nci-cidc-schemas 0.28.3__py2.py3-none-any.whl → 0.28.13__py2.py3-none-any.whl

cidc_schemas/schemas/assays/mif_assay.json

@@ -4,7 +4,7 @@
   "title": "mIF Assay",
   "type": "object",
 
-	"$comment": "description used in docs/index.html and docs/assays.mif.html",
+  "$comment": "description used in docs/index.html and docs/assays.mif.html",
   "description": "Multiplex immunofluorescence.",
   
   "additionalProperties": false,
@@ -28,7 +28,14 @@
     "imaging_status": {"$ref": "assays/components/imaging_data.json#properties/imaging_status"},
 
     "qc_report": {"$ref": "artifacts/artifact_zip.json"},
-
+    "batch_id": {
+      "description": "Batch identification number. Unique to every upload.",
+      "type": "string"
+    },
+    "optional_id": {
+      "description": "User provided optional id. Currently comes from CIDC Submission ID",
+      "type": "string"
+    },
     "panel": {
       "type": "string",
       "enum": [
@@ -65,6 +72,6 @@
       }
     }
   },
-  "required": ["records", "panel", "antibodies"],
+  "required": ["records", "panel", "antibodies", "batch_id"],
   "mergeStrategy": "objectMerge"
 }

cidc_schemas/schemas/assays/mihc_assay.json

@@ -46,7 +46,10 @@
             "description": "Batch identification number. Unique to every upload.",
             "type": "string"
         },
-
+        "optional_id": {
+            "description": "User provided optional id. Currently comes from CIDC Submission ID",
+            "type": "string"
+        },
         "samples_file": {"$ref": "artifacts/artifact_csv.json"},
 
         "panel": {"type": "string"},

cidc_schemas/schemas/assays/misc_data.json

@@ -43,6 +43,14 @@
         "assay_creator": {
             "$ref": "assays/components/assay_core.json#properties/assay_creator"
         },
+        "batch_id": {
+            "description": "Batch identification number. Unique to every upload.",
+            "type": "string"
+        },
+        "optional_id": {
+            "description": "User provided optional id. Currently comes from CIDC Submission ID",
+            "type": "string"
+        },
         "files": {
             "type": "array",
             "description": "A single file containing miscellaneous data.",
@@ -59,4 +67,4 @@
         "files",
         "assay_creator"
     ]
-}
+}

cidc_schemas/schemas/assays/nanostring_assay.json

@@ -61,6 +61,10 @@
       "type": "string",
       "description": "A unique ID that separates the different batches of Nanostring."
     },
+    "optional_id": {
+      "description": "User provided optional id. Currently comes from CIDC Submission ID",
+      "type": "string"
+    },
     "data": {
       "type": "object",
       "additionalProperties": false,
@@ -82,5 +86,5 @@
       "items": { "$ref": "assays/nanostring_assay.json#definitions/run" }
     }
   },
-  "required": ["data", "runs"]
+  "required": ["data", "runs", "batch_id"]
 }

cidc_schemas/schemas/assays/nulisa_assay.json

@@ -35,6 +35,10 @@
             "description": "Batch identification number. Unique to every upload.",
             "type": "string"
         },
+        "optional_id": {
+            "description": "User provided optional id. Currently comes from CIDC Submission ID",
+            "type": "string"
+        },
         "npq_file": {
             "$ref": "artifacts/artifact_csv.json"
         },

cidc_schemas/schemas/assays/olink_assay.json

@@ -119,6 +119,10 @@
           "type": "string",
           "description": "A unique identifier for this Olink upload"
         },
+        "optional_id": {
+          "description": "User provided optional id. Currently comes from CIDC Submission ID",
+          "type": "string"
+        },
         "assay_creator": {
           "$ref": "assays/components/assay_core.json#properties/assay_creator"
         },

