +PAT16 25DEC1997 V 0 +PAT17 29SEP1991 V 0 diff --git a/test_data/test_logic/dropzone/clinic/RDP-Patient.tab.sha1 b/test_data/test_logic/dropzone/clinic/RDP-Patient.tab.sha1 new file mode 100644 index 0000000..22e83aa --- /dev/null +++ b/test_data/test_logic/dropzone/clinic/RDP-Patient.tab.sha1 @@ -0,0 +1 @@ +67082ab768b32dfc28c0d9d665d646f4f355140f RDP-Patient.tab diff --git a/test_data/test_logic/dropzone/laboratory/biomaterial.txt b/test_data/test_logic/dropzone/laboratory/biomaterial.txt new file mode 100644 index 0000000..5ed6131 --- /dev/null +++ b/test_data/test_logic/dropzone/laboratory/biomaterial.txt @@ -0,0 +1,22 @@ +biomaterial_id biomaterial_date type src_biosource_id src_biomaterial_id description label +BIOM1 07/03/2018 genomic DNA BIOS1 genomic DNA isolated from 1222TI 1222TI_DNA +BIOM2 05/06/2011 genomic DNA BIOS2 neuroblastoma DNA NBL_DNA +BIOM3 05/06/2011 mRNA BIOS3 neuroblastoma DNA NBL_DNA +BIOM4 07/03/2018 mRNA BIOS4 genomic DNA isolated from 1222TI 1222TI_DNA +BIOM5 05/06/2011 mRNA BIOS5 neuroblastoma DNA NBL_DNA +BIOM6 05/06/2011 mRNA DNA BIOS6 neuroblastoma DNA NBL_DNA +BIOM7 07/03/2018 mRNA DNA BIOS7 genomic DNA isolated from 1222TI 1222TI_DNA +BIOM8 05/06/2011 mRNA DNA BIOS8 neuroblastoma DNA NBL_DNA +BIOM9 05/06/2011 genomic DNA BIOS9 neuroblastoma DNA NBL_DNA +BIOM10 07/03/2018 genomic DNA BIOS10 genomic DNA isolated from 1222TI 1222TI_DNA +BIOM11 05/06/2011 genomic DNA BIOS11 neuroblastoma DNA NBL_DNA +BIOM12 05/06/2011 genomic DNA BIOS12 neuroblastoma DNA NBL_DNA +BIOM13 07/03/2018 mRNA BIOS13 genomic DNA isolated from 1222TI 1222TI_DNA +BIOM14 05/06/2011 mRNA BIOS14 neuroblastoma DNA NBL_DNA +BIOM15 05/06/2011 genomic DNA BIOS15 neuroblastoma DNA NBL_DNA +BIOM16 07/03/2018 genomic DNA BIOS16 genomic DNA isolated from 1222TI 1222TI_DNA +BIOM17 05/06/2011 genomic DNA BIOS17 neuroblastoma DNA NBL_DNA +BIOM18 05/06/2011 mRNA BIOS18 neuroblastoma DNA NBL_DNA +BIOM19 07/03/2018 mRNA BIOS19 genomic DNA isolated from 1222TI 1222TI_DNA +BIOM20 05/06/2011 mRNA BIOS11 BIOM11 neuroblastoma DNA NBL_DNA +BIOM21 05/06/2011 genomic DNA BIOS12 BIOM12 neuroblastoma DNA NBL_DNA diff --git a/test_data/test_logic/dropzone/laboratory/biomaterial.txt.sha1 b/test_data/test_logic/dropzone/laboratory/biomaterial.txt.sha1 new file mode 100644 index 0000000..de247b6 --- /dev/null +++ b/test_data/test_logic/dropzone/laboratory/biomaterial.txt.sha1 @@ -0,0 +1 @@ +f15c2071e6a478d8e227264029fd563dbe7027a2 biomaterial.txt diff --git a/test_data/test_logic/dropzone/laboratory/biosource.txt b/test_data/test_logic/dropzone/laboratory/biosource.txt new file mode 100644 index 0000000..fff2811 --- /dev/null +++ b/test_data/test_logic/dropzone/laboratory/biosource.txt @@ -0,0 +1,20 @@ +biosource_id biosource_dedicated tissue biosource_date disease_status individual_id diagnosis_id src_biosource_id tumor_percentage label description +BIOS1 no eye 25/01/2018 primary tumor PAT1 DIA1 0 NBL_normal tumor surrounding normal nerve tissue +BIOS2 no nerve 24/01/2018 primary tumor PAT2 DIA2 5 NBL neuroblastoma +BIOS3 yes eye 24/01/2018 unaffected PAT3 DIA3 5 NBL neuroblastoma +BIOS4 yes nerve 25/01/2018 primary tumor PAT4 DIA4 0 NBL_normal tumor surrounding normal nerve tissue +BIOS5 yes eye 24/01/2018 primary tumor PAT5 DIA5 5 NBL neuroblastoma +BIOS6 yes nerve 24/01/2018 unaffected PAT6 DIA6 5 NBL neuroblastoma +BIOS7 yes eye 25/01/2018 primary tumor PAT7 DIA7 0 NBL_normal tumor surrounding normal nerve tissue +BIOS8 yes nerve 24/01/2018 primary tumor PAT8 DIA8 5 NBL neuroblastoma +BIOS9 no eye 24/01/2018 unaffected PAT9 DIA9 5 NBL neuroblastoma +BIOS10 yes eye 25/01/2018 primary tumor PAT10 DIA10 0 NBL_normal tumor surrounding normal nerve tissue +BIOS11 yes eye 24/01/2018 primary tumor PAT11 DIA11 5 NBL neuroblastoma +BIOS12 yes eye 24/01/2018 unaffected PAT12 DIA12 5 NBL neuroblastoma +BIOS13 yes nerve 25/01/2018 primary tumor PAT13 DIA13 0 NBL_normal tumor surrounding normal nerve tissue +BIOS14 yes nerve 24/01/2018 primary tumor PAT14 DIA14 5 NBL neuroblastoma +BIOS15 no nerve 24/01/2018 unaffected PAT15 DIA15 5 NBL neuroblastoma +BIOS16 no nerve 25/01/2018 primary tumor PAT16 DIA16 0 NBL_normal tumor surrounding normal nerve tissue +BIOS17 yes nerve 24/01/2018 primary tumor PAT17 DIA17 5 NBL neuroblastoma +BIOS18 yes nerve 25/01/2018 primary tumor PAT1 DIA18 BIOS1 10 NBL_normal tumor surrounding normal nerve tissue +BIOS19 no nerve 24/01/2018 primary tumor PAT2 DIA19 BIOS2 15 NBL neuroblastoma diff --git a/test_data/test_logic/dropzone/laboratory/biosource.txt.sha1 b/test_data/test_logic/dropzone/laboratory/biosource.txt.sha1 new file mode 100644 index 0000000..9ba7118 --- /dev/null +++ b/test_data/test_logic/dropzone/laboratory/biosource.txt.sha1 @@ -0,0 +1 @@ +554be16054dc041fe0e482ddd214b1b36bab7c92 biosource.txt diff --git a/test_data/test_logic/dropzone/studies/PMCST000AAA_death.txt b/test_data/test_logic/dropzone/studies/PMCST000AAA_death.txt new file mode 100644 index 0000000..92e457e --- /dev/null +++ b/test_data/test_logic/dropzone/studies/PMCST000AAA_death.txt @@ -0,0 +1,4 @@ +"MARK:","ID","IDAA","INDIVIDUAL_ID","STATUSA","IDAABB","DTDEATH" +,217,8000217,PAT10,1,07/03/2017 0:00:00,10/08/2016 0:00:00 +,217,8000238,PAT11,1,15/01/2016 0:00:00,06/07/2015 0:00:00 +,217,8000251,PAT12,1,24/02/2016 0:00:00,07/09/2015 0:00:00 diff --git a/test_data/test_logic/dropzone/studies/PMCST000AAA_death.txt.sha1 b/test_data/test_logic/dropzone/studies/PMCST000AAA_death.txt.sha1 new file mode 100644 index 0000000..65d0d74 --- /dev/null +++ b/test_data/test_logic/dropzone/studies/PMCST000AAA_death.txt.sha1 @@ -0,0 +1 @@ +b886a68f4d69de8dd1e76739af4fa3c688520f8e PMCST000AAA_death.txt diff --git a/test_data/test_logic/dropzone/studies/PMCST000AAA_death_codebook.txt b/test_data/test_logic/dropzone/studies/PMCST000AAA_death_codebook.txt new file mode 100644 index 0000000..9d23109 --- /dev/null +++ b/test_data/test_logic/dropzone/studies/PMCST000AAA_death_codebook.txt @@ -0,0 +1 @@ +1 SEX 1 male 2 female 9 unknown 2 SIGYN IFCGIV IFCMAT IFCCOM IFCREF NOREGIS CLEXPYN CYTOLYN HISTOYN IMAGEYN TMARKYN PATDCOGR PROTYN ELIGYN TXSTART SIGYNX SIGYNY 1 yes 2 no 8 not applicable 8 HOSPREC HOSPDIAG HOSPASS HOSPTRAN 200 AMC 201 UMCG 202 AZM 203 CZE 204 ErasmusMC 207 JBZ 208 LUMC 213 EZT 214 Radboudumc 216 VUMC 217 UMCU 220 PMC 332 DIAGCD PDGCD1 PDGCD2 PDGCD3 61000 FanconiÔs anaemia 61900 Aplastic anaemia 70000 KostmannÔs disease 76100 HLH 80000 "Neoplasm, benign" 80001 "Neoplasm, uncertain whether benign or malignant" 80003 "Neoplasm, malignant" 80010 "Tumor cells, benign" 80011 "Tumor cells, uncertain whether benign or mal..." 80013 "Tumor cells, malignant" 80023 "Malignant tumor, small cell type" 80033 "Malignant tumor, giant cell type" 80043 "Malignant tumor, spindle cell type" 80050 "Clear cell tumor, NOS" 80053 "Malignant tumor, clear cell type" 80100 "Epithelial tumor, benign" 80102 "Carcinoma in situ, NOS" 80103 "Carcinoma, NOS" 80113 "Epithelioma, malignant" 80123 "Large cell carcinoma, NOS" 80133 Large cell neuroendocrine carcinoma 80143 Large cell carcinoma with rhabdoid phenotype 80153 Glassy cell carcinoma 80203 "Carcinoma, undifferentiated type, NOS" 80213 "Carcinoma, anaplastic type, NOS" 80223 Pleomorphic carcinoma 80303 Giant cell and spindle cell carcinoma 80313 Giant cell carcinoma 80323 Spindle cell carcinoma 80333 Pseudosarcomatous carcinoma 80343 Polygonal cell carcinoma 80353 Carcinoma with osteoclast-like giant cells 80413 "Small cell carcinoma, NOS" 80423 Oat cell carcinoma 80433 "Small cell carcinoma, fusiform cell" 80443 "Small cell carcinoma, intermediate cell" 80453 Combined small cell carcinoma 80463 Non-small cell carcinoma 80502 Papillary carcinoma in situ 80503 "Papillary carcinoma, NOS" 80513 "Verrucous carcinoma, NOS" 80522 "Papillary squamous cell carcinoma, non-invasive" 80523 Papillary squamous cell carcinoma 80702 "Squamous cell carcinoma in situ, NOS" 80703 "Squamous cell carcinoma, NOS" 80713 "Sq. cell carcinoma, keratinizing, NOS" 80723 "Sq. cell carcinoma, lg. cell, non-ker." 80733 "Sq. cell carcinoma, sm. cell, non-ker." 80743 "Sq. cell carcinoma, spindle cell" 80753 "Squamous cell carcinoma, adenoid" 80762 Sq. cell carc. in situ with question. stroma... 80763 "Sq. cell carcinoma, micro-invasive" 80770 "Squamous intraepithelial neoplasia, low grade" 80772 "Squamous intraepithelial neoplasia, high grade" 80783 Squamous cell carcinoma with horn formation 80802 Queyrat erythroplasia 80812 Bowen disease 80823 Lymphoepithelial carcinoma 80833 Basaloid squamous cell carcinoma 80843 "Squamous cell carcinoma, clear cell type" 80903 "Basal cell carcinoma, NOS" 80913 Multifocal superficial basal cell carcinoma 80923 "Infiltrating basal cell carcinoma, NOS" 80933 "Basal cell carcinoma, fibroepithelial" 80943 Basosquamous carcinoma 80953 Metatypical carcinoma 80973 "Basal cell carcinoma, nodular" 80983 Adenoid basal cell carcinoma 81023 Trichilemmocarcinoma 81103 Pilomatrix carcinoma 81202 Transitional cell carcinoma in situ 81203 "Transitional cell carcinoma, NOS" 81213 Schneiderian carcinoma 81223 "Trans. cell carcinoma, spindle cell" 81233 Basaloid carcinoma 81243 Cloacogenic carcinoma 81302 "Papillary trans. cell carcinoma, non-invasive" 81303 Papillary trans. cell carcinoma 81313 "Transitional cell carcinoma, micropapillary" 81400 "Adenoma, NOS" 81402 Adenocarcinoma in situ 81403 "Adenocarcinoma, NOS" 81413 Scirrhous adenocarcinoma 81423 Linitis plastica 81433 Superficial spreading adenocarcinoma 81443 "Adenocarcinoma, intestinal type" 81453 "Carcinoma, diffuse type" 81460 Monomorphic adenoma 81473 Basal cell adenocarcinoma 81480 "Glandular intraepithelial neoplasia, low grade" 81482 "Glandular intraepithelial neoplasia, high grade" 81500 "Pancreatic endocrine tumor, benign" 81501 "Pancreatic endocrine tumor, NOS" 81503 "Pancreatic endocrine tumor, malignant" 81513 "Insulinoma, malignant" 81523 "Glucagonoma, malignant" 81533 "Gastrinoma, malignant" 81543 "Mix. pancreatic endocrine&exocrine tumor, mal" 81553 Vipoma 81563 "Somatostatinoma, malignant" 81573 "Enteroglucagonoma, malignant" 81581 "Endocrine tumor, functioning, NOS" 81603 Cholangiocarcinoma 81613 Bile duct cystadenocarcinoma 81623 Klatskin tumor 81630 "Pancreatobiliary neoplasm, non-invasive" 81632 "Pap. neoplasm,pancreatobiliary-type,high gr. int" 81633 Pancreatobiliary-type carcinoma 81703 "Hepatocellular carcinoma, NOS" 81713 "Hepatocellular carcinoma, fibrolamellar" 81723 "Hepatocellular carcinoma, scirrhous" 81733 "Hepatocellular carcinoma, spindle cell variant" 81743 "Hepatocellular carcinoma, clear cell type" 81753 "Hepatocellular carcinoma, pleomorphic type" 81803 Comb. hepatocel. carcinoma & cholangiocarcinoma 81903 Trabecular adenocarcinoma 82003 Adenoid cystic carcinoma 82012 Cribriform carcinoma in situ 82013 Cribriform carcinoma 82102 Adenocarcinoma in situ in adenomatous polyp 82103 Adenocarcinoma in adenomatous polyp 82113 Tubular adenocarcinoma 82133 Serrated adenocarcinoma 82143 Parietal cell carcinoma 82153 Adenocarcinoma of anal glands 82202 Adenocarcinoma in situ in familial polyp. coli 82203 Adenocarcinoma in adenoma. polyposis coli 82212 Adenocarc. in situ in mult. adenomatous polyps 82213 Adenocarcinoma in mult. adenomatous polyps 82302 "Duct carcinoma in situ, solid type" 82303 "Solid carcinoma, NOS" 82313 Carcinoma simplex 82401 Carcinoid tumor of uncertain malignant potential 82403 "Carcinoid tumor, malignant" 82413 Enterochromaffin cell carcinoid 82423 "Enterochromaffin-like cell tumor, malignant" 82433 Goblet cell carcinoid 82443 Mixed adenoneuroendocrine carcinoma 82453 Adenocarcinoid tumor 82463 Neuroendocrine carcinoma 82473 Merkel cell carcinoma 82493 Atypical carcinoid tumor 82503 Bronchiolo-alveolar adenocarcinoma 82513 Alveolar adenocarcinoma 82523 "Bronchiolo-alveolar carcinoma, non-mucinous" 82533 "Bronchiolo-alveolar carcinoma, mucinous" 82543 "Bronch.-alv. carc., mixed mucin. and non-muc..." 82553 Adenocarcinoma with mixed subtypes 82600 "Papillary adenoma, NOS" 82603 "Papillary adenocarcinoma, NOS" 82612 Adenocarcinoma in situ in villous adenoma 82613 Adenocarcinoma in villous adenoma 82623 Villous adenocarcinoma 82632 Adenocarcinoma in situ in tubulovillous adenoma 82633 Adenocarcinoma in tubulovillous adenoma 82653 "Micropapillary carcinoma, NOS" 82700 Chromophobe adenoma 82703 Chromophobe carcinoma 82710 Prolactinoma 82720 "Pituitary adenoma, NOS" 82723 "Pituitary carcinoma, NOS" 82800 Acidophil adenoma 82803 Acidophil carcinoma 82810 Mixed acidophil-basophil adenoma 82813 Mixed acidophil-basophil carcinoma 82900 Oxyphilic adenoma 82903 Oxyphilic adenocarcinoma 83000 Basophil adenoma 83003 Basophil carcinoma 83100 Clear cell adenoma 83103 "Clear cell adenocarcinoma, NOS" 83123 Renal cell carcinoma 83133 Clear cell adenocarcinofibroma 83143 Lipid-rich carcinoma 83153 Glycogen-rich carcinoma 83163 Cyst-associated renal cell carcinoma 83173 "Renal cell carcinoma, chromophobe type" 83183 "Renal cell carcinoma, sarcomatoid" 83193 Collecting duct carcinoma 83203 Granular cell carcinoma 83223 Water-clear cell adenocarcinoma 83230 Mixed cell adenoma 83233 Mixed cell adenocarcinoma 83303 "Follicular adenocarcinoma, NOS" 83313 Follicular adenocarcinoma well diff. 83323 Follicular adenocarcinoma trabecular 83333 Fetal adenocarcinoma 83353 "Follicular carcinoma, minimally invasive" 83373 Insular carcinoma 83403 "Papillary carcinoma, follicular variant" 83413 Papillary microcarcinoma 83423 "Papillary carcinoma, oxyphilic cell" 83433 "Papillary carcinoma, encapsulated" 83443 "Papillary carcinoma, columnar cell" 83453 Medullary carcinoma with amyloid stroma 83463 Mixed medullary-follicular carcinoma 83473 Mixed medullary-papillary carcinoma 83503 Nonencapsulated sclerosing carcinoma 83700 "Adrenal cortical adenoma, NOS" 83703 Adrenal cortical carcinoma 83803 Endometrioid carcinoma 83813 "Endometrioid adenofibroma, malignant" 83823 "Endometrioid adenocarcinoma, secretory variant" 83833 "Endometrioid adenocarcinoma, ciliated cell v..." 83843 "Adenocarcinoma, endocervical type" 83903 Skin appendage carcinoma 84003 Sweat gland adenocarcinoma 84013 Apocrine adenocarcinoma 84023 "Nodular hidradenoma, malignant" 84033 Malignant eccrine spiradenoma 84073 Sclerosing sweat duct carcinoma 84083 Eccrine papillary adenocarcinoma 84093 "Eccrine poroma, malignant" 84103 Sebaceous adenocarcinoma 84133 Eccrine adenocarcinoma 84203 Ceruminous adenocarcinoma 84303 Mucoepidermoid carcinoma 84403 "Cystadenocarcinoma, NOS" 84413 "Serous cystadenocarcinoma, NOS" 84421 "Serous cystadenoma, borderline malignancy (C..." 84503 "Papillary cystadenocarcinoma, NOS" 84511 "Papillary cystadenoma, borderline malignancy..." 84523 Solid pseudopapillary carcinoma 84532 "Intraductal papillary-mucinous carcinoma, no..." 84533 "Intraductal papillary-mucinous carcinoma, in..." 84603 Papillary serous cystadenocarcinoma 84613 Serous surface papillary carcinoma 84621 Serous papillary cystic tumor of borderline ... 84702 "Mucinous cystadenocarcinoma, non-invasive" 84703 "Mucinous cystadenocarcinoma, NOS" 84713 Papillary mucinous cystadenocarcinoma 84721 Mucinous cystic tumor of borderline malignan... 84731 "Papillary mucinous cystadenoma, borderline m..." 84803 Mucinous adenocarcinoma 84813 Mucin-producing adenocarcinoma 84823 "Mucinous adenocarcinoma, endocervical type" 84903 Signet ring cell carcinoma 85002 "Intraductal carcinoma, noninfiltrating, NOS" 85003 "Infiltrating duct carcinoma, NOS" 85012 "Comedocarcinoma, non-infiltrating" 85013 "Comedocarcinoma, NOS" 85023 Secretory carcinoma of breast 85032 Noninfiltrating intraductal papillary adenoc... 85033 Intraductal papillary adenocarcinoma with in... 85042 Noninfiltrating intracystic carcinoma 85043 "Intracystic carcinoma, NOS" 85072 Intraductal micropapillary carcinoma 85083 Cystic hypersecretory carcinoma 85103 "Medullary carcinoma, NOS" 85123 Medullary carcinoma with lymphoid stroma 85133 Atypical medullary carcinoma 85143 "Duct carcinoma, desmoplastic type" 85202 Lobular carcinoma in situ 85203 "Lobular carcinoma, NOS" 85213 Infiltrating ductular carcinoma 85222 Intraductal and lobular in situ carcinoma 85223 Infiltrating duct and lobular carcinoma 85233 Infiltr. duct mixed with other types of carc... 85243 Infiltrating lobular mixed with other types ... 