nci-cidc-schemas 0.26.33__py2.py3-none-any.whl → 0.26.35__py2.py3-none-any.whl

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"

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/",

cidc_schemas/schemas/artifacts/artifact_core.json

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

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"
+}

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"
     },

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"
+  ]
+}

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"
+  ]
+}

cidc_schemas/schemas/assays/mibi_assay.json

@@ -6,10 +6,10 @@
     "$comment": "description used in docs/index.html and docs/assays.mibi.html",
     "description": "Multiplexed Ion Beam Imaging (MIBI) assay",
     "additionalProperties": false,
-    "mergeStrategy": "objectMerge",
     "definitions": {
         "record": {
             "type": "object",
+            "mergeStrategy": "objectMerge",
             "description": "A single data record from a MIBI assay.",
             "additionalProperties": false,
             "properties": {
@@ -17,58 +17,13 @@
                     "description": "Id of an sample within this clinical trial, that this assay record is based upon.",
                     "$ref": "sample.json#properties/cimac_id"
                 },
-                "regions_of_interest": {
-                    "type": "array",
-                    "items": {
-                        "$ref": "assays/mibi_assay.json#definitions/region_of_interest"
-                    },
-                    "mergeStrategy": "arrayMergeById",
-                    "mergeOptions": {
-                        "idRef": "roi_id"
-                    }
+                "files": {
+                    "$ref": "assays/components/mibi_imaging/mibi_input.json"
                 }
             },
             "required": [
                 "cimac_id",
-                "regions_of_interest"
-            ]
-        },
-        "region_of_interest": {
-            "type": "object",
-            "description": "A region of interest (ROI) is a portion of an image which has been analyzed using image processing software.",
-            "additionalProperties": false,
-            "properties": {
-                "roi_id": {
-                    "description": "Identifier of a region of interest within one mIF slide, e.g. 1, 2, 3 or [123x321]",
-                    "type": "string"
-                },
-                "multichannel_image": {
-                    "description": "Analysis-ready multichannel image in OME TIFF format",
-                    "$ref": "artifacts/artifact_image.json"
-                },
-                "cluster_labels": {
-                    "description": "Cluster-labelled image in TIFF format",
-                    "$ref": "artifacts/artifact_image.json"
-                },
-                "channel_names": {
-                    "description": "Channel names table in CSV format",
-                    "$ref": "artifacts/artifact_csv.json"
-                },
-                "single_cell_table": {
-                    "description": "Single cell data table in CSV format",
-                    "$ref": "artifacts/artifact_csv.json"
-                },
-                "roi_description": {
-                    "description": "A text description of this ROI. Eg: decidua",
-                    "type": "string"
-                },
-                "comment": {
-                    "description": "A text comment regarding this slide.",
-                    "type": "string"
-                }
-            },
-            "required": [
-                "roi_id"
+                "files"
             ]
         }
     },
@@ -101,15 +56,13 @@
             "items": {
                 "$ref": "assays/mibi_assay.json#definitions/record"
             },
-            "mergeStrategy": "arrayMergeById",
-            "mergeOptions": {
-                "idRef": "cimac_id"
-            }
+            "mergeStrategy": "append"
         }
     },
     "required": [
         "batch_id",
         "records",
-        "assay_creator"
+        "assay_creator",
+        "antibodies"
     ]
-}
+}

cidc_schemas/schemas/shipping_core.json

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

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 @@
             }
         }
     }
-}
+}

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.dist-info → nci_cidc_schemas-0.26.35.dist-info}/METADATA

@@ -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.dist-info → nci_cidc_schemas-0.26.35.dist-info}/RECORD

