nci-cidc-api-modules 1.1.34__tar.gz → 1.1.35__tar.gz

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Files changed (33) hide show
  1. {nci_cidc_api_modules-1.1.34/nci_cidc_api_modules.egg-info → nci_cidc_api_modules-1.1.35}/PKG-INFO +2 -2
  2. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/cidc_api/models/files/details.py +31 -0
  3. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/cidc_api/models/files/facets.py +57 -0
  4. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35/nci_cidc_api_modules.egg-info}/PKG-INFO +2 -2
  5. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/nci_cidc_api_modules.egg-info/requires.txt +1 -1
  6. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/requirements.modules.txt +1 -1
  7. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/LICENSE +0 -0
  8. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/MANIFEST.in +0 -0
  9. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/README.md +0 -0
  10. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/cidc_api/config/__init__.py +0 -0
  11. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/cidc_api/config/db.py +0 -0
  12. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/cidc_api/config/logging.py +0 -0
  13. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/cidc_api/config/secrets.py +0 -0
  14. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/cidc_api/config/settings.py +0 -0
  15. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/cidc_api/models/__init__.py +0 -0
  16. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/cidc_api/models/files/__init__.py +0 -0
  17. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/cidc_api/models/migrations.py +0 -0
  18. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/cidc_api/models/models.py +0 -0
  19. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/cidc_api/models/schemas.py +0 -0
  20. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/cidc_api/shared/__init__.py +0 -0
  21. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/cidc_api/shared/auth.py +0 -0
  22. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/cidc_api/shared/emails.py +0 -0
  23. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/cidc_api/shared/gcloud_client.py +0 -0
  24. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/cidc_api/shared/jose.py +0 -0
  25. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/cidc_api/shared/rest_utils.py +0 -0
  26. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/nci_cidc_api_modules.egg-info/SOURCES.txt +0 -0
  27. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/nci_cidc_api_modules.egg-info/dependency_links.txt +0 -0
  28. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/nci_cidc_api_modules.egg-info/not-zip-safe +0 -0
  29. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/nci_cidc_api_modules.egg-info/top_level.txt +0 -0
  30. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/pyproject.toml +0 -0
  31. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/setup.cfg +0 -0
  32. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/setup.py +0 -0
  33. {nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/tests/test_api.py +0 -0
{nci_cidc_api_modules-1.1.34/nci_cidc_api_modules.egg-info → nci_cidc_api_modules-1.1.35}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: nci_cidc_api_modules
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- Version: 1.1.34
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+ Version: 1.1.35
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  Summary: SQLAlchemy data models and configuration tools used in the NCI CIDC API
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  Home-page: https://github.com/NCI-CIDC/cidc-api-gae
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  License: MIT license
@@ -28,7 +28,7 @@ Requires-Dist: python-dotenv==0.10.3
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  Requires-Dist: requests==2.32.4
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  Requires-Dist: jinja2==3.1.6
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  Requires-Dist: certifi==2024.7.4
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- Requires-Dist: nci-cidc-schemas==0.27.25
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+ Requires-Dist: nci-cidc-schemas==0.27.26
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  Dynamic: description
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  Dynamic: description-content-type
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  Dynamic: home-page
{nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/cidc_api/models/files/details.py RENAMED
@@ -993,4 +993,35 @@ details_dict = {
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  "",
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  "",
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  ),
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+ # scrna
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+ "/scrnaseq/samples_metadata.csv": FileDetails("source", "", ""),
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+ "/scrnaseq/read_1.gz": FileDetails("source", "", ""),
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+ "/scrnaseq/read_2.gz": FileDetails("source", "", ""),
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+ "/scrnaseq_analysis/samples_metadata.csv": FileDetails("source", "", ""),
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+ "/scrnaseq_analysis/config.yaml": FileDetails("source", "", ""),
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+ "/scrnaseq_analysis/R_package_versions.csv": FileDetails("source", "", ""),
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+ "/scrnaseq_analysis/integration.rds": FileDetails("source", "", ""),
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+ "/scrnaseq_analysis/integration_heatmap_plots.zip": FileDetails("source", "", ""),
