diff --git a/test_data/test_data_NGS/config/ontology_config.json b/test_data/test_data_NGS/config/ontology_config.json index 0e8f1e5..e85bc27 100644 --- a/test_data/test_data_NGS/config/ontology_config.json +++ b/test_data/test_data_NGS/config/ontology_config.json @@ -118,6 +118,14 @@ { "name": "03. Biomaterial type", "concept_code": "Biomaterial.type" + }, + { + "name": "04. Library strategy", + "concept_code": "Biomaterial.library_strategy" + }, + { + "name": "05. Analysis type", + "concept_code": "Biomaterial.analysis_type" } ] }, diff --git a/test_data/test_data_NGS/config/sources_config.json b/test_data/test_data_NGS/config/sources_config.json index f45354f..5ccc239 100644 --- a/test_data/test_data_NGS/config/sources_config.json +++ b/test_data/test_data_NGS/config/sources_config.json @@ -382,7 +382,8 @@ "codebooks": { "studies/individual.txt": "studies/individual_codebook.txt", "studies/diagnosis.txt": "studies/diagnosis_codebook.txt", - "studies/death.txt": "studies/death_codebook.txt" + "studies/death.txt": "studies/death_codebook.txt", + "clinic/RDP-Patient.tab": "clinic/RDP-Patient_codebook.txt" }, "file_format": { "studies/individual.txt": { diff --git a/test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test1.maf.gz b/test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test1_WGS.maf.gz similarity index 100% rename from test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test1.maf.gz rename to test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test1_WGS.maf.gz diff --git a/test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test1.maf.gz.sha1 b/test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test1_WGS.maf.gz.sha1 similarity index 100% rename from test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test1.maf.gz.sha1 rename to test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test1_WGS.maf.gz.sha1 diff --git a/test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test2.maf.gz b/test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test2_WGS.maf.gz similarity index 100% rename from test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test2.maf.gz rename to test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test2_WGS.maf.gz diff --git a/test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test2.maf.gz.sha1 b/test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test2_WGS.maf.gz.sha1 similarity index 100% rename from test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test2.maf.gz.sha1 rename to test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test2_WGS.maf.gz.sha1 diff --git a/test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test.seg b/test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test_WXS.seg similarity index 100% rename from test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test.seg rename to test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test_WXS.seg diff --git a/test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test.seg.sha1 b/test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test_WXS.seg.sha1 similarity index 100% rename from test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test.seg.sha1 rename to test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test_WXS.seg.sha1 diff --git a/test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test_all_data_by_genes.txt b/test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test_WXS_all_data_by_genes.txt similarity index 100% rename from test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test_all_data_by_genes.txt rename to test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test_WXS_all_data_by_genes.txt diff --git a/test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test_all_data_by_genes.txt.sha1 b/test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test_WXS_all_data_by_genes.txt.sha1 similarity index 100% rename from test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test_all_data_by_genes.txt.sha1 rename to test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test_WXS_all_data_by_genes.txt.sha1 diff --git a/test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test_all_thresholded.by_genes.txt b/test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test_WXS_all_thresholded.by_genes.txt similarity index 100% rename from test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test_all_thresholded.by_genes.txt rename to test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test_WXS_all_thresholded.by_genes.txt diff --git a/test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test_all_thresholded.by_genes.txt.sha1 b/test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test_WXS_all_thresholded.by_genes.txt.sha1 similarity index 100% rename from test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test_all_thresholded.by_genes.txt.sha1 rename to test_data/test_data_NGS/dropzone/alternative/NGS/pmc_test_WXS_all_thresholded.by_genes.txt.sha1 diff --git a/test_data/test_data_NGS/dropzone/alternative/clinic/RDP-Patient_codebook.txt b/test_data/test_data_NGS/dropzone/alternative/clinic/RDP-Patient_codebook.txt new file mode 100644 index 