URL checks error reformatting

CHANGELOG.md

@@ -22,6 +22,7 @@
 - Update GeoMx NGS directory schema
 - Ported murine from SenNet
 - Update Histology directory schema
+- Converted upload `_url_checks` to use `_get_method` for SenNet compatibility
 
 ## v0.0.17
 

examples/dataset-examples/bad-cedar-assay-histology/README.md

@@ -5,27 +5,26 @@ Upload Errors:
       column 'contributors_path', value './contributors.tsv'
     : CEDAR Validation Errors:
         examples/dataset-examples/bad-cedar-assay-histology/upload/contributors.tsv:
-          examples/dataset-examples/bad-cedar-assay-histology/upload/contributors.tsv:
-          - Validation Errors:
-            - On row 0, column "orcid", value "0000-0002-8928-abcd" fails because
-              of error "invalidValueFormat".
+          Validation Errors:
+          - On row 0, column "orcid", value "0000-0002-8928-abcd" fails because of
+            error "invalidValueFormat".
 Metadata TSV Validation Errors:
   CEDAR Validation Errors:
     examples/dataset-examples/bad-cedar-assay-histology/upload/bad-histology-metadata.tsv:
-      examples/dataset-examples/bad-cedar-assay-histology/upload/bad-histology-metadata.tsv:
-      - URL Errors:
-        - 'Row 2, field "parent_sample_id" with value "wrong": Field value is not
-          valid; URL https://entity.api.hubmapconsortium.org/entities/wrong returned
-          a 400 Error.'
-        Validation Errors:
-        - On row 0, column "parent_sample_id", value "wrong" fails because of error
-          "invalidValueFormat".
-        - On row 1, column "contributors_path", value "" fails because of error "missingRequired".
+      URL Errors:
+      - 'On row 2, column "parent_sample_id", value "wrong" fails because of error
+        "HTTPError": 401 Client Error: Unauthorized for url: https://entity.api.hubmapconsortium.org/entities/wrong.'
+      - 'On row 3, column "parent_sample_id", value "HBM854.FXDQ.783" fails because
+        of error "HTTPError": 401 Client Error: Unauthorized for url: https://entity.api.hubmapconsortium.org/entities/HBM854.FXDQ.783'
+      Validation Errors:
+      - On row 0, column "parent_sample_id", value "wrong" fails because of error
+        "invalidValueFormat".
+      - On row 1, column "contributors_path", value "" fails because of error "missingRequired".
 Reference Errors:
   No References:
     Files:
     - unreferenced_file.
 Hint: 'If validation fails because of extra whitespace in the TSV, try:
 
   src/cleanup_whitespace.py --tsv_in original.tsv --tsv_out clean.tsv.'
-```
+```

examples/dataset-examples/bad-cedar-assay-histology/fixtures.json

@@ -1 +1 @@
-{"assaytype": {"Histology": {"assaytype": "h-and-e", "contains-pii": false, "dataset-type": "Histology", "description": "H&E Stained Microscopy", "dir-schema": "histology-v2", "primary": true, "vitessce-hints": []}}, "validation": {"h-and-e": {"examples/dataset-examples/bad-cedar-assay-histology/upload/bad-histology-metadata.tsv": [{"URL Errors": ["Row 2, field 'parent_sample_id' with value 'wrong': 400 Client Error: Bad Request for url: https://entity.api.hubmapconsortium.org/entities/wrong"], "Validation Errors": ["On row 0, column \"parent_sample_id\", value \"wrong\" fails because of error \"invalidValueFormat\"", "On row 1, column \"contributors_path\", value \"\" fails because of error \"missingRequired\""]}]}, "contributors": {"examples/dataset-examples/bad-cedar-assay-histology/upload/contributors.tsv": [{"Validation Errors": ["On row 0, column \"orcid\", value \"0000-0002-8928-abcd\" fails because of error \"invalidValueFormat\""]}]}}}
+{"assaytype": {"Histology": {"assaytype": "h-and-e", "contains-pii": false, "dataset-type": "Histology", "description": "H&E Stained Microscopy", "dir-schema": "histology-v2", "primary": true, "vitessce-hints": []}}, "validation": {"h-and-e": {"URL Errors": ["On row 2, column \"parent_sample_id\", value \"wrong\" fails because of error \"HTTPError\": 400 Client Error: Bad Request for url: https://entity.api.hubmapconsortium.org/entities/wrong"], "Validation Errors": ["On row 0, column \"parent_sample_id\", value \"wrong\" fails because of error \"invalidValueFormat\"", "On row 1, column \"contributors_path\", value \"\" fails because of error \"missingRequired\""]}, "contributors": {"Validation Errors": ["On row 0, column \"orcid\", value \"0000-0002-8928-abcd\" fails because of error \"invalidValueFormat\""]}}}