@@ -1,9 +1,9 @@
-cidc_schemas/__init__.py,sha256=xBaOLwy5XV4zmqGjfPUr8jM1S-oKNZtijjJ9xJjc_c8,136
+cidc_schemas/__init__.py,sha256=ADFA3YhRSz91I9C5rj115esQzZvq9FJA6KKjjerNOFo,136
 cidc_schemas/cli.py,sha256=gWiktRlraNH8Q0zNUae9dohKjPwBmcY0BJwdcQ_fIic,4099
 cidc_schemas/constants.py,sha256=RULs7pGuBAVq1teXymrfbVsK23ZowJvLuZlv0KcjL-Y,698
 cidc_schemas/json_validation.py,sha256=SyZSW7AAS-qlYLUUV_ri4393utkNsDexcWB73rEmFLs,20035
 cidc_schemas/migrations.py,sha256=Amg_T4cFgMzySD7yNnT_PWpqP7hwlTWGeHlI_RSXuRI,14766
-cidc_schemas/template.py,sha256=J41S65-2w4VdmpLDVY-icyHWAsbH1Gtg-pMlL_TGo6A,49891
+cidc_schemas/template.py,sha256=gM6Xp1fOZaF8wOLzY5HGdxi4p8cEYhYXRpqRPncYua0,49865
 cidc_schemas/template_reader.py,sha256=xXtLRKu1y4FrPj8RgyGOmB2hlsCDXcuvMBWami2_jV8,13119
 cidc_schemas/template_writer.py,sha256=faOhvSDTp4nuPhOtVQR_J7YNnFzx-vh7oyNpFdee1mY,18236
 cidc_schemas/unprism.py,sha256=5EeqNKedVEf15CJiMQ-ImXd1wIbNnzihv21rAMClZyc,13325
@@ -11,7 +11,7 @@ cidc_schemas/util.py,sha256=ZCQ--ROZyXYVB034fHHmxZXb5F0G2GwzPwSfyfegtGk,4348
 cidc_schemas/metaschema/strict_meta_schema.json,sha256=3FiS0r2dAXgfPsruJwZYbQoQnHhC_yl-3mclX8gfiQU,6428
 cidc_schemas/pipeline_configs/rna_level1_analysis_config.yaml.j2,sha256=6no9sFqwzb1T61RZGD-owDt2K5R8G_fPTzflV4fOroo,2832
 cidc_schemas/prism/__init__.py,sha256=J5Tj0X7Di6cyxAjaduOUp2aVyvl8UI67bgxEkgttvcU,530
-cidc_schemas/prism/constants.py,sha256=fFiXfFFMiGqG07mKlt_ejcRZrnMD6g66pwnB6s4Dfgk,2379
+cidc_schemas/prism/constants.py,sha256=b5pgxrzwJvKWWIEE9V72cvKwl_ARRaANPHzKk4yo4M4,2325
 cidc_schemas/prism/core.py,sha256=PQgsRAEleT6gO3VyE4uFTYa3qK_VXjFcErV1YwWV1nQ,19294
 cidc_schemas/prism/extra_metadata.py,sha256=wZjhUGKSvfupr6qZ1WuPepKnf_FG1nGfsDai_kBFZ50,8559
 cidc_schemas/prism/merger.py,sha256=Kf5o9NWT80XqYZASbH0dJsQ0dkwMl3HtoR_p7wqUypI,12431
@@ -21,7 +21,7 @@ cidc_schemas/schemas/clinical_data.json,sha256=ubt2dqTLCbDuxuOXrBObT_xLHVSArMBx4
 cidc_schemas/schemas/clinical_trial.json,sha256=mqvpCTqWGimKA8-S4F32YMDBoHcJkawpr9iTwUgH56w,4652
 cidc_schemas/schemas/participant.json,sha256=vCtxbUfVGTjvZ8SPPNLvWJkJIBZUK2NSHpYzJgdoSaY,2991
 cidc_schemas/schemas/sample.json,sha256=TRWgxQBybtj4WjLBNZAdpoShpbDTGl8iT3FceGx2gD8,16296
-cidc_schemas/schemas/shipping_core.json,sha256=MYnULNUnXYmOOHvF6T7oSBfMsT5f1waFdzlgdknnMD0,3299
+cidc_schemas/schemas/shipping_core.json,sha256=ouekd6KNf4EKVz4IsE2yjibvIjpCE8CZBxCRXlJ7p_U,3315