cidc_schemas/schemas/assays/olink_ht_assay.json

@@ -0,0 +1,100 @@
+{
+    "$schema": "metaschema/strict_meta_schema.json#",
+    "$id": "olink_ht_assay",
+    "title": "Olink HT Assay",
+    "type": "object",
+    "$comment": "description used in docs/index.html and docs/assays.olink_ht.html",
+    "description": "Olink HT assay",
+    "additionalProperties": false,
+    "definitions": {
+        "record": {
+            "type": "object",
+            "mergeStrategy": "objectMerge",
+            "description": "A single data record from an Olink HT assay.",
+            "additionalProperties": false,
+            "required": [
+                "cimac_id",
+                "npx_run_file",
+                "instrument",
+                "npx_manager_version"
+            ],
+            "properties": {
+                "cimac_id": {
+                    "description": "Id of an sample within this clinical trial, that this assay record is based upon.",
+                    "$ref": "sample.json#properties/cimac_id"
+                },
+                "npx_run_file": {
+                    "$ref": "artifacts/artifact_parquet.json",
+                    "$comment": "Parquet file of the overall run the sample was in."
+                },
+                "instrument": {
+                    "description": "Instrument used for the Olink HT assay.",
+                    "type": "string"
+                },
+                "npx_manager_version": {
+                    "description": "Version of NPX manager used for the analysis.",
+                    "type": "string"
+                },
+                "comments": {
+                    "description": "Comments on the Olink HT assay sample.",
+                    "type": "string"
+                }
+            }
+        }
+    },
+    "properties": {
+        "assay_creator": {
+            "$ref": "assays/components/assay_core.json#properties/assay_creator"
+        },
+        "batch_id": {
+            "description": "Batch identification number. Unique to every upload.",
+            "type": "string"
+        },
+        "optional_id": {
+            "description": "User provided optional id. Currently comes from CIDC Submission ID",
+            "type": "string"
+        },
+        "panel": {
+            "description": "Panel used for the assay.",
+            "type": "string"
+        },
+        "assay_panel_lot": {
+            "description": "Lot number of the assay panel.",
+            "type": "string"
+        },
+        "study_level_combined_file": {
+            "$comment": "Parquet file of the study level run.",
+            "$ref": "artifacts/artifact_parquet.json"
+        },
+        "study_level_combined_npx_manager_version": {
+            "description": "Version of NPX manager used for the analysis.",
+            "type": "string"
+        },
+        "batch_level_combined_file": {
+            "$comment": "Parquet file of the batch level run.",
+            "$ref": "artifacts/artifact_parquet.json"
+        },
+        "batch_level_combined_npx_manager_version": {
+            "description": "Version of NPX manager used for the analysis.",
+            "type": "string"
+        },
+        "records": {
+            "type": "array",
+            "description": "A single data record from an Olink HT assay.",
+            "items": {
+                "$ref": "assays/olink_ht_assay.json#definitions/record"
+            },
+            "mergeStrategy": "append"
+        }
+    },
+    "required": [
+        "assay_creator",
+        "batch_id",
+        "panel",
+        "assay_panel_lot",
+        "study_level_combined_file",
+        "study_level_combined_npx_manager_version",
+        "batch_level_combined_file",
+        "batch_level_combined_npx_manager_version"
+    ]
+}

cidc_schemas/schemas/assays/rna_assay-v0.json

@@ -8,6 +8,7 @@
   "mergeStrategy": "objectMerge",
   
   "required": [
+    "batch_id",
     "assay_creator",
     "enrichment_method",
     "records",
@@ -21,6 +22,14 @@
 
   "properties": {
     "assay_creator": { "$ref": "assays/components/assay_core.json#properties/assay_creator" },
+    "batch_id": {
+      "description": "Batch identification number. Unique to every upload.",
+      "type": "string"
+    },
+    "optional_id": {
+      "description": "User provided optional id. Currently comes from CIDC Submission ID",
+      "type": "string"
+    },
     "sequencer_platform": { "$ref": "assays/components/ngs_assay_core.json#properties/sequencer_platform" },
     "library_kit": { "$ref": "assays/components/ngs_assay_core.json#properties/library_kit" },
     "paired_end_reads": { "$ref": "assays/components/ngs_assay_core.json#properties/paired_end_reads" },

cidc_schemas/schemas/assays/scrnaseq_analysis.json

@@ -78,6 +78,10 @@
         "batch_id":{
             "$ref": "assays/scrnaseq_assay.json#properties/batch_id"
         },
+        "optional_id": {
+            "description": "User provided optional id. Currently comes from CIDC Submission ID",
+            "type": "string"
+        },
         "records": {
             "type": "array",
             "mergeStrategy": "arrayMergeById",