85253 Polymorphous low grade adenocarcinoma 85303 Inflammatory carcinoma 85403 "Paget disease, mammary" 85413 Paget dis. & infil. duct carcinoma 85423 "Paget disease, extramammary" 85433 Paget disease and intraductal ca. 85503 Acinar cell carcinoma 85513 Acinar cell cystadenocarcinoma 85603 Adenosquamous carcinoma 85613 "Warthin tumor, malignant" 85623 Epithelial-myoepithelial carcinoma 85703 Adenocarcinoma with squamous metaplasia 85713 Adenocarcinoma w cartilag. & oss. metaplas. 85723 Adenocarcinoma with spindle cell mataplasia 85733 Adenocarcinoma with apocrine metaplasia 85743 Adenocarcinoma with neuroendocrine differen. 85753 "Metaplastic carcinoma, NOS" 85763 Hepatoid adenocarcinoma 85803 "Thymoma, malignant, NOS" 85813 "Thymoma, type A, malignant" 85823 "Thymoma, type AB, malignant" 85833 "Thymoma, type B1, malignant" 85843 "Thymoma, type B2, malignant" 85853 "Thymoma, type B3, malignant" 85863 "Thymic carcinoma, NOS" 85883 Spindle epithelial tumor with thymus-like el... 85893 Carcinoma showing thymus-like element 85903 "Ovarian stromal tumor, mal." 86003 "Thecoma, malignant" 86201 "Granulosa cell tumor, adult type" 86203 "Granulosa cell tumor, malignant" 86211 Granulosa cell-theca cell tumor 86221 "Granulosa cell tumor, juvenile" 86303 "Androblastoma, malignant" 86311 Sertoli-Leydig cell tumor of intermediate differ 86313 "Sertoli-Leydig cell tumor, poorly differenti..." 86323 "Gynandroblastoma, malignant" 86343 "Sertoli-Leydig cl tum., p.d. w heterologous ..." 86401 "Sertoli cell tumor, NOS" 86403 Sertoli cell carcinoma 86501 "Leydig cell tumor, NOS" 86503 "Leydig cell tumor, malignant" 86703 "Steroid cell tumor, malignant" 86801 "Paraganglioma, NOS" 86803 "Paraganglioma, malignant" 86913 "Aortic body tumor, malignant" 86923 "Carotid body tumor, malignant" 86933 "Extra-adrenal paraganglioma, malignant" 87000 Pheochromocytoma NOS 87003 Pheochromocytoma 87103 Glomangiosarcoma 87202 Melanoma in situ 87203 "Malignant melanoma, NOS" 87213 Nodular melanoma 87223 Balloon cell melanoma 87233 "Malignant melanoma, regressing" 87280 Diffuse melanocytosis 87281 Meningeal melanocytoma 87283 Meningeal melanomatosis 87303 Amelanotic melanoma 87403 Mal. melanoma in junctional nevus 87412 "Precancerous melanosis, NOS" 87413 Mal. melanoma in precan. melanosis 87422 Lentigo maligna 87423 Lentigo maligna melanoma 87433 Superficial spreading melanoma 87443 "Acral lentiginous melanoma, malig." 87453 "Desmoplastic melanoma, malignant" 87463 Mucosal lentiginous melanoma 87613 Mal. melanoma in giant pigmented nevus 87703 Mixed epithel. & spindle cell melanoma 87713 Epithelioid cell melanoma 87723 "Spindle cell melanoma, NOS" 87733 "Spindle cell melanoma, type A" 87743 "Spindle cell melanoma, type B" 87803 "Blue nevus, malignant" 88000 "Soft tissue tumor, benign" 88003 "Sarcoma, NOS" 88013 Spindle cell sarcoma 88023 Giant cell sarcoma 88033 Small cell sarcoma 88043 Epithelioid sarcoma 88053 Undifferentiated sarcoma 88063 Desmoplastic small round cell tumor 88100 "Fibroma, NOS" 88103 "Fibrosarcoma, NOS" 88113 Fibromyxosarcoma 88123 Periosteal fibrosarcoma 88133 Fascial fibrosarcoma 88143 Infantile fibrosarcoma 88150 Solitary fibrous tumor 88153 "Solitary fibrous tumor, malignant" 88211 "Fibromatosis, aggressive" 88240 Myofibroma 88241 Myofibromatosis 88251 "Myofibroblastic tumor, NOS" 88300 "Fibrous histiocytoma, benign" 88303 "Fibrous histiocytoma, malignant" 88323 "Dermatofibrosarcoma, NOS" 88333 Pigmented dermatofibrosarcoma protuberans 88341 Giant cell fibroblastoma 88351 Plexiform fibrohistiocytic tumor 88361 Angiomatoid fibrous histiocytoma 88403 Myxosarcoma 88411 Angiomyxoma 88500 "Lipoma, NOS" 88501 Atypical lipoma 88503 "Liposarcoma, NOS" 88510 Fibrolipoma 88513 "Liposarcoma, well differentiated" 88523 Myxoid liposarcoma 88533 Round cell liposarcoma 88543 Pleomorphic liposarcoma 88553 Mixed type liposarcoma 88573 Fibroblastic liposarcoma 88583 Dedifferentiated liposarcoma 88610 "Angiolipoma, NOS" 88900 "Leiomyoma, NOS" 88901 "Leiomyomatosis, NOS" 88903 "Leiomyosarcoma, NOS" 88913 Epithelioid leiomyosarcoma 88943 Angiomyosarcoma 88953 Myosarcoma 88963 Myxoid leiomyosarcoma 88971 "Smooth muscle tumor, NOS" 89000 "Rhabdomyoma, NOS" 89003 "Rhabdomyosarcoma, NOS" 89013 "Pleomorphic rhabdomyosarcoma, adult type" 89023 Mixed type rhabdomyosarcoma 89103 Embryonal rhabdomyosarcoma 89123 Spindle cell rhabdomyosarcoma 89203 Alveolar rhabdomyosarcoma 89213 Rhabdomyosarcoma with ganglionic differentia... 89303 Endometrial stromal sarcoma 89313 "Endometrial stromal sarcoma, low grade" 89333 Adenosarcoma 89343 Carcinofibroma 89353 "Stromal sarcoma, NOS" 89361 "Gastrointestinal stromal tumor, NOS" 89363 Gastrointestinal stromal sarcoma 89403 "Mixed tumor, malignant, NOS" 89413 Carcinoma in pleomorphic adenoma 89503 Mullerian mixed tumor 89513 Mesodermal mixed tumor 89590 Benign Cystic nephroma 89591 Cystic partially differentiated nephroblastoma 89593 Malignant cystic nephroma 89601 Mesoblastic nephroma 89603 "Nephroblastoma, NOS" 89633 Malignant rhabdoid tumor 89643 Clear cell sarcoma of kidney 89703 Hepatoblastoma 89713 Pancreatoblastoma 89723 Pulmonary blastoma 89733 Pleuropulmonary blastoma 89741 Sialoblastoma 89751 Calcifying nested epithelial stromal tumor 89803 "Carcinosarcoma, NOS" 89813 "Carcinosarcoma, embryonal type" 89823 Malignant myoepithelioma 89901 "Mesenchymoma, NOS" 89903 "Mesenchymoma, malignant" 89913 Embryonal sarcoma 90003 "Brenner tumor, malignant" 90143 Serous adenocarcinofibroma 90153 Mucinous adenocarcinofibroma 90203 "Phyllodes tumor, malignant" 90403 "Synovial sarcoma, NOS" 90413 "Synovial sarcoma, spindle cell" 90423 "Synovial sarcoma, epithelioid cell" 90433 "Synovial sarcoma, biphasic" 90443 "Clear cell sarcoma,NOS (except of kidney M-8..." 90503 "Mesothelioma, malignant" 90513 "Fibrous mesothelioma, malignant" 90523 "Epithel. mesothelioma, mal." 90533 "Mesothelioma, biphasic, malignant" 90603 Dysgerminoma 90613 "Seminoma, NOS" 90623 "Seminoma, anaplastic" 90633 Spermatocytic seminoma 90642 Intratubular malignant germ cells 90643 Germinoma 90653 "Germ cell tumor, nonseminomatous" 90703 "Embryonal carcinoma, NOS" 90713 Yolk sac tumor 90723 Polyembryoma 90800 "Teratoma, benign" 90801 "Teratoma, NOS" 90803 "Teratoma, malignant, NOS" 90813 Teratocarcinoma 90823 "Malignant teratoma, undiff." 90833 "Malignant teratoma, intermediate" 90840 "Dermoid cyst, NOS" 90843 Teratoma with malig. transformation 90853 Mixed germ cell tumor 90903 "Struma ovarii, malignant" 91003 Choriocarcinoma 91013 Choriocarcinoma combined w/ other germ cell ... 91023 "Malignant teratoma, trophoblastic" 91043 Malignant placental site trophoblastic tumor 91053 "Trophoblastic tumor, epithelioid" 91103 "Mesonephroma, malignant" 91200 "Hemangioma, NOS" 91203 Hemangiosarcoma 91210 Cavernous hemangioma 91220 Venous hemangioma 91243 Kupffer cell sarcoma 91300 "Hemangioendothelioma, benign" 91301 "Hemangioendothelioma, NOS" 91303 "Hemangioendothelioma, malignant" 91310 Capillary hemangioma 91333 "Epithelioid hemangioendothelioma, malignant" 91403 Kaposi sarcoma 91500 "Hemangiopericytoma, benign" 91501 "Hemangiopericytoma, NOS" 91503 "Hemangiopericytoma, malignant" 91611 Hemangioblastoma 91703 Lymphangiosarcoma 91803 "Osteosarcoma, NOS" 91813 Chondroblastic osteosarcoma 91823 Fibroblastic osteosarcoma 91833 Telangiectatic osteosarcoma 91843 Osteosarcoma in Paget disease 91853 Small cell osteosarcoma 91863 Central osteosarcoma 91873 Instrosseous well differentiated osteosarcoma 91923 Parosteal osteosarcoma 91933 Periosteal osteosarcoma 91943 High grade surface osteosarcoma 91953 Intracortical osteosarcoma 92203 "Chondrosarcoma, NOS" 92213 Juxtacortical chondrosarcoma 92303 "Chondroblastoma, malignant" 92313 Myxoid chondrosarcoma 92403 Mesenchymal chondrosarcoma 92423 Clear cell chondrosarcoma 92433 Dedifferentiated chondrosarcoma 92501 "Giant cell tumor of bone, NOS" 92503 "Giant cell tumor of bone, malignant" 92511 Giant cell tumor of soft parts 92513 Malignant giant cell tumor of soft parts 92523 Malignant tenosynovial giant cell tumor 92603 Ewing sarcoma 92613 Adamantinoma of long bones 92703 "Odontogenic tumor, malignant" 92903 Ameloblastic odontosarcoma 93103 "Ameloblastoma, malignant" 93303 Ameloblastic fibrosarcoma 93423 Odontogenic carcinosarcoma 93501 Craniopharyngioma 93511 Adamantinomatous craniopharyngioma 93521 Papillary craniopharyngioma 93601 "Pinealoma, NOS" 93611 Pineocytoma 93623 Pineoblastoma 93630 Melanotic neuroectodermal tumor 93643 Peripheral neuroectodermal tumor 93653 Askin tumor 93703 "Chordoma, NOS" 93713 Chondroid chordoma 93723 Dedifferentiated chordoma 93803 "Glioma, malignant" 93813 Gliomatosis cerebri 93823 Mixed glioma 93831 Subependymoma 93841 Supependymal giant cell astrocytoma 93900 "Choroid plexus papilloma, NOS" 93901 Atypical choroid plexus papilloma 93903 "Choroid plexus papilloma, malignant" 93913 "Ependymoma, NOS" 93923 "Ependymoma, anaplastic" 93933 Papillary ependymoma 93941 Myxopapillary ependymoma 93953 Papillary tumor of the pineal region 94003 "Astrocytoma, NOS" 94013 "Astrocytoma, anaplastic" 94103 Protoplasmic astrocytoma 94113 Gemistocytic astrocytoma 94121 Desmoplastic infantile astrocytoma 94130 Dysembryoplastic neuroepithelial tumor 94203 Fibrillary astrocytoma 94211 Pilocytic astrocytoma 94233 Polar spongioblastoma 94243 Pleomorphic xanthoastrocytoma 94253 Pilomyxoid astrocytoma 94303 Astroblastoma 94311 Angiocentric glioma 94321 Pituicytoma 94403 "Glioblastoma, NOS" 94413 Giant cell glioblastoma 94421 Gliofibroma 94423 Gliosarcoma 94441 Chordoid glioma 94503 "Oligodendroglioma, NOS" 94513 "Oligodendroglioma, anaplastic" 94603 Oligodendroblastoma 94703 "Medulloblastoma, NOS" 94713 Desmoplastic medulloblastoma 94723 Medullomyoblastoma 94733 Primitive neuroectodermal tumor 94743 Large cell medulloblastoma 94803 "Cerebellar sarcoma, NOS" 94900 Ganglioneuroma 94903 Ganglioneuroblastoma 94920 Gangliocytoma 94930 Dysplastic gangliocytoma of cerebellum (Lher... 95003 "Neuroblastoma, NOS" 95013 "Medulloepithelioma, NOS" 95023 Teratoid medulloepithelioma 95033 "Neuroepithelioma, NOS" 95043 Spongioneuroblastoma 95051 "Ganglioglioma, NOS" 95053 "Ganglioglioma, anaplastic" 95061 Centrol neurocytoma 95083 Atypical teratoid/rhabdoid tumor 95091 Papillary glioneuronal tumor 95103 "Retinoblastoma, NOS" 95113 "Retinoblastoma, differentiated" 95123 "Retinoblastoma, undifferentiated" 95133 "Retinoblastoma, diffuse" 95203 Olfactory neurogenic tumor 95213 Olfactory neurocytoma 95223 Olfactory neuroblastoma 95233 Olfactory neuroepithelioma 95300 "Meningioma, NOS" 95301 "Meningiomatosis, NOS" 95303 "Meningioma, malignant" 95310 Meningothelial meningioma 95320 Fibrous meningioma 95330 Psammomatous meningioma 95340 Angiomatous meningioma 95370 Transitional meningioma 95381 Clear cell meningioma 95383 Papillary meningioma 95391 Atypical meningioma 95393 Meningeal sarcomatosis 95400 "Neurofibroma, NOS" 95401 "Neurofibromatosis, NOS" 95403 Malignant peripheral nerve sheath tumor 95410 Melanotic neurofibroma 95500 Plexiform neurofibroma 95600 "Neurilemoma, NOS" 95601 Neurinomatosis 95603 "Neurilemmoma, malignant" 95613 MPNST with rhabdomyoblastic differentiation 95620 Neurothekeoma 95700 "Neuroma, NOS" 95710 "Perineurioma, NOS" 95713 "Perineurioma, malignant" 95800 "Granular cell tumor, NOS" 95803 "Granular cell tumor, malignant" 95813 Alveolar soft part sarcoma 95903 "Malignant lymphoma, NOS" 95913 "Malignant lymphoma, non-Hodgkin" 95963 Composite Hodgkin and non-Hodgkin lymphoma 95973 Primary cutaneous follicle centre lymphoma 96503 "Hodgkin lymphoma, NOS" 96513 "Hodgkin lymphoma, lymphocyte-rich" 96523 "Hodgkin lymphoma, mixed cellularity, NOS" 96533 "Hodgkin lymphoma, lymphocytic deplet., NOS" 96543 "Hodgkin lymph., lymphocyt. deplet., diffuse ..." 96553 "Hodgkin lymphoma, lymphocyt. deplet., reticular" 96593 "Hodgkin lymph., nodular lymphocyte predom." 96613 Hodgkin granuloma [obs] 96623 Hodgkin sarcoma [obs] 96633 "Hodgkin lymphoma, nodular sclerosis, NOS" 96643 "Hodgkin lymphoma, nod. scler., cellular phase" 96653 "Hodgkin lymphoma, nod. scler., grade 1" 96673 "Hodgkin lymphoma, nod. scler., grade 2" 96703 "ML, small B lymphocytic, NOS" 96713 "ML, lymphoplasmacytic" 96733 Mantle cell lymphoma 96753 "ML, mixed sm. and lg. cell, diffuse" 96783 Primary effusion lymphoma 96793 Mediastinal large B-cell lymphoma 96803 "ML, large B-cell, diffuse" 96843 "ML, large B-cell, diffuse, immunoblastic, NOS" 96873 "Burkitt lymphoma, NOS" 96883 T-cell/histiocyte rich large B-cell lymphoma 96893 Splenic marginal zone B-cell lymphoma 96903 "Follicular lymphoma, NOS" 96913 "Follicular lymphoma, grade 2" 96953 "Follicular lymphoma, grade 1" 96983 "Follicular lymphoma, grade 3" 96993 "Marginal zone B-cell lymphoma, NOS" 97003 Mycosis fungoides 97013 Sezary syndrome 97023 "Mature T-cell lymphoma, NOS" 97053 Angioimmunoblastic T-cell lymphoma 97083 Subcutaneous panniculitis-like T-cell lymphoma 97093 "Cutaneous T-cell lymphoma, NOS" 97123 Intravascular large B-cell lymphoma 97143 "Anaplastic large cell lymphoma, T-cell and N..." 97163 Hepatosplenic T-cell lymphoma 97173 Intestinal T-cell lymphoma 97183 Primary cutan. CD30+ T-cell lymphoprolif. di... 97193 "NK/T-cell lymphoma, nasal and nasal-type" 97243 Syst. EBV pos. T-cell lymphoprol. disease 97253 Hydroa vacciniforme-like lymphoma 97263 Primary cutaneous gamma-delta T-cell lymphoma 97273 "Precursor cell lymphoblastic lymphoma, NOS" 97283 Precursor B-cell lymphoblastic lymphoma 97293 Precursor T-cell lymphoblastic lymphoma 97313 "Plasmacytoma, NOS" 97323 Multiple myeloma 97333 Plasma cell leukemia 97343 "Plasmacytoma, extramedullary" 97353 Plasmablastic lymphoma 97373 ALK postive large B-cell lymphoma 97383 Large B-cell lymph. arising in HHV8-assoc. multi 97403 Mast cell sarcoma 97411 Indolent systemic mastocytosis 97413 Malignant mastocytosis 97423 Mast cell leukemia 97503 Malignant histiocytosis 97511 "Langerhans cell histiocytosis, NOS" 97513 "Langerhans cell histiocytosis, NOS" 97521 "Langerhans cell histiocytosis, unifocal" 97531 "Langerhans cell histiocytosis, multifocal" 97543 "Langerhans cell histiocytosis, disseminated" 97553 Histiocytic sarcoma 97563 Langerhans cell sarcoma 97573 Interdigitating dendritic cell sarcoma 97583 Follicular dendritic cell sarcoma 97593 Fibroblastic reticular cell tumor 97603 "Immunoproliferative disease, NOS" 97613 Waldenstrom macroglobulinemia 97623 "Heavy chain disease, NOS" 97643 Immunoproliferative small intestinal disease 98003 "Leukemia, NOS" 98013 "Acute leukemia, NOS" 98053 Acute biphenotypic leukemia 98063 Mix. phenotype ac. leukemia with t;BCR-ABL1 98073 Mix. phenotype ac. leukemia with t;MLL rearrange 98083 "Mixed phenotype acute leukemia, B/myeloid, NOS" 98093 "Mixed phenotype acute leukemia, T/myeloid, NOS" 98113 "B lymphoblastic leukemia/lymphoma, NOS" 98123 B lymphoblast. leukemia/lymphoma with t;BCR-ABL1 98133 B lymphoblast. leukemia/lymphoma with t;MLL rear 98143 B lymphoblast. leukemia/lymphoma with t;TEL-AML1 98153 B lymphoblastic leukemia/lymphoma with hyperdipl 98163 B lymphoblast. leukemia/lymph. with hypodiploidy 98173 B lymphoblast. leukemia/lymphoma with t;IL3-IGH 98183 B lymphoblast. leukemia/lymphoma with t;E2A PBX1 98203 "Lymphoid leukemia, NOS" 98233 B-cell chr. lymph. leuk./small lymphocytic l... 98263 Burkitt cell leukemia 98273 Adult T-cell leukemia/lymphoma (HTLV-1 pos.) 98283 "Acute lymphoblastic leukemia, L2 type, NOS" 98313 T-cell large granular lymphocytic leukemia 98323 "Prolymphocytic leukemia, NOS" 98333 "Prolymphocytic leukemia, B-cell type" 98343 "Prolymphocytic leukemia, T-cell type" 98353 "Precursor cell lymphoblastic leukemia, NOS" 98363 Precursor B-cell lymphoblastic leukemia 98373 Precursor T-cell lymphoblastic leukemia 98403 "Acute myeloid leukemia, M6 type" 98603 "Myeloid leukemia, NOS" 98613 Acute myeloid leukemia 98633 "Chronic myeloid leukemia, NOS" 98653 Acute myeloid leukemia with t;DEK-NUP214 98663 "Acute promyelocytic leuk.,t(15;17)(q22;q11-12)" 98673 Acute myelomonocytic leukemia 98693 Acute myeloid leukemia with inv or t;RPN1-EVI1 98703 Acute basophilic leukemia 98713 Ac. myelomonocytic leuk. w abn. mar. eosinop... 