 cidc_schemas/schemas/artifacts/artifact_bam.json,sha256=nPy3qx07--arLyb9VgfdVK6OJoMPhr6rnp-3AF6o82Q,1653
 cidc_schemas/schemas/artifacts/artifact_bam_bai.json,sha256=S1LxCZVyN3v-Hxhs7TEDbGcV-y7LVdAoLzGblT9IhEk,1671
 cidc_schemas/schemas/artifacts/artifact_bed.json,sha256=nGPKiAd2GQGJ6JkdLaqZhfOuyDmsAdUqril1Yao2qmE,1653
@@ -32,7 +32,7 @@ cidc_schemas/schemas/artifacts/artifact_clinical_docx.json,sha256=9Lbq9H0mhPIRDA
 cidc_schemas/schemas/artifacts/artifact_clinical_xlsx.json,sha256=IOQD7NBS3lvJV2Dts0Z6y0QoyYeB2jc2OLFgjSSTEn4,2232
 cidc_schemas/schemas/artifacts/artifact_cncf.json,sha256=IrawYPFqZ4HV0bClCKgOpO8Xh6d2GD8rP7tjS5ASv_o,1657
 cidc_schemas/schemas/artifacts/artifact_cns.json,sha256=R9RItkDV_kqnfLqr-WBa7yJmeDc2kblJg3xx7hNjtAk,1653
-cidc_schemas/schemas/artifacts/artifact_core.json,sha256=Fmm6LSnEBzEutpXtTpB3pQgzObCXl4Ymu9BbvN_5aHM,3140
+cidc_schemas/schemas/artifacts/artifact_core.json,sha256=dNVhgD7CYaSjANH6EN_rxatqwAKOtOyEravE6N_-9Ds,3160
 cidc_schemas/schemas/artifacts/artifact_csv.json,sha256=BPqogQ3DMjyRs9N-sk9c1Q7gKTNumOHhhwwn5gCHbGM,1665
 cidc_schemas/schemas/artifacts/artifact_elisa_xlsx.json,sha256=1Erw2HG4YJPiNop40hs9LigHr7O66_WRlrZ3wWSQzBs,2216
 cidc_schemas/schemas/artifacts/artifact_fastq_gz.json,sha256=k8So4mBtC7YWp6-PSeCKNvp3v0MNPNfdPWRQWoASNvA,1683
@@ -47,6 +47,7 @@ cidc_schemas/schemas/artifacts/artifact_log.json,sha256=TvHQLsxAfnB9WbnHt-otYObK
 cidc_schemas/schemas/artifacts/artifact_maf.json,sha256=MyJOs8A0aHrl8i9l5Q1m4ADm8dqcTyJ_YtUJDS48Bjk,1653
 cidc_schemas/schemas/artifacts/artifact_narrowPeak.json,sha256=EOGIAmpo46qZdSzZj3Gi7WKLS81OH1xUTJzeu7_I75c,1681
 cidc_schemas/schemas/artifacts/artifact_npx.json,sha256=I0o8C9ilOrbLBmLpTOQ1ARFyQHyaSd321mPjuJMGUUw,2134
+cidc_schemas/schemas/artifacts/artifact_ome_tiff.json,sha256=wSIQPf2mi00BwikFlz8qL3wmVvtYWhuOxrHLc3ngzS0,1673
 cidc_schemas/schemas/artifacts/artifact_pdf.json,sha256=t-RR4gftGD-wjB7t40lb1TbnKLosPQCDyP-SL1V5dWc,1674
 cidc_schemas/schemas/artifacts/artifact_png.json,sha256=cGzHZQg3qbungIkxvLh6TY8iqKjtutBU2XmBnRyiijQ,1653
 cidc_schemas/schemas/artifacts/artifact_rcc.json,sha256=IyqqsxPdFZjRoFuBpnkBKBLbc-SoWvrQoqFWeNLU_as,1704
@@ -60,14 +61,13 @@ cidc_schemas/schemas/artifacts/artifact_xlsx.json,sha256=PmQ3NY_8ywS3iFa4vvLzcXb
 cidc_schemas/schemas/artifacts/artifact_yaml.json,sha256=Eey5T68k4jXqiFXfgWTVi3ZoiY5EZxc75rWCEvaZscE,1657
