nci-cidc-schemas 0.26.33__tar.gz → 0.26.35__tar.gz

{nci_cidc_schemas-0.26.33/nci_cidc_schemas.egg-info → nci_cidc_schemas-0.26.35}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nci_cidc_schemas
-Version: 0.26.33
+Version: 0.26.35
 Summary: The CIDC data model and tools for working with it.
 Home-page: https://github.com/NCI-CIDC/cidc-schemas
 Author: NCI
@@ -24,7 +24,7 @@ Requires-Dist: openpyxl==3.0.7
 Requires-Dist: jsonmerge==1.6.1
 Requires-Dist: deepdiff~=4.3.0
 Requires-Dist: jsonpointer==2.0
-Requires-Dist: pandas==1.2.4
+Requires-Dist: pandas==1.5.3
 Requires-Dist: jinja2~=3.1.3
 Requires-Dist: nci-cidc-ngs-pipeline-api==0.1.25
 Requires-Dist: markupsafe==2.1.5

{nci_cidc_schemas-0.26.33 → nci_cidc_schemas-0.26.35}/cidc_schemas/__init__.py

@@ -2,4 +2,4 @@
 
 __author__ = """NCI"""
 __email__ = "nci-cidc-tools-admin@mail.nih.gov"
-__version__ = "0.26.33"
+__version__ = "0.26.35"

{nci_cidc_schemas-0.26.33 → nci_cidc_schemas-0.26.35}/cidc_schemas/prism/constants.py

@@ -51,7 +51,6 @@ SUPPORTED_ANALYSES = [
     "tcr_analysis",
     "wes_analysis",
     "wes_tumor_only_analysis",
-    "ctdna_analysis",
 ]
 
 SUPPORTED_TEMPLATES = SUPPORTED_ASSAYS + SUPPORTED_MANIFESTS + SUPPORTED_ANALYSES
@@ -63,7 +62,6 @@ ASSAY_TO_FILEPATH: Dict[str, str] = {
     "rna_level1_analysis": "rna/",
     "wes_analysis": "wes/",
     "wes_tumor_only_analysis": "wes_tumor_only/",
-    "ctdna_analysis": "ctdna/",
     # assay specifics removed
     "atacseq_fastq": "atacseq/",
     "rna_bam": "rna/",

{nci_cidc_schemas-0.26.33 → nci_cidc_schemas-0.26.35}/cidc_schemas/schemas/artifacts/artifact_core.json

@@ -90,6 +90,7 @@
         "YAML",
         "PDF",
         "RDATA",
+        "OME.TIFF",
         "[NOT SET]"
       ]
     },

nci_cidc_schemas-0.26.35/cidc_schemas/schemas/artifacts/artifact_ome_tiff.json

@@ -0,0 +1,51 @@
+{
+  "$schema": "metaschema/strict_meta_schema.json#",
+  "$id": "ome_tiff_artifact",
+  "title": "Ome Tiff Artifact",
+  "type": "object",
+  "description": "Information about a ome tiff file.",
+  "additionalProperties": false,
+  "properties": {
+    "data_format": {
+      "description": "Data format.",
+      "const": "OME.TIFF"
+    },
+    "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-0.26.33 → nci_cidc_schemas-0.26.35}/cidc_schemas/schemas/assays/components/available_ngs_analyses.json

@@ -13,9 +13,6 @@
     "wes_tumor_only_analysis": {
       "$ref": "assays/wes_tumor_only_analysis.json"
     },
-    "ctdna_analysis": {
-      "$ref": "assays/ctdna_analysis.json"
-    },
     "wes_analysis_old": {
       "$ref": "assays/wes_analysis.json"
     },

nci_cidc_schemas-0.26.35/cidc_schemas/schemas/assays/components/mibi_imaging/mibi_files.json