0000000..76336f2 --- /dev/null +++ b/test_data/test_data_NGS/dropzone/alternative/clinic/RDP-Patient_codebook.txt @@ -0,0 +1 @@ +1 Geslacht M male V female \ No newline at end of file diff --git a/test_data/test_data_NGS/dropzone/alternative/clinic/RDP-Patient_codebook.txt.sha1 b/test_data/test_data_NGS/dropzone/alternative/clinic/RDP-Patient_codebook.txt.sha1 new file mode 100644 index 0000000..7a26340 --- /dev/null +++ b/test_data/test_data_NGS/dropzone/alternative/clinic/RDP-Patient_codebook.txt.sha1 @@ -0,0 +1 @@ +7854a94ee9adb8f765a65db17cd17fcc9fea708d RDP-Patient_codebook.txt diff --git a/test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test1.maf.gz b/test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test1_WGS.maf.gz similarity index 100% rename from test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test1.maf.gz rename to test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test1_WGS.maf.gz diff --git a/test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test1.maf.gz.sha1 b/test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test1_WGS.maf.gz.sha1 similarity index 100% rename from test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test1.maf.gz.sha1 rename to test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test1_WGS.maf.gz.sha1 diff --git a/test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test2.maf.gz b/test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test2_WGS.maf.gz similarity index 100% rename from test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test2.maf.gz rename to test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test2_WGS.maf.gz diff --git a/test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test2.maf.gz.sha1 b/test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test2_WGS.maf.gz.sha1 similarity index 100% rename from test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test2.maf.gz.sha1 rename to test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test2_WGS.maf.gz.sha1 diff --git a/test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test.seg b/test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test_WXS.seg similarity index 100% rename from test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test.seg rename to test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test_WXS.seg diff --git a/test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test.seg.sha1 b/test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test_WXS.seg.sha1 similarity index 100% rename from test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test.seg.sha1 rename to test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test_WXS.seg.sha1 diff --git a/test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test_all_data_by_genes.txt b/test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test_WXS_all_data_by_genes.txt similarity index 100% rename from test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test_all_data_by_genes.txt rename to test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test_WXS_all_data_by_genes.txt diff --git a/test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test_all_data_by_genes.txt.sha1 b/test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test_WXS_all_data_by_genes.txt.sha1 similarity index 100% rename from test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test_all_data_by_genes.txt.sha1 rename to test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test_WXS_all_data_by_genes.txt.sha1 diff --git a/test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test_all_thresholded.by_genes.txt b/test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test_WXS_all_thresholded.by_genes.txt similarity index 100% rename from test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test_all_thresholded.by_genes.txt rename to test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test_WXS_all_thresholded.by_genes.txt diff --git a/test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test_all_thresholded.by_genes.txt.sha1 b/test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test_WXS_all_thresholded.by_genes.txt.sha1 similarity index 100% rename from test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test_all_thresholded.by_genes.txt.sha1 rename to test_data/test_data_NGS/dropzone/full_dataset/NGS/pmc_test_WXS_all_thresholded.by_genes.txt.sha1 diff --git a/test_data/test_data_NGS/dropzone/full_dataset/clinic/RDP-Patient_codebook.txt b/test_data/test_data_NGS/dropzone/full_dataset/clinic/RDP-Patient_codebook.txt new file mode 100644 index 0000000..76336f2 --- /dev/null +++ b/test_data/test_data_NGS/dropzone/full_dataset/clinic/RDP-Patient_codebook.txt @@ -0,0 +1 @@ +1 Geslacht M male V female \ No newline at end of file diff --git a/test_data/test_data_NGS/dropzone/full_dataset/clinic/RDP-Patient_codebook.txt.sha1 b/test_data/test_data_NGS/dropzone/full_dataset/clinic/RDP-Patient_codebook.txt.sha1 new file mode 100644 index 0000000..7a26340 --- /dev/null +++ b/test_data/test_data_NGS/dropzone/full_dataset/clinic/RDP-Patient_codebook.txt.sha1 @@ -0,0 +1 @@ +7854a94ee9adb8f765a65db17cd17fcc9fea708d RDP-Patient_codebook.txt