 cidc_schemas/schemas/artifacts/artifact_zip.json,sha256=L9TyKfKm2j0jUo7ED7Lb43Z6VRHP7hEirC349viEBhQ,1653
 cidc_schemas/schemas/assays/atacseq_assay.json,sha256=5ezVeJmrwOWuXLtf9-gH8iYKhLCys9Ii2VamezNI_hM,2547
-cidc_schemas/schemas/assays/ctdna_analysis.json,sha256=8HTya0iwtxle0myQ4Dj6VaTII0RuqqiR14SUrmPKPAM,1513
 cidc_schemas/schemas/assays/ctdna_assay.json,sha256=1AwUYiE93XEVDg_FPFyV2OgaD7Ry7pWoD4AH2DAXasA,3503
 cidc_schemas/schemas/assays/cytof_assay.json,sha256=rf0vebcoHY_dS4wlqkoBY9rclSAE3CRdxeGLXAbhScM,3659
 cidc_schemas/schemas/assays/cytof_assay_core.json,sha256=Vwg3RmEEdCpZtDDaVAWBDCKTMnSxagsdqSJq4AiDu9w,8828
 cidc_schemas/schemas/assays/elisa_assay.json,sha256=YHeoxYmgdpefLWkBXNg60JUig2Ccqg8thWZ5M5q3hyw,2233
 cidc_schemas/schemas/assays/hande_assay.json,sha256=NhLyBiBOgeZ9woeGO4EEIod-y_Wzz6WamsP3ZNzxtS0,3192
 cidc_schemas/schemas/assays/ihc_assay.json,sha256=g1WuTUrN6M3mmQL7TCURsKL442An8jlmXaxddg2Ayak,6738
-cidc_schemas/schemas/assays/mibi_assay.json,sha256=gxUdCKzsNpL5FB8muT8Gq-3cqbOTGiOax-kFjI4myCA,4187
+cidc_schemas/schemas/assays/mibi_assay.json,sha256=0DnK6Tl_DZbzKuLcleaBYMW19OBpI3ociSqqeK0bG04,2164
 cidc_schemas/schemas/assays/microbiome_assay.json,sha256=4eSEKRylf86yLV7QKCIlMzzjj_XHKMfQpA0njLHBs00,2078
 cidc_schemas/schemas/assays/mif_assay.json,sha256=IG-s80kl8PUUi4U6FGmJbziG0nJf5Or_WTzfb5d46uQ,2599
 cidc_schemas/schemas/assays/misc_data.json,sha256=R6q-B8E-fIihlDNbe34gy7_aQeU1eIL9R_Yolg8SotU,2005
@@ -84,7 +84,7 @@ cidc_schemas/schemas/assays/wes_tumor_only_analysis.json,sha256=dU3oaeBbPnEv2Xjy
 cidc_schemas/schemas/assays/components/antibody.json,sha256=vfLxXkXIcaJ1BXeUjCaJehrRCdVrBW3gxibwrD7zzd4,960
 cidc_schemas/schemas/assays/components/assay_core.json,sha256=QGuLiArVb7lEF2t1Ml4Qt7g4SXY58WuGBPFVgvOLI5w,485
 cidc_schemas/schemas/assays/components/available_assays.json,sha256=RiyOd6-awMmELxYj-UbAo5dQxQv_rEMI3TuYAk4TCiU,3540
-cidc_schemas/schemas/assays/components/available_ngs_analyses.json,sha256=-827aY2HoYDWc_zjqEBFCqPH6DFgSqFRberrn7E96zc,1237
+cidc_schemas/schemas/assays/components/available_ngs_analyses.json,sha256=dmC10wI7roGVwbf5T8DxIW1geIjks-Sl-GHJkJXc6eQ,1163
 cidc_schemas/schemas/assays/components/composite_image.json,sha256=k9EaBG3y9j-lvg3nQNZbfVpo9fK_gUz1-9iTwjlTDfE,733
 cidc_schemas/schemas/assays/components/controls.json,sha256=_Wxz7W2msTGJ2Ei4XZg0Qy1t8A5_rLSHNvdPurC073E,458