@@ -0,0 +1,55 @@
+{
+  "$schema": "metaschema/strict_meta_schema.json#",
+  "$id": "mibi_files",
+  "description": "A region of interest (ROI) is a portion of an image which has been analyzed using image processing software.",
+  "type": "object",
+  "properties": {
+    "roi_id": {
+        "description": "Identifier of a region of interest within one mibi slide, e.g. 1, 2, 3 or [123 x 321]",
+        "type": "string"
+    },
+    "dataset": {
+      "description": "Dataset the record belongs to",
+      "type": "string"
+    },
+    "mibi_ome_tiff_file_name": {
+      "type": "string",
+      "description": "A (short) name of the file. Do not include the .ome.tiff extension"
+    },
+    "mibi_ome_tiff_file": {
+      "description": "Image for MIBI in OME TIFF format",
+      "$ref": "artifacts/artifact_ome_tiff.json"
+    },
+    "roi_description": {
+      "description": "A text description of this ROI",
+      "type": "string"
+    },
+    "he_file": {
+      "inheritableBase": true,
+      "mergeStrategy": "objectMerge",
+      "anyOf": [
+        {
+          "$comment": "Path to the H & E image in SVS format.",
+          "$ref": "artifacts/artifact_image.json"
+        },
+        {
+          "$comment": "Path to the H & E image in JPG format.",
+          "$ref": "artifacts/artifact_jpg.json"
+        }
+      ]
+    },
+    "comment": {
+      "description": "A text comment regarding this slide.",
+      "type": "string"
+    }
+  },
+  "inheritableBase": true,
+  "required": [
+    "roi_id",
+    "dataset",
+    "mibi_ome_tiff_file_name",
+    "mibi_ome_tiff_file",
+    "roi_description",
+    "he_file"
+  ]
+}

nci_cidc_schemas-0.26.35/cidc_schemas/schemas/assays/components/mibi_imaging/mibi_input.json

@@ -0,0 +1,56 @@
+{
+  "$schema": "metaschema/strict_meta_schema.json#",
+  "$id": "mibi_input",
+  "title": "MIBI Input Files",
+  "type": "object",
+  "description": "MIBI assay input files.",
+  "inheritableBase": true,
+  "properties": {
+    "roi_id": {
+      "description": "Identifier of a region of interest within one mibi slide, e.g. 1, 2, 3 or [123 x 321]",
+      "type": "string"
+    },
+    "dataset": {
+      "description": "Dataset the record belongs to",
+      "type": "string"
+    },
+    "mibi_ome_tiff_file_name": {
+      "type": "string",
+      "description": "A (short) name of the file. Do not include the .ome.tiff extension"
+    },
+    "mibi_ome_tiff_file": {
+      "description": "Image for MIBI in OME TIFF format",
+      "$ref": "artifacts/artifact_ome_tiff.json"
+    },
+    "roi_description": {
+      "description": "A text description of this ROI",
+      "type": "string"
+    },
+    "he_file": {
+      "inheritableBase": true,
+      "mergeStrategy": "objectMerge",
+      "anyOf": [
+        {
+          "$comment": "Path to the H & E image in SVS format.",
+          "$ref": "artifacts/artifact_image.json"
+        },
+        {
+          "$comment": "Path to the H & E image in JPG format.",
+          "$ref": "artifacts/artifact_jpg.json"
+        }
+      ]
+    },
+    "comment": {
+      "description": "A text comment regarding this slide.",
+      "type": "string"
+    }
+  },
+  "required": [
+    "roi_id",
+    "dataset",
+    "mibi_ome_tiff_file_name",
+    "mibi_ome_tiff_file",
+    "roi_description",
+    "he_file"
+  ]
+}

nci_cidc_schemas-0.26.35/cidc_schemas/schemas/assays/mibi_assay.json

@@ -0,0 +1,68 @@
+{
+    "$schema": "metaschema/strict_meta_schema.json#",
+    "$id": "mibi_assay",
+    "title": "MIBI Assay",
+    "type": "object",
+    "$comment": "description used in docs/index.html and docs/assays.mibi.html",
+    "description": "Multiplexed Ion Beam Imaging (MIBI) assay",
+    "additionalProperties": false,
+    "definitions": {
+        "record": {
+            "type": "object",
+            "mergeStrategy": "objectMerge",
+            "description": "A single data record from a MIBI assay.",
+            "additionalProperties": false,
+            "properties": {
+                "cimac_id": {
+                    "description": "Id of an sample within this clinical trial, that this assay record is based upon.",
+                    "$ref": "sample.json#properties/cimac_id"
+                },
+                "files": {
+                    "$ref": "assays/components/mibi_imaging/mibi_input.json"
+                }
+            },
+            "required": [
+                "cimac_id",
+                "files"
+            ]
+        }
+    },
+    "properties": {
+        "assay_creator": {
+            "$ref": "assays/components/assay_core.json#properties/assay_creator"
+        },
+        "batch_id": {
+            "type": "string",
+            "description": "Batch identification number. Unique to every batch."
+        },
+        "metadata_tsv": {
+            "description": "Deidentified metadata as a TSV file",
+            "$ref": "artifacts/artifact_tsv.json"
+        },
+
+        "antibodies": {
+            "type": "array",
+            "items": {
+                "$ref": "assays/components/mibi_antibody.json"
+            },
+            "mergeStrategy": "arrayMergeById",
+            "mergeOptions": {
+                "idRef": "antibody"
+            }
+        },
+        "records": {
+            "type": "array",
+            "description": "A single data record from a MIBI assay.",
+            "items": {
+                "$ref": "assays/mibi_assay.json#definitions/record"
+            },
+            "mergeStrategy": "append"
+        }
+    },
+    "required": [
+        "batch_id",
+        "records",
+        "assay_creator",
+        "antibodies"
+    ]
+}