cidc_schemas/schemas/assays/scrnaseq_assay.json

@@ -35,6 +35,10 @@
             "description": "Batch identification number. Unique to every upload.",
             "type": "string"
         },
+        "optional_id": {
+            "description": "User provided optional id. Currently comes from CIDC Submission ID",
+            "type": "string"
+        },
         "azimuth_reference": {
             "$ref": "assays/components/scrnaseq_preamble.json#properties/azimuth_reference"
         },

cidc_schemas/schemas/assays/tcr_analysis.json

@@ -12,6 +12,10 @@
       "required": ["batch_id"],
       "properties": {
         "batch_id": {"$ref": "assays/tcr_assay.json#properties/batch_id"},
+        "optional_id": {
+          "description": "User provided optional id. Currently comes from CIDC Submission ID",
+          "type": "string"
+        },
         "report_trial": {"$ref": "artifacts/artifact_gz.json"},
         "summary_info": {"$ref": "artifacts/artifact_csv.json"},
         "excluded_samples": {"$ref": "assays/components/excluded_samples.json"},

cidc_schemas/schemas/assays/tcr_assay.json

@@ -127,6 +127,10 @@
         "description": "TCRseq batch identification number.",
         "type": "string"
     },
+    "optional_id": {
+        "description": "User provided optional id. Currently comes from CIDC Submission ID",
+        "type": "string"
+    },
     "controls": {
       "type": "array",
       "description": "Data records from TCRseq assay for a control for this batch.",

cidc_schemas/schemas/assays/tcrseq_rna_assay.json

@@ -0,0 +1,64 @@
+{
+    "$schema": "metaschema/strict_meta_schema.json#",
+    "$id": "tcrseq_rna_assay",
+    "title": "TCR RNA Assay",
+    "type": "object",
+    "$comment": "description used in docs/index.html and docs/assays.tcrseq_rna.html",
+    "description": "TCR RNA assay",
+    "additionalProperties": false,
+    "definitions": {
+        "record": {
+            "type": "object",
+            "mergeStrategy": "objectMerge",
+            "description": "A single data record from a TCR RNA assay.",
+            "additionalProperties": false,
+            "required": [
+                "cimac_id",
+                "alpha_results_file",
+                "beta_results_file"
+            ],
+            "properties": {
+                "cimac_id": {
+                    "description": "Id of an sample within this clinical trial, that this assay record is based upon.",
+                    "$ref": "sample.json#properties/cimac_id"
+                },
+                "alpha_results_file": {"$ref":  "artifacts/artifact_csv.json"},
+                "beta_results_file": {"$ref":  "artifacts/artifact_csv.json"}
+            }
+        }
+    },
+    "properties": {
+        "assay_creator": {
+            "$ref": "assays/components/assay_core.json#properties/assay_creator"
+        },
+        "batch_id": {
+            "description": "Batch identification number. Unique to every upload.",
+            "type": "string"
+        },
+        "optional_id": {
+            "description": "User provided optional id. Currently comes from CIDC Submission ID",
+            "type": "string"
+        },
+        "sequencer_platform": {"$ref": "assays/components/ngs_assay_core.json#properties/sequencer_platform"},
+        "sequencing_run_date": {
+            "description": "Date when the TCR sequencing was run.",
+            "type": "string",
+            "format": "date"
+        },
+        "records": {
+            "type": "array",
+            "description": "A single data record from a TCR RNA assay.",
+            "items": {
+                "$ref": "assays/tcrseq_rna_assay.json#definitions/record"
+            },
+            "mergeStrategy": "append"
+        }
+    },
+    "required": [
+        "assay_creator",
+        "batch_id",
+        "sequencer_platform",
+        "sequencing_run_date",
+        "records"
+    ]
+}

cidc_schemas/schemas/assays/visium_analysis.json

@@ -43,6 +43,10 @@
         "batch_id":{
             "$ref": "assays/scrnaseq_assay.json#properties/batch_id"
         },
+        "optional_id": {
+            "description": "User provided optional id. Currently comes from CIDC Submission ID",
+            "type": "string"
+        },
         "records": {
             "type": "array",
             "mergeStrategy": "arrayMergeById",