 cidc_schemas/schemas/assays/components/enrichment_core.json,sha256=zC5G7q-QyNrdynCOoPCCSfOuSKq8TiDH-Pl6gITNfVQ,813
@@ -104,6 +104,8 @@ cidc_schemas/schemas/assays/components/imaging/mif_entry.json,sha256=0jYCSMD3j5r
 cidc_schemas/schemas/assays/components/imaging/mif_export.json,sha256=CVGCpIVcHkTnIQvBibU4HkdYcm2lYzGYu3pXGm4bUa8,1728
 cidc_schemas/schemas/assays/components/imaging/mif_input.json,sha256=Hf1PKkk6pHRLcGGJrVmkhC6SApOA5pD6XJFRscM9ee0,1000
 cidc_schemas/schemas/assays/components/imaging/mif_roi.json,sha256=XL80pl3_5xj40Y4fpE0THDjCDNYojtxDpjtatoFcNAA,1112
+cidc_schemas/schemas/assays/components/mibi_imaging/mibi_files.json,sha256=zylVuDxUKxJ2wXPuTphuT1yY8YYl_vm42a80Xpl3tfc,1580
+cidc_schemas/schemas/assays/components/mibi_imaging/mibi_input.json,sha256=JvigxrK5namtAjUHvBm6QVBZWePVLXWTNaORoUH_aBA,1522
 cidc_schemas/schemas/assays/components/ngs/ngs_assay_record.json,sha256=DwHKyRNDQ6h8PUz0KdBfmcd0Pz1Q1rOeqWpKfUIwjZM,615
 cidc_schemas/schemas/assays/components/ngs/atacseq/atacseq_analysis.json,sha256=kDhS8GHGLF05v4427J6E73J6MiOh0R8Lh6RHrSD5Ak0,2283
 cidc_schemas/schemas/assays/components/ngs/rna/fusion.json,sha256=lgGWX9unADhT4xNDGqQD_VbC6cUo1JMgH9Ii7ZBvofQ,392
@@ -117,7 +119,6 @@ cidc_schemas/schemas/assays/components/ngs/rna/salmon.json,sha256=GRJaC4MhupuRrE
 cidc_schemas/schemas/assays/components/ngs/rna/star.json,sha256=XoL1Ro8YDr-ZQQOmYZC8NnREDW-7qzR6IzJi3tLQ2ks,772
 cidc_schemas/schemas/assays/components/ngs/rna/trust4.json,sha256=o-fxkTL-1Tho1kPkJ6CcMUp5kE5mnkZU8cdSCzHR5cQ,382
 cidc_schemas/schemas/templates/analyses/atacseq_analysis_template.json,sha256=7vBdwVD6HEd9Pj8AkEoa34fQjIynztsNaKvfn2KoFFc,5403
-cidc_schemas/schemas/templates/analyses/ctdna_analysis_template.json,sha256=WSuNoR4cFoYOH3_VHD0FY0m8TD578Yl6MSESQPMDMQo,7408
 cidc_schemas/schemas/templates/analyses/cytof_analysis_template.json,sha256=d6qOGbYXXx1c8rb-saM4D_tMuK8n4ydbyW9_xaW6xhk,6381
 cidc_schemas/schemas/templates/analyses/rna_level1_analysis_template.json,sha256=vMHXSQNZz8sFxwiBUnRXb5o08GxgbKZjMu8ZPjNn4TI,15944
 cidc_schemas/schemas/templates/analyses/tcr_analysis_template.json,sha256=ai5KUp6q5GGTxDybOHBaseOnvQCVqIRh4SurETz5Vx0,3054
@@ -130,7 +131,7 @@ cidc_schemas/schemas/templates/assays/cytof_template.json,sha256=YGaLt7DKsz32o3n
 cidc_schemas/schemas/templates/assays/elisa_template.json,sha256=Q8cv5ZpaRZUfvr6e4PC4uvMqhhaDGLdvVMN_s8Uiajw,2259