98723 "Acute myeloid leukemia, minimal differentiation" 98733 Acute myeloid leukemia without maturation 98743 Acute myeloid leukemia with maturation 98753 "Chronic myelogenous leukemia, BCR/ABL positive" 98763 "Atypical chronic myeloid leuk., BCR/ABL nega..." 98913 Acute monocytic leukemia 98953 Acute myeloid leuk. with myelodysplasia-related 98963 "Acute myeloid leukemia, t(8;21)(q22;q22)" 98973 "Acute myeloid leukemia, 11q23 abnormalities" 98981 Transient abnormal myelopoiesis 98983 Myeloid leukemia associated with Down Syndrome 99103 Acute megakaryoblastic leukemia 99113 Acute myeloid leukemia (megakar. blast.) with t; 99203 Therapy related myeloid neoplasm 99303 Myeloid sarcoma 99313 Acute panmyelosis with myelofibrosis 99403 Hairy cell leukemia 99453 "Chronic myelomonocytic leukemia, NOS" 99463 Juvenile myelomonocytic leukemia 99483 Aggressive NK-cell leukemia 99503 Polycythemia vera 99603 "Myeloproliferative neoplasm, NOS" 99613 Primary myelofibrosis 99623 Essential thrombocythemia 99633 Chronic neutrophilic leukemia 99643 "Chronic eosinophilic leukemia, NOS" 99653 Myeloid&lymphoid neoplasms with PDGFRB rearrange 99663 Myeloid neoplasms with PDGFRB rearrangement 99673 Myeloid&lymphoid neoplasm with FGFR1 abnormaliti 99701 "Lymphoproliferative disorder, NOS" 99711 "Post transplant lymphoproliferative disorder, NO" 99713 Polymorphic post transplant lymphoproliferative 99751 "Myeloproliferative disease, NOS" 99753 "Myeloproliferative neoplasm, unclassifiable" 99803 Refractory anemia 99823 Refractory anemia with sideroblasts 99833 Refractory anemia with excess blasts 99843 Refract. anemia with excess blasts in transf... 99853 Refractory cytopenia with multilineage dyspl... 99863 Myelodysplastic syndr. with 5q deletion synd... 99873 "Therapy-related myelodysplastic syndrome, NOS" 99893 "Myelodysplastic syndrome, NOS" 99913 Refractory neutropenia 99923 Refractory thrombocytopenia 341 PLOCCD PLCCD1 PLCCD2 PLCCD3 0 external upper lip 1 external lower lip 2 "external lip, NOS" 3 mucose of uppper lip 4 mucosa of lower lip 5 "mucosa of lip, NOS" 6 commissure of lip 8 overlapping lesion of lip 9 "lip, NOS" 19 base of tongue 20 "dorsal surface of tongue, NOS" 21 border of tongue 22 "ventral surface of tongue, NOS" 23 anterior 2/3 of tongue 24 lingual tonsil 28 overlapping lesion of tongue 29 "tongue, NOS" 30 upper gum 31 lower gum 39 "gum, NOS" 40 anterior floor of mouth 41 lateral floor of mouth 48 overlapping lesion of floor of mouth 49 "floor of mouth, NOS" 50 hard palate 51 "soft palate, NOS" 52 uvula 58 overlapping lesion of palate 59 "palate, NOS" 60 cheek mucosa 61 vestibule of mouth 62 retromolar area 68 overlappinglesionofotherandunspecifiedpartso... 69 "mouth, NOS" 79 parotid gland 80 submandibular gland 81 sublingual gland 88 overlapping lesion of major salivary glands 89 "major salivary gland, NOS" 90 tonsillar fossa 91 tonsillar pillar 98 overlapping lesion of tonsil 99 "tonsil, NOS" 100 vallecula 101 anterior surface of epiglottis 102 lateral wall of oropharynx 103 posterior wall of oropharynx 104 branchial cleft 108 overlapping lesion of oropharynx 109 "oropharynx, NOS" 110 superior wall of nasopharyx 111 posterior wall of nasopharyx 112 lateral wall of nasopharyx 113 anterior wall of nasopharyx 118 overlapping lesion of nasopharyx 119 "nasopharyx, NOS" 129 "nasopharyxyriform sinus, NOS" 130 postcricoid region 131 hypopharyngeal aspect of aryepiglottic fold 132 posterior wall of hypopharynx 138 overlapping lesion of hypopharyx 139 "hypopharyx, NOS" 140 "pharyx, NOS" 142 waldeyer ring 148 "overlappinglesionoflip,oralcavityandpharynx" 150 cervical esophagus 151 thoracic esophagus 152 abdominal esophagus 153 upper third of esophagus 154 middle third of esophagus 155 lower third of esophagus 158 overlapping lesion of esophagus 159 "esophagus, NOS" 160 "cardia, NOS" 161 fundus of stomach 162 body of stomach 163 gastric antrum 164 pylorus 165 lesser curvature of stomach 166 greater curvature of stomach 168 overlapping lesion of stomach 169 "stomach, NOS" 170 duodenum 171 jejunum 172 ileum 173 Meckel diverticulum 178 overlapping lesion of small intestine 179 "small intestine, NOS" 180 cecum 181 appendix 182 ascending colon 183 hepatic flexure of colon 184 transverse colon 185 splenic flexure of colon 186 descending colon 187 sigmoid colon 188 overlapping lesion of colon 189 "colon, NOS" 199 rectosigmoid junction 209 "rectum, NOS" 210 "anus, NOS" 211 anal canal 212 cloacogenic zone 218 "overlappinglesionofrectum,anusandanalcanal" 220 liver 221 intrahepatic bile duct 239 "gallbladder, NOS" 240 extrahepatic bile duct 241 ampulla of Vater 248 overlapping lesion of biliary tract 249 "billary tract, NOS" 250 head of pancreas 251 body of pancreas 252 tail of pancreas 253 pancreatic duct 254 islets of Langerhans 257 other specified parts of pancreas 258 overlapping lesion of pancreas 259 "pancreas, NOS" 260 "intestinal tract, NOS" 268 overlapping lesion of digestive system 269 "gastrointestinal tract, NOS" 300 nasal cavity 301 middle ear 310 maxillary sinus 311 ethmoid sinus 312 frontal sinus 313 sphenoid sinus 318 overlapping lesion of accessory sinuses 319 "accessory sinus, NOS" 320 glottis 321 supraglottis 322 subglottis 323 laryngeal cartilage 328 overlapping lesion of larynx 329 "larynx, NOS" 339 trachea 340 main bronchus 341 "upper lobe, lung" 342 "middle lobe, lung" 343 "lower lobe, lung" 348 overlapping lesion of lung 349 "lung, NOS" 379 thymus 380 heart 381 anterior mediastinum 382 posterior mediastinum 383 "mediastinum, NOS" 384 "pleura, NOS" 388 "overlappinglesionofheart,mediastinumandpleura" 390 "upper respiratory tract, NOS" 398 overlappinglesionofrespiratorysystemandintra... 399 ill-defined sites within respiratory system 400 "longboneofupperlimb,scapulaandassociatedjoints" 401 short bone of upper limb and associated joints 402 long bones of lower limb and associated joints 403 short bones of lower limb and associated joints 408 "overlappinglesionofbones,jointsandarticularc..." 409 "bones of lomb, NOS" 410 bones of skull and face and associated joints 411 mandible 412 vertebral column 413 "rib, sternum, clavicle and associated joints" 414 "pelvicbones,sacrum,coccyxandassociatedjoints" 418 "overlappinglesionofbones,jointsandarticularc..." 419 "bone, NOS" 420 blood 421 bone marrow 422 spleen 423 "reticuloendothelial system, NOS" 424 "hematopoietic system, NOS" 440 "skin of lip, NOS" 441 eyelid 442 external ear 443 skin of other and unspecified parts of face 444 skin of scalp and neck 445 skin of trunc 446 skin of upper limb and shoulder 447 skin of lower limb and hip 448 overlapping lesion of skin 449 "skin, NOS" 470 peripheralnervesandautonomicnervoussystemofh... 471 peripheralnervesandautonomicnervoussystemofu... 472 peripheralnervesandautonomicnervoussystemofl... 473 peripheralnervesandautonomicnervoussystemoft... 474 peripheralnervesandautonomicnervoussystemofa... 475 peripheralnervesandautonomicnervoussystemofp... 476 peripheralnervesandautonomicnervoussystemoft... 478 overlappinglesionofperipheralnervesandautono... 479 "autonomic nervous system, NOS" 480 retroperitoneum 481 specified parts of peritoneum 482 "peritoneum, NOS" 488 overlapping lesion of retroperitoneum 490 "connective,subcutaneousandothersofttissuesof..." 491 "connective,subcutaneousandothersofttissuesof..." 492 "connective,subcutaneousandothersofttissuesof..." 493 "connective,subcutaneousandothersofttissuesof..." 494 "connective,subcutaneousandothersofttissuesof..." 495 "connective,subcutaneousandothersofttissuesof..." 496 "connective,subcutaneousandothersofttissuesof..." 498 "overlappinglesionofconnective,subcutaneousan..." 499 "connective,subcutaneousandothersofttissues,NOS" 500 nipple 501 central portion of breast 502 upper-inner quadrant of breast 503 lower-inner quadrant of breast 504 upper-outer quadrant of breast 505 upper-outer quadrant of breast 506 axillary tail of breast 508 overlapping lesion of breast 509 "breast, NOS" 510 labium majus 511 labium minus 512 clitoris 518 overlapping lesion of vulva 519 "vulva, NOS" 529 "vagina, NOS" 530 endocervix 531 exocervix 538 overlapping lesion of cervix uteri 539 "cervix uteri, NOS" 540 isthmus uteri 541 endometrium 542 myometrium 543 fundus uteri 548 overlapping lesion of corpus uteri 549 "corpus uteri, NOS" 559 "uterus, NOS" 569 "ovary, NOS" 570 fallopian tube 571 broad ligament 572 round ligament 573 parametrium 574 uterine adnexa 577 other specified parts of female genital organs 578 overlapping lesion of female genital organs 579 "female genital tract, NOS" 589 "placenta, NOS" 600 prepuce 601 glans penis 602 body of penis 608 overlapping lesion of penis 609 "penis, NOS" 619 prostate gland 620 undescended testis 621 descended testis 629 "testis, NOS" 630 epididymis 631 spermatic cord 632 "scrotum, NOS" 637 other specified parts of male genital organs 638 overlapping lesion of male genital organs 639 "male genital tract, NOS" 649 "kidney, NOS" 659 renal pelvis 669 ureter 670 trigone of bladder 671 dome of bladder 672 lateral wall of bladder 673 anterior wall of bladder 674 posterior of bladder 675 bladder neck 676 ureteric orifice 677 urachus 678 overlapping lesion of bladder 679 "bladder, NOS" 680 urethra 681 paraurethral gland 688 overlapping lesion of urinary organs 689 "urinary system, NOS" 690 conjuctiva 691 "cornea, NOS" 692 retina 693 choroid 694 ciliary body 695 lacrimal gland 696 "orbit, NOS" 698 overlapping lesion of eye and adnexa 699 "eye, NOS" 700 cerebral meninges 701 spinal meninges 709 "meninges, NOS" 710 cerebrum 711 frontal lobe 712 temperal lobe 713 parietal lobe 714 occipital lobe 715 "ventricle, NOS" 716 cerebellum 717 brain stem 718 overlapping lesion of brain 719 "brain, NOS" 720 spinal cord 721 cauda equina 722 olfactory nerve 723 optic nerve 724 acoustic nerve 725 "cranial nerve, NOS" 728 overlappinglesionofbrainandcentralnervoussystem 729 "nervous system, NOS" 739 "thyroid gland, NOS" 740 cortex of adrenal gland 741 medulla of adrenal gland 749 "adrenal gland, NOS" 750 parathyroid gland 751 pituitary gland 752 craniopharyngeal duct 753 pineal gland 754 carotid body 755 aortic body and other paraganglia 758 overlappinglesionofendocrineglandsandrelated... 759 "endocrine gland, NOS" 760 "head, face or neck, NOS" 761 "thorax, NOS" 762 "abdomen, NOS" 763 "pelvis, NOS" 764 "upper limb, NOS" 765 "lower limb, NOS" 767 other ill-defined sites 768 overlapping lesion of ill-defined sites 770 "lymph nodes of head, face and neck" 771 intrathoracic lymph nodes 772 intra-abdominal lymph nodes 773 lymph nodes of axilla of arm 774 lymph nodes of inguinal region or leg 775 pelvic lymph nodes 778 lymph nodes of multiple regions 779 "lymph node, NOS" 809 unknown primary sites 343 IFCDATR 1 yes 2 no 3 statement by physician 4 IC will follow \ No newline at end of file diff --git a/test_data/test_logic/dropzone/studies/PMCST000AAA_death_codebook.txt.sha1 b/test_data/test_logic/dropzone/studies/PMCST000AAA_death_codebook.txt.sha1 new file mode 100644 index 0000000..c7ec326 --- /dev/null +++ b/test_data/test_logic/dropzone/studies/PMCST000AAA_death_codebook.txt.sha1 @@ -0,0 +1 @@ +8cc20a3917db3e251d9426d078ce74969e531931 PMCST000AAA_death_codebook.txt diff --git a/test_data/test_logic/dropzone/studies/PMCST000AAA_diagnosis.txt b/test_data/test_logic/dropzone/studies/PMCST000AAA_diagnosis.txt new file mode 100644 index 0000000..197d37c --- /dev/null +++ b/test_data/test_logic/dropzone/studies/PMCST000AAA_diagnosis.txt @@ -0,0 +1,20 @@ +"MARK:","ID","IDAA","INDIVIDUAL_ID","CIDDIAG","HOSPDIAG","DIAGCD","PLOCCD","DIAGGRSTX","IDAABA" +,217,8000208,PAT1,DIA1,217,95913,771,,10/04/2003 0:00:00 +,217,8000216,PAT2,DIA2,217,95913,421,,17/04/2003 0:00:00 +,217,8000233,PAT3,DIA3,217,95913,421,,04/05/2003 0:00:00 +,217,8000250,PAT4,DIA4,217,95913,421,,21/05/2003 0:00:00 +,217,8000268,PAT5,DIA5,217,95913,421,,05/06/2003 0:00:00 +,217,8000273,PAT6,DIA6,217,95913,421,,29/09/2003 0:00:00 +,217,8000323,PAT7,DIA7,217,95913,421,,17/08/2003 0:00:00 +,217,8000333,PAT8,DIA8,217,95913,421,,28/08/2003 0:00:00 +,217,8000345,PAT9,DIA9,217,95913,778,,06/08/2003 0:00:00 +,217,8000217,PAT10,DIA10,217,95913,778,,06/08/2003 0:00:00 +,217,8000238,PAT11,DIA11,217,97053,778,,06/08/2003 0:00:00 +,217,8000251,PAT12,DIA12,217,95913,778,,06/08/2003 0:00:00 +,217,8000269,PAT13,DIA13,217,95913,778,,06/08/2003 0:00:00 +,217,8000274,PAT14,DIA14,217,97053,778,,06/08/2003 0:00:00 +,217,8000324,PAT15,DIA15,217,97053,778,,06/08/2003 0:00:00 +,217,8000334,PAT16,DIA16,217,97053,778,,06/08/2003 0:00:00 +,217,8000346,PAT17,DIA17,217,97053,778,,06/08/2003 0:00:00 +,217,8000208,PAT1,DIA18,217,97053,778,,06/08/2003 0:00:00 +,217,8000216,PAT2,DIA19,217,97053,778,,06/08/2003 0:00:00 diff --git a/test_data/test_logic/dropzone/studies/PMCST000AAA_diagnosis.txt.sha1 b/test_data/test_logic/dropzone/studies/PMCST000AAA_diagnosis.txt.sha1 new file mode 100644 index 0000000..fac1e34 --- /dev/null +++ b/test_data/test_logic/dropzone/studies/PMCST000AAA_diagnosis.txt.sha1 @@ -0,0 +1 @@ +c2c862477e73c9059b5b2e8cc7b8049a74099ea7 PMCST000AAA_diagnosis.txt diff --git a/test_data/test_logic/dropzone/studies/PMCST000AAA_diagnosis_codebook.txt b/test_data/test_logic/dropzone/studies/PMCST000AAA_diagnosis_codebook.txt new file mode 100644 index 0000000..9d23109 --- /dev/null +++ b/test_data/test_logic/dropzone/studies/PMCST000AAA_diagnosis_codebook.txt @@ -0,0 +1 @@ +1 SEX 1 male 2 female 9 unknown 2 SIGYN IFCGIV IFCMAT IFCCOM IFCREF NOREGIS CLEXPYN CYTOLYN HISTOYN IMAGEYN TMARKYN PATDCOGR PROTYN ELIGYN TXSTART SIGYNX SIGYNY 1 yes 2 no 8 not applicable 8 HOSPREC HOSPDIAG HOSPASS HOSPTRAN 200 AMC 201 UMCG 202 AZM 203 CZE 204 ErasmusMC 207 JBZ 208 LUMC 213 EZT 214 Radboudumc 216 VUMC 217 UMCU 220 PMC 332 DIAGCD PDGCD1 PDGCD2 PDGCD3 61000 FanconiÔs anaemia 61900 Aplastic anaemia 70000 KostmannÔs disease 76100 HLH 80000 "Neoplasm, benign" 80001 "Neoplasm, uncertain whether benign or malignant" 80003 "Neoplasm, malignant" 80010 "Tumor cells, benign" 80011 "Tumor cells, uncertain whether benign or mal..." 80013 "Tumor cells, malignant" 80023 "Malignant tumor, small cell type" 80033 "Malignant tumor, giant cell type" 80043 "Malignant tumor, spindle cell type" 80050 "Clear cell tumor, NOS" 80053 "Malignant tumor, clear cell type" 80100 "Epithelial tumor, benign" 80102 "Carcinoma in situ, NOS" 80103 "Carcinoma, NOS" 80113 "Epithelioma, malignant" 80123 "Large cell carcinoma, NOS" 80133 Large cell neuroendocrine carcinoma 80143 Large cell carcinoma with rhabdoid phenotype 80153 Glassy cell carcinoma 80203 "Carcinoma, undifferentiated type, NOS" 80213 "Carcinoma, anaplastic type, NOS" 80223 Pleomorphic carcinoma 80303 Giant cell and spindle cell carcinoma 80313 Giant cell carcinoma 80323 Spindle cell carcinoma 80333 Pseudosarcomatous carcinoma 80343 Polygonal cell carcinoma 80353 Carcinoma with osteoclast-like giant cells 80413 "Small cell carcinoma, NOS" 80423 Oat cell carcinoma 80433 "Small cell carcinoma, fusiform cell" 80443 "Small cell carcinoma, intermediate cell" 80453 Combined small cell carcinoma 80463 Non-small cell carcinoma 80502 Papillary carcinoma in situ 80503 "Papillary carcinoma, NOS" 80513 "Verrucous carcinoma, NOS" 80522 "Papillary squamous cell carcinoma, non-invasive" 80523 Papillary squamous cell carcinoma 80702 "Squamous cell carcinoma in situ, NOS" 80703 "Squamous cell carcinoma, NOS" 80713 "Sq. cell carcinoma, keratinizing, NOS" 80723 "Sq. cell carcinoma, lg. cell, non-ker." 80733 "Sq. cell carcinoma, sm. cell, non-ker." 80743 "Sq. cell carcinoma, spindle cell" 80753 "Squamous cell carcinoma, adenoid" 80762 Sq. cell carc. in situ with question. stroma... 