nci-cidc-schemas 0.27.10__tar.gz → 0.27.12__tar.gz

{nci_cidc_schemas-0.27.10/nci_cidc_schemas.egg-info → nci_cidc_schemas-0.27.12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_schemas
-Version: 0.27.10
+Version: 0.27.12
 Summary: The CIDC data model and tools for working with it.
 Home-page: https://github.com/NCI-CIDC/cidc-schemas
 Author: NCI

{nci_cidc_schemas-0.27.10 → nci_cidc_schemas-0.27.12}/cidc_schemas/__init__.py

@@ -2,4 +2,4 @@
 
 __author__ = """NCI"""
 __email__ = "nci-cidc-tools-admin@mail.nih.gov"
-__version__ = "0.27.10"
+__version__ = "0.27.12"

{nci_cidc_schemas-0.27.10 → nci_cidc_schemas-0.27.12}/cidc_schemas/json_validation.py

@@ -7,6 +7,7 @@ import copy
 import functools
 import json
 import collections.abc
+import logging
 from contextlib import contextmanager
 from typing import Optional, Callable, Union
 
@@ -19,6 +20,8 @@ from jsonpointer import resolve_pointer
 from .constants import SCHEMA_DIR, METASCHEMA_PATH
 from .util import JSON
 
+logger = logging.getLogger("cidc_schemas.json_validation")
+
 
 class InDocRefNotFoundError(ValidationError):
     pass
@@ -115,12 +118,13 @@ class _Validator(jsonschema.Draft7Validator):
 
                     # protect against None cache
                     if self._in_doc_refs_cache is None:
-                        print(f"_in_doc_refs_cache: {self._in_doc_refs_cache}")
-                        print(f"scope '{scope}'")
-                        raise RuntimeError(
+                        logger.info(f"_in_doc_refs_cache: {self._in_doc_refs_cache}")
+                        logger.info(f"scope '{scope}'")
+                        logger.info(
                             "Internal error: _in_doc_refs_cache is None when trying to build cache. "
                             "This usually means the validation context was improperly set up."
                         )
+                        self._in_doc_refs_cache = dict()
 
                     # If there are no cached values for this ref path pattern, collect them
                     if ref_path_pattern not in self._in_doc_refs_cache:

{nci_cidc_schemas-0.27.10 → nci_cidc_schemas-0.27.12}/cidc_schemas/prism/constants.py

@@ -25,6 +25,7 @@ SUPPORTED_ASSAYS = [
     "misc_data",
     "ctdna",
     "microbiome",
+    "mihc",
 ]
 
 SUPPORTED_SHIPPING_MANIFESTS = [
@@ -91,6 +92,7 @@ ASSAY_TO_FILEPATH: Dict[str, str] = {
             "misc_data",
             "nanostring",
             "olink",
+            "mihc",
         ]
     },
 }

nci_cidc_schemas-0.27.12/cidc_schemas/schemas/artifacts/artifact_h5ad.json

@@ -0,0 +1,51 @@
+{
+  "$schema": "metaschema/strict_meta_schema.json#",
+  "$id": "h5ad_artifact",
+  "title": "H5AD Artifact",
+  "type": "object",
+  "description": "Information about a h5ad file.",
+  "additionalProperties": false,
+  "properties": {
+    "data_format": {
+      "description": "Data format.",
+      "const": "H5AD"
+    },
+    "upload_placeholder": {
+      "$ref": "artifacts/artifact_core.json#properties/upload_placeholder"
+    },
+    "artifact_creator": {
+      "$ref": "artifacts/artifact_core.json#properties/artifact_creator"
+    },
+    "uploader": { "$ref": "artifacts/artifact_core.json#properties/uploader" },
+    "uuid": { "$ref": "artifacts/artifact_core.json#properties/uuid" },
+    "file_name": {
+      "$ref": "artifacts/artifact_core.json#properties/file_name"
+    },
+    "object_url": {
+      "$ref": "artifacts/artifact_core.json#properties/object_url"
+    },
+    "uploaded_timestamp": {
+      "$ref": "artifacts/artifact_core.json#properties/uploaded_timestamp"
+    },
+    "file_size_bytes": {
+      "$ref": "artifacts/artifact_core.json#properties/file_size_bytes"
+    },
+    "md5_hash": { "$ref": "artifacts/artifact_core.json#properties/md5_hash" },
+    "crc32c_hash": {
+      "$ref": "artifacts/artifact_core.json#properties/crc32c_hash"
+    },
+    "visible": { "$ref": "artifacts/artifact_core.json#properties/visible" },
+    "artifact_category": {
+      "$ref": "artifacts/artifact_core.json#properties/artifact_category"
+    },
+    "facet_group": {
+      "$ref": "artifacts/artifact_core.json#properties/facet_group"
+    }
+  },
+  "allOf": [
+    {
+      "$ref": "artifacts/artifact_core.json"
+    }
+  ],
+  "mergeStrategy": "objectMerge"
+}