 cidc_schemas/schemas/templates/assays/hande_template.json,sha256=BNMQO4JpBrjuD8ITH1x7cJfkqI4bgKZilvN9yqavaqs,4293
 cidc_schemas/schemas/templates/assays/ihc_template.json,sha256=lOSP6v24FMk-WN7Za4IYQkM94R-1TEvrnllRopEEYa4,7341
-cidc_schemas/schemas/templates/assays/mibi_template.json,sha256=wy-LeCZRVYpvkpD7S04GZgL6P8ZvtoGroIzzijpti6M,8984
+cidc_schemas/schemas/templates/assays/mibi_template.json,sha256=T5gAgsmWpUkkO6CI7aFpyD4efSTZsNmbsLLBrHXpNzg,7787
 cidc_schemas/schemas/templates/assays/microbiome_template.json,sha256=2qaTB8W-tG6NhbSJ3KAEIacp1E4g-cFBGMOMc5zTafo,3578
 cidc_schemas/schemas/templates/assays/mif_template.json,sha256=ozyMdziNxtAReTL7guFIwTiJGhEWam9Hsb_fOhIYXIY,19272
 cidc_schemas/schemas/templates/assays/misc_data_template.json,sha256=88GBWq7hrALrYmmgfqStrhocNtPWWYOMeUk9i8_uFRg,1896
@@ -152,9 +153,9 @@ cidc_schemas/schemas/templates/manifests/tissue_slide_template.json,sha256=sFPyt
 cidc_schemas/schemas/templates/manifests/tumor_normal_pairing_template.json,sha256=lVJrGb28n-vyfjGBzhrzjn1lMKw1b4HXXmWtwA603v0,2797
 cidc_schemas/schemas/templates/manifests/tumor_tissue_dna_template.json,sha256=D4ICMeHQgKXFDwaMOqrcLcUEF-dYGalagGYDUFAploU,13276
 cidc_schemas/schemas/templates/manifests/tumor_tissue_rna_template.json,sha256=MpJTjoaTdIlNBAIIxSfmItVevA5BXnajqu_jaEXxBmo,12568
-nci_cidc_schemas-0.26.33.dist-info/LICENSE,sha256=zK77-w4rYCZBHAYJEGkcFuPXwKIsP7jMPZ2iQOXjzko,1072
-nci_cidc_schemas-0.26.33.dist-info/METADATA,sha256=cb3K4hIn3QTCETgLcKIXF2A3OlRg2hrFPlYZf3sXOAM,4436
-nci_cidc_schemas-0.26.33.dist-info/WHEEL,sha256=DZajD4pwLWue70CAfc7YaxT1wLUciNBvN_TTcvXpltE,110
-nci_cidc_schemas-0.26.33.dist-info/entry_points.txt,sha256=kSyTzXeJQrJp_2ZX0GS_NnbJR8ceQKLBSgER46PM0hs,55
-nci_cidc_schemas-0.26.33.dist-info/top_level.txt,sha256=Wwb5Cu7QrnbmSJxI2d00e3-Mir36t0jTRnSulmfhi30,13
-nci_cidc_schemas-0.26.33.dist-info/RECORD,,
+nci_cidc_schemas-0.26.35.dist-info/LICENSE,sha256=zK77-w4rYCZBHAYJEGkcFuPXwKIsP7jMPZ2iQOXjzko,1072
+nci_cidc_schemas-0.26.35.dist-info/METADATA,sha256=_JLgHeJXExaE0Ojart8M35025nFtBsi3RyrmdUzJaD0,4436
+nci_cidc_schemas-0.26.35.dist-info/WHEEL,sha256=4h2DkfJSb0e6Ob8eR1zE5-yQ9f6nK3Do8SfsDGV3_YQ,109
+nci_cidc_schemas-0.26.35.dist-info/entry_points.txt,sha256=kSyTzXeJQrJp_2ZX0GS_NnbJR8ceQKLBSgER46PM0hs,55
+nci_cidc_schemas-0.26.35.dist-info/top_level.txt,sha256=Wwb5Cu7QrnbmSJxI2d00e3-Mir36t0jTRnSulmfhi30,13
+nci_cidc_schemas-0.26.35.dist-info/RECORD,,