cidc_schemas/schemas/assays/visium_assay.json

@@ -35,6 +35,10 @@
             "description": "Batch identification number. Unique to every upload.",
             "type": "string"
         },
+        "optional_id": {
+            "description": "User provided optional id. Currently comes from CIDC Submission ID",
+            "type": "string"
+        },
         "azimuth_reference": {
             "$ref": "assays/components/scrnaseq_preamble.json#properties/azimuth_reference"
         },

cidc_schemas/schemas/assays/wes_analysis.json

@@ -72,9 +72,17 @@
     }
   },
 
-  "required": [],
+  "required": ["batch_id"],
   "additionalProperties": false,
   "properties": {
+    "batch_id": {
+      "description": "Batch identification number. Unique to every upload.",
+      "type": "string"
+    },
+    "optional_id": {
+      "description": "User provided optional id. Currently comes from CIDC Submission ID",
+      "type": "string"
+    },
     "pair_runs": {
       "type": "array",
       "items": {

cidc_schemas/schemas/assays/wes_assay.json

@@ -61,23 +61,45 @@
   "required": [
     "records",
     "bait_set",
-    "read_length"
+    "read_length",
+    "batch_id"
   ],
   "additionalProperties": false,
   "properties": {
       "assay_creator": {"$ref": "assays/components/assay_core.json#properties/assay_creator"},
+      "batch_id": {
+          "description": "Batch identification number. Unique to every upload.",
+          "type": "string"
+      },
+      "optional_id": {
+          "description": "User provided optional id. Currently comes from CIDC Submission ID",
+          "type": "string"
+      },
       "sequencer_platform": {"$ref": "assays/components/ngs_assay_core.json#properties/sequencer_platform"},
       "library_kit": {"$ref": "assays/components/ngs_assay_core.json#properties/library_kit"},
       "paired_end_reads": {"$ref": "assays/components/ngs_assay_core.json#properties/paired_end_reads"},
       "sequencing_protocol": {
           "description": "Protocol and version used for the sequencing.",
           "type": "string",
-          "enum": ["Express Somatic Human WES (Deep Coverage) v1.1", "Somatic Human WES v6", "TWIST Custom Panel PN 101042", "TWIST"]
+          "enum": [
+            "Express Somatic Human WES (Deep Coverage) v1.1",
+            "Somatic Human WES v4",
+            "Somatic Human WES v6",
+            "TWIST Custom Panel PN 101042",
+            "TWIST"
+          ]
       },
       "bait_set": {
           "description": "Bait set ID.",
           "type": "string",
-          "enum": ["whole_exome_illumina_coding_v1","broad_custom_exome_v1","TWIST Dana Farber Custom Panel", "TWIST Custom Panel PN 101042", "TWIST Clin Research Exome PN 104033"]
+          "enum": [
+            "whole_exome_illumina_coding_v1",
+            "broad_custom_exome_v1",
+            "TWIST Dana Farber Custom Panel",
+            "TWIST Custom Panel PN 101042",
+            "TWIST Clin Research Exome PN 104033",
+            "Agilent SS Human All Exon V4"
+          ]
       },
       "read_length": {
           "description": "Number of cycles for each sequencing read.",

cidc_schemas/schemas/assays/wes_tumor_only_analysis.json

@@ -38,9 +38,17 @@
     }
   },
 
-  "required": [],
+  "required": ["batch_id"],
   "additionalProperties": false,
   "properties": {
+    "batch_id": {
+      "description": "Batch identification number. Unique to every upload.",
+      "type": "string"
+    },
+    "optional_id": {
+      "description": "User provided optional id. Currently comes from CIDC Submission ID",
+      "type": "string"
+    },
     "runs": {
       "type": "array",
       "items": {