{nci_cidc_schemas-0.27.10 → nci_cidc_schemas-0.27.12}/cidc_schemas/schemas/assays/components/available_assays.json

@@ -119,6 +119,13 @@
         "idRef": "batch_id"
       }
     },
+    "mihc": {
+      "type": "array",
+      "description": "mIHC",
+      "items": {
+        "$ref": "assays/mihc_assay.json"
+      }
+    },
     "nanostring": {
       "type": "array",
       "description": "Nanostring",

{nci_cidc_schemas-0.27.10 → nci_cidc_schemas-0.27.12}/cidc_schemas/schemas/assays/components/image.json

@@ -9,12 +9,12 @@
     "slide_scanner_model": {
       "description": "Model version of the slide scanner instrument.",
       "type": "string",
-      "enum": ["Vectra 2.0", "Hamamatsu", "VectraPolaris/3.0.3", "Not Provided"]
+      "enum": ["Vectra 2.0", "Hamamatsu", "VectraPolaris/3.0.3", "Aperio AT2","Not Provided"]
     },
     "image_analysis_software": {
       "description": "Source software for digital pathology and image analysis.",
       "type": "string",
-      "enum": ["InForm", "QuPath"]
+      "enum": ["InForm", "QuPath", "MARQO", "Not Provided"]
     },
     "image_analysis_software_version": {
       "description": "Source software version for digital pathology and image analysis.",
@@ -28,7 +28,7 @@
     "positive_cell_detection": {
       "description": "Model used for positive cell detection in imaging experiment.",
       "type": "string",
-      "enum": ["proprietary", "random forest classifier"]
+      "enum": ["proprietary", "random forest classifier", "Not Provided"]
     }
   },
   "required": ["slide_scanner_model"]

nci_cidc_schemas-0.27.12/cidc_schemas/schemas/assays/components/mihc_antibody.json

@@ -0,0 +1,66 @@
+{
+  "$schema": "metaschema/strict_meta_schema.json#",
+  "$id": "mihc_antibody",
+  "title": "mIHC antibody",
+  "description": "Data specific to antibody preparation on the mIHC platform",
+  "additionalProperties": false,
+  "type": "object",
+  "allOf": [{ "$ref": "assays/components/antibody.json" }],
+  "properties": {
+
+    "antibody": {"$ref": "assays/components/antibody.json#properties/antibody"},
+    "clone": {"$ref": "assays/components/antibody.json#properties/clone"},
+    "company": {"$ref": "assays/components/antibody.json#properties/company"},
+    "cat_num": {"$ref": "assays/components/antibody.json#properties/cat_num"},
+    "lot_num": {"$ref": "assays/components/antibody.json#properties/lot_num"},
+
+    "export_name": {
+      "description": "Name of this antibody in InForm export, e.g. 'CD8 (Opal 520)'",
+      "type": "string"
+    },
+    "staining_order": {
+      "description": "Order of staining applied",
+      "type": "integer"
+    },
+    "fluor_wavelength": {
+      "description": "Wavelength registered for Alexa Fluor processing.",
+      "type": "integer"
+    },
+    "primary_ab_dilution": {
+      "description": "Concentration ratio for primary antibody dilution.",
+      "type": "string"
+    },
+    "dilutent": {
+      "description": "Dilution agent used for antibody sample.",
+      "type": "string"
+    },
+    "fluor_dilution": {
+      "description": "Concentration ratio for fluor dilution agent.",
+      "type": "string"
+    },
+    "antigen_retrieval_time": {
+      "description": "Length of time needed for antigen retrieval.",
+      "type": "string",
+      "format": "time"
+    },
+    "primary_incubation_time": {
+      "description": "Length of time for primary antibody incubation.",
+      "type": "string",
+      "format": "time"
+    },
+    "amplification_time": {
+      "description": "Length of time required for amplified signal detection.",
+      "type": "string",
+      "format": "time"
+    }
+  },
+  "mergeStrategy": "objectMerge",
+  "required": [
+    "primary_ab_dilution",
+    "dilutent",
+    "fluor_dilution",
+    "antigen_retrieval_time",
+    "primary_incubation_time",
+    "amplification_time"
+  ]
+}