examples/dataset-examples/bad-cedar-multi-assay-visium-bad-child-metadata/README.md

@@ -2,19 +2,18 @@
 Metadata TSV Validation Errors:
   CEDAR Validation Errors:
     examples/dataset-examples/bad-cedar-multi-assay-visium-bad-child-metadata/upload/bad-visium-rnaseq-metadata.tsv:
-      examples/dataset-examples/bad-cedar-multi-assay-visium-bad-child-metadata/upload/bad-visium-rnaseq-metadata.tsv:
-      - URL Errors:
-        - 'Row 3, field "parent_sample_id" with value "": 404 Client Error: Not Found
-          for url: https://entity.api.hubmapconsortium.org/entities/.'
-        Validation Errors:
-        - On row 1, column "parent_sample_id", value "" fails because of error "missingRequired".
-        - On row 2, column "preparation_protocol_doi", value "wrong" fails because
-          of error "invalidUrl".
+      URL Errors:
+      - 'On row 3, column "parent_sample_id", value "" fails because of error "HTTPError":
+        404 Client Error: Not Found for url: https://entity.api.hubmapconsortium.org/entities/.'
+      Validation Errors:
+      - On row 1, column "parent_sample_id", value "" fails because of error "missingRequired".
+      - On row 2, column "preparation_protocol_doi", value "wrong" fails because of
+        error "invalidUrl".
 Reference Errors:
   No References:
     Files:
     - unreferenced_file.
 Hint: 'If validation fails because of extra whitespace in the TSV, try:
 
   src/cleanup_whitespace.py --tsv_in original.tsv --tsv_out clean.tsv.'
-```
+```

examples/dataset-examples/bad-cedar-multi-assay-visium-bad-child-metadata/fixtures.json