{nci_cidc_schemas-0.26.33 → nci_cidc_schemas-0.26.35}/cidc_schemas/schemas/shipping_core.json

@@ -53,7 +53,8 @@
         "ATACseq",
         "ctDNA",
         "Microbiome",
-        "Nanostring"
+        "Nanostring",
+        "MIBI"
       ]
     },
     "courier": {

{nci_cidc_schemas-0.26.33 → nci_cidc_schemas-0.26.35}/cidc_schemas/schemas/templates/assays/mibi_template.json

@@ -6,7 +6,7 @@
     "properties": {
         "worksheets": {
             "MIBI": {
-                "prism_data_object_pointer": "/records/0/regions_of_interest/-",
+                "prism_data_object_pointer": "/records/-",
                 "preamble_rows": {
                     "protocol identifier": {
                         "merge_pointer": "3/protocol_identifier",
@@ -20,82 +20,59 @@
                         "merge_pointer": "0/assay_creator",
                         "type_ref": "assays/components/assay_core.json#properties/assay_creator"
                     },
-                    "folder": {
-                        "do_not_merge": true,
-                        "type": "string",
-                        "allow_empty": true
-                    },
                     "metadata tsv": {
+                        "merge_pointer": "0/metadata_tsv",
+                        "gcs_uri_format": "{protocol identifier}/mibi/{batch id}/metadata.tsv",
+                        "is_artifact": 1,
                         "type_ref": "assays/components/local_file.json#properties/file_path",
-                        "do_not_merge": true,
-                        "allow_empty": true,
-                        "process_as": [
-                            {
-                                "parse_through": "lambda metadata_tsv: f'{folder or \"\"}{metadata_tsv}'",
-                                "gcs_uri_format": "{protocol identifier}/mibi/{batch id}/metadata.tsv",
-                                "type_ref": "assays/components/local_file.json#properties/file_path",
-                                "merge_pointer": "0/metadata_tsv",
-                                "is_artifact": 1
-                            }
-                        ]
+                        "allow_empty": true
                     }
                 },
                 "data_columns": {
                     "Samples": {
-                        "Cimac id": {
-                            "merge_pointer": "2/cimac_id",
+                        "cimac id": {
+                            "merge_pointer": "0/cimac_id",
                             "type_ref": "sample.json#properties/cimac_id"
                         },
-                        "Roi id": {
-                            "merge_pointer": "0/roi_id",
-                            "type_ref": "assays/mibi_assay.json#definitions/region_of_interest/properties/roi_id"
+                        "roi id": {
+                            "merge_pointer": "0/files/roi_id",
+                            "type_ref": "assays/components/mibi_imaging/mibi_files.json#properties/roi_id"
                         },
                         "Dataset": {
+                            "merge_pointer": "0/files/dataset",
+                            "type_ref": "assays/components/mibi_imaging/mibi_files.json#properties/dataset",
+                            "allow_empty": true
+                        },
+                        "HE file type": {
                             "do_not_merge": true,
                             "type": "string",
-                            "process_as": [
-                                {
-                                    "parse_through": "lambda dataset: f'{folder or \"\"}{dataset}/3D_image_stack.ome.tiff'",
-                                    "merge_pointer": "/multichannel_image",
-                                    "gcs_uri_format": "{protocol identifier}/mibi/{batch id}/{cimac id}/{roi id}/multichannel_image.ome.tiff",
-                                    "type_ref": "assays/components/local_file.json#properties/file_path",
-                                    "is_artifact": 1,
-                                    "allow_empty": true
-                                },
-                                {
-                                    "parse_through": "lambda dataset: f'{folder or \"\"}{dataset}/Mapping/cluster_labels_image.tif'",
-                                    "merge_pointer": "/cluster_labels",
-                                    "gcs_uri_format": "{protocol identifier}/mibi/{batch id}/{cimac id}/{roi id}/cluster_labels.tif",
-                                    "type_ref": "assays/components/local_file.json#properties/file_path",
-                                    "is_artifact": 1,
-                                    "allow_empty": true
-                                },
-                                {
-                                    "parse_through": "lambda dataset: f'{folder or \"\"}{dataset}/mcd/channelnames_report.csv'",
-                                    "merge_pointer": "/channel_names",
-                                    "gcs_uri_format": "{protocol identifier}/mibi/{batch id}/{cimac id}/{roi id}/channel_names.csv",
-                                    "type_ref": "assays/components/local_file.json#properties/file_path",
-                                    "is_artifact": 1,
-                                    "allow_empty": true
-                                },
-                                {
-                                    "parse_through": "lambda dataset: f'{folder or \"\"}{dataset}/SingleCellData/cells.csv'",
-                                    "merge_pointer": "/single_cell_table",
-                                    "gcs_uri_format": "{protocol identifier}/mibi/{batch id}/{cimac id}/{roi id}/single_cell_table.csv",
-                                    "type_ref": "assays/components/local_file.json#properties/file_path",
-                                    "is_artifact": 1,
-                                    "allow_empty": true
-                                }
-                            ]
+                            "enum": ["svs", "jpg"]
+                        },
+                        "HE file name": {
+                            "merge_pointer": "0/files/he_file",
+                            "is_artifact": 1,
+                            "gcs_uri_format": "{protocol identifier}/mibi/{batch id}/{cimac id}/{roi id}/he_file.{he file type}",
+                            "type_ref": "assays/components/local_file.json#properties/file_path"
                         },
                         "Roi description": {
-                            "merge_pointer": "0/roi_description",
-                            "type_ref": "assays/mibi_assay.json#definitions/region_of_interest/properties/roi_description",
+                            "merge_pointer": "0/files/roi_description",
+                            "type_ref": "assays/components/mibi_imaging/mibi_files.json#properties/roi_description",
                             "allow_empty": true
                         },
+                        "MIBI OME Tiff File": {
+                            "merge_pointer": "0/files/mibi_ome_tiff_file",
+                            "type_ref": "assays/components/local_file.json#properties/file_path",
+                            "is_artifact": 1,
+                            "gcs_uri_format": "{protocol identifier}/mibi/{batch id}/{cimac id}/{roi id}/{mibi ome tiff file name}.ome.tiff"
+                        },
+                        "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"
+                        },
+
                         "Comment": {
-                            "merge_pointer": "0/comment",
-                            "type_ref": "assays/mibi_assay.json#definitions/region_of_interest/properties/comment",
+                            "merge_pointer": "0/files/comment",
+                            "type_ref": "assays/components/mibi_imaging/mibi_files.json#properties/comment",
                             "allow_empty": true
                         }
                     }
@@ -115,6 +92,16 @@
                             "merge_pointer": "0/antibody",
                             "type_ref": "assays/components/antibody.json#properties/antibody"
                         },
+                        "Clone": {
+                            "merge_pointer": "0/clone",
+                            "type_ref": "assays/components/antibody.json#properties/clone",
+                            "allow_empty": true
+                        },
+                        "Company": {
+                            "merge_pointer": "0/company",
+                            "type_ref": "assays/components/antibody.json#properties/clone",
+                            "allow_empty": true
+                        },
                         "Scicrunch rrid": {
                             "merge_pointer": "0/scicrunch_rrid",
                             "type_ref": "assays/components/mibi_antibody.json#properties/scicrunch_rrid",
@@ -160,4 +147,4 @@
             }
         }
     }
-}
+}