{nci_cidc_schemas-0.26.33.dist-info → nci_cidc_schemas-0.26.35.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: setuptools (71.0.3)
 Root-Is-Purelib: true
 Tag: py2-none-any
 Tag: py3-none-any

cidc_schemas/schemas/assays/ctdna_analysis.json

@@ -1,52 +0,0 @@
-{
-  "$schema": "metaschema/strict_meta_schema.json#",
-  "$id": "ctdna_analysis",
-  "title": "ctDNA analysis",
-  "type": "object",
-  "description": "Combined analysis files for the ctDNA assay.",
-
-  "definitions": {
-    "sample_analysis": {
-      "type": "object",
-      "description": "ctDNA assay output files for a tumor normal pair of samples.",
-
-      "required": [
-        "run_id",
-        "tumor"
-      ],
-      "additionalProperties": false,
-      "properties": {
-        "run_id": {
-          "type": "string",
-          "description": "An id used as if this was a paired analysis run."
-        },
-        "error": { "$ref": "assays/wes_core.json#properties/error" },
-        "tumor": { "$ref": "assays/wes_assay.json#definitions/sample_analysis" },
-        "comments": {
-          "type": "string",
-          "description": "Comments on the tumor-only analysis run."
-        }
-      }
-    }
-  },
-
-  "required": [],
-  "additionalProperties": false,
-  "properties": {
-    "runs": {
-      "type": "array",
-      "items": {
-        "$ref": "assays/ctdna_analysis.json#definitions/sample_analysis"
-      },
-      "mergeStrategy": "arrayMergeById",
-      "mergeOptions": {
-        "$comment": "TODO fix to merge by a pair of normal and tumor ids. It requires improvements to the merge strategy code.",
-        "idRef": "/run_id"
-      }
-    },
-    "batch_id": {"$ref": "assays/tcr_assay.json#properties/batch_id"},
-    "excluded_samples": {
-      "$ref": "assays/components/excluded_samples.json"
-    }
-  }
-}