@@ -1 +1 @@
-{"assaytype": {"RNAseq": {"assaytype": "scRNAseq-10Genomics-v3", "contains-pii": true, "dataset-type": "RNAseq", "description": "scRNA-seq (10x Genomics v3)", "dir-schema": "rnaseq-v2", "primary": true, "vitessce-hints": []}, "Visium (no probes)": {"assaytype": "visium-no-probes", "contains-pii": true, "dataset-type": "Visium (no probes)", "description": "Visium (No probes)", "dir-schema": "visium-no-probes-v2", "is-multi-assay": true, "must-contain": ["Histology", "RNAseq"], "primary": true, "vitessce-hints": []}, "Histology": {"assaytype": "h-and-e", "contains-pii": false, "dataset-type": "Histology", "description": "H&E Stained Microscopy", "dir-schema": "histology-v2", "primary": true, "vitessce-hints": []}}, "validation": {"scRNAseq-10Genomics-v3": {"examples/dataset-examples/bad-cedar-multi-assay-visium-bad-child-metadata/upload/bad-visium-rnaseq-metadata.tsv": [{"URL Errors": ["Row 3, field 'parent_sample_id' with value '': 404 Client Error: Not Found for url: https://entity.api.hubmapconsortium.org/entities/"], "Validation Errors": ["On row 1, column \"parent_sample_id\", value \"\" fails because of error \"missingRequired\"", "On row 2, column \"preparation_protocol_doi\", value \"wrong\" fails because of error \"invalidUrl\""]}]}, "contributors": null, "visium-no-probes": null, "h-and-e": null}}
+{"assaytype": {"RNAseq": {"assaytype": "scRNAseq-10xGenomics-v3", "contains-pii": true, "dataset-type": "RNAseq", "description": "scRNA-seq (10x Genomics v3)", "dir-schema": "rnaseq-v2", "primary": true, "vitessce-hints": []}, "Visium (no probes)": {"assaytype": "visium-no-probes", "contains-pii": true, "dataset-type": "Visium (no probes)", "description": "Visium (no probes)", "dir-schema": "visium-no-probes-v2", "is-multi-assay": true, "must-contain": ["Histology", "RNAseq"], "primary": true, "vitessce-hints": []}, "Histology": {"assaytype": "h-and-e", "contains-pii": false, "dataset-type": "Histology", "description": "H&E Stained Microscopy", "dir-schema": "histology-v2", "primary": true, "vitessce-hints": []}}, "validation": {"scRNAseq-10xGenomics-v3": {"URL Errors": ["On row 3, column \"parent_sample_id\", value \"\" fails because of error \"HTTPError\": 404 Client Error: Not Found for url: https://entity.api.hubmapconsortium.org/entities/"], "Validation Errors": ["On row 1, column \"parent_sample_id\", value \"\" fails because of error \"missingRequired\"", "On row 2, column \"preparation_protocol_doi\", value \"wrong\" fails because of error \"invalidUrl\""]}, "contributors": null, "visium-no-probes": null, "h-and-e": null}}

examples/dataset-examples/bad-cedar-multi-assay-visium-bad-dir-structure/fixtures.json

@@ -1 +1 @@
-{"assaytype": {"Visium (no probes)": {"assaytype": "visium-no-probes", "contains-pii": true, "dataset-type": "Visium (no probes)", "description": "Visium (No probes)", "dir-schema": "visium-no-probes-v2", "is-multi-assay": true, "must-contain": ["Histology", "RNAseq"], "primary": true, "vitessce-hints": []}, "Histology": {"assaytype": "h-and-e", "contains-pii": false, "dataset-type": "Histology", "description": "H&E Stained Microscopy", "dir-schema": "histology-v2", "primary": true, "vitessce-hints": []}, "RNAseq": {"assaytype": "scRNAseq-10Genomics-v3", "contains-pii": true, "dataset-type": "RNAseq", "description": "scRNA-seq (10x Genomics v3)", "dir-schema": "rnaseq-v2", "primary": true, "vitessce-hints": []}}, "validation": {"visium-no-probes": null, "contributors": null, "h-and-e": null, "scRNAseq-10Genomics-v3": null}}
+{"assaytype": {"Visium (no probes)": {"assaytype": "visium-no-probes", "contains-pii": true, "dataset-type": "Visium (no probes)", "description": "Visium (no probes)", "dir-schema": "visium-no-probes-v2", "is-multi-assay": true, "must-contain": ["Histology", "RNAseq"], "primary": true, "vitessce-hints": []}, "Histology": {"assaytype": "h-and-e", "contains-pii": false, "dataset-type": "Histology", "description": "H&E Stained Microscopy", "dir-schema": "histology-v2", "primary": true, "vitessce-hints": []}, "RNAseq": {"assaytype": "scRNAseq-10xGenomics-v3", "contains-pii": true, "dataset-type": "RNAseq", "description": "scRNA-seq (10x Genomics v3)", "dir-schema": "rnaseq-v2", "primary": true, "vitessce-hints": []}}, "validation": {"visium-no-probes": null, "contributors": null, "h-and-e": null, "scRNAseq-10xGenomics-v3": null}}

examples/dataset-examples/bad-cedar-multi-assay-visium-missing-child/fixtures.json