cidc_schemas/schemas/clinical_data.json

@@ -40,6 +40,14 @@
     "assay_creator": {
       "$ref": "assays/components/assay_core.json#properties/assay_creator"
     },
+    "batch_id": {
+      "description": "ctDNA batch identification number. Unique to every batch.",
+      "type": "string"
+    },
+    "optional_id": {
+      "description": "User provided optional id. Currently comes from CIDC Submission ID",
+      "type": "string"
+    },
     "records": {
       "type": "array",
       "description": "A single file from clinical data upload.",

cidc_schemas/schemas/shipping_core.json

@@ -62,7 +62,9 @@
         "MIBI",
         "scRNAseq",
         "snRNA-Seq",
-        "Visium"
+        "Visium",
+        "Olink HT",
+        "TCRseq RNA"
       ]
     },
     "courier": {

cidc_schemas/schemas/templates/analyses/atacseq_analysis_template.json

@@ -16,9 +16,13 @@
                         "type": "string",
                         "allow_empty": true
                     },
-                    "batch id": {
+                    "CIMAC Batch ID": {
                         "merge_pointer": "0/batch_id",
                         "type_ref": "assays/atacseq_assay.json#properties/batch_id"
+                    },
+                    "CIDC Submission ID": {
+                        "merge_pointer": "0/optional_id",
+                        "type_ref": "assays/atacseq_assay.json#properties/optional_id"
                     }
                 },
                 "prism_data_object_pointer": "/records/-",
@@ -90,4 +94,4 @@
             }
         }
     }
-}
+}

cidc_schemas/schemas/templates/analyses/cytof_analysis_template.json

@@ -15,26 +15,30 @@
                         "merge_pointer": "3/protocol_identifier",
                         "type_ref": "clinical_trial.json#properties/protocol_identifier"
                     },
-                    "batch id": {
+                    "CIMAC Batch ID": {
                         "merge_pointer": "0/batch_id",
                         "type_ref": "assays/cytof_assay_core.json#properties/batch_id"
                     },
+                    "CIDC Submission ID": {
+                        "merge_pointer": "0/optional_id",
+                        "type_ref": "assays/cytof_assay_core.json#properties/optional_id"
+                    },
                     "astrolabe reports": {
                         "merge_pointer": "0/astrolabe_reports",
                         "type_ref": "assays/components/local_file.json#properties/file_path",
-                        "gcs_uri_format": "{protocol identifier}/cytof_analysis/{assay run id}/{batch id}/reports.zip",
+                        "gcs_uri_format": "{protocol identifier}/cytof_analysis/{assay run id}/{cimac batch id}/reports.zip",
                         "is_artifact": 1
                     },
                     "astrolabe analysis": {
                         "merge_pointer": "0/astrolabe_analysis",
                         "type_ref": "assays/components/local_file.json#properties/file_path",
-                        "gcs_uri_format": "{protocol identifier}/cytof_analysis/{assay run id}/{batch id}/analysis.zip",
+                        "gcs_uri_format": "{protocol identifier}/cytof_analysis/{assay run id}/{cimac batch id}/analysis.zip",
                         "is_artifact": 1
                     },
                     "control files package": {
                         "merge_pointer": "0/control_files_analysis",
                         "type_ref": "assays/components/local_file.json#properties/file_path",
-                        "gcs_uri_format": "{protocol identifier}/cytof_analysis/{assay run id}/{batch id}/control_files_analysis.zip",
+                        "gcs_uri_format": "{protocol identifier}/cytof_analysis/{assay run id}/{cimac batch id}/control_files_analysis.zip",
                         "is_artifact": 1,
                         "allow_empty": true
                     }
@@ -49,43 +53,43 @@
                         "fcs file": {
                             "merge_pointer": "0/output_files/fcs_file",
                             "type_ref": "assays/components/local_file.json#properties/file_path",
-                            "gcs_uri_format": "{protocol identifier}/cytof_analysis/{assay run id}/{batch id}/{cimac id}/source.fcs",
+                            "gcs_uri_format": "{protocol identifier}/cytof_analysis/{assay run id}/{cimac batch id}/{cimac id}/source.fcs",
                             "is_artifact": 1
                         },
                         "assignment": {
                             "merge_pointer": "0/output_files/assignment",
                             "type_ref": "assays/components/local_file.json#properties/file_path",
-                            "gcs_uri_format": "{protocol identifier}/cytof_analysis/{assay run id}/{batch