80763 "Sq. cell carcinoma, micro-invasive" 80770 "Squamous intraepithelial neoplasia, low grade" 80772 "Squamous intraepithelial neoplasia, high grade" 80783 Squamous cell carcinoma with horn formation 80802 Queyrat erythroplasia 80812 Bowen disease 80823 Lymphoepithelial carcinoma 80833 Basaloid squamous cell carcinoma 80843 "Squamous cell carcinoma, clear cell type" 80903 "Basal cell carcinoma, NOS" 80913 Multifocal superficial basal cell carcinoma 80923 "Infiltrating basal cell carcinoma, NOS" 80933 "Basal cell carcinoma, fibroepithelial" 80943 Basosquamous carcinoma 80953 Metatypical carcinoma 80973 "Basal cell carcinoma, nodular" 80983 Adenoid basal cell carcinoma 81023 Trichilemmocarcinoma 81103 Pilomatrix carcinoma 81202 Transitional cell carcinoma in situ 81203 "Transitional cell carcinoma, NOS" 81213 Schneiderian carcinoma 81223 "Trans. cell carcinoma, spindle cell" 81233 Basaloid carcinoma 81243 Cloacogenic carcinoma 81302 "Papillary trans. cell carcinoma, non-invasive" 81303 Papillary trans. cell carcinoma 81313 "Transitional cell carcinoma, micropapillary" 81400 "Adenoma, NOS" 81402 Adenocarcinoma in situ 81403 "Adenocarcinoma, NOS" 81413 Scirrhous adenocarcinoma 81423 Linitis plastica 81433 Superficial spreading adenocarcinoma 81443 "Adenocarcinoma, intestinal type" 81453 "Carcinoma, diffuse type" 81460 Monomorphic adenoma 81473 Basal cell adenocarcinoma 81480 "Glandular intraepithelial neoplasia, low grade" 81482 "Glandular intraepithelial neoplasia, high grade" 81500 "Pancreatic endocrine tumor, benign" 81501 "Pancreatic endocrine tumor, NOS" 81503 "Pancreatic endocrine tumor, malignant" 81513 "Insulinoma, malignant" 81523 "Glucagonoma, malignant" 81533 "Gastrinoma, malignant" 81543 "Mix. pancreatic endocrine&exocrine tumor, mal" 81553 Vipoma 81563 "Somatostatinoma, malignant" 81573 "Enteroglucagonoma, malignant" 81581 "Endocrine tumor, functioning, NOS" 81603 Cholangiocarcinoma 81613 Bile duct cystadenocarcinoma 81623 Klatskin tumor 81630 "Pancreatobiliary neoplasm, non-invasive" 81632 "Pap. neoplasm,pancreatobiliary-type,high gr. int" 81633 Pancreatobiliary-type carcinoma 81703 "Hepatocellular carcinoma, NOS" 81713 "Hepatocellular carcinoma, fibrolamellar" 81723 "Hepatocellular carcinoma, scirrhous" 81733 "Hepatocellular carcinoma, spindle cell variant" 81743 "Hepatocellular carcinoma, clear cell type" 81753 "Hepatocellular carcinoma, pleomorphic type" 81803 Comb. hepatocel. carcinoma & cholangiocarcinoma 81903 Trabecular adenocarcinoma 82003 Adenoid cystic carcinoma 82012 Cribriform carcinoma in situ 82013 Cribriform carcinoma 82102 Adenocarcinoma in situ in adenomatous polyp 82103 Adenocarcinoma in adenomatous polyp 82113 Tubular adenocarcinoma 82133 Serrated adenocarcinoma 82143 Parietal cell carcinoma 82153 Adenocarcinoma of anal glands 82202 Adenocarcinoma in situ in familial polyp. coli 82203 Adenocarcinoma in adenoma. polyposis coli 82212 Adenocarc. in situ in mult. adenomatous polyps 82213 Adenocarcinoma in mult. adenomatous polyps 82302 "Duct carcinoma in situ, solid type" 82303 "Solid carcinoma, NOS" 82313 Carcinoma simplex 82401 Carcinoid tumor of uncertain malignant potential 82403 "Carcinoid tumor, malignant" 82413 Enterochromaffin cell carcinoid 82423 "Enterochromaffin-like cell tumor, malignant" 82433 Goblet cell carcinoid 82443 Mixed adenoneuroendocrine carcinoma 82453 Adenocarcinoid tumor 82463 Neuroendocrine carcinoma 82473 Merkel cell carcinoma 82493 Atypical carcinoid tumor 82503 Bronchiolo-alveolar adenocarcinoma 82513 Alveolar adenocarcinoma 82523 "Bronchiolo-alveolar carcinoma, non-mucinous" 82533 "Bronchiolo-alveolar carcinoma, mucinous" 82543 "Bronch.-alv. carc., mixed mucin. and non-muc..." 82553 Adenocarcinoma with mixed subtypes 82600 "Papillary adenoma, NOS" 82603 "Papillary adenocarcinoma, NOS" 82612 Adenocarcinoma in situ in villous adenoma 82613 Adenocarcinoma in villous adenoma 82623 Villous adenocarcinoma 82632 Adenocarcinoma in situ in tubulovillous adenoma 82633 Adenocarcinoma in tubulovillous adenoma 82653 "Micropapillary carcinoma, NOS" 82700 Chromophobe adenoma 82703 Chromophobe carcinoma 82710 Prolactinoma 82720 "Pituitary adenoma, NOS" 82723 "Pituitary carcinoma, NOS" 82800 Acidophil adenoma 82803 Acidophil carcinoma 82810 Mixed acidophil-basophil adenoma 82813 Mixed acidophil-basophil carcinoma 82900 Oxyphilic adenoma 82903 Oxyphilic adenocarcinoma 83000 Basophil adenoma 83003 Basophil carcinoma 83100 Clear cell adenoma 83103 "Clear cell adenocarcinoma, NOS" 83123 Renal cell carcinoma 83133 Clear cell adenocarcinofibroma 83143 Lipid-rich carcinoma 83153 Glycogen-rich carcinoma 83163 Cyst-associated renal cell carcinoma 83173 "Renal cell carcinoma, chromophobe type" 83183 "Renal cell carcinoma, sarcomatoid" 83193 Collecting duct carcinoma 83203 Granular cell carcinoma 83223 Water-clear cell adenocarcinoma 83230 Mixed cell adenoma 83233 Mixed cell adenocarcinoma 83303 "Follicular adenocarcinoma, NOS" 83313 Follicular adenocarcinoma well diff. 83323 Follicular adenocarcinoma trabecular 83333 Fetal adenocarcinoma 83353 "Follicular carcinoma, minimally invasive" 83373 Insular carcinoma 83403 "Papillary carcinoma, follicular variant" 83413 Papillary microcarcinoma 83423 "Papillary carcinoma, oxyphilic cell" 83433 "Papillary carcinoma, encapsulated" 83443 "Papillary carcinoma, columnar cell" 83453 Medullary carcinoma with amyloid stroma 83463 Mixed medullary-follicular carcinoma 83473 Mixed medullary-papillary carcinoma 83503 Nonencapsulated sclerosing carcinoma 83700 "Adrenal cortical adenoma, NOS" 83703 Adrenal cortical carcinoma 83803 Endometrioid carcinoma 83813 "Endometrioid adenofibroma, malignant" 83823 "Endometrioid adenocarcinoma, secretory variant" 83833 "Endometrioid adenocarcinoma, ciliated cell v..." 83843 "Adenocarcinoma, endocervical type" 83903 Skin appendage carcinoma 84003 Sweat gland adenocarcinoma 84013 Apocrine adenocarcinoma 84023 "Nodular hidradenoma, malignant" 84033 Malignant eccrine spiradenoma 84073 Sclerosing sweat duct carcinoma 84083 Eccrine papillary adenocarcinoma 84093 "Eccrine poroma, malignant" 84103 Sebaceous adenocarcinoma 84133 Eccrine adenocarcinoma 84203 Ceruminous adenocarcinoma 84303 Mucoepidermoid carcinoma 84403 "Cystadenocarcinoma, NOS" 84413 "Serous cystadenocarcinoma, NOS" 84421 "Serous cystadenoma, borderline malignancy (C..." 84503 "Papillary cystadenocarcinoma, NOS" 84511 "Papillary cystadenoma, borderline malignancy..." 84523 Solid pseudopapillary carcinoma 84532 "Intraductal papillary-mucinous carcinoma, no..." 84533 "Intraductal papillary-mucinous carcinoma, in..." 84603 Papillary serous cystadenocarcinoma 84613 Serous surface papillary carcinoma 84621 Serous papillary cystic tumor of borderline ... 84702 "Mucinous cystadenocarcinoma, non-invasive" 84703 "Mucinous cystadenocarcinoma, NOS" 84713 Papillary mucinous cystadenocarcinoma 84721 Mucinous cystic tumor of borderline malignan... 84731 "Papillary mucinous cystadenoma, borderline m..." 84803 Mucinous adenocarcinoma 84813 Mucin-producing adenocarcinoma 84823 "Mucinous adenocarcinoma, endocervical type" 84903 Signet ring cell carcinoma 85002 "Intraductal carcinoma, noninfiltrating, NOS" 85003 "Infiltrating duct carcinoma, NOS" 85012 "Comedocarcinoma, non-infiltrating" 85013 "Comedocarcinoma, NOS" 85023 Secretory carcinoma of breast 85032 Noninfiltrating intraductal papillary adenoc... 85033 Intraductal papillary adenocarcinoma with in... 85042 Noninfiltrating intracystic carcinoma 85043 "Intracystic carcinoma, NOS" 85072 Intraductal micropapillary carcinoma 85083 Cystic hypersecretory carcinoma 85103 "Medullary carcinoma, NOS" 85123 Medullary carcinoma with lymphoid stroma 85133 Atypical medullary carcinoma 85143 "Duct carcinoma, desmoplastic type" 85202 Lobular carcinoma in situ 85203 "Lobular carcinoma, NOS" 85213 Infiltrating ductular carcinoma 85222 Intraductal and lobular in situ carcinoma 85223 Infiltrating duct and lobular carcinoma 85233 Infiltr. duct mixed with other types of carc... 85243 Infiltrating lobular mixed with other types ... 85253 Polymorphous low grade adenocarcinoma 85303 Inflammatory carcinoma 85403 "Paget disease, mammary" 85413 Paget dis. & infil. duct carcinoma 85423 "Paget disease, extramammary" 85433 Paget disease and intraductal ca. 85503 Acinar cell carcinoma 85513 Acinar cell cystadenocarcinoma 85603 Adenosquamous carcinoma 85613 "Warthin tumor, malignant" 85623 Epithelial-myoepithelial carcinoma 85703 Adenocarcinoma with squamous metaplasia 85713 Adenocarcinoma w cartilag. & oss. metaplas. 85723 Adenocarcinoma with spindle cell mataplasia 85733 Adenocarcinoma with apocrine metaplasia 85743 Adenocarcinoma with neuroendocrine differen. 85753 "Metaplastic carcinoma, NOS" 85763 Hepatoid adenocarcinoma 85803 "Thymoma, malignant, NOS" 85813 "Thymoma, type A, malignant" 85823 "Thymoma, type AB, malignant" 85833 "Thymoma, type B1, malignant" 85843 "Thymoma, type B2, malignant" 85853 "Thymoma, type B3, malignant" 85863 "Thymic carcinoma, NOS" 85883 Spindle epithelial tumor with thymus-like el... 85893 Carcinoma showing thymus-like element 85903 "Ovarian stromal tumor, mal." 86003 "Thecoma, malignant" 86201 "Granulosa cell tumor, adult type" 86203 "Granulosa cell tumor, malignant" 86211 Granulosa cell-theca cell tumor 86221 "Granulosa cell tumor, juvenile" 86303 "Androblastoma, malignant" 86311 Sertoli-Leydig cell tumor of intermediate differ 86313 "Sertoli-Leydig cell tumor, poorly differenti..." 86323 "Gynandroblastoma, malignant" 86343 "Sertoli-Leydig cl tum., p.d. w heterologous ..." 86401 "Sertoli cell tumor, NOS" 86403 Sertoli cell carcinoma 86501 "Leydig cell tumor, NOS" 86503 "Leydig cell tumor, malignant" 86703 "Steroid cell tumor, malignant" 86801 "Paraganglioma, NOS" 86803 "Paraganglioma, malignant" 86913 "Aortic body tumor, malignant" 86923 "Carotid body tumor, malignant" 86933 "Extra-adrenal paraganglioma, malignant" 87000 Pheochromocytoma NOS 87003 Pheochromocytoma 87103 Glomangiosarcoma 87202 Melanoma in situ 87203 "Malignant melanoma, NOS" 87213 Nodular melanoma 87223 Balloon cell melanoma 87233 "Malignant melanoma, regressing" 87280 Diffuse melanocytosis 87281 Meningeal melanocytoma 87283 Meningeal melanomatosis 87303 Amelanotic melanoma 87403 Mal. melanoma in junctional nevus 87412 "Precancerous melanosis, NOS" 87413 Mal. melanoma in precan. melanosis 87422 Lentigo maligna 87423 Lentigo maligna melanoma 87433 Superficial spreading melanoma 87443 "Acral lentiginous melanoma, malig." 87453 "Desmoplastic melanoma, malignant" 87463 Mucosal lentiginous melanoma 87613 Mal. melanoma in giant pigmented nevus 87703 Mixed epithel. & spindle cell melanoma 87713 Epithelioid cell melanoma 87723 "Spindle cell melanoma, NOS" 87733 "Spindle cell melanoma, type A" 87743 "Spindle cell melanoma, type B" 87803 "Blue nevus, malignant" 88000 "Soft tissue tumor, benign" 88003 "Sarcoma, NOS" 88013 Spindle cell sarcoma 88023 Giant cell sarcoma 88033 Small cell sarcoma 88043 Epithelioid sarcoma 88053 Undifferentiated sarcoma 88063 Desmoplastic small round cell tumor 88100 "Fibroma, NOS" 88103 "Fibrosarcoma, NOS" 88113 Fibromyxosarcoma 88123 Periosteal fibrosarcoma 88133 Fascial fibrosarcoma 88143 Infantile fibrosarcoma 88150 Solitary fibrous tumor 88153 "Solitary fibrous tumor, malignant" 88211 "Fibromatosis, aggressive" 88240 Myofibroma 88241 Myofibromatosis 88251 "Myofibroblastic tumor, NOS" 88300 "Fibrous histiocytoma, benign" 88303 "Fibrous histiocytoma, malignant" 88323 "Dermatofibrosarcoma, NOS" 88333 Pigmented dermatofibrosarcoma protuberans 88341 Giant cell fibroblastoma 88351 Plexiform fibrohistiocytic tumor 88361 Angiomatoid fibrous histiocytoma 88403 Myxosarcoma 88411 Angiomyxoma 88500 "Lipoma, NOS" 88501 Atypical lipoma 88503 "Liposarcoma, NOS" 88510 Fibrolipoma 88513 "Liposarcoma, well differentiated" 88523 Myxoid liposarcoma 88533 Round cell liposarcoma 88543 Pleomorphic liposarcoma 88553 Mixed type liposarcoma 88573 Fibroblastic liposarcoma 88583 Dedifferentiated liposarcoma 88610 "Angiolipoma, NOS" 88900 "Leiomyoma, NOS" 88901 "Leiomyomatosis, NOS" 88903 "Leiomyosarcoma, NOS" 88913 Epithelioid leiomyosarcoma 88943 Angiomyosarcoma 88953 Myosarcoma 88963 Myxoid leiomyosarcoma 88971 "Smooth muscle tumor, NOS" 89000 "Rhabdomyoma, NOS" 89003 "Rhabdomyosarcoma, NOS" 89013 "Pleomorphic rhabdomyosarcoma, adult type" 89023 Mixed type rhabdomyosarcoma 89103 Embryonal rhabdomyosarcoma 89123 Spindle cell rhabdomyosarcoma 89203 Alveolar rhabdomyosarcoma 89213 Rhabdomyosarcoma with ganglionic differentia... 89303 Endometrial stromal sarcoma 89313 "Endometrial stromal sarcoma, low grade" 89333 Adenosarcoma 89343 Carcinofibroma 89353 "Stromal sarcoma, NOS" 89361 "Gastrointestinal stromal tumor, NOS" 89363 Gastrointestinal stromal sarcoma 89403 "Mixed tumor, malignant, NOS" 89413 Carcinoma in pleomorphic adenoma 89503 Mullerian mixed tumor 89513 Mesodermal mixed tumor 89590 Benign Cystic nephroma 89591 Cystic partially differentiated nephroblastoma 89593 Malignant cystic nephroma 89601 Mesoblastic nephroma 89603 "Nephroblastoma, NOS" 89633 Malignant rhabdoid tumor 89643 Clear cell sarcoma of kidney 89703 Hepatoblastoma 89713 Pancreatoblastoma 89723 Pulmonary blastoma 89733 Pleuropulmonary blastoma 89741 Sialoblastoma 89751 Calcifying nested epithelial stromal tumor 89803 "Carcinosarcoma, NOS" 89813 "Carcinosarcoma, embryonal type" 89823 Malignant myoepithelioma 89901 "Mesenchymoma, NOS" 89903 "Mesenchymoma, malignant" 89913 Embryonal sarcoma 90003 "Brenner tumor, malignant" 90143 Serous adenocarcinofibroma 90153 Mucinous adenocarcinofibroma 90203 "Phyllodes tumor, malignant" 90403 "Synovial sarcoma, NOS" 90413 "Synovial sarcoma, spindle cell" 90423 "Synovial sarcoma, epithelioid cell" 90433 "Synovial sarcoma, biphasic" 90443 "Clear cell sarcoma,NOS (except of kidney M-8..." 90503 "Mesothelioma, malignant" 90513 "Fibrous mesothelioma, malignant" 90523 "Epithel. mesothelioma, mal." 90533 "Mesothelioma, biphasic, malignant" 90603 Dysgerminoma 90613 "Seminoma, NOS" 90623 "Seminoma, anaplastic" 90633 Spermatocytic seminoma 90642 Intratubular malignant germ cells 90643 Germinoma 90653 "Germ cell tumor, nonseminomatous" 90703 "Embryonal carcinoma, NOS" 90713 Yolk sac tumor 90723 Polyembryoma 90800 "Teratoma, benign" 90801 "Teratoma, NOS" 90803 "Teratoma, malignant, NOS" 90813 Teratocarcinoma 90823 "Malignant teratoma, undiff." 90833 "Malignant teratoma, intermediate" 90840 "Dermoid cyst, NOS" 90843 Teratoma with malig. transformation 90853 Mixed germ cell tumor 90903 "Struma ovarii, malignant" 91003 Choriocarcinoma 91013 Choriocarcinoma combined w/ other germ cell ... 91023 "Malignant teratoma, trophoblastic" 91043 Malignant placental site trophoblastic tumor 91053 "Trophoblastic tumor, epithelioid" 91103 "Mesonephroma, malignant" 91200 "Hemangioma, NOS" 91203 Hemangiosarcoma 91210 Cavernous hemangioma 91220 Venous hemangioma 91243 Kupffer cell sarcoma 91300 "Hemangioendothelioma, benign" 91301 "Hemangioendothelioma, NOS" 91303 "Hemangioendothelioma, malignant" 91310 Capillary hemangioma 91333 "Epithelioid hemangioendothelioma, malignant" 91403 Kaposi sarcoma 91500 "Hemangiopericytoma, benign" 91501 "Hemangiopericytoma, NOS" 91503 "Hemangiopericytoma, malignant" 91611 Hemangioblastoma 91703 Lymphangiosarcoma 91803 "Osteosarcoma, NOS" 91813 Chondroblastic osteosarcoma 91823 Fibroblastic osteosarcoma 91833 Telangiectatic osteosarcoma 91843 Osteosarcoma in Paget disease 91853 Small cell osteosarcoma 91863 Central osteosarcoma 91873 Instrosseous well differentiated osteosarcoma 91923 Parosteal osteosarcoma 91933 Periosteal osteosarcoma 91943 High grade surface osteosarcoma 91953 Intracortical osteosarcoma 92203 "Chondrosarcoma, NOS" 92213 Juxtacortical chondrosarcoma 92303 "Chondroblastoma, malignant" 92313 Myxoid chondrosarcoma 92403 Mesenchymal chondrosarcoma 92423 Clear cell chondrosarcoma 92433 Dedifferentiated chondrosarcoma 92501 "Giant cell tumor of bone, NOS" 92503 "Giant cell tumor of bone, malignant" 92511 Giant cell tumor of soft parts 92513 Malignant giant cell tumor of soft parts 92523 Malignant tenosynovial giant cell tumor 92603 Ewing sarcoma 92613 Adamantinoma of long bones 92703 "Odontogenic tumor, malignant" 92903 Ameloblastic odontosarcoma 93103 "Ameloblastoma, malignant" 93303 Ameloblastic fibrosarcoma 93423 Odontogenic carcinosarcoma 93501 Craniopharyngioma 93511 Adamantinomatous craniopharyngioma 93521 Papillary craniopharyngioma 93601 "Pinealoma, NOS" 93611 Pineocytoma 93623 Pineoblastoma 93630 Melanotic neuroectodermal tumor 93643 Peripheral neuroectodermal tumor 93653 Askin tumor 93703 "Chordoma, NOS" 93713 Chondroid chordoma 93723 Dedifferentiated chordoma 93803 "Glioma, malignant" 93813 Gliomatosis cerebri 93823 Mixed glioma 93831 Subependymoma 93841 Supependymal giant cell astrocytoma 93900 "Choroid plexus papilloma, NOS" 93901 Atypical choroid plexus papilloma 93903 "Choroid plexus papilloma, malignant" 93913 "Ependymoma, NOS" 93923 "Ependymoma, anaplastic" 93933 Papillary ependymoma 93941 Myxopapillary ependymoma 93953 Papillary tumor of the pineal region 94003 "Astrocytoma, NOS" 94013 "Astrocytoma, anaplastic" 94103 Protoplasmic astrocytoma 94113 Gemistocytic astrocytoma 94121 Desmoplastic infantile astrocytoma 94130 Dysembryoplastic neuroepithelial tumor 94203 Fibrillary astrocytoma 94211 Pilocytic astrocytoma 94233 Polar spongioblastoma 94243 Pleomorphic xanthoastrocytoma 94253 Pilomyxoid astrocytoma 94303 Astroblastoma 94311 Angiocentric glioma 94321 Pituicytoma 94403 "Glioblastoma, NOS" 94413 Giant cell glioblastoma 94421 Gliofibroma 94423 Gliosarcoma 94441 Chordoid glioma 94503 "Oligodendroglioma, NOS" 94513 "Oligodendroglioma, anaplastic" 94603 Oligodendroblastoma 94703 "Medulloblastoma, NOS" 94713 Desmoplastic medulloblastoma 94723 Medullomyoblastoma 94733 Primitive neuroectodermal tumor 94743 Large cell medulloblastoma 94803 "Cerebellar sarcoma, NOS" 94900 Ganglioneuroma 94903 Ganglioneuroblastoma 94920 Gangliocytoma 94930 Dysplastic gangliocytoma of cerebellum (Lher... 95003 "Neuroblastoma, NOS" 95013 "Medulloepithelioma, NOS" 95023 Teratoid medulloepithelioma 95033 "Neuroepithelioma, NOS" 95043 Spongioneuroblastoma 95051 "Ganglioglioma, NOS" 95053 "Ganglioglioma, anaplastic" 95061 Centrol neurocytoma 95083 Atypical teratoid/rhabdoid tumor 95091 Papillary glioneuronal tumor 95103 "Retinoblastoma, NOS" 95113 "Retinoblastoma, differentiated" 95123 "Retinoblastoma, undifferentiated" 95133 "Retinoblastoma, diffuse" 95203 Olfactory neurogenic tumor 95213 Olfactory neurocytoma 95223 Olfactory neuroblastoma 95233 Olfactory neuroepithelioma 95300 "Meningioma, NOS" 95301 "Meningiomatosis, NOS" 95303 "Meningioma, malignant" 95310 Meningothelial meningioma 95320 Fibrous meningioma 95330 Psammomatous meningioma 95340 Angiomatous meningioma 95370 Transitional meningioma 95381 Clear cell meningioma 95383 Papillary meningioma 95391 Atypical meningioma 95393 Meningeal sarcomatosis 95400 "Neurofibroma, NOS" 95401 "Neurofibromatosis, NOS" 95403 Malignant peripheral nerve sheath tumor 95410 Melanotic neurofibroma 95500 Plexiform neurofibroma 95600 "Neurilemoma, NOS" 95601 Neurinomatosis 95603 "Neurilemmoma, malignant" 95613 MPNST with rhabdomyoblastic differentiation 95620 Neurothekeoma 95700 "Neuroma, NOS" 95710 "Perineurioma, NOS" 95713 "Perineurioma, malignant" 95800 "Granular cell tumor, NOS" 95803 "Granular cell tumor, malignant" 95813 Alveolar soft part sarcoma 95903 "Malignant lymphoma, NOS" 95913 "Malignant lymphoma, non-Hodgkin" 95963 Composite Hodgkin and non-Hodgkin lymphoma 95973 Primary cutaneous follicle centre lymphoma 96503 "Hodgkin lymphoma, NOS" 96513 "Hodgkin lymphoma, lymphocyte-rich" 96523 "Hodgkin lymphoma, mixed cellularity, NOS" 96533 "Hodgkin lymphoma, lymphocytic deplet., NOS" 96543 "Hodgkin lymph., lymphocyt. deplet., diffuse ..." 