@@ -1 +1 @@
-{"assaytype": {"Visium (no probes)": {"assaytype": "visium-no-probes", "contains-pii": true, "dataset-type": "Visium (no probes)", "description": "Visium (No probes)", "dir-schema": "visium-no-probes-v2", "is-multi-assay": true, "must-contain": ["Histology", "RNAseq"], "primary": true, "vitessce-hints": []}, "Histology": {"assaytype": "h-and-e", "contains-pii": false, "dataset-type": "Histology", "description": "H&E Stained Microscopy", "dir-schema": "histology-v2", "primary": true, "vitessce-hints": []}}, "validation": {}}
+{"assaytype": {"Visium (no probes)": {"assaytype": "visium-no-probes", "contains-pii": true, "dataset-type": "Visium (no probes)", "description": "Visium (no probes)", "dir-schema": "visium-no-probes-v2", "is-multi-assay": true, "must-contain": ["Histology", "RNAseq"], "primary": true, "vitessce-hints": []}, "Histology": {"assaytype": "h-and-e", "contains-pii": false, "dataset-type": "Histology", "description": "H&E Stained Microscopy", "dir-schema": "histology-v2", "primary": true, "vitessce-hints": []}}, "validation": {}}

examples/dataset-examples/bad-cedar-multi-assay-visium-unreferenced-parent-path/fixtures.json

@@ -1 +1 @@
-{"assaytype": {"Visium (no probes)": {"assaytype": "visium-no-probes", "contains-pii": true, "dataset-type": "Visium (no probes)", "description": "Visium (No probes)", "dir-schema": "visium-no-probes-v2", "is-multi-assay": true, "must-contain": ["Histology", "RNAseq"], "primary": true, "vitessce-hints": []}, "Histology": {"assaytype": "h-and-e", "contains-pii": false, "dataset-type": "Histology", "description": "H&E Stained Microscopy", "dir-schema": "histology-v2", "primary": true, "vitessce-hints": []}, "RNAseq": {"assaytype": "scRNAseq-10Genomics-v3", "contains-pii": true, "dataset-type": "RNAseq", "description": "scRNA-seq (10x Genomics v3)", "dir-schema": "rnaseq-v2", "primary": true, "vitessce-hints": []}}, "validation": {}}
+{"assaytype": {"Visium (no probes)": {"assaytype": "visium-no-probes", "contains-pii": true, "dataset-type": "Visium (no probes)", "description": "Visium (no probes)", "dir-schema": "visium-no-probes-v2", "is-multi-assay": true, "must-contain": ["Histology", "RNAseq"], "primary": true, "vitessce-hints": []}, "Histology": {"assaytype": "h-and-e", "contains-pii": false, "dataset-type": "Histology", "description": "H&E Stained Microscopy", "dir-schema": "histology-v2", "primary": true, "vitessce-hints": []}, "RNAseq": {"assaytype": "scRNAseq-10xGenomics-v3", "contains-pii": true, "dataset-type": "RNAseq", "description": "scRNA-seq (10x Genomics v3)", "dir-schema": "rnaseq-v2", "primary": true, "vitessce-hints": []}}, "validation": {}}

examples/dataset-examples/bad-cedar-multi-assay-visium-with-standalone-histology/fixtures.json