cidc_schemas/schemas/templates/analyses/ctdna_analysis_template.json

@@ -1,121 +0,0 @@
-{
-    "title": "ctDNA analysis template",
-    "description": "ctDNA analysis submission.",
-    "prism_template_root_object_schema": "assays/ctdna_analysis.json",
-    "prism_template_root_object_pointer": "/analysis/ctdna_analysis",
-    "properties": {
-        "worksheets": {
-            "ctDNA Analysis": {
-                "preamble_rows": {
-                    "protocol identifier": {
-                        "merge_pointer": "2/protocol_identifier",
-                        "type_ref": "clinical_trial.json#properties/protocol_identifier"
-                    },
-                    "folder": {
-                        "do_not_merge": true,
-                        "type": "string",
-                        "allow_empty": true
-                    },
-                    "batch id": {
-                        "merge_pointer": "0/batch_id",
-                        "type_ref": "assays/tcr_assay.json#properties/batch_id"
-                    }
-                },
-                "prism_data_object_pointer": "/runs/-",
-                "data_columns": {
-                    "ctDNA Runs": {
-                        "run id": {
-                            "merge_pointer": "/run_id",
-                            "type_ref": "assays/ctdna_analysis.json#definitions/sample_analysis/properties/run_id",
-                            "process_as": [
-                                {
-                                    "parse_through": "lambda run: f'{folder or \"\"}analysis/{run}_error.yaml'",
-                                    "merge_pointer": "/error",
-                                    "gcs_uri_format": "{protocol identifier}/ctdna/{run id}/analysis/error.yaml",
-                                    "type_ref": "assays/components/local_file.json#properties/file_path",
-                                    "is_artifact": 1,
-                                    "allow_empty": true
-                                }
-                            ]
-                        },
-                        "cimac id": {
-                            "merge_pointer": "/tumor/cimac_id",
-                            "type_ref": "sample.json#properties/cimac_id",
-                            "process_as": [
-                                {
-                                    "parse_through": "lambda id: f'{folder or \"\"}analysis/align/{id}/{id}.sorted.dedup.bam'",
-                                    "merge_pointer": "/tumor/alignment/align_sorted_dedup",
-                                    "gcs_uri_format": "{protocol identifier}/ctdna/{run id}/analysis/tumor/{cimac id}/sorted.dedup.bam",
-                                    "type_ref": "assays/components/local_file.json#properties/file_path",
-                                    "is_artifact": 1
-                                },
-                                {
-                                    "parse_through": "lambda id: f'{folder or \"\"}analysis/align/{id}/{id}.sorted.dedup.bam.bai'",
-                                    "merge_pointer": "/tumor/alignment/align_sorted_dedup_index",
-                                    "gcs_uri_format": "{protocol identifier}/ctdna/{run id}/analysis/tumor/{cimac id}/sorted.dedup.bam.bai",
-                                    "type_ref": "assays/components/local_file.json#properties/file_path",
-                                    "is_artifact": 1
-                                },
-                                {
-                                    "parse_through": "lambda id: f'{folder or \"\"}analysis/align/{id}/{id}_recalibrated.bam'",
-                                    "merge_pointer": "/tumor/alignment/align_recalibrated",
-                                    "gcs_uri_format": "{protocol identifier}/ctdna/{run id}/analysis/tumor/{cimac id}/recalibrated.bam",
-                                    "type_ref": "assays/components/local_file.json#properties/file_path",
-                                    "is_artifact": 1
-                                },
-                                {
-                                    "parse_through": "lambda id: f'{folder or \"\"}analysis/align/{id}/{id}_recalibrated.bam.bai'",
-                                    "merge_pointer": "/tumor/alignment/align_recalibrated_index",
-                                    "gcs_uri_format": "{protocol identifier}/ctdna/{run id}/analysis/tumor/{cimac id}/recalibrated.bam.bai",
-                                    "type_ref": "assays/components/local_file.json#properties/file_path",
-                                    "is_artifact": 1
-                                },
-                                {
-                                    "parse_through": "lambda id: f'{folder or \"\"}analysis/hlahd/{id}/result/{id}_final.result.txt'",
-                                    "merge_pointer": "/tumor/hla/hla_final_result",
-                                    "gcs_uri_format": "{protocol identifier}/ctdna/{run id}/analysis/tumor/{cimac id}/hla_final_result.txt",
-                                    "type_ref": "assays/components/local_file.json#properties/file_path",
-                                    "is_artifact": 1
-                                },
-                                {
-                                    "parse_through": "lambda id: f'{folder or \"\"}analysis/optitype/{id}/{id}_result.tsv'",
-                                    "merge_pointer": "/tumor/hla/optitype_result",
-                                    "gcs_uri_format": "{protocol identifier}/ctdna/{run id}/analysis/tumor/{cimac id}/optitype_result.tsv",
-                                    "type_ref": "assays/components/local_file.json#properties/file_path",
-                                    "is_artifact": 1
-                                },
-                                {
-                                    "parse_through": "lambda id: f'{folder or \"\"}analysis/xhla/{id}/report-{id}-hla.json'",
-                                    "merge_pointer": "/tumor/hla/xhla_report_hla",
-                                    "gcs_uri_format": "{protocol identifier}/ctdna/{run id}/analysis/tumor/{cimac id}/xhla_report_hla.json",
-                                    "type_ref": "assays/components/local_file.json#properties/file_path",
-                                    "is_artifact": 1
-                                }
-                            ]
-                        },
-                        "comments": {
-                            "type_ref": "assays/ctdna_analysis.json#definitions/sample_analysis/properties/comments",
-                            "merge_pointer": "0/comments",
-                            "allow_empty": true
-                        }
-                    }
-                }
-            },
-            "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"
-                        }
-                    }
-                }
-            }
-        }
-    }
-}