nci-cidc-api-modules 1.1.33__py3-none-any.whl → 1.1.35__py3-none-any.whl

cidc_api/models/files/details.py

@@ -993,4 +993,35 @@ details_dict = {
         "",
         "",
     ),
+    # scrna
+    "/scrnaseq/samples_metadata.csv": FileDetails("source", "", ""),
+    "/scrnaseq/read_1.gz": FileDetails("source", "", ""),
+    "/scrnaseq/read_2.gz": FileDetails("source", "", ""),
+    "/scrnaseq_analysis/samples_metadata.csv": FileDetails("source", "", ""),
+    "/scrnaseq_analysis/config.yaml": FileDetails("source", "", ""),
+    "/scrnaseq_analysis/R_package_versions.csv": FileDetails("source", "", ""),
+    "/scrnaseq_analysis/integration.rds": FileDetails("source", "", ""),
+    "/scrnaseq_analysis/integration_heatmap_plots.zip": FileDetails("source", "", ""),
+    "/scrnaseq_analysis/integration_markers.zip": FileDetails("source", "", ""),
+    "/scrnaseq_analysis/integration_split_percent_plots.zip": FileDetails("source", "", ""),
+    "/scrnaseq_analysis/integration_split_umap_plots.zip": FileDetails("source", "", ""),
+    "/scrnaseq_analysis/integration_umap_plots.zip": FileDetails("source", "", ""),
+    "/scrnaseq_analysis/clustering.rds": FileDetails("source", "", ""),
+    "/scrnaseq_analysis/report.html": FileDetails("source", "", ""),
+    "/scrnaseq_analysis/star_sorted_by_cord.bam": FileDetails("source", "", ""),
+    "/scrnaseq_analysis/star_sorted_by_cord.bam.bai": FileDetails("source", "", ""),
+    "/scrnaseq_analysis/log_final.out": FileDetails("source", "", ""),
+    "/scrnaseq_analysis/log.out": FileDetails("source", "", ""),
+    "/scrnaseq_analysis/log_progress.out": FileDetails("source", "", ""),
+    "/scrnaseq_analysis/sj_out.tab": FileDetails("source", "", ""),
+    "/scrnaseq_analysis/barcodes.stats": FileDetails("source", "", ""),
+    "/scrnaseq_analysis/gene_features.stats": FileDetails("source", "", ""),
+    "/scrnaseq_analysis/gene_summary.csv": FileDetails("source", "", ""),
+    "/scrnaseq_analysis/gene_umi_per_cell_sorted.txt": FileDetails("source", "", ""),
+    "/scrnaseq_analysis/gene_filtered_features.tsv": FileDetails("source", "", ""),
+    "/scrnaseq_analysis/gene_filtered_barcodes.tsv": FileDetails("source", "", ""),
+    "/scrnaseq_analysis/gene_filtered_matrix.mtx": FileDetails("source", "", ""),
+    "/scrnaseq_analysis/gene_raw_features.tsv": FileDetails("source", "", ""),
+    "/scrnaseq_analysis/gene_raw_barcodes.tsv": FileDetails("source", "", ""),
+    "/scrnaseq_analysis/gene_raw_matrix.mtx": FileDetails("source", "", ""),
 }

cidc_api/models/files/facets.py

@@ -346,6 +346,21 @@ assay_facets: Facets = {
             "H and E file from MIBI analysis",
         ),
     },
+    "scRNA": {
+        "Samples Metadata": FacetConfig(["/scrnaseq/samples_metadata.csv"], "Sample metadata for scRNA run"),
+        "Read 1 gz": FacetConfig(["/scrnaseq/read_1.gz"], "Gz file for read 1"),
+        "Read 2 gz": FacetConfig(["/scrnaseq/read_2.gz"], "Gz file for read 2"),
+    },
+    "Visium": {
+        "Samples Metadata": FacetConfig(["/visium/samples_metadata.csv"], "Sample metadata for visium run"),
+        "Read 1 fastq gz": FacetConfig(["/visium/R1_001.fastq.gz"], "Gz file for read 1"),
+        "Read 2 fastq gz": FacetConfig(["/visium/R2_001.fastq.gz"], "Gz file for read 2"),
+        "loupe alignment file": FacetConfig(["/visium/loupe_alignment_file.json"]),
+        "brightfield image": FacetConfig(["/visium/brightfield.tiff"]),
+        "dark image": FacetConfig(["/visium/dark_image.tiff"]),
+        "colorized image": FacetConfig(["/visium/colorized.tiff"]),
+        "cytassist image": FacetConfig(["/visium/cytassist.tiff"]),
+    },
     "mIHC": {
         "Samples Report": FacetConfig(["/mihc/sample_report.csv"], "Samples report for mIHC run"),
         "Multitiffs": FacetConfig(["/mihc/multitiffs.tar.gz"], "Multi Tiffs file from mIHC run"),
@@ -549,6 +564,48 @@ analysis_ready_facets = {
     "WES Analysis": FacetConfig(["/wes/analysis/report.tar.gz"]),
     "TCR": FacetConfig(["/tcr_analysis/report_trial.tar.gz"]),
     "mIF": FacetConfig(["/mif/roi_/cell_seg_data.txt"]),
+    "scRNA": FacetConfig(
+        [
+            "/scrnaseq_analysis/samples_metadata.csv",
+            "/scrnaseq_analysis/config.yaml",
+            "/scrnaseq_analysis/R_package_versions.csv",
+            "/scrnaseq_analysis/integration.rds",
+            "/scrnaseq_analysis/integration_heatmap_plots.zip",
+            "/scrnaseq_analysis/integration_markers.zip",
+            "/scrnaseq_analysis/integration_split_percent_plots.zip",
+            "/scrnaseq_analysis/integration_split_umap_plots.zip",
+            "/scrnaseq_analysis/integration_umap_plots.zip",
+            "/scrnaseq_analysis/clustering.rds",
+            "/scrnaseq_analysis/report.html",
+            "/scrnaseq_analysis/star_sorted_by_cord.bam",
+            "/scrnaseq_analysis/star_sorted_by_cord.bam.bai",
+            "/scrnaseq_analysis/log_final.out",
+            "/scrnaseq_analysis/log.out",
+            "/scrnaseq_analysis/log_progress.out",
+            "/scrnaseq_analysis/sj_out.tab",
+            "/scrnaseq_analysis/barcodes.stats",
+            "/scrnaseq_analysis/gene_features.stats",
+            "/scrnaseq_analysis/gene_summary.csv",
+            "/scrnaseq_analysis/gene_umi_per_cell_sorted.txt",
+            "/scrnaseq_analysis/gene_filtered_features.tsv",
+            "/scrnaseq_analysis/gene_filtered_barcodes.tsv",
+            "/scrnaseq_analysis/gene_filtered_matrix.mtx",
+            "/scrnaseq_analysis/gene_raw_features.tsv",
+            "/scrnaseq_analysis/gene_raw_barcodes.tsv",
+            "/scrnaseq_analysis/gene_raw_matrix.mtx",
+        ]
+    ),
+    "Visium": FacetConfig(
+        [
+            "/visium_analysis/samples_metadata.csv",
+            "/visium_analysis/config.yaml",
+            "/visium_analysis/R_package_versions.csv",
+            "/visium_analysis/merged.rds",
+            "/visium_analysis/spatial_variable_features.rds",
+            "/visium_analysis/report.html",
+            "/visium_analysis/visium_spaceranger_output.zip",
+        ]
+    ),
 }
 