@@ -1 +1 @@
-{"assaytype": {"Visium (no probes)": {"assaytype": "visium-no-probes", "contains-pii": true, "dataset-type": "Visium (no probes)", "description": "Visium (No probes)", "dir-schema": "visium-no-probes-v2", "is-multi-assay": true, "must-contain": ["Histology", "RNAseq"], "primary": true, "vitessce-hints": []}, "Histology": {"assaytype": "h-and-e", "contains-pii": false, "dataset-type": "Histology", "description": "H&E Stained Microscopy", "dir-schema": "histology-v2", "primary": true, "vitessce-hints": []}, "RNAseq": {"assaytype": "scRNAseq-10Genomics-v3", "contains-pii": true, "dataset-type": "RNAseq", "description": "scRNA-seq (10x Genomics v3)", "dir-schema": "rnaseq-v2", "primary": true, "vitessce-hints": []}}, "validation": {}}
+{"assaytype": {"Visium (no probes)": {"assaytype": "visium-no-probes", "contains-pii": true, "dataset-type": "Visium (no probes)", "description": "Visium (no probes)", "dir-schema": "visium-no-probes-v2", "is-multi-assay": true, "must-contain": ["Histology", "RNAseq"], "primary": true, "vitessce-hints": []}, "Histology": {"assaytype": "h-and-e", "contains-pii": false, "dataset-type": "Histology", "description": "H&E Stained Microscopy", "dir-schema": "histology-v2", "primary": true, "vitessce-hints": []}, "RNAseq": {"assaytype": "scRNAseq-10xGenomics-v3", "contains-pii": true, "dataset-type": "RNAseq", "description": "scRNA-seq (10x Genomics v3)", "dir-schema": "rnaseq-v2", "primary": true, "vitessce-hints": []}}, "validation": {}}

examples/dataset-examples/bad-cedar-multi-assay-visium-wrong-child/fixtures.json

@@ -1 +1 @@
-{"assaytype": {"RNAseq (with probes)": {"assaytype": "scRNAseq-visium-with-probes", "contains-pii": true, "dataset-type": "RNAseq (with probes)", "description": "Visium RNAseq with probes", "dir-schema": "rnaseq-with-probes-v2", "primary": true, "vitessce-hints": []}, "Visium (no probes)": {"assaytype": "visium-no-probes", "contains-pii": true, "dataset-type": "Visium (no probes)", "description": "Visium (No probes)", "dir-schema": "visium-no-probes-v2", "is-multi-assay": true, "must-contain": ["Histology", "RNAseq"], "primary": true, "vitessce-hints": []}, "Histology": {"assaytype": "h-and-e", "contains-pii": false, "dataset-type": "Histology", "description": "H&E Stained Microscopy", "dir-schema": "histology-v2", "primary": true, "vitessce-hints": []}}, "validation": {}}
+{"assaytype": {"RNAseq (with probes)": {"assaytype": "scRNAseq-visium-with-probes", "contains-pii": true, "dataset-type": "RNAseq (with probes)", "description": "Visium RNAseq with probes", "dir-schema": "rnaseq-with-probes-v2", "primary": true, "vitessce-hints": []}, "Visium (no probes)": {"assaytype": "visium-no-probes", "contains-pii": true, "dataset-type": "Visium (no probes)", "description": "Visium (no probes)", "dir-schema": "visium-no-probes-v2", "is-multi-assay": true, "must-contain": ["Histology", "RNAseq"], "primary": true, "vitessce-hints": []}, "Histology": {"assaytype": "h-and-e", "contains-pii": false, "dataset-type": "Histology", "description": "H&E Stained Microscopy", "dir-schema": "histology-v2", "primary": true, "vitessce-hints": []}}, "validation": {}}

examples/dataset-examples/good-cedar-multi-assay-visium/README.md

@@ -13,7 +13,7 @@ TSVs:
     Metadata schema version: '2'
     Directory schema versions: histology-v2
   good-visium-rnaseq-metadata.tsv:
-    Schema: scRNAseq-10Genomics-v3-v2
+    Schema: scRNAseq-10xGenomics-v3-v2
     Metadata schema version: '2'
     Directory schema versions: rnaseq-v2
 