96553 "Hodgkin lymphoma, lymphocyt. deplet., reticular" 96593 "Hodgkin lymph., nodular lymphocyte predom." 96613 Hodgkin granuloma [obs] 96623 Hodgkin sarcoma [obs] 96633 "Hodgkin lymphoma, nodular sclerosis, NOS" 96643 "Hodgkin lymphoma, nod. scler., cellular phase" 96653 "Hodgkin lymphoma, nod. scler., grade 1" 96673 "Hodgkin lymphoma, nod. scler., grade 2" 96703 "ML, small B lymphocytic, NOS" 96713 "ML, lymphoplasmacytic" 96733 Mantle cell lymphoma 96753 "ML, mixed sm. and lg. cell, diffuse" 96783 Primary effusion lymphoma 96793 Mediastinal large B-cell lymphoma 96803 "ML, large B-cell, diffuse" 96843 "ML, large B-cell, diffuse, immunoblastic, NOS" 96873 "Burkitt lymphoma, NOS" 96883 T-cell/histiocyte rich large B-cell lymphoma 96893 Splenic marginal zone B-cell lymphoma 96903 "Follicular lymphoma, NOS" 96913 "Follicular lymphoma, grade 2" 96953 "Follicular lymphoma, grade 1" 96983 "Follicular lymphoma, grade 3" 96993 "Marginal zone B-cell lymphoma, NOS" 97003 Mycosis fungoides 97013 Sezary syndrome 97023 "Mature T-cell lymphoma, NOS" 97053 Angioimmunoblastic T-cell lymphoma 97083 Subcutaneous panniculitis-like T-cell lymphoma 97093 "Cutaneous T-cell lymphoma, NOS" 97123 Intravascular large B-cell lymphoma 97143 "Anaplastic large cell lymphoma, T-cell and N..." 97163 Hepatosplenic T-cell lymphoma 97173 Intestinal T-cell lymphoma 97183 Primary cutan. CD30+ T-cell lymphoprolif. di... 97193 "NK/T-cell lymphoma, nasal and nasal-type" 97243 Syst. EBV pos. T-cell lymphoprol. disease 97253 Hydroa vacciniforme-like lymphoma 97263 Primary cutaneous gamma-delta T-cell lymphoma 97273 "Precursor cell lymphoblastic lymphoma, NOS" 97283 Precursor B-cell lymphoblastic lymphoma 97293 Precursor T-cell lymphoblastic lymphoma 97313 "Plasmacytoma, NOS" 97323 Multiple myeloma 97333 Plasma cell leukemia 97343 "Plasmacytoma, extramedullary" 97353 Plasmablastic lymphoma 97373 ALK postive large B-cell lymphoma 97383 Large B-cell lymph. arising in HHV8-assoc. multi 97403 Mast cell sarcoma 97411 Indolent systemic mastocytosis 97413 Malignant mastocytosis 97423 Mast cell leukemia 97503 Malignant histiocytosis 97511 "Langerhans cell histiocytosis, NOS" 97513 "Langerhans cell histiocytosis, NOS" 97521 "Langerhans cell histiocytosis, unifocal" 97531 "Langerhans cell histiocytosis, multifocal" 97543 "Langerhans cell histiocytosis, disseminated" 97553 Histiocytic sarcoma 97563 Langerhans cell sarcoma 97573 Interdigitating dendritic cell sarcoma 97583 Follicular dendritic cell sarcoma 97593 Fibroblastic reticular cell tumor 97603 "Immunoproliferative disease, NOS" 97613 Waldenstrom macroglobulinemia 97623 "Heavy chain disease, NOS" 97643 Immunoproliferative small intestinal disease 98003 "Leukemia, NOS" 98013 "Acute leukemia, NOS" 98053 Acute biphenotypic leukemia 98063 Mix. phenotype ac. leukemia with t;BCR-ABL1 98073 Mix. phenotype ac. leukemia with t;MLL rearrange 98083 "Mixed phenotype acute leukemia, B/myeloid, NOS" 98093 "Mixed phenotype acute leukemia, T/myeloid, NOS" 98113 "B lymphoblastic leukemia/lymphoma, NOS" 98123 B lymphoblast. leukemia/lymphoma with t;BCR-ABL1 98133 B lymphoblast. leukemia/lymphoma with t;MLL rear 98143 B lymphoblast. leukemia/lymphoma with t;TEL-AML1 98153 B lymphoblastic leukemia/lymphoma with hyperdipl 98163 B lymphoblast. leukemia/lymph. with hypodiploidy 98173 B lymphoblast. leukemia/lymphoma with t;IL3-IGH 98183 B lymphoblast. leukemia/lymphoma with t;E2A PBX1 98203 "Lymphoid leukemia, NOS" 98233 B-cell chr. lymph. leuk./small lymphocytic l... 98263 Burkitt cell leukemia 98273 Adult T-cell leukemia/lymphoma (HTLV-1 pos.) 98283 "Acute lymphoblastic leukemia, L2 type, NOS" 98313 T-cell large granular lymphocytic leukemia 98323 "Prolymphocytic leukemia, NOS" 98333 "Prolymphocytic leukemia, B-cell type" 98343 "Prolymphocytic leukemia, T-cell type" 98353 "Precursor cell lymphoblastic leukemia, NOS" 98363 Precursor B-cell lymphoblastic leukemia 98373 Precursor T-cell lymphoblastic leukemia 98403 "Acute myeloid leukemia, M6 type" 98603 "Myeloid leukemia, NOS" 98613 Acute myeloid leukemia 98633 "Chronic myeloid leukemia, NOS" 98653 Acute myeloid leukemia with t;DEK-NUP214 98663 "Acute promyelocytic leuk.,t(15;17)(q22;q11-12)" 98673 Acute myelomonocytic leukemia 98693 Acute myeloid leukemia with inv or t;RPN1-EVI1 98703 Acute basophilic leukemia 98713 Ac. myelomonocytic leuk. w abn. mar. eosinop... 98723 "Acute myeloid leukemia, minimal differentiation" 98733 Acute myeloid leukemia without maturation 98743 Acute myeloid leukemia with maturation 98753 "Chronic myelogenous leukemia, BCR/ABL positive" 98763 "Atypical chronic myeloid leuk., BCR/ABL nega..." 98913 Acute monocytic leukemia 98953 Acute myeloid leuk. with myelodysplasia-related 98963 "Acute myeloid leukemia, t(8;21)(q22;q22)" 98973 "Acute myeloid leukemia, 11q23 abnormalities" 98981 Transient abnormal myelopoiesis 98983 Myeloid leukemia associated with Down Syndrome 99103 Acute megakaryoblastic leukemia 99113 Acute myeloid leukemia (megakar. blast.) with t; 99203 Therapy related myeloid neoplasm 99303 Myeloid sarcoma 99313 Acute panmyelosis with myelofibrosis 99403 Hairy cell leukemia 99453 "Chronic myelomonocytic leukemia, NOS" 99463 Juvenile myelomonocytic leukemia 99483 Aggressive NK-cell leukemia 99503 Polycythemia vera 99603 "Myeloproliferative neoplasm, NOS" 99613 Primary myelofibrosis 99623 Essential thrombocythemia 99633 Chronic neutrophilic leukemia 99643 "Chronic eosinophilic leukemia, NOS" 99653 Myeloid&lymphoid neoplasms with PDGFRB rearrange 99663 Myeloid neoplasms with PDGFRB rearrangement 99673 Myeloid&lymphoid neoplasm with FGFR1 abnormaliti 99701 "Lymphoproliferative disorder, NOS" 99711 "Post transplant lymphoproliferative disorder, NO" 99713 Polymorphic post transplant lymphoproliferative 99751 "Myeloproliferative disease, NOS" 99753 "Myeloproliferative neoplasm, unclassifiable" 99803 Refractory anemia 99823 Refractory anemia with sideroblasts 99833 Refractory anemia with excess blasts 99843 Refract. anemia with excess blasts in transf... 99853 Refractory cytopenia with multilineage dyspl... 99863 Myelodysplastic syndr. with 5q deletion synd... 99873 "Therapy-related myelodysplastic syndrome, NOS" 99893 "Myelodysplastic syndrome, NOS" 99913 Refractory neutropenia 99923 Refractory thrombocytopenia 341 PLOCCD PLCCD1 PLCCD2 PLCCD3 0 external upper lip 1 external lower lip 2 "external lip, NOS" 3 mucose of uppper lip 4 mucosa of lower lip 5 "mucosa of lip, NOS" 6 commissure of lip 8 overlapping lesion of lip 9 "lip, NOS" 19 base of tongue 20 "dorsal surface of tongue, NOS" 21 border of tongue 22 "ventral surface of tongue, NOS" 23 anterior 2/3 of tongue 24 lingual tonsil 28 overlapping lesion of tongue 29 "tongue, NOS" 30 upper gum 31 lower gum 39 "gum, NOS" 40 anterior floor of mouth 41 lateral floor of mouth 48 overlapping lesion of floor of mouth 49 "floor of mouth, NOS" 50 hard palate 51 "soft palate, NOS" 52 uvula 58 overlapping lesion of palate 59 "palate, NOS" 60 cheek mucosa 61 vestibule of mouth 62 retromolar area 68 overlappinglesionofotherandunspecifiedpartso... 69 "mouth, NOS" 79 parotid gland 80 submandibular gland 81 sublingual gland 88 overlapping lesion of major salivary glands 89 "major salivary gland, NOS" 90 tonsillar fossa 91 tonsillar pillar 98 overlapping lesion of tonsil 99 "tonsil, NOS" 100 vallecula 101 anterior surface of epiglottis 102 lateral wall of oropharynx 103 posterior wall of oropharynx 104 branchial cleft 108 overlapping lesion of oropharynx 109 "oropharynx, NOS" 110 superior wall of nasopharyx 111 posterior wall of nasopharyx 112 lateral wall of nasopharyx 113 anterior wall of nasopharyx 118 overlapping lesion of nasopharyx 119 "nasopharyx, NOS" 129 "nasopharyxyriform sinus, NOS" 130 postcricoid region 131 hypopharyngeal aspect of aryepiglottic fold 132 posterior wall of hypopharynx 138 overlapping lesion of hypopharyx 139 "hypopharyx, NOS" 140 "pharyx, NOS" 142 waldeyer ring 148 "overlappinglesionoflip,oralcavityandpharynx" 150 cervical esophagus 151 thoracic esophagus 152 abdominal esophagus 153 upper third of esophagus 154 middle third of esophagus 155 lower third of esophagus 158 overlapping lesion of esophagus 159 "esophagus, NOS" 160 "cardia, NOS" 161 fundus of stomach 162 body of stomach 163 gastric antrum 164 pylorus 165 lesser curvature of stomach 166 greater curvature of stomach 168 overlapping lesion of stomach 169 "stomach, NOS" 170 duodenum 171 jejunum 172 ileum 173 Meckel diverticulum 178 overlapping lesion of small intestine 179 "small intestine, NOS" 180 cecum 181 appendix 182 ascending colon 183 hepatic flexure of colon 184 transverse colon 185 splenic flexure of colon 186 descending colon 187 sigmoid colon 188 overlapping lesion of colon 189 "colon, NOS" 199 rectosigmoid junction 209 "rectum, NOS" 210 "anus, NOS" 211 anal canal 212 cloacogenic zone 218 "overlappinglesionofrectum,anusandanalcanal" 220 liver 221 intrahepatic bile duct 239 "gallbladder, NOS" 240 extrahepatic bile duct 241 ampulla of Vater 248 overlapping lesion of biliary tract 249 "billary tract, NOS" 250 head of pancreas 251 body of pancreas 252 tail of pancreas 253 pancreatic duct 254 islets of Langerhans 257 other specified parts of pancreas 258 overlapping lesion of pancreas 259 "pancreas, NOS" 260 "intestinal tract, NOS" 268 overlapping lesion of digestive system 269 "gastrointestinal tract, NOS" 300 nasal cavity 301 middle ear 310 maxillary sinus 311 ethmoid sinus 312 frontal sinus 313 sphenoid sinus 318 overlapping lesion of accessory sinuses 319 "accessory sinus, NOS" 320 glottis 321 supraglottis 322 subglottis 323 laryngeal cartilage 328 overlapping lesion of larynx 329 "larynx, NOS" 339 trachea 340 main bronchus 341 "upper lobe, lung" 342 "middle lobe, lung" 343 "lower lobe, lung" 348 overlapping lesion of lung 349 "lung, NOS" 379 thymus 380 heart 381 anterior mediastinum 382 posterior mediastinum 383 "mediastinum, NOS" 384 "pleura, NOS" 388 "overlappinglesionofheart,mediastinumandpleura" 390 "upper respiratory tract, NOS" 398 overlappinglesionofrespiratorysystemandintra... 399 ill-defined sites within respiratory system 400 "longboneofupperlimb,scapulaandassociatedjoints" 401 short bone of upper limb and associated joints 402 long bones of lower limb and associated joints 403 short bones of lower limb and associated joints 408 "overlappinglesionofbones,jointsandarticularc..." 409 "bones of lomb, NOS" 410 bones of skull and face and associated joints 411 mandible 412 vertebral column 413 "rib, sternum, clavicle and associated joints" 414 "pelvicbones,sacrum,coccyxandassociatedjoints" 418 "overlappinglesionofbones,jointsandarticularc..." 419 "bone, NOS" 420 blood 421 bone marrow 422 spleen 423 "reticuloendothelial system, NOS" 424 "hematopoietic system, NOS" 440 "skin of lip, NOS" 441 eyelid 442 external ear 443 skin of other and unspecified parts of face 444 skin of scalp and neck 445 skin of trunc 446 skin of upper limb and shoulder 447 skin of lower limb and hip 448 overlapping lesion of skin 449 "skin, NOS" 470 peripheralnervesandautonomicnervoussystemofh... 471 peripheralnervesandautonomicnervoussystemofu... 472 peripheralnervesandautonomicnervoussystemofl... 473 peripheralnervesandautonomicnervoussystemoft... 474 peripheralnervesandautonomicnervoussystemofa... 475 peripheralnervesandautonomicnervoussystemofp... 476 peripheralnervesandautonomicnervoussystemoft... 478 overlappinglesionofperipheralnervesandautono... 479 "autonomic nervous system, NOS" 480 retroperitoneum 481 specified parts of peritoneum 482 "peritoneum, NOS" 488 overlapping lesion of retroperitoneum 490 "connective,subcutaneousandothersofttissuesof..." 491 "connective,subcutaneousandothersofttissuesof..." 492 "connective,subcutaneousandothersofttissuesof..." 493 "connective,subcutaneousandothersofttissuesof..." 494 "connective,subcutaneousandothersofttissuesof..." 495 "connective,subcutaneousandothersofttissuesof..." 496 "connective,subcutaneousandothersofttissuesof..." 498 "overlappinglesionofconnective,subcutaneousan..." 499 "connective,subcutaneousandothersofttissues,NOS" 500 nipple 501 central portion of breast 502 upper-inner quadrant of breast 503 lower-inner quadrant of breast 504 upper-outer quadrant of breast 505 upper-outer quadrant of breast 506 axillary tail of breast 508 overlapping lesion of breast 509 "breast, NOS" 510 labium majus 511 labium minus 512 clitoris 518 overlapping lesion of vulva 519 "vulva, NOS" 529 "vagina, NOS" 530 endocervix 531 exocervix 538 overlapping lesion of cervix uteri 539 "cervix uteri, NOS" 540 isthmus uteri 541 endometrium 542 myometrium 543 fundus uteri 548 overlapping lesion of corpus uteri 549 "corpus uteri, NOS" 559 "uterus, NOS" 569 "ovary, NOS" 570 fallopian tube 571 broad ligament 572 round ligament 573 parametrium 574 uterine adnexa 577 other specified parts of female genital organs 578 overlapping lesion of female genital organs 579 "female genital tract, NOS" 589 "placenta, NOS" 600 prepuce 601 glans penis 602 body of penis 608 overlapping lesion of penis 609 "penis, NOS" 619 prostate gland 620 undescended testis 621 descended testis 629 "testis, NOS" 630 epididymis 631 spermatic cord 632 "scrotum, NOS" 637 other specified parts of male genital organs 638 overlapping lesion of male genital organs 639 "male genital tract, NOS" 649 "kidney, NOS" 659 renal pelvis 669 ureter 670 trigone of bladder 671 dome of bladder 672 lateral wall of bladder 673 anterior wall of bladder 674 posterior of bladder 675 bladder neck 676 ureteric orifice 677 urachus 678 overlapping lesion of bladder 679 "bladder, NOS" 680 urethra 681 paraurethral gland 688 overlapping lesion of urinary organs 689 "urinary system, NOS" 690 conjuctiva 691 "cornea, NOS" 692 retina 693 choroid 694 ciliary body 695 lacrimal gland 696 "orbit, NOS" 698 overlapping lesion of eye and adnexa 699 "eye, NOS" 700 cerebral meninges 701 spinal meninges 709 "meninges, NOS" 710 cerebrum 711 frontal lobe 712 temperal lobe 713 parietal lobe 714 occipital lobe 715 "ventricle, NOS" 716 cerebellum 717 brain stem 718 overlapping lesion of brain 719 "brain, NOS" 720 spinal cord 721 cauda equina 722 olfactory nerve 723 optic nerve 724 acoustic nerve 725 "cranial nerve, NOS" 728 overlappinglesionofbrainandcentralnervoussystem 729 "nervous system, NOS" 739 "thyroid gland, NOS" 740 cortex of adrenal gland 741 medulla of adrenal gland 749 "adrenal gland, NOS" 750 parathyroid gland 751 pituitary gland 752 craniopharyngeal duct 753 pineal gland 754 carotid body 755 aortic body and other paraganglia 758 overlappinglesionofendocrineglandsandrelated... 