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+ "/scrnaseq_analysis/integration_markers.zip": FileDetails("source", "", ""),
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+ "/scrnaseq_analysis/integration_split_percent_plots.zip": FileDetails("source", "", ""),
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+ "/scrnaseq_analysis/integration_split_umap_plots.zip": FileDetails("source", "", ""),
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+ "/scrnaseq_analysis/integration_umap_plots.zip": FileDetails("source", "", ""),
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+ "/scrnaseq_analysis/clustering.rds": FileDetails("source", "", ""),
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+ "/scrnaseq_analysis/report.html": FileDetails("source", "", ""),
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+ "/scrnaseq_analysis/star_sorted_by_cord.bam": FileDetails("source", "", ""),
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+ "/scrnaseq_analysis/star_sorted_by_cord.bam.bai": FileDetails("source", "", ""),
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+ "/scrnaseq_analysis/log_final.out": FileDetails("source", "", ""),
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+ "/scrnaseq_analysis/log.out": FileDetails("source", "", ""),
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+ "/scrnaseq_analysis/log_progress.out": FileDetails("source", "", ""),
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+ "/scrnaseq_analysis/sj_out.tab": FileDetails("source", "", ""),
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+ "/scrnaseq_analysis/barcodes.stats": FileDetails("source", "", ""),
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+ "/scrnaseq_analysis/gene_features.stats": FileDetails("source", "", ""),
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+ "/scrnaseq_analysis/gene_summary.csv": FileDetails("source", "", ""),
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+ "/scrnaseq_analysis/gene_umi_per_cell_sorted.txt": FileDetails("source", "", ""),
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+ "/scrnaseq_analysis/gene_filtered_features.tsv": FileDetails("source", "", ""),
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+ "/scrnaseq_analysis/gene_filtered_barcodes.tsv": FileDetails("source", "", ""),
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+ "/scrnaseq_analysis/gene_filtered_matrix.mtx": FileDetails("source", "", ""),
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+ "/scrnaseq_analysis/gene_raw_features.tsv": FileDetails("source", "", ""),
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+ "/scrnaseq_analysis/gene_raw_barcodes.tsv": FileDetails("source", "", ""),
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+ "/scrnaseq_analysis/gene_raw_matrix.mtx": FileDetails("source", "", ""),
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  }
{nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/cidc_api/models/files/facets.py RENAMED
@@ -346,6 +346,21 @@ assay_facets: Facets = {
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  "H and E file from MIBI analysis",
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  ),
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  },
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+ "scRNA": {
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+ "Samples Metadata": FacetConfig(["/scrnaseq/samples_metadata.csv"], "Sample metadata for scRNA run"),
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+ "Read 1 gz": FacetConfig(["/scrnaseq/read_1.gz"], "Gz file for read 1"),
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+ "Read 2 gz": FacetConfig(["/scrnaseq/read_2.gz"], "Gz file for read 2"),
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+ },
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+ "Visium": {
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+ "Samples Metadata": FacetConfig(["/visium/samples_metadata.csv"], "Sample metadata for visium run"),
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+ "Read 1 fastq gz": FacetConfig(["/visium/R1_001.fastq.gz"], "Gz file for read 1"),
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+ "Read 2 fastq gz": FacetConfig(["/visium/R2_001.fastq.gz"], "Gz file for read 2"),
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+ "loupe alignment file": FacetConfig(["/visium/loupe_alignment_file.json"]),
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+ "brightfield image": FacetConfig(["/visium/brightfield.tiff"]),
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+ "dark image": FacetConfig(["/visium/dark_image.tiff"]),
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+ "colorized image": FacetConfig(["/visium/colorized.tiff"]),
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+ "cytassist image": FacetConfig(["/visium/cytassist.tiff"]),
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+ },
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  "mIHC": {
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  "Samples Report": FacetConfig(["/mihc/sample_report.csv"], "Samples report for mIHC run"),
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  "Multitiffs": FacetConfig(["/mihc/multitiffs.tar.gz"], "Multi Tiffs file from mIHC run"),
@@ -549,6 +564,48 @@ analysis_ready_facets = {
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  "WES Analysis": FacetConfig(["/wes/analysis/report.tar.gz"]),
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  "TCR": FacetConfig(["/tcr_analysis/report_trial.tar.gz"]),
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  "mIF": FacetConfig(["/mif/roi_/cell_seg_data.txt"]),
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+ "scRNA": FacetConfig(
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+ [
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+ "/scrnaseq_analysis/samples_metadata.csv",
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+ "/scrnaseq_analysis/config.yaml",