nci_cidc_schemas-0.27.12/cidc_schemas/schemas/assays/mihc_assay.json

@@ -0,0 +1,108 @@
+{
+    "$schema": "metaschema/strict_meta_schema.json#",
+    "$id": "mihc_assay",
+    "title": "mIHC Assay",
+    "type": "object",
+    "$comment": "description used in docs/index.html and docs/assays.mihc.html",
+    "description": "Mulitplex Immunohistochemestry (mIHC) assay",
+    "additionalProperties": false,
+    "definitions": {
+        "record": {
+            "type": "object",
+            "mergeStrategy": "objectMerge",
+            "description": "A single data record from a mIHC assay.",
+            "additionalProperties": false,
+            "required": [
+                "cimac_id",
+                "tilemap_file",
+                "tilestats_file",
+                "h5ad_file",
+                "multitiffs_gzip",
+                "stain_zip",
+                "geojsons_zip"
+            ],
+            "properties": {
+                "cimac_id": {
+                    "description": "Id of an sample within this clinical trial, that this assay record is based upon.",
+                    "$ref": "sample.json#properties/cimac_id"
+                },
+                "tilemap_file": {
+                    "$ref": "artifacts/artifact_ome_tiff.json"
+                },
+                "tilestats_file": {
+                    "$ref": "artifacts/artifact_csv.json"
+                },
+                "h5ad_file": {
+                    "$ref": "artifacts/artifact_h5ad.json"
+                },
+                "multitiffs_gzip": {
+                    "$ref": "artifacts/artifact_gz.json"
+                },
+                "stain_zip": {
+                    "$ref": "artifacts/artifact_zip.json"
+                },
+                "geojsons_zip": {
+                    "$ref": "artifacts/artifact_zip.json"
+                }
+            }
+        }
+    },
+    "properties": {
+        "assay_creator": {
+            "$ref": "assays/components/assay_core.json#properties/assay_creator"
+        },
+        "slide_scanner_model": {"$ref": "assays/components/image.json#properties/slide_scanner_model"},
+        "image_analysis_software": {"$ref": "assays/components/image.json#properties/image_analysis_software"},
+        "image_analysis_software_version": {"$ref": "assays/components/image.json#properties/image_analysis_software_version"},
+        "cell_segmentation_model": {"$ref": "assays/components/image.json#properties/cell_segmentation_model"},
+        "positive_cell_detection": {"$ref": "assays/components/image.json#properties/positive_cell_detection"},
+
+        "staining": {"$ref": "assays/components/imaging_data.json#properties/staining"},
+        "staining_date": {"$ref": "assays/components/imaging_data.json#properties/staining_date"},
+        "imaging_date": {"$ref": "assays/components/imaging_data.json#properties/imaging_date"},
+        "imaging_status": {"$ref": "assays/components/imaging_data.json#properties/imaging_status"},
+
+        "batch_id": {
+            "description": "Batch identification number. Unique to every upload.",
+            "type": "string"
+        },
+
+        "samples_file": {"$ref": "artifacts/artifact_csv.json"},
+
+        "panel": {"type": "string"},
+
+        "antibodies": {
+            "type": "array",
+            "items": {
+                "$ref": "assays/components/mihc_antibody.json"
+            },
+            "mergeStrategy": "arrayMergeById",
+            "mergeOptions": {
+                "idRef": "antibody"
+            }
+        },
+
+
+        "excluded_samples": {
+            "$ref": "assays/components/excluded_samples.json"
+        },
+
+        "records": {
+            "type": "array",
+            "description": "A single data record from a mIHC assay.",
+            "items": {
+                "$ref": "assays/mihc_assay.json#definitions/record"
+            },
+            "mergeStrategy": "append"
+        }
+    },
+    "required": [
+        "assay_creator",
+        "batch_id",
+        "samples_file",
+        "records",
+        "panel",
+        "antibodies"
+    ]
+}
+