759 "endocrine gland, NOS" 760 "head, face or neck, NOS" 761 "thorax, NOS" 762 "abdomen, NOS" 763 "pelvis, NOS" 764 "upper limb, NOS" 765 "lower limb, NOS" 767 other ill-defined sites 768 overlapping lesion of ill-defined sites 770 "lymph nodes of head, face and neck" 771 intrathoracic lymph nodes 772 intra-abdominal lymph nodes 773 lymph nodes of axilla of arm 774 lymph nodes of inguinal region or leg 775 pelvic lymph nodes 778 lymph nodes of multiple regions 779 "lymph node, NOS" 809 unknown primary sites 343 IFCDATR 1 yes 2 no 3 statement by physician 4 IC will follow \ No newline at end of file diff --git a/test_data/test_logic/dropzone/studies/PMCST000AAA_diagnosis_codebook.txt.sha1 b/test_data/test_logic/dropzone/studies/PMCST000AAA_diagnosis_codebook.txt.sha1 new file mode 100644 index 0000000..24531c1 --- /dev/null +++ b/test_data/test_logic/dropzone/studies/PMCST000AAA_diagnosis_codebook.txt.sha1 @@ -0,0 +1 @@ +8cc20a3917db3e251d9426d078ce74969e531931 PMCST000AAA_diagnosis_codebook.txt diff --git a/test_data/test_logic/dropzone/studies/PMCST000AAA_individual.txt b/test_data/test_logic/dropzone/studies/PMCST000AAA_individual.txt new file mode 100644 index 0000000..4d7974e --- /dev/null +++ b/test_data/test_logic/dropzone/studies/PMCST000AAA_individual.txt @@ -0,0 +1,18 @@ +"MARK:","ID","IDAA","INDIVIDUAL_ID","SEX","IFCDATR","IFCGIV","IFCMAT","IFCCOM","DTOB" +,217,8000208,PAT1,1,2,,,,15/09/2000 0:00:00 +,217,8000216,PAT2,1,2,,,,18/02/1989 0:00:00 +,217,8000233,PAT3,1,2,,,,07/11/2001 0:00:00 +,217,8000250,PAT4,1,2,,,,23/06/1998 0:00:00 +,217,8000268,PAT5,1,2,,,,23/04/2001 0:00:00 +,217,8000273,PAT6,1,2,,,,28/03/2001 0:00:00 +,217,8000323,PAT7,1,2,,,,08/01/1999 0:00:00 +,217,8000333,PAT8,1,2,,,,25/12/1997 0:00:00 +,217,8000345,PAT9,1,2,,,,29/09/1991 0:00:00 +,217,8000217,PAT10,1,2,,,,18/02/1989 0:00:00 +,217,8000238,PAT11,1,2,,,,07/11/2001 0:00:00 +,217,8000251,PAT12,2,2,,,,23/06/1998 0:00:00 +,217,8000269,PAT13,2,2,,,,23/04/2001 0:00:00 +,217,8000274,PAT14,2,2,,,,28/03/2001 0:00:00 +,217,8000324,PAT15,2,2,,,,08/01/1999 0:00:00 +,217,8000334,PAT16,2,2,,,,25/12/1997 0:00:00 +,217,8000346,PAT17,2,2,,,,29/09/1991 0:00:00 diff --git a/test_data/test_logic/dropzone/studies/PMCST000AAA_individual.txt.sha1 b/test_data/test_logic/dropzone/studies/PMCST000AAA_individual.txt.sha1 new file mode 100644 index 0000000..92c2fd7 --- /dev/null +++ b/test_data/test_logic/dropzone/studies/PMCST000AAA_individual.txt.sha1 @@ -0,0 +1 @@ +d70a6c8727d3d8dd40eaf2cf87eb71d9ee581387 PMCST000AAA_individual.txt diff --git a/test_data/test_logic/dropzone/studies/PMCST000AAA_individual_codebook.txt b/test_data/test_logic/dropzone/studies/PMCST000AAA_individual_codebook.txt new file mode 100644 index 0000000..9d23109 --- /dev/null +++ b/test_data/test_logic/dropzone/studies/PMCST000AAA_individual_codebook.txt @@ -0,0 +1 @@ +1 SEX 1 male 2 female 9 unknown 2 SIGYN IFCGIV IFCMAT IFCCOM IFCREF NOREGIS CLEXPYN CYTOLYN HISTOYN IMAGEYN TMARKYN PATDCOGR PROTYN ELIGYN TXSTART SIGYNX SIGYNY 1 yes 2 no 8 not applicable 8 HOSPREC HOSPDIAG HOSPASS HOSPTRAN 200 AMC 201 UMCG 202 AZM 203 CZE 204 ErasmusMC 207 JBZ 208 LUMC 213 EZT 214 Radboudumc 216 VUMC 217 UMCU 220 PMC 332 DIAGCD PDGCD1 PDGCD2 PDGCD3 61000 FanconiÔs anaemia 61900 Aplastic anaemia 70000 KostmannÔs disease 76100 HLH 80000 "Neoplasm, benign" 80001 "Neoplasm, uncertain whether benign or malignant" 80003 "Neoplasm, malignant" 80010 "Tumor cells, benign" 80011 "Tumor cells, uncertain whether benign or mal..." 80013 "Tumor cells, malignant" 80023 "Malignant tumor, small cell type" 80033 "Malignant tumor, giant cell type" 80043 "Malignant tumor, spindle cell type" 80050 "Clear cell tumor, NOS" 80053 "Malignant tumor, clear cell type" 80100 "Epithelial tumor, benign" 80102 "Carcinoma in situ, NOS" 80103 "Carcinoma, NOS" 80113 "Epithelioma, malignant" 80123 "Large cell carcinoma, NOS" 80133 Large cell neuroendocrine carcinoma 80143 Large cell carcinoma with rhabdoid phenotype 80153 Glassy cell carcinoma 80203 "Carcinoma, undifferentiated type, NOS" 80213 "Carcinoma, anaplastic type, NOS" 80223 Pleomorphic carcinoma 80303 Giant cell and spindle cell carcinoma 80313 Giant cell carcinoma 80323 Spindle cell carcinoma 80333 Pseudosarcomatous carcinoma 80343 Polygonal cell carcinoma 80353 Carcinoma with osteoclast-like giant cells 80413 "Small cell carcinoma, NOS" 80423 Oat cell carcinoma 80433 "Small cell carcinoma, fusiform cell" 80443 "Small cell carcinoma, intermediate cell" 80453 Combined small cell carcinoma 80463 Non-small cell carcinoma 80502 Papillary carcinoma in situ 80503 "Papillary carcinoma, NOS" 80513 "Verrucous carcinoma, NOS" 80522 "Papillary squamous cell carcinoma, non-invasive" 80523 Papillary squamous cell carcinoma 80702 "Squamous cell carcinoma in situ, NOS" 80703 "Squamous cell carcinoma, NOS" 80713 "Sq. cell carcinoma, keratinizing, NOS" 80723 "Sq. cell carcinoma, lg. cell, non-ker." 80733 "Sq. cell carcinoma, sm. cell, non-ker." 80743 "Sq. cell carcinoma, spindle cell" 80753 "Squamous cell carcinoma, adenoid" 80762 Sq. cell carc. in situ with question. stroma... 80763 "Sq. cell carcinoma, micro-invasive" 80770 "Squamous intraepithelial neoplasia, low grade" 80772 "Squamous intraepithelial neoplasia, high grade" 80783 Squamous cell carcinoma with horn formation 80802 Queyrat erythroplasia 80812 Bowen disease 80823 Lymphoepithelial carcinoma 80833 Basaloid squamous cell carcinoma 80843 "Squamous cell carcinoma, clear cell type" 80903 "Basal cell carcinoma, NOS" 80913 Multifocal superficial basal cell carcinoma 80923 "Infiltrating basal cell carcinoma, NOS" 80933 "Basal cell carcinoma, fibroepithelial" 80943 Basosquamous carcinoma 80953 Metatypical carcinoma 80973 "Basal cell carcinoma, nodular" 80983 Adenoid basal cell carcinoma 81023 Trichilemmocarcinoma 81103 Pilomatrix carcinoma 81202 Transitional cell carcinoma in situ 81203 "Transitional cell carcinoma, NOS" 81213 Schneiderian carcinoma 81223 "Trans. cell carcinoma, spindle cell" 81233 Basaloid carcinoma 81243 Cloacogenic carcinoma 81302 "Papillary trans. cell carcinoma, non-invasive" 81303 Papillary trans. cell carcinoma 81313 "Transitional cell carcinoma, micropapillary" 81400 "Adenoma, NOS" 81402 Adenocarcinoma in situ 81403 "Adenocarcinoma, NOS" 81413 Scirrhous adenocarcinoma 81423 Linitis plastica 81433 Superficial spreading adenocarcinoma 81443 "Adenocarcinoma, intestinal type" 81453 "Carcinoma, diffuse type" 81460 Monomorphic adenoma 81473 Basal cell adenocarcinoma 81480 "Glandular intraepithelial neoplasia, low grade" 81482 "Glandular intraepithelial neoplasia, high grade" 81500 "Pancreatic endocrine tumor, benign" 81501 "Pancreatic endocrine tumor, NOS" 81503 "Pancreatic endocrine tumor, malignant" 81513 "Insulinoma, malignant" 81523 "Glucagonoma, malignant" 81533 "Gastrinoma, malignant" 81543 "Mix. pancreatic endocrine&exocrine tumor, mal" 81553 Vipoma 81563 "Somatostatinoma, malignant" 81573 "Enteroglucagonoma, malignant" 81581 "Endocrine tumor, functioning, NOS" 81603 Cholangiocarcinoma 81613 Bile duct cystadenocarcinoma 81623 Klatskin tumor 81630 "Pancreatobiliary neoplasm, non-invasive" 81632 "Pap. neoplasm,pancreatobiliary-type,high gr. int" 81633 Pancreatobiliary-type carcinoma 81703 "Hepatocellular carcinoma, NOS" 81713 "Hepatocellular carcinoma, fibrolamellar" 81723 "Hepatocellular carcinoma, scirrhous" 81733 "Hepatocellular carcinoma, spindle cell variant" 81743 "Hepatocellular carcinoma, clear cell type" 81753 "Hepatocellular carcinoma, pleomorphic type" 81803 Comb. hepatocel. carcinoma & cholangiocarcinoma 81903 Trabecular adenocarcinoma 82003 Adenoid cystic carcinoma 82012 Cribriform carcinoma in situ 82013 Cribriform carcinoma 82102 Adenocarcinoma in situ in adenomatous polyp 82103 Adenocarcinoma in adenomatous polyp 82113 Tubular adenocarcinoma 82133 Serrated adenocarcinoma 82143 Parietal cell carcinoma 82153 Adenocarcinoma of anal glands 82202 Adenocarcinoma in situ in familial polyp. coli 82203 Adenocarcinoma in adenoma. polyposis coli 82212 Adenocarc. in situ in mult. adenomatous polyps 82213 Adenocarcinoma in mult. adenomatous polyps 82302 "Duct carcinoma in situ, solid type" 82303 "Solid carcinoma, NOS" 82313 Carcinoma simplex 82401 Carcinoid tumor of uncertain malignant potential 82403 "Carcinoid tumor, malignant" 82413 Enterochromaffin cell carcinoid 82423 "Enterochromaffin-like cell tumor, malignant" 82433 Goblet cell carcinoid 82443 Mixed adenoneuroendocrine carcinoma 82453 Adenocarcinoid tumor 82463 Neuroendocrine carcinoma 82473 Merkel cell carcinoma 82493 Atypical carcinoid tumor 82503 Bronchiolo-alveolar adenocarcinoma 82513 Alveolar adenocarcinoma 82523 "Bronchiolo-alveolar carcinoma, non-mucinous" 82533 "Bronchiolo-alveolar carcinoma, mucinous" 82543 "Bronch.-alv. carc., mixed mucin. and non-muc..." 82553 Adenocarcinoma with mixed subtypes 82600 "Papillary adenoma, NOS" 82603 "Papillary adenocarcinoma, NOS" 82612 Adenocarcinoma in situ in villous adenoma 82613 Adenocarcinoma in villous adenoma 82623 Villous adenocarcinoma 82632 Adenocarcinoma in situ in tubulovillous adenoma 82633 Adenocarcinoma in tubulovillous adenoma 82653 "Micropapillary carcinoma, NOS" 82700 Chromophobe adenoma 82703 Chromophobe carcinoma 82710 Prolactinoma 82720 "Pituitary adenoma, NOS" 82723 "Pituitary carcinoma, NOS" 82800 Acidophil adenoma 82803 Acidophil carcinoma 82810 Mixed acidophil-basophil adenoma 82813 Mixed acidophil-basophil carcinoma 82900 Oxyphilic adenoma 82903 Oxyphilic adenocarcinoma 83000 Basophil adenoma 83003 Basophil carcinoma 83100 Clear cell adenoma 83103 "Clear cell adenocarcinoma, NOS" 83123 Renal cell carcinoma 83133 Clear cell adenocarcinofibroma 83143 Lipid-rich carcinoma 83153 Glycogen-rich carcinoma 83163 Cyst-associated renal cell carcinoma 83173 "Renal cell carcinoma, chromophobe type" 83183 "Renal cell carcinoma, sarcomatoid" 83193 Collecting duct carcinoma 83203 Granular cell carcinoma 83223 Water-clear cell adenocarcinoma 83230 Mixed cell adenoma 83233 Mixed cell adenocarcinoma 83303 "Follicular adenocarcinoma, NOS" 83313 Follicular adenocarcinoma well diff. 83323 Follicular adenocarcinoma trabecular 83333 Fetal adenocarcinoma 83353 "Follicular carcinoma, minimally invasive" 83373 Insular carcinoma 83403 "Papillary carcinoma, follicular variant" 83413 Papillary microcarcinoma 83423 "Papillary carcinoma, oxyphilic cell" 83433 "Papillary carcinoma, encapsulated" 83443 "Papillary carcinoma, columnar cell" 83453 Medullary carcinoma with amyloid stroma 83463 Mixed medullary-follicular carcinoma 83473 Mixed medullary-papillary carcinoma 83503 Nonencapsulated sclerosing carcinoma 83700 "Adrenal cortical adenoma, NOS" 83703 Adrenal cortical carcinoma 83803 Endometrioid carcinoma 83813 "Endometrioid adenofibroma, malignant" 83823 "Endometrioid adenocarcinoma, secretory variant" 83833 "Endometrioid adenocarcinoma, ciliated cell v..." 83843 "Adenocarcinoma, endocervical type" 83903 Skin appendage carcinoma 84003 Sweat gland adenocarcinoma 84013 Apocrine adenocarcinoma 84023 "Nodular hidradenoma, malignant" 84033 Malignant eccrine spiradenoma 84073 Sclerosing sweat duct carcinoma 84083 Eccrine papillary adenocarcinoma 84093 "Eccrine poroma, malignant" 84103 Sebaceous adenocarcinoma 84133 Eccrine adenocarcinoma 84203 Ceruminous adenocarcinoma 84303 Mucoepidermoid carcinoma 84403 "Cystadenocarcinoma, NOS" 84413 "Serous cystadenocarcinoma, NOS" 84421 "Serous cystadenoma, borderline malignancy (C..." 84503 "Papillary cystadenocarcinoma, NOS" 84511 "Papillary cystadenoma, borderline malignancy..." 84523 Solid pseudopapillary carcinoma 84532 "Intraductal papillary-mucinous carcinoma, no..." 84533 "Intraductal papillary-mucinous carcinoma, in..." 84603 Papillary serous cystadenocarcinoma 84613 Serous surface papillary carcinoma 84621 Serous papillary cystic tumor of borderline ... 84702 "Mucinous cystadenocarcinoma, non-invasive" 84703 "Mucinous cystadenocarcinoma, NOS" 84713 Papillary mucinous cystadenocarcinoma 84721 Mucinous cystic tumor of borderline malignan... 84731 "Papillary mucinous cystadenoma, borderline m..." 84803 Mucinous adenocarcinoma 84813 Mucin-producing adenocarcinoma 84823 "Mucinous adenocarcinoma, endocervical type" 84903 Signet ring cell carcinoma 85002 "Intraductal carcinoma, noninfiltrating, NOS" 85003 "Infiltrating duct carcinoma, NOS" 85012 "Comedocarcinoma, non-infiltrating" 85013 "Comedocarcinoma, NOS" 85023 Secretory carcinoma of breast 85032 Noninfiltrating intraductal papillary adenoc... 85033 Intraductal papillary adenocarcinoma with in... 85042 Noninfiltrating intracystic carcinoma 85043 "Intracystic carcinoma, NOS" 85072 Intraductal micropapillary carcinoma 85083 Cystic hypersecretory carcinoma 85103 "Medullary carcinoma, NOS" 85123 Medullary carcinoma with lymphoid stroma 85133 Atypical medullary carcinoma 85143 "Duct carcinoma, desmoplastic type" 85202 Lobular carcinoma in situ 85203 "Lobular carcinoma, NOS" 85213 Infiltrating ductular carcinoma 85222 Intraductal and lobular in situ carcinoma 85223 Infiltrating duct and lobular carcinoma 85233 Infiltr. duct mixed with other types of carc... 85243 Infiltrating lobular mixed with other types ... 85253 Polymorphous low grade adenocarcinoma 85303 Inflammatory carcinoma 85403 "Paget disease, mammary" 85413 Paget dis. & infil. duct carcinoma 85423 "Paget disease, extramammary" 85433 Paget disease and intraductal ca. 85503 Acinar cell carcinoma 85513 Acinar cell cystadenocarcinoma 85603 Adenosquamous carcinoma 85613 "Warthin tumor, malignant" 85623 Epithelial-myoepithelial carcinoma 85703 Adenocarcinoma with squamous metaplasia 85713 Adenocarcinoma w cartilag. & oss. metaplas. 85723 Adenocarcinoma with spindle cell mataplasia 85733 Adenocarcinoma with apocrine metaplasia 85743 Adenocarcinoma with neuroendocrine differen. 85753 "Metaplastic carcinoma, NOS" 85763 Hepatoid adenocarcinoma 85803 "Thymoma, malignant, NOS" 85813 "Thymoma, type A, malignant" 85823 "Thymoma, type AB, malignant" 85833 "Thymoma, type B1, malignant" 85843 "Thymoma, type B2, malignant" 85853 "Thymoma, type B3, malignant" 85863 "Thymic carcinoma, NOS" 85883 Spindle epithelial tumor with thymus-like el... 85893 Carcinoma showing thymus-like element 85903 "Ovarian stromal tumor, mal." 86003 "Thecoma, malignant" 86201 "Granulosa cell tumor, adult type" 86203 "Granulosa cell tumor, malignant" 86211 Granulosa cell-theca cell tumor 86221 "Granulosa cell tumor, juvenile" 86303 "Androblastoma, malignant" 86311 Sertoli-Leydig cell tumor of intermediate differ 86313 "Sertoli-Leydig cell tumor, poorly differenti..." 86323 "Gynandroblastoma, malignant" 86343 "Sertoli-Leydig cl tum., p.d. w heterologous ..." 86401 "Sertoli cell tumor, NOS" 86403 Sertoli cell carcinoma 86501 "Leydig cell tumor, NOS" 86503 "Leydig cell tumor, malignant" 86703 "Steroid cell tumor, malignant" 86801 "Paraganglioma, NOS" 86803 "Paraganglioma, malignant" 86913 "Aortic body tumor, malignant" 86923 "Carotid body tumor, malignant" 86933 "Extra-adrenal paraganglioma, malignant" 87000 Pheochromocytoma NOS 87003 Pheochromocytoma 87103 Glomangiosarcoma 87202 Melanoma in situ 87203 "Malignant melanoma, NOS" 87213 Nodular melanoma 87223 Balloon cell melanoma 87233 "Malignant melanoma, regressing" 87280 Diffuse melanocytosis 87281 Meningeal melanocytoma 87283 Meningeal melanomatosis 87303 Amelanotic melanoma 87403 Mal. melanoma in junctional nevus 87412 "Precancerous melanosis, NOS" 87413 Mal. melanoma in precan. melanosis 87422 Lentigo maligna 87423 Lentigo maligna melanoma 87433 Superficial spreading melanoma 87443 "Acral lentiginous melanoma, malig." 