{nci_cidc_schemas-0.26.33 → nci_cidc_schemas-0.26.35}/cidc_schemas/template.py

@@ -232,7 +232,6 @@ def _initialize_template_schema(name: str, title: str, pointer: str):
         "rna": "RNA sequencing Level 1",
         "wes": "Whole Exome Sequencing (WES) Tumor-Normal Paired",
         "wes_tumor_only": "Whole Exome Sequencing (WES) Tumor-Only",
-        "ctDNA": "ctDNA",
     }[name]
 
     # static

{nci_cidc_schemas-0.26.33 → nci_cidc_schemas-0.26.35/nci_cidc_schemas.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nci_cidc_schemas
-Version: 0.26.33
+Version: 0.26.35
 Summary: The CIDC data model and tools for working with it.
 Home-page: https://github.com/NCI-CIDC/cidc-schemas
 Author: NCI
@@ -24,7 +24,7 @@ Requires-Dist: openpyxl==3.0.7
 Requires-Dist: jsonmerge==1.6.1
 Requires-Dist: deepdiff~=4.3.0
 Requires-Dist: jsonpointer==2.0
-Requires-Dist: pandas==1.2.4
+Requires-Dist: pandas==1.5.3
 Requires-Dist: jinja2~=3.1.3
 Requires-Dist: nci-cidc-ngs-pipeline-api==0.1.25
 Requires-Dist: markupsafe==2.1.5