examples/dataset-examples/good-cedar-multi-assay-visium/fixtures.json

@@ -1 +1 @@
-{"assaytype": {"Visium (no probes)": {"assaytype": "visium-no-probes", "contains-pii": true, "dataset-type": "Visium (no probes)", "description": "Visium (No probes)", "dir-schema": "visium-no-probes-v2", "is-multi-assay": true, "must-contain": ["Histology", "RNAseq"], "primary": true, "vitessce-hints": []}, "Histology": {"assaytype": "h-and-e", "contains-pii": false, "dataset-type": "Histology", "description": "H&E Stained Microscopy", "dir-schema": "histology-v2", "primary": true, "vitessce-hints": []}, "RNAseq": {"assaytype": "scRNAseq-10Genomics-v3", "contains-pii": true, "dataset-type": "RNAseq", "description": "scRNA-seq (10x Genomics v3)", "dir-schema": "rnaseq-v2", "primary": true, "vitessce-hints": []}}, "validation": {"visium-no-probes": null, "contributors": null, "h-and-e": null, "scRNAseq-10Genomics-v3": null}}
+{"assaytype": {"Visium (no probes)": {"assaytype": "visium-no-probes", "contains-pii": true, "dataset-type": "Visium (no probes)", "description": "Visium (no probes)", "dir-schema": "visium-no-probes-v2", "is-multi-assay": true, "must-contain": ["Histology", "RNAseq"], "primary": true, "vitessce-hints": []}, "Histology": {"assaytype": "h-and-e", "contains-pii": false, "dataset-type": "Histology", "description": "H&E Stained Microscopy", "dir-schema": "histology-v2", "primary": true, "vitessce-hints": []}, "RNAseq": {"assaytype": "scRNAseq-10xGenomics-v3", "contains-pii": true, "dataset-type": "RNAseq", "description": "scRNA-seq (10x Genomics v3)", "dir-schema": "rnaseq-v2", "primary": true, "vitessce-hints": []}}, "validation": {"visium-no-probes": null, "contributors": null, "h-and-e": null, "scRNAseq-10xGenomics-v3": null}}

examples/plugin-tests/expected-failure/fixtures.json

@@ -1 +1 @@
-{"assaytype": {"Visium (no probes)": {"assaytype": "visium-no-probes", "contains-pii": true, "dataset-type": "Visium (no probes)", "description": "Visium (No probes)", "dir-schema": "visium-no-probes-v2", "is-multi-assay": true, "must-contain": ["Histology", "RNAseq"], "primary": true, "vitessce-hints": []}, "Histology": {"assaytype": "h-and-e", "contains-pii": false, "dataset-type": "Histology", "description": "H&E Stained Microscopy", "dir-schema": "histology-v2", "primary": true, "vitessce-hints": []}, "RNAseq": {"assaytype": "scRNAseq-10Genomics-v3", "contains-pii": true, "dataset-type": "RNAseq", "description": "scRNA-seq (10x Genomics v3)", "dir-schema": "rnaseq-v2", "primary": true, "vitessce-hints": []}}, "validation": {"visium-no-probes": null, "contributors": null, "h-and-e": null, "scRNAseq-10Genomics-v3": null}}
+{"assaytype": {"Visium (no probes)": {"assaytype": "visium-no-probes", "contains-pii": true, "dataset-type": "Visium (no probes)", "description": "Visium (no probes)", "dir-schema": "visium-no-probes-v2", "is-multi-assay": true, "must-contain": ["Histology", "RNAseq"], "primary": true, "vitessce-hints": []}, "Histology": {"assaytype": "h-and-e", "contains-pii": false, "dataset-type": "Histology", "description": "H&E Stained Microscopy", "dir-schema": "histology-v2", "primary": true, "vitessce-hints": []}, "RNAseq": {"assaytype": "scRNAseq-10xGenomics-v3", "contains-pii": true, "dataset-type": "RNAseq", "description": "scRNA-seq (10x Genomics v3)", "dir-schema": "rnaseq-v2", "primary": true, "vitessce-hints": []}}, "validation": {"visium-no-probes": null, "contributors": null, "h-and-e": null, "scRNAseq-10xGenomics-v3": null}}