87453 "Desmoplastic melanoma, malignant" 87463 Mucosal lentiginous melanoma 87613 Mal. melanoma in giant pigmented nevus 87703 Mixed epithel. & spindle cell melanoma 87713 Epithelioid cell melanoma 87723 "Spindle cell melanoma, NOS" 87733 "Spindle cell melanoma, type A" 87743 "Spindle cell melanoma, type B" 87803 "Blue nevus, malignant" 88000 "Soft tissue tumor, benign" 88003 "Sarcoma, NOS" 88013 Spindle cell sarcoma 88023 Giant cell sarcoma 88033 Small cell sarcoma 88043 Epithelioid sarcoma 88053 Undifferentiated sarcoma 88063 Desmoplastic small round cell tumor 88100 "Fibroma, NOS" 88103 "Fibrosarcoma, NOS" 88113 Fibromyxosarcoma 88123 Periosteal fibrosarcoma 88133 Fascial fibrosarcoma 88143 Infantile fibrosarcoma 88150 Solitary fibrous tumor 88153 "Solitary fibrous tumor, malignant" 88211 "Fibromatosis, aggressive" 88240 Myofibroma 88241 Myofibromatosis 88251 "Myofibroblastic tumor, NOS" 88300 "Fibrous histiocytoma, benign" 88303 "Fibrous histiocytoma, malignant" 88323 "Dermatofibrosarcoma, NOS" 88333 Pigmented dermatofibrosarcoma protuberans 88341 Giant cell fibroblastoma 88351 Plexiform fibrohistiocytic tumor 88361 Angiomatoid fibrous histiocytoma 88403 Myxosarcoma 88411 Angiomyxoma 88500 "Lipoma, NOS" 88501 Atypical lipoma 88503 "Liposarcoma, NOS" 88510 Fibrolipoma 88513 "Liposarcoma, well differentiated" 88523 Myxoid liposarcoma 88533 Round cell liposarcoma 88543 Pleomorphic liposarcoma 88553 Mixed type liposarcoma 88573 Fibroblastic liposarcoma 88583 Dedifferentiated liposarcoma 88610 "Angiolipoma, NOS" 88900 "Leiomyoma, NOS" 88901 "Leiomyomatosis, NOS" 88903 "Leiomyosarcoma, NOS" 88913 Epithelioid leiomyosarcoma 88943 Angiomyosarcoma 88953 Myosarcoma 88963 Myxoid leiomyosarcoma 88971 "Smooth muscle tumor, NOS" 89000 "Rhabdomyoma, NOS" 89003 "Rhabdomyosarcoma, NOS" 89013 "Pleomorphic rhabdomyosarcoma, adult type" 89023 Mixed type rhabdomyosarcoma 89103 Embryonal rhabdomyosarcoma 89123 Spindle cell rhabdomyosarcoma 89203 Alveolar rhabdomyosarcoma 89213 Rhabdomyosarcoma with ganglionic differentia... 89303 Endometrial stromal sarcoma 89313 "Endometrial stromal sarcoma, low grade" 89333 Adenosarcoma 89343 Carcinofibroma 89353 "Stromal sarcoma, NOS" 89361 "Gastrointestinal stromal tumor, NOS" 89363 Gastrointestinal stromal sarcoma 89403 "Mixed tumor, malignant, NOS" 89413 Carcinoma in pleomorphic adenoma 89503 Mullerian mixed tumor 89513 Mesodermal mixed tumor 89590 Benign Cystic nephroma 89591 Cystic partially differentiated nephroblastoma 89593 Malignant cystic nephroma 89601 Mesoblastic nephroma 89603 "Nephroblastoma, NOS" 89633 Malignant rhabdoid tumor 89643 Clear cell sarcoma of kidney 89703 Hepatoblastoma 89713 Pancreatoblastoma 89723 Pulmonary blastoma 89733 Pleuropulmonary blastoma 89741 Sialoblastoma 89751 Calcifying nested epithelial stromal tumor 89803 "Carcinosarcoma, NOS" 89813 "Carcinosarcoma, embryonal type" 89823 Malignant myoepithelioma 89901 "Mesenchymoma, NOS" 89903 "Mesenchymoma, malignant" 89913 Embryonal sarcoma 90003 "Brenner tumor, malignant" 90143 Serous adenocarcinofibroma 90153 Mucinous adenocarcinofibroma 90203 "Phyllodes tumor, malignant" 90403 "Synovial sarcoma, NOS" 90413 "Synovial sarcoma, spindle cell" 90423 "Synovial sarcoma, epithelioid cell" 90433 "Synovial sarcoma, biphasic" 90443 "Clear cell sarcoma,NOS (except of kidney M-8..." 90503 "Mesothelioma, malignant" 90513 "Fibrous mesothelioma, malignant" 90523 "Epithel. mesothelioma, mal." 90533 "Mesothelioma, biphasic, malignant" 90603 Dysgerminoma 90613 "Seminoma, NOS" 90623 "Seminoma, anaplastic" 90633 Spermatocytic seminoma 90642 Intratubular malignant germ cells 90643 Germinoma 90653 "Germ cell tumor, nonseminomatous" 90703 "Embryonal carcinoma, NOS" 90713 Yolk sac tumor 90723 Polyembryoma 90800 "Teratoma, benign" 90801 "Teratoma, NOS" 90803 "Teratoma, malignant, NOS" 90813 Teratocarcinoma 90823 "Malignant teratoma, undiff." 90833 "Malignant teratoma, intermediate" 90840 "Dermoid cyst, NOS" 90843 Teratoma with malig. transformation 90853 Mixed germ cell tumor 90903 "Struma ovarii, malignant" 91003 Choriocarcinoma 91013 Choriocarcinoma combined w/ other germ cell ... 91023 "Malignant teratoma, trophoblastic" 91043 Malignant placental site trophoblastic tumor 91053 "Trophoblastic tumor, epithelioid" 91103 "Mesonephroma, malignant" 91200 "Hemangioma, NOS" 91203 Hemangiosarcoma 91210 Cavernous hemangioma 91220 Venous hemangioma 91243 Kupffer cell sarcoma 91300 "Hemangioendothelioma, benign" 91301 "Hemangioendothelioma, NOS" 91303 "Hemangioendothelioma, malignant" 91310 Capillary hemangioma 91333 "Epithelioid hemangioendothelioma, malignant" 91403 Kaposi sarcoma 91500 "Hemangiopericytoma, benign" 91501 "Hemangiopericytoma, NOS" 91503 "Hemangiopericytoma, malignant" 91611 Hemangioblastoma 91703 Lymphangiosarcoma 91803 "Osteosarcoma, NOS" 91813 Chondroblastic osteosarcoma 91823 Fibroblastic osteosarcoma 91833 Telangiectatic osteosarcoma 91843 Osteosarcoma in Paget disease 91853 Small cell osteosarcoma 91863 Central osteosarcoma 91873 Instrosseous well differentiated osteosarcoma 91923 Parosteal osteosarcoma 91933 Periosteal osteosarcoma 91943 High grade surface osteosarcoma 91953 Intracortical osteosarcoma 92203 "Chondrosarcoma, NOS" 92213 Juxtacortical chondrosarcoma 92303 "Chondroblastoma, malignant" 92313 Myxoid chondrosarcoma 92403 Mesenchymal chondrosarcoma 92423 Clear cell chondrosarcoma 92433 Dedifferentiated chondrosarcoma 92501 "Giant cell tumor of bone, NOS" 92503 "Giant cell tumor of bone, malignant" 92511 Giant cell tumor of soft parts 92513 Malignant giant cell tumor of soft parts 92523 Malignant tenosynovial giant cell tumor 92603 Ewing sarcoma 92613 Adamantinoma of long bones 92703 "Odontogenic tumor, malignant" 92903 Ameloblastic odontosarcoma 93103 "Ameloblastoma, malignant" 93303 Ameloblastic fibrosarcoma 93423 Odontogenic carcinosarcoma 93501 Craniopharyngioma 93511 Adamantinomatous craniopharyngioma 93521 Papillary craniopharyngioma 93601 "Pinealoma, NOS" 93611 Pineocytoma 93623 Pineoblastoma 93630 Melanotic neuroectodermal tumor 93643 Peripheral neuroectodermal tumor 93653 Askin tumor 93703 "Chordoma, NOS" 93713 Chondroid chordoma 93723 Dedifferentiated chordoma 93803 "Glioma, malignant" 93813 Gliomatosis cerebri 93823 Mixed glioma 93831 Subependymoma 93841 Supependymal giant cell astrocytoma 93900 "Choroid plexus papilloma, NOS" 93901 Atypical choroid plexus papilloma 93903 "Choroid plexus papilloma, malignant" 93913 "Ependymoma, NOS" 93923 "Ependymoma, anaplastic" 93933 Papillary ependymoma 93941 Myxopapillary ependymoma 93953 Papillary tumor of the pineal region 94003 "Astrocytoma, NOS" 94013 "Astrocytoma, anaplastic" 94103 Protoplasmic astrocytoma 94113 Gemistocytic astrocytoma 94121 Desmoplastic infantile astrocytoma 94130 Dysembryoplastic neuroepithelial tumor 94203 Fibrillary astrocytoma 94211 Pilocytic astrocytoma 94233 Polar spongioblastoma 94243 Pleomorphic xanthoastrocytoma 94253 Pilomyxoid astrocytoma 94303 Astroblastoma 94311 Angiocentric glioma 94321 Pituicytoma 94403 "Glioblastoma, NOS" 94413 Giant cell glioblastoma 94421 Gliofibroma 94423 Gliosarcoma 94441 Chordoid glioma 94503 "Oligodendroglioma, NOS" 94513 "Oligodendroglioma, anaplastic" 94603 Oligodendroblastoma 94703 "Medulloblastoma, NOS" 94713 Desmoplastic medulloblastoma 94723 Medullomyoblastoma 94733 Primitive neuroectodermal tumor 94743 Large cell medulloblastoma 94803 "Cerebellar sarcoma, NOS" 94900 Ganglioneuroma 94903 Ganglioneuroblastoma 94920 Gangliocytoma 94930 Dysplastic gangliocytoma of cerebellum (Lher... 95003 "Neuroblastoma, NOS" 95013 "Medulloepithelioma, NOS" 95023 Teratoid medulloepithelioma 95033 "Neuroepithelioma, NOS" 95043 Spongioneuroblastoma 95051 "Ganglioglioma, NOS" 95053 "Ganglioglioma, anaplastic" 95061 Centrol neurocytoma 95083 Atypical teratoid/rhabdoid tumor 95091 Papillary glioneuronal tumor 95103 "Retinoblastoma, NOS" 95113 "Retinoblastoma, differentiated" 95123 "Retinoblastoma, undifferentiated" 95133 "Retinoblastoma, diffuse" 95203 Olfactory neurogenic tumor 95213 Olfactory neurocytoma 95223 Olfactory neuroblastoma 95233 Olfactory neuroepithelioma 95300 "Meningioma, NOS" 95301 "Meningiomatosis, NOS" 95303 "Meningioma, malignant" 95310 Meningothelial meningioma 95320 Fibrous meningioma 95330 Psammomatous meningioma 95340 Angiomatous meningioma 95370 Transitional meningioma 95381 Clear cell meningioma 95383 Papillary meningioma 95391 Atypical meningioma 95393 Meningeal sarcomatosis 95400 "Neurofibroma, NOS" 95401 "Neurofibromatosis, NOS" 95403 Malignant peripheral nerve sheath tumor 95410 Melanotic neurofibroma 95500 Plexiform neurofibroma 95600 "Neurilemoma, NOS" 95601 Neurinomatosis 95603 "Neurilemmoma, malignant" 95613 MPNST with rhabdomyoblastic differentiation 95620 Neurothekeoma 95700 "Neuroma, NOS" 95710 "Perineurioma, NOS" 95713 "Perineurioma, malignant" 95800 "Granular cell tumor, NOS" 95803 "Granular cell tumor, malignant" 95813 Alveolar soft part sarcoma 95903 "Malignant lymphoma, NOS" 95913 "Malignant lymphoma, non-Hodgkin" 95963 Composite Hodgkin and non-Hodgkin lymphoma 95973 Primary cutaneous follicle centre lymphoma 96503 "Hodgkin lymphoma, NOS" 96513 "Hodgkin lymphoma, lymphocyte-rich" 96523 "Hodgkin lymphoma, mixed cellularity, NOS" 96533 "Hodgkin lymphoma, lymphocytic deplet., NOS" 96543 "Hodgkin lymph., lymphocyt. deplet., diffuse ..." 96553 "Hodgkin lymphoma, lymphocyt. deplet., reticular" 96593 "Hodgkin lymph., nodular lymphocyte predom." 96613 Hodgkin granuloma [obs] 96623 Hodgkin sarcoma [obs] 96633 "Hodgkin lymphoma, nodular sclerosis, NOS" 96643 "Hodgkin lymphoma, nod. scler., cellular phase" 96653 "Hodgkin lymphoma, nod. scler., grade 1" 96673 "Hodgkin lymphoma, nod. scler., grade 2" 96703 "ML, small B lymphocytic, NOS" 96713 "ML, lymphoplasmacytic" 96733 Mantle cell lymphoma 96753 "ML, mixed sm. and lg. cell, diffuse" 96783 Primary effusion lymphoma 96793 Mediastinal large B-cell lymphoma 96803 "ML, large B-cell, diffuse" 96843 "ML, large B-cell, diffuse, immunoblastic, NOS" 96873 "Burkitt lymphoma, NOS" 96883 T-cell/histiocyte rich large B-cell lymphoma 96893 Splenic marginal zone B-cell lymphoma 96903 "Follicular lymphoma, NOS" 96913 "Follicular lymphoma, grade 2" 96953 "Follicular lymphoma, grade 1" 96983 "Follicular lymphoma, grade 3" 96993 "Marginal zone B-cell lymphoma, NOS" 97003 Mycosis fungoides 97013 Sezary syndrome 97023 "Mature T-cell lymphoma, NOS" 97053 Angioimmunoblastic T-cell lymphoma 97083 Subcutaneous panniculitis-like T-cell lymphoma 97093 "Cutaneous T-cell lymphoma, NOS" 97123 Intravascular large B-cell lymphoma 97143 "Anaplastic large cell lymphoma, T-cell and N..." 97163 Hepatosplenic T-cell lymphoma 97173 Intestinal T-cell lymphoma 97183 Primary cutan. CD30+ T-cell lymphoprolif. di... 97193 "NK/T-cell lymphoma, nasal and nasal-type" 97243 Syst. EBV pos. T-cell lymphoprol. disease 97253 Hydroa vacciniforme-like lymphoma 97263 Primary cutaneous gamma-delta T-cell lymphoma 97273 "Precursor cell lymphoblastic lymphoma, NOS" 97283 Precursor B-cell lymphoblastic lymphoma 97293 Precursor T-cell lymphoblastic lymphoma 97313 "Plasmacytoma, NOS" 97323 Multiple myeloma 97333 Plasma cell leukemia 97343 "Plasmacytoma, extramedullary" 97353 Plasmablastic lymphoma 97373 ALK postive large B-cell lymphoma 97383 Large B-cell lymph. arising in HHV8-assoc. multi 97403 Mast cell sarcoma 97411 Indolent systemic mastocytosis 97413 Malignant mastocytosis 97423 Mast cell leukemia 97503 Malignant histiocytosis 97511 "Langerhans cell histiocytosis, NOS" 97513 "Langerhans cell histiocytosis, NOS" 97521 "Langerhans cell histiocytosis, unifocal" 97531 "Langerhans cell histiocytosis, multifocal" 97543 "Langerhans cell histiocytosis, disseminated" 97553 Histiocytic sarcoma 97563 Langerhans cell sarcoma 97573 Interdigitating dendritic cell sarcoma 97583 Follicular dendritic cell sarcoma 97593 Fibroblastic reticular cell tumor 97603 "Immunoproliferative disease, NOS" 97613 Waldenstrom macroglobulinemia 97623 "Heavy chain disease, NOS" 97643 Immunoproliferative small intestinal disease 98003 "Leukemia, NOS" 98013 "Acute leukemia, NOS" 98053 Acute biphenotypic leukemia 98063 Mix. phenotype ac. leukemia with t;BCR-ABL1 98073 Mix. phenotype ac. leukemia with t;MLL rearrange 98083 "Mixed phenotype acute leukemia, B/myeloid, NOS" 98093 "Mixed phenotype acute leukemia, T/myeloid, NOS" 98113 "B lymphoblastic leukemia/lymphoma, NOS" 98123 B lymphoblast. leukemia/lymphoma with t;BCR-ABL1 98133 B lymphoblast. leukemia/lymphoma with t;MLL rear 98143 B lymphoblast. leukemia/lymphoma with t;TEL-AML1 98153 B lymphoblastic leukemia/lymphoma with hyperdipl 98163 B lymphoblast. leukemia/lymph. with hypodiploidy 98173 B lymphoblast. leukemia/lymphoma with t;IL3-IGH 98183 B lymphoblast. leukemia/lymphoma with t;E2A PBX1 98203 "Lymphoid leukemia, NOS" 98233 B-cell chr. lymph. leuk./small lymphocytic l... 98263 Burkitt cell leukemia 98273 Adult T-cell leukemia/lymphoma (HTLV-1 pos.) 98283 "Acute lymphoblastic leukemia, L2 type, NOS" 98313 T-cell large granular lymphocytic leukemia 98323 "Prolymphocytic leukemia, NOS" 98333 "Prolymphocytic leukemia, B-cell type" 98343 "Prolymphocytic leukemia, T-cell type" 98353 "Precursor cell lymphoblastic leukemia, NOS" 98363 Precursor B-cell lymphoblastic leukemia 98373 Precursor T-cell lymphoblastic leukemia 98403 "Acute myeloid leukemia, M6 type" 98603 "Myeloid leukemia, NOS" 98613 Acute myeloid leukemia 98633 "Chronic myeloid leukemia, NOS" 98653 Acute myeloid leukemia with t;DEK-NUP214 98663 "Acute promyelocytic leuk.,t(15;17)(q22;q11-12)" 98673 Acute myelomonocytic leukemia 98693 Acute myeloid leukemia with inv or t;RPN1-EVI1 98703 Acute basophilic leukemia 98713 Ac. myelomonocytic leuk. w abn. mar. eosinop... 98723 "Acute myeloid leukemia, minimal differentiation" 98733 Acute myeloid leukemia without maturation 98743 Acute myeloid leukemia with maturation 98753 "Chronic myelogenous leukemia, BCR/ABL positive" 98763 "Atypical chronic myeloid leuk., BCR/ABL nega..." 98913 Acute monocytic leukemia 98953 Acute myeloid leuk. with myelodysplasia-related 98963 "Acute myeloid leukemia, t(8;21)(q22;q22)" 98973 "Acute myeloid leukemia, 11q23 abnormalities" 98981 Transient abnormal myelopoiesis 98983 Myeloid leukemia associated with Down Syndrome 99103 Acute megakaryoblastic leukemia 99113 Acute myeloid leukemia (megakar. blast.) with t; 99203 Therapy related myeloid neoplasm 99303 Myeloid sarcoma 99313 Acute panmyelosis with myelofibrosis 99403 Hairy cell leukemia 99453 "Chronic myelomonocytic leukemia, NOS" 99463 Juvenile myelomonocytic leukemia 99483 Aggressive NK-cell leukemia 99503 Polycythemia vera 99603 "Myeloproliferative neoplasm, NOS" 99613 Primary myelofibrosis 99623 Essential thrombocythemia 99633 Chronic neutrophilic leukemia 99643 "Chronic eosinophilic leukemia, NOS" 99653 Myeloid&lymphoid neoplasms with PDGFRB rearrange 99663 Myeloid neoplasms with PDGFRB rearrangement 99673 Myeloid&lymphoid neoplasm with FGFR1 abnormaliti 99701 "Lymphoproliferative disorder, NOS" 99711 "Post transplant lymphoproliferative disorder, NO" 99713 Polymorphic post transplant lymphoproliferative 99751 "Myeloproliferative disease, NOS" 99753 "Myeloproliferative neoplasm, unclassifiable" 99803 Refractory anemia 99823 Refractory anemia with sideroblasts 99833 Refractory anemia with excess blasts 99843 Refract. anemia with excess blasts in transf... 99853 Refractory cytopenia with multilineage dyspl... 99863 Myelodysplastic syndr. with 5q deletion synd... 99873 "Therapy-related myelodysplastic syndrome, NOS" 99893 "Myelodysplastic syndrome, NOS" 99913 Refractory neutropenia 99923 Refractory thrombocytopenia 341 PLOCCD PLCCD1 PLCCD2 PLCCD3 0 external upper lip 1 external lower lip 2 "external lip, NOS" 3 mucose of uppper lip 4 mucosa of lower lip 5 "mucosa of lip, NOS" 6 commissure of lip 8 overlapping lesion of lip 9 "lip, NOS" 19 base of tongue 20 "dorsal surface of tongue, NOS" 21 border of tongue 22 "ventral surface of tongue, NOS" 23 anterior 2/3 of tongue 24 lingual tonsil 28 overlapping lesion of tongue 29 "tongue, NOS" 30 upper gum 31 lower gum 39 "gum, NOS" 40 anterior floor of mouth 41 lateral floor of mouth 48 overlapping lesion of floor of mouth 49 "floor of mouth, NOS" 50 hard palate 51 "soft palate, NOS" 52 uvula 58 overlapping lesion of palate 59 "palate, NOS" 60 cheek mucosa 61 vestibule of mouth 62 retromolar area 68 overlappinglesionofotherandunspecifiedpartso... 