 facets_dict: Dict[str, Facets] = {

{nci_cidc_api_modules-1.1.33.dist-info → nci_cidc_api_modules-1.1.35.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.1.33
+Version: 1.1.35
 Summary: SQLAlchemy data models and configuration tools used in the NCI CIDC API
 Home-page: https://github.com/NCI-CIDC/cidc-api-gae
 License: MIT license
@@ -28,7 +28,7 @@ Requires-Dist: python-dotenv==0.10.3
 Requires-Dist: requests==2.32.4
 Requires-Dist: jinja2==3.1.6
 Requires-Dist: certifi==2024.7.4
-Requires-Dist: nci-cidc-schemas==0.27.24
+Requires-Dist: nci-cidc-schemas==0.27.26
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page

{nci_cidc_api_modules-1.1.33.dist-info → nci_cidc_api_modules-1.1.35.dist-info}/RECORD

@@ -8,16 +8,16 @@ cidc_api/models/migrations.py,sha256=gp9vtkYbA9FFy2s-7woelAmsvQbJ41LO2_DY-YkFIrQ
 cidc_api/models/models.py,sha256=JceOfSBetV6ifhYIPL4Qp0T3YpG55M016YvEajLUQ8o,132587
 cidc_api/models/schemas.py,sha256=7tDYtmULuzTt2kg7RorWhte06ffalgpQKrFiDRGcPEQ,2711
 cidc_api/models/files/__init__.py,sha256=8BMTnUSHzUbz0lBeEQY6NvApxDD3GMWMduoVMos2g4Y,213
-cidc_api/models/files/details.py,sha256=WrWPxJqlsteinoNbGTaQ3fcxgvChqLGJ9vY7H829jtk,62842
-cidc_api/models/files/facets.py,sha256=JqCmwcjYYSz7XK4bAokSE9i71C8t9EQ4Jtbv7npth7M,29391
+cidc_api/models/files/details.py,sha256=sZkGM7iEV4-J6IDQCdiMV6KBDLbPxCOqUMaU3aY9rX8,65153
+cidc_api/models/files/facets.py,sha256=WqjfqtYJgY2tBnZ598Yc0eJdQUo2slFNLyTDaqPx_DE,32318
 cidc_api/shared/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cidc_api/shared/auth.py,sha256=PHqmVGkqDjbmUofytVFwD_9ssgUomESl3fFtFHPwZYQ,9062
 cidc_api/shared/emails.py,sha256=GY-l0EkoVU_3hjV0g-xo7N9d1iyCdluyq_arftEPPe0,4989
 cidc_api/shared/gcloud_client.py,sha256=oD7Y3Glp1ZrPYkonv7DvX1koGtF30lgm3ENXYQ7G5cI,35634
 cidc_api/shared/jose.py,sha256=-qzGzEDAlokEp9E7WtBtQkXyyfPWTYXlwYpCqVJWmqM,1830
 cidc_api/shared/rest_utils.py,sha256=RwR30WOUAYCxL7V-i2totEyeriG30GbBDvBcpLXhM9w,6594
-nci_cidc_api_modules-1.1.33.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
-nci_cidc_api_modules-1.1.33.dist-info/METADATA,sha256=a-Cbt8kytToYJwtADZu_hjRC7x5MXobefSYCV6V_lSI,41285
-nci_cidc_api_modules-1.1.33.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-nci_cidc_api_modules-1.1.33.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
-nci_cidc_api_modules-1.1.33.dist-info/RECORD,,
+nci_cidc_api_modules-1.1.35.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
+nci_cidc_api_modules-1.1.35.dist-info/METADATA,sha256=udkDYU-7dGtR_Msaw1vAFABYr8M5rq_RSbb8kjkyDbI,41285
+nci_cidc_api_modules-1.1.35.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+nci_cidc_api_modules-1.1.35.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
+nci_cidc_api_modules-1.1.35.dist-info/RECORD,,