{nci_cidc_schemas-0.26.33 → nci_cidc_schemas-0.26.35}/nci_cidc_schemas.egg-info/SOURCES.txt

@@ -53,6 +53,7 @@ cidc_schemas/schemas/artifacts/artifact_log.json
 cidc_schemas/schemas/artifacts/artifact_maf.json
 cidc_schemas/schemas/artifacts/artifact_narrowPeak.json
 cidc_schemas/schemas/artifacts/artifact_npx.json
+cidc_schemas/schemas/artifacts/artifact_ome_tiff.json
 cidc_schemas/schemas/artifacts/artifact_pdf.json
 cidc_schemas/schemas/artifacts/artifact_png.json
 cidc_schemas/schemas/artifacts/artifact_rcc.json
@@ -66,7 +67,6 @@ cidc_schemas/schemas/artifacts/artifact_xlsx.json
 cidc_schemas/schemas/artifacts/artifact_yaml.json
 cidc_schemas/schemas/artifacts/artifact_zip.json
 cidc_schemas/schemas/assays/atacseq_assay.json
-cidc_schemas/schemas/assays/ctdna_analysis.json
 cidc_schemas/schemas/assays/ctdna_assay.json
 cidc_schemas/schemas/assays/cytof_assay.json
 cidc_schemas/schemas/assays/cytof_assay_core.json
@@ -110,6 +110,8 @@ cidc_schemas/schemas/assays/components/imaging/mif_entry.json
 cidc_schemas/schemas/assays/components/imaging/mif_export.json
 cidc_schemas/schemas/assays/components/imaging/mif_input.json
 cidc_schemas/schemas/assays/components/imaging/mif_roi.json
+cidc_schemas/schemas/assays/components/mibi_imaging/mibi_files.json
+cidc_schemas/schemas/assays/components/mibi_imaging/mibi_input.json
 cidc_schemas/schemas/assays/components/ngs/ngs_assay_record.json
 cidc_schemas/schemas/assays/components/ngs/atacseq/atacseq_analysis.json
 cidc_schemas/schemas/assays/components/ngs/rna/fusion.json
@@ -123,7 +125,6 @@ cidc_schemas/schemas/assays/components/ngs/rna/salmon.json
 cidc_schemas/schemas/assays/components/ngs/rna/star.json
 cidc_schemas/schemas/assays/components/ngs/rna/trust4.json
 cidc_schemas/schemas/templates/analyses/atacseq_analysis_template.json
-cidc_schemas/schemas/templates/analyses/ctdna_analysis_template.json
 cidc_schemas/schemas/templates/analyses/cytof_analysis_template.json
 cidc_schemas/schemas/templates/analyses/rna_level1_analysis_template.json
 cidc_schemas/schemas/templates/analyses/tcr_analysis_template.json
@@ -213,7 +214,6 @@ tests/data/schemas/invalid_ref.json
 tests/data/schemas/d1/3.json
 tests/data/schemas/d1/d2/2.json
 tests/data/schemas/target-templates/atacseq_analysis_template.json
-tests/data/schemas/target-templates/ctdna_analysis_template.json
 tests/data/schemas/target-templates/rna_level1_analysis_template.json
 tests/data/schemas/target-templates/wes_analysis_template.json
 tests/data/schemas/target-templates/wes_tumor_only_analysis_template.json

{nci_cidc_schemas-0.26.33 → nci_cidc_schemas-0.26.35}/nci_cidc_schemas.egg-info/requires.txt

@@ -7,7 +7,7 @@ openpyxl==3.0.7
 jsonmerge==1.6.1
 deepdiff~=4.3.0
 jsonpointer==2.0
-pandas==1.2.4
+pandas==1.5.3
 jinja2~=3.1.3
 nci-cidc-ngs-pipeline-api==0.1.25
 markupsafe==2.1.5

{nci_cidc_schemas-0.26.33 → nci_cidc_schemas-0.26.35}/requirements.txt

@@ -7,7 +7,7 @@ openpyxl==3.0.7
 jsonmerge==1.6.1
 deepdiff~=4.3.0
 jsonpointer==2.0
-pandas==1.2.4
+pandas==1.5.3
 jinja2~=3.1.3
 nci-cidc-ngs-pipeline-api==0.1.25
 markupsafe==2.1.5