69 "mouth, NOS" 79 parotid gland 80 submandibular gland 81 sublingual gland 88 overlapping lesion of major salivary glands 89 "major salivary gland, NOS" 90 tonsillar fossa 91 tonsillar pillar 98 overlapping lesion of tonsil 99 "tonsil, NOS" 100 vallecula 101 anterior surface of epiglottis 102 lateral wall of oropharynx 103 posterior wall of oropharynx 104 branchial cleft 108 overlapping lesion of oropharynx 109 "oropharynx, NOS" 110 superior wall of nasopharyx 111 posterior wall of nasopharyx 112 lateral wall of nasopharyx 113 anterior wall of nasopharyx 118 overlapping lesion of nasopharyx 119 "nasopharyx, NOS" 129 "nasopharyxyriform sinus, NOS" 130 postcricoid region 131 hypopharyngeal aspect of aryepiglottic fold 132 posterior wall of hypopharynx 138 overlapping lesion of hypopharyx 139 "hypopharyx, NOS" 140 "pharyx, NOS" 142 waldeyer ring 148 "overlappinglesionoflip,oralcavityandpharynx" 150 cervical esophagus 151 thoracic esophagus 152 abdominal esophagus 153 upper third of esophagus 154 middle third of esophagus 155 lower third of esophagus 158 overlapping lesion of esophagus 159 "esophagus, NOS" 160 "cardia, NOS" 161 fundus of stomach 162 body of stomach 163 gastric antrum 164 pylorus 165 lesser curvature of stomach 166 greater curvature of stomach 168 overlapping lesion of stomach 169 "stomach, NOS" 170 duodenum 171 jejunum 172 ileum 173 Meckel diverticulum 178 overlapping lesion of small intestine 179 "small intestine, NOS" 180 cecum 181 appendix 182 ascending colon 183 hepatic flexure of colon 184 transverse colon 185 splenic flexure of colon 186 descending colon 187 sigmoid colon 188 overlapping lesion of colon 189 "colon, NOS" 199 rectosigmoid junction 209 "rectum, NOS" 210 "anus, NOS" 211 anal canal 212 cloacogenic zone 218 "overlappinglesionofrectum,anusandanalcanal" 220 liver 221 intrahepatic bile duct 239 "gallbladder, NOS" 240 extrahepatic bile duct 241 ampulla of Vater 248 overlapping lesion of biliary tract 249 "billary tract, NOS" 250 head of pancreas 251 body of pancreas 252 tail of pancreas 253 pancreatic duct 254 islets of Langerhans 257 other specified parts of pancreas 258 overlapping lesion of pancreas 259 "pancreas, NOS" 260 "intestinal tract, NOS" 268 overlapping lesion of digestive system 269 "gastrointestinal tract, NOS" 300 nasal cavity 301 middle ear 310 maxillary sinus 311 ethmoid sinus 312 frontal sinus 313 sphenoid sinus 318 overlapping lesion of accessory sinuses 319 "accessory sinus, NOS" 320 glottis 321 supraglottis 322 subglottis 323 laryngeal cartilage 328 overlapping lesion of larynx 329 "larynx, NOS" 339 trachea 340 main bronchus 341 "upper lobe, lung" 342 "middle lobe, lung" 343 "lower lobe, lung" 348 overlapping lesion of lung 349 "lung, NOS" 379 thymus 380 heart 381 anterior mediastinum 382 posterior mediastinum 383 "mediastinum, NOS" 384 "pleura, NOS" 388 "overlappinglesionofheart,mediastinumandpleura" 390 "upper respiratory tract, NOS" 398 overlappinglesionofrespiratorysystemandintra... 399 ill-defined sites within respiratory system 400 "longboneofupperlimb,scapulaandassociatedjoints" 401 short bone of upper limb and associated joints 402 long bones of lower limb and associated joints 403 short bones of lower limb and associated joints 408 "overlappinglesionofbones,jointsandarticularc..." 409 "bones of lomb, NOS" 410 bones of skull and face and associated joints 411 mandible 412 vertebral column 413 "rib, sternum, clavicle and associated joints" 414 "pelvicbones,sacrum,coccyxandassociatedjoints" 418 "overlappinglesionofbones,jointsandarticularc..." 419 "bone, NOS" 420 blood 421 bone marrow 422 spleen 423 "reticuloendothelial system, NOS" 424 "hematopoietic system, NOS" 440 "skin of lip, NOS" 441 eyelid 442 external ear 443 skin of other and unspecified parts of face 444 skin of scalp and neck 445 skin of trunc 446 skin of upper limb and shoulder 447 skin of lower limb and hip 448 overlapping lesion of skin 449 "skin, NOS" 470 peripheralnervesandautonomicnervoussystemofh... 471 peripheralnervesandautonomicnervoussystemofu... 472 peripheralnervesandautonomicnervoussystemofl... 473 peripheralnervesandautonomicnervoussystemoft... 474 peripheralnervesandautonomicnervoussystemofa... 475 peripheralnervesandautonomicnervoussystemofp... 476 peripheralnervesandautonomicnervoussystemoft... 478 overlappinglesionofperipheralnervesandautono... 479 "autonomic nervous system, NOS" 480 retroperitoneum 481 specified parts of peritoneum 482 "peritoneum, NOS" 488 overlapping lesion of retroperitoneum 490 "connective,subcutaneousandothersofttissuesof..." 491 "connective,subcutaneousandothersofttissuesof..." 492 "connective,subcutaneousandothersofttissuesof..." 493 "connective,subcutaneousandothersofttissuesof..." 494 "connective,subcutaneousandothersofttissuesof..." 495 "connective,subcutaneousandothersofttissuesof..." 496 "connective,subcutaneousandothersofttissuesof..." 498 "overlappinglesionofconnective,subcutaneousan..." 499 "connective,subcutaneousandothersofttissues,NOS" 500 nipple 501 central portion of breast 502 upper-inner quadrant of breast 503 lower-inner quadrant of breast 504 upper-outer quadrant of breast 505 upper-outer quadrant of breast 506 axillary tail of breast 508 overlapping lesion of breast 509 "breast, NOS" 510 labium majus 511 labium minus 512 clitoris 518 overlapping lesion of vulva 519 "vulva, NOS" 529 "vagina, NOS" 530 endocervix 531 exocervix 538 overlapping lesion of cervix uteri 539 "cervix uteri, NOS" 540 isthmus uteri 541 endometrium 542 myometrium 543 fundus uteri 548 overlapping lesion of corpus uteri 549 "corpus uteri, NOS" 559 "uterus, NOS" 569 "ovary, NOS" 570 fallopian tube 571 broad ligament 572 round ligament 573 parametrium 574 uterine adnexa 577 other specified parts of female genital organs 578 overlapping lesion of female genital organs 579 "female genital tract, NOS" 589 "placenta, NOS" 600 prepuce 601 glans penis 602 body of penis 608 overlapping lesion of penis 609 "penis, NOS" 619 prostate gland 620 undescended testis 621 descended testis 629 "testis, NOS" 630 epididymis 631 spermatic cord 632 "scrotum, NOS" 637 other specified parts of male genital organs 638 overlapping lesion of male genital organs 639 "male genital tract, NOS" 649 "kidney, NOS" 659 renal pelvis 669 ureter 670 trigone of bladder 671 dome of bladder 672 lateral wall of bladder 673 anterior wall of bladder 674 posterior of bladder 675 bladder neck 676 ureteric orifice 677 urachus 678 overlapping lesion of bladder 679 "bladder, NOS" 680 urethra 681 paraurethral gland 688 overlapping lesion of urinary organs 689 "urinary system, NOS" 690 conjuctiva 691 "cornea, NOS" 692 retina 693 choroid 694 ciliary body 695 lacrimal gland 696 "orbit, NOS" 698 overlapping lesion of eye and adnexa 699 "eye, NOS" 700 cerebral meninges 701 spinal meninges 709 "meninges, NOS" 710 cerebrum 711 frontal lobe 712 temperal lobe 713 parietal lobe 714 occipital lobe 715 "ventricle, NOS" 716 cerebellum 717 brain stem 718 overlapping lesion of brain 719 "brain, NOS" 720 spinal cord 721 cauda equina 722 olfactory nerve 723 optic nerve 724 acoustic nerve 725 "cranial nerve, NOS" 728 overlappinglesionofbrainandcentralnervoussystem 729 "nervous system, NOS" 739 "thyroid gland, NOS" 740 cortex of adrenal gland 741 medulla of adrenal gland 749 "adrenal gland, NOS" 750 parathyroid gland 751 pituitary gland 752 craniopharyngeal duct 753 pineal gland 754 carotid body 755 aortic body and other paraganglia 758 overlappinglesionofendocrineglandsandrelated... 759 "endocrine gland, NOS" 760 "head, face or neck, NOS" 761 "thorax, NOS" 762 "abdomen, NOS" 763 "pelvis, NOS" 764 "upper limb, NOS" 765 "lower limb, NOS" 767 other ill-defined sites 768 overlapping lesion of ill-defined sites 770 "lymph nodes of head, face and neck" 771 intrathoracic lymph nodes 772 intra-abdominal lymph nodes 773 lymph nodes of axilla of arm 774 lymph nodes of inguinal region or leg 775 pelvic lymph nodes 778 lymph nodes of multiple regions 779 "lymph node, NOS" 809 unknown primary sites 343 IFCDATR 1 yes 2 no 3 statement by physician 4 IC will follow \ No newline at end of file diff --git a/test_data/test_logic/dropzone/studies/PMCST000AAA_individual_codebook.txt.sha1 b/test_data/test_logic/dropzone/studies/PMCST000AAA_individual_codebook.txt.sha1 new file mode 100644 index 0000000..e05732f --- /dev/null +++ b/test_data/test_logic/dropzone/studies/PMCST000AAA_individual_codebook.txt.sha1 @@ -0,0 +1 @@ +8cc20a3917db3e251d9426d078ce74969e531931 PMCST000AAA_individual_codebook.txt diff --git a/test_data/test_logic/dropzone/studies/individual_study.txt b/test_data/test_logic/dropzone/studies/individual_study.txt new file mode 100644 index 0000000..f0da77b --- /dev/null +++ b/test_data/test_logic/dropzone/studies/individual_study.txt @@ -0,0 +1,18 @@ +STUDY_ID,INDIVIDUAL_ID,INDIVIDUAL_STUDY_ID +PMCST000AAC,PAT1,8301 +PMCST000AAC,PAT2,8337 +PMCST000AAC,PAT3,8355 +PMCST000AAC,PAT4,8409 +PMCST000AAC,PAT5,8419 +PMCST000AAC,PAT6,8436 +PMCST000AAC,PAT7,8448 +PMCST000AAB,PAT8,8592 +PMCST000AAB,PAT9,8637 +PMCST000AAB,PAT10,8962 +PMCST000AAB,PAT11,9162 +PMCST000AAC,PAT12,9174 +PMCST000AAC,PAT13,9383 +PMCST000AAC,PAT14,9571 +PMCST000AAC,PAT15,9676 +PMCST000AAB,PAT16,9875 +PMCST000AAB,PAT17,9931 diff --git a/test_data/test_logic/dropzone/studies/individual_study.txt.sha1 b/test_data/test_logic/dropzone/studies/individual_study.txt.sha1 new file mode 100644 index 0000000..e18a847 --- /dev/null +++ b/test_data/test_logic/dropzone/studies/individual_study.txt.sha1 @@ -0,0 +1 @@ +0c8cea524414911e8a3fd0e55e2fd88847da06e8 individual_study.txt diff --git a/test_data/test_logic/dropzone/studies/study.txt b/test_data/test_logic/dropzone/studies/study.txt new file mode 100644 index 0000000..44103c2 --- /dev/null +++ b/test_data/test_logic/dropzone/studies/study.txt @@ -0,0 +1,3 @@ +"STUDY_ID","acronym","title","description","datadictionary" +PMCST000AAC,STUDYA,Treatment study protocol of the Dutch Childhood Oncology Group for children and adolescents (1-19 year) with newly diagnosed acute lymphoblastic leukemia.,Intial ALL treatment <1 year,xls bestand +PMCST000AAB,STUDYB,International collaborative treatment protocol for infants under one year with acute lymphoblastic or biphenotypic leukemia. ,Intial ALL treatment 1-19 years,xls bestand diff --git a/test_data/test_logic/dropzone/studies/study.txt.sha1 b/test_data/test_logic/dropzone/studies/study.txt.sha1 new file mode 100644 index 0000000..f729831 --- /dev/null +++ b/test_data/test_logic/dropzone/studies/study.txt.sha1 @@ -0,0 +1 @@ +683f607214f3b53c06a0431a2303c0322cc99ce6 study.txt From db23e4fa0eaee2936a54f568430c1ecce2c2ca6e Mon Sep 17 00:00:00 2001 From: Gijs Kant Date: Wed, 16 Oct 2019 14:28:37 +0200 Subject: [PATCH 03/10] Add requests dependency. --- requirements/requirements.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements/requirements.txt b/requirements/requirements.txt index 2241b52..a9a31ad 100644 --- a/requirements/requirements.txt +++ b/requirements/requirements.txt @@ -11,3 +11,4 @@ numpy==1.17.1 chardet==3.0.4 psycopg2-binary==2.7.4 click>=7.0,<8.0 +requests>= 2.22.0,<2.23.0 From 49a80efc47cc039f724e9f40d68084855eb97558 Mon Sep 17 00:00:00 2001 From: Gijs Kant Date: Wed, 16 Oct 2019 14:48:07 +0200 Subject: [PATCH 04/10] Add empty NGS directory to test_logic test data set. --- test_data/test_logic/dropzone/NGS/.gitignore | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 test_data/test_logic/dropzone/NGS/.gitignore diff --git a/test_data/test_logic/dropzone/NGS/.gitignore b/test_data/test_logic/dropzone/NGS/.gitignore new file mode 100644 index 0000000..e69de29 From 36511a1e1acf21bdc54bef5c3cdaefb576f2df24 Mon Sep 17 00:00:00 2001 From: ewelinagr Date: Wed, 16 Oct 2019 15:18:55 +0200 Subject: [PATCH 05/10] Update csr2transmart to version 0.0.20 --- requirements/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements/requirements.txt b/requirements/requirements.txt index a9a31ad..6eeda48 100644 --- a/requirements/requirements.txt +++ b/requirements/requirements.txt @@ -1,4 +1,4 @@ -csr2transmart==0.0.19 +csr2transmart==0.0.20 docutils==0.14 lockfile==0.12.2 luigi==2.8.0 From 28398bd16ec1511a2bec512d5a42e54b2a97e0c9 Mon Sep 17 00:00:00 2001 From: ewelinagr Date: Wed, 16 Oct 2019 15:26:12 +0200 Subject: [PATCH 06/10] Pass ngs_dir as None to csr2cbioportal if it does not exist --- luigi-pipeline/main.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/luigi-pipeline/main.py b/luigi-pipeline/main.py index 66e0012..c70d3db 100644 --- a/luigi-pipeline/main.py +++ b/luigi-pipeline/main.py @@ -147,6 +147,8 @@ class CbioportalDataTransformation(BaseTask): def run(self): clinical_input_file = os.path.join(config.working_dir) ngs_dir = os.path.join(config.input_data_dir, 'NGS') + if not os.path.isdir(ngs_dir): + ngs_dir = None csr2cbioportal.csr2cbioportal(input_dir=clinical_input_file, ngs_dir=ngs_dir, output_dir=config.cbioportal_staging_dir) From 42e46915f7ae286e706b8fc26c86925294a2bca7 Mon Sep 17 00:00:00 2001 From: Gijs Kant Date: Wed, 16 Oct 2019 15:44:47 +0200 Subject: [PATCH 07/10] Update cBioPortal validation image. --- luigi.cfg-sample | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/luigi.cfg-sample b/luigi.cfg-sample index 8089162..b5ad7e5 100644 --- a/luigi.cfg-sample +++ b/luigi.cfg-sample @@ -63,11 +63,11 @@ offline_token = [CbioportalDataValidation] -docker_image = cbioportal-image +docker_image = cbioportal-hg38:1.10.2 [CbioportalDataLoading] -docker_image = cbioportal-image +docker_image = cbioportal-hg38:1.10.2 server_name = pmc-cbioportal-test From 09275661199e77ae2e29e2ed7bbc185188af74ff Mon Sep 17 00:00:00 2001 From: Gijs Kant Date: Wed, 16 Oct 2019 21:26:56 +0200 Subject: [PATCH 08/10] Update csr2transmart. --- requirements/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements/requirements.txt b/requirements/requirements.txt index 6eeda48..3a0c471 100644 --- a/requirements/requirements.txt +++ b/requirements/requirements.txt @@ -1,4 +1,4 @@ -csr2transmart==0.0.20 +csr2transmart==0.0.21 docutils==0.14 lockfile==0.12.2 luigi==2.8.0 From 6c9d63c9fc4d5b8bec986a47ddb5c7dfa6156281 Mon Sep 17 00:00:00 2001 From: Gijs Kant Date: Wed, 16 Oct 2019 23:01:29 +0200 Subject: [PATCH 09/10] Fix git commit in empty repo. --- luigi-pipeline/main.py | 2 +- scripts/git_commons.py | 38 ++++++++++++++++++++++---------------- 2 files changed, 23 insertions(+), 17 deletions(-) diff --git a/luigi-pipeline/main.py b/luigi-pipeline/main.py index c70d3db..e04d57a 100644 --- a/luigi-pipeline/main.py +++ b/luigi-pipeline/main.py @@ -89,7 +89,7 @@ class GitCommit(BaseTask): def run(self): with git_lock: repo.index.add([self.directory_to_add]) - if not repo.index.diff('HEAD'): + if repo.is_dirty(): repo.index.commit(self.commit_message) logger.info('Commit changes in {} directory.'.format(self.directory_to_add)) else: diff --git a/scripts/git_commons.py b/scripts/git_commons.py index 41d24a8..a3314ce 100644 --- a/scripts/git_commons.py +++ b/scripts/git_commons.py @@ -1,11 +1,11 @@ import os import logging -import git +from git import Repo, InvalidGitRepositoryError logger = logging.getLogger(__name__) -def get_git_repo(repo_dir): +def get_git_repo(repo_dir: str) -> Repo: """ Returns the git repository used for VCS of source and transformed data files. As well as load logs. If it does not exist, it will create one. @@ -14,26 +14,32 @@ def get_git_repo(repo_dir): """ if not os.path.exists(repo_dir): return init_git_repo(repo_dir) - try: - return git.Repo(repo_dir) - except git.InvalidGitRepositoryError: + repo = Repo(repo_dir) + init_gitignore(repo) + return repo + except InvalidGitRepositoryError: return init_git_repo(repo_dir) -def init_git_repo(repo_dir): - os.makedirs(repo_dir, exist_ok=True) - logger.info('Initializing git repository: {}'.format(repo_dir)) - r = git.Repo.init(os.path.realpath(repo_dir)) - ignore_list = ['.done-*', '.DS_Store'] - logger.debug('Git ignore list: {}'.format(ignore_list)) - - gitignore = os.path.realpath(os.path.join(repo_dir, '.gitignore')) +def init_gitignore(repo: Repo): + gitignore = os.path.realpath(os.path.join(repo.working_tree_dir, '.gitignore')) + if os.path.isfile(gitignore): + return + ignore_list = ['.done-*', '.DS_Store'] logger.debug('Writing git ignore file') with open(gitignore, 'w') as f: f.write('\n'.join(ignore_list)) + f.write('\n') + + repo.index.add([gitignore]) + repo.index.commit('Initial commit.') + - r.index.add([gitignore]) - r.index.commit('Initial commit.') - return r +def init_git_repo(repo_dir) -> Repo: + os.makedirs(repo_dir, exist_ok=True) + logger.info('Initializing git repository: {}'.format(repo_dir)) + repo = Repo.init(os.path.realpath(repo_dir)) + init_gitignore(repo) + return repo From f365446f7b50d03aaa360ce4d02c5ed96494e777 Mon Sep 17 00:00:00 2001 From: ewelinagr Date: Thu, 17 Oct 2019 16:28:10 +0200 Subject: [PATCH 10/10] Update csr2transmart to 0.0.23. --- requirements/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements/requirements.txt b/requirements/requirements.txt index 3a0c471..71e5038 100644 --- a/requirements/requirements.txt +++ b/requirements/requirements.txt @@ -1,4 +1,4 @@ -csr2transmart==0.0.21 +csr2transmart==0.0.23 docutils==0.14 lockfile==0.12.2 luigi==2.8.0