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+ "/scrnaseq_analysis/R_package_versions.csv",
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+ "/scrnaseq_analysis/integration.rds",
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+ "/scrnaseq_analysis/integration_heatmap_plots.zip",
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+ "/scrnaseq_analysis/integration_markers.zip",
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+ "/scrnaseq_analysis/integration_split_percent_plots.zip",
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+ "/scrnaseq_analysis/integration_split_umap_plots.zip",
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+ "/scrnaseq_analysis/integration_umap_plots.zip",
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+ "/scrnaseq_analysis/clustering.rds",
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+ "/scrnaseq_analysis/report.html",
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+ "/scrnaseq_analysis/star_sorted_by_cord.bam",
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+ "/scrnaseq_analysis/star_sorted_by_cord.bam.bai",
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+ "/scrnaseq_analysis/log_final.out",
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+ "/scrnaseq_analysis/log.out",
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+ "/scrnaseq_analysis/log_progress.out",
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+ "/scrnaseq_analysis/sj_out.tab",
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+ "/scrnaseq_analysis/barcodes.stats",
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+ "/scrnaseq_analysis/gene_features.stats",
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+ "/scrnaseq_analysis/gene_summary.csv",
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+ "/scrnaseq_analysis/gene_umi_per_cell_sorted.txt",
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+ "/scrnaseq_analysis/gene_filtered_features.tsv",
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+ "/scrnaseq_analysis/gene_filtered_barcodes.tsv",
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+ "/scrnaseq_analysis/gene_filtered_matrix.mtx",
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+ "/scrnaseq_analysis/gene_raw_features.tsv",
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+ "/scrnaseq_analysis/gene_raw_barcodes.tsv",
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+ "/scrnaseq_analysis/gene_raw_matrix.mtx",
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+ ]
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+ ),
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+ "Visium": FacetConfig(
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+ [
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+ "/visium_analysis/samples_metadata.csv",
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+ "/visium_analysis/config.yaml",
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+ "/visium_analysis/R_package_versions.csv",
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+ "/visium_analysis/merged.rds",
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+ "/visium_analysis/spatial_variable_features.rds",
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+ "/visium_analysis/report.html",
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+ "/visium_analysis/visium_spaceranger_output.zip",
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+ ]
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+ ),
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  }
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  facets_dict: Dict[str, Facets] = {
{nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35/nci_cidc_api_modules.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: nci_cidc_api_modules
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- Version: 1.1.34
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+ Version: 1.1.35
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  Summary: SQLAlchemy data models and configuration tools used in the NCI CIDC API
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  Home-page: https://github.com/NCI-CIDC/cidc-api-gae
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  License: MIT license
@@ -28,7 +28,7 @@ Requires-Dist: python-dotenv==0.10.3
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  Requires-Dist: requests==2.32.4
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  Requires-Dist: jinja2==3.1.6
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  Requires-Dist: certifi==2024.7.4
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- Requires-Dist: nci-cidc-schemas==0.27.25
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+ Requires-Dist: nci-cidc-schemas==0.27.26
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  Dynamic: description
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  Dynamic: description-content-type
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  Dynamic: home-page
{nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/nci_cidc_api_modules.egg-info/requires.txt RENAMED
@@ -19,4 +19,4 @@ python-dotenv==0.10.3
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  requests==2.32.4
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  jinja2==3.1.6
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  certifi==2024.7.4
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- nci-cidc-schemas==0.27.25
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+ nci-cidc-schemas==0.27.26
{nci_cidc_api_modules-1.1.34 → nci_cidc_api_modules-1.1.35}/requirements.modules.txt RENAMED
@@ -19,4 +19,4 @@ python-dotenv==0.10.3
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  requests==2.32.4
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  jinja2==3.1.6
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  certifi==2024.7.4
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- nci-cidc-schemas==0.27.25
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+ nci-cidc-schemas==0.27.26