{nci_cidc_schemas-0.27.10 → nci_cidc_schemas-0.27.12}/cidc_schemas/schemas/templates/assays/mibi_template.json

@@ -36,11 +36,11 @@
                         },
                         "roi id": {
                             "merge_pointer": "0/files/roi_id",
-                            "type_ref": "assays/components/mibi_imaging/mibi_files.json#properties/roi_id"
+                            "type_ref": "assays/components/mibi_imaging/mibi_input.json#properties/roi_id"
                         },
                         "Dataset": {
                             "merge_pointer": "0/files/dataset",
-                            "type_ref": "assays/components/mibi_imaging/mibi_files.json#properties/dataset",
+                            "type_ref": "assays/components/mibi_imaging/mibi_input.json#properties/dataset",
                             "allow_empty": true
                         },
                         "HE file type": {
@@ -56,7 +56,7 @@
                         },
                         "Roi description": {
                             "merge_pointer": "0/files/roi_description",
-                            "type_ref": "assays/components/mibi_imaging/mibi_files.json#properties/roi_description",
+                            "type_ref": "assays/components/mibi_imaging/mibi_input.json#properties/roi_description",
                             "allow_empty": true
                         },
                         "MIBI OME Tiff File": {
@@ -67,12 +67,12 @@
                         },
                         "MIBI OME Tiff File Name": {
                             "merge_pointer": "0/files/mibi_ome_tiff_file_name",
-                            "type_ref": "assays/components/mibi_imaging/mibi_files.json#properties/mibi_ome_tiff_file_name"
+                            "type_ref": "assays/components/mibi_imaging/mibi_input.json#properties/mibi_ome_tiff_file_name"
                         },
 
                         "Comment": {
                             "merge_pointer": "0/files/comment",
-                            "type_ref": "assays/components/mibi_imaging/mibi_files.json#properties/comment",
+                            "type_ref": "assays/components/mibi_imaging/mibi_input.json#properties/comment",
                             "allow_empty": true
                         }
                     }

nci_cidc_schemas-0.27.12/cidc_schemas/schemas/templates/assays/mihc_template.json

@@ -0,0 +1,244 @@
+{    "title": "mIHC assay template",
+    "description": "Multiplex Immunohistochemistry (mIHC) submission.",
+    "prism_template_root_object_schema": "assays/mihc_assay.json",
+    "prism_template_root_object_pointer": "/assays/mihc/0",
+    "properties":
+    {
+        "worksheets":
+        {
+            "mIHC":
+            {
+                "preamble_rows":
+                {
+                    "protocol identifier":
+                    {
+                        "merge_pointer": "3/protocol_identifier",
+                        "type_ref": "clinical_trial.json#properties/protocol_identifier"
+                    },
+                    "assay creator":
+                    {
+                        "merge_pointer": "0/assay_creator",
+                        "type_ref": "assays/mihc_assay.json#properties/assay_creator"
+                    },
+                    "slide scanner model":
+                    {
+                        "merge_pointer": "0/slide_scanner_model",
+                        "type_ref": "assays/mihc_assay.json#properties/slide_scanner_model"
+                    },
+                    "image analysis software":
+                    {
+                        "merge_pointer": "0/image_analysis_software",
+                        "type_ref": "assays/mihc_assay.json#properties/image_analysis_software",
+                        "allow_empty": true
+                    },
+                    "image analysis software version":
+                    {
+                        "merge_pointer": "0/image_analysis_software_version",
+                        "type_ref": "assays/mihc_assay.json#properties/image_analysis_software_version",
+                        "allow_empty": true
+                    },
+                    "cell segmentation model":
+                    {
+                        "merge_pointer": "0/cell_segmentation_model",
+                        "type_ref": "assays/mihc_assay.json#properties/cell_segmentation_model",
+                        "allow_empty": true
+                    },
+                    "positive cell detection model":
+                    {
+                        "merge_pointer": "0/positive_cell_detection",
+                        "type_ref": "assays/mihc_assay.json#properties/positive_cell_detection",
+                        "allow_empty": true
+                    },
+                    "staining":
+                    {
+                        "merge_pointer": "0/staining",
+                        "type_ref": "assays/mihc_assay.json#properties/staining",
+                        "allow_empty": true
+                    },
+                    "staining date":
+                    {
+                        "merge_pointer": "0/staining_date",
+                        "type_ref": "assays/components/imaging_data.json#properties/staining_date",
+                        "allow_empty": true
+                    },
+                    "imaging date":
+                    {
+                        "merge_pointer": "0/imaging_date",
+                        "type_ref": "assays/components/imaging_data.json#properties/imaging_date",
+                        "allow_empty": true
+                    },
+                    "imaging status":
+                    {
+                        "merge_pointer": "0/imaging_status",
+                        "type_ref": "assays/components/imaging_data.json#properties/imaging_status",
+                        "allow_empty": true
+                    },
+                    "panel":
+                    {
+                        "merge_pointer": "0/panel",
+                        "type_ref": "assays/mihc_assay.json#properties/panel"
+                    },
+                    "batch id": {
+                        "merge_pointer": "0/batch_id",
+                        "type_ref": "assays/mihc_assay.json#properties/batch_id"
+                    },
+                    "sample mapping report": {
+                        "merge_pointer": "0/samples_file",
+                        "type_ref": "assays/components/local_file.json#properties/file_path",
+                        "gcs_uri_format": "{protocol identifier}/mihc/{batch id}/sample_report.csv",
+                        "is_artifact": 1,
+                        "allow_empty": true
+                    }
+                },
+                "prism_data_object_pointer": "/records/-",
+                "data_columns":
+                {
+                    "Samples":
+                    {
+                        "CIMAC ID":
+                        {
+                            "merge_pointer": "0/cimac_id",
+                            "type_ref": "sample.json#properties/cimac_id"
+                        }
+                    },
+                    "Run info":
+                    {
+                        "Tilemap file": {
+                            "merge_pointer": "0/tilemap_file",
+                            "is_artifact": 1,
+                            "gcs_uri_format": "{protocol identifier}/mihc/{cimac id}/tilemap.ome.tiff",
+                            "type_ref": "assays/components/local_file.json#properties/file_path"
+                        },
+                        "Tilestats file": {
+                            "merge_pointer": "0/tilestats_file",
+                            "is_artifact": 1,
+                            "gcs_uri_format": "{protocol identifier}/mihc/{cimac id}/tilestats.csv",
+                            "type_ref": "assays/components/local_file.json#properties/file_path"
+                        },
+                        "H5ad file": {
+                            "merge_pointer": "0/h5ad_file",
+                            "is_artifact": 1,
+                            "gcs_uri_format": "{protocol identifier}/mihc/{cimac id}/h5ad.h5ad",
+                            "type_ref": "assays/components/local_file.json#properties/file_path"
+                        },
+                        "Multitiffs gzip": {
+                            "merge_pointer": "0/multitiffs_gzip",
+                            "is_artifact": 1,
+                            "gcs_uri_format": "{protocol identifier}/mihc/{cimac id}/multitiffs.tar.gz",
+                            "type_ref": "assays/components/local_file.json#properties/file_path"
+                        },
+                        "Stain Zip": {
+                            "merge_pointer": "0/stain_zip",
+                            "is_artifact": 1,
+                            "gcs_uri_format": "{protocol identifier}/mihc/{cimac id}/stains.zip",
+                            "type_ref": "assays/components/local_file.json#properties/file_path"
+                        },
+                        "Geojsons Zip": {
+                            "merge_pointer": "0/geojsons_zip",
+                            "is_artifact": 1,
+                            "gcs_uri_format": "{protocol identifier}/mihc/{cimac id}/geo_jsons.zip",
+                            "type_ref": "assays/components/local_file.json#properties/file_path"
+                        }
+                    }
+                }
+            },
+            "Antibodies":
+            {
+                "prism_data_object_pointer": "/antibodies/-",
+                "data_columns":
+                {
+                    "antibodies":
+                    {
+                        "Antibody":
+                        {
+                            "merge_pointer": "0/antibody",
+                            "type_ref": "assays/components/antibody.json#properties/antibody"
+                        },
+                        "Export name":
+                        {
+                            "merge_pointer": "0/export_name",
+                            "allow_empty": true,
+                            "type_ref": "assays/components/mihc_antibody.json#properties/export_name"
+                        },
+                        "Clone":
+                        {
+                            "merge_pointer": "0/clone",
+                            "type_ref": "assays/components/antibody.json#properties/clone"
+                        },
+                        "Antibody Company":
+                        {
+                            "merge_pointer": "0/company",
+                            "type_ref": "assays/components/antibody.json#properties/company"
+                        },
+                        "Cat#":
+                        {
+                            "merge_pointer": "0/cat_num",
+                            "type_ref": "assays/components/antibody.json#properties/cat_num"
+                        },
+                        "Lot#":
+                        {
+                            "merge_pointer": "0/lot_num",
+                            "type_ref": "assays/components/antibody.json#properties/lot_num"
+                        },
+                        "Staining Order":
+                        {
+                            "merge_pointer": "0/staining_order",
+                            "type_ref": "assays/components/mihc_antibody.json#properties/staining_order"
+                        },
+                        "Fluor Wavelength":
+                        {
+                            "merge_pointer": "0/fluor_wavelength",
+                            "allow_empty": true,
+                            "type_ref": "assays/components/mihc_antibody.json#properties/fluor_wavelength"
+                        },
+                        "Primary ab Dilution":
+                        {
+                            "merge_pointer": "0/primary_ab_dilution",
+                            "type_ref": "assays/components/mihc_antibody.json#properties/primary_ab_dilution"
+                        },
+                        "Dilutent":
+                        {
+                            "merge_pointer": "0/dilutent",
+                            "type_ref": "assays/components/mihc_antibody.json#properties/dilutent"
+                        },
+                        "Fluor dilution":
+                        {
+                            "merge_pointer": "0/fluor_dilution",
+                            "type_ref": "assays/components/mihc_antibody.json#properties/fluor_dilution"
+                        },
+                        "Antigen Retrieval Time":
+                        {
+                            "merge_pointer": "0/antigen_retrieval_time",
+                            "type_ref": "assays/components/mihc_antibody.json#properties/antigen_retrieval_time"
+                        },
+                        "Primary Incubation Time":
+                        {
+                            "merge_pointer": "0/primary_incubation_time",
+                            "type_ref": "assays/components/mihc_antibody.json#properties/primary_incubation_time"
+                        },
+                        "Amplification Time":
+                        {
+                            "merge_pointer": "0/amplification_time",
+                            "type_ref": "assays/components/mihc_antibody.json#properties/amplification_time"
+                        }
+                    }
+                }
+            },
+            "Excluded Samples": {
+                "prism_data_object_pointer": "/excluded_samples/-",
+                "data_columns": {
+                  "Samples Excluded From Analysis": {
+                    "cimac id": {
+                      "type_ref": "sample.json#properties/cimac_id",
+                      "merge_pointer": "0/cimac_id"
+                    },
+                    "reason": {
+                      "type_ref": "assays/components/excluded_samples.json#items/properties/reason_excluded",
+                      "merge_pointer": "0/reason_excluded"
+                    }
+                  }
+                }
+            }
+        }
+    }
+}

{nci_cidc_schemas-0.27.10 → nci_cidc_schemas-0.27.12/nci_cidc_schemas.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_schemas
-Version: 0.27.10
+Version: 0.27.12
 Summary: The CIDC data model and tools for working with it.
 Home-page: https://github.com/NCI-CIDC/cidc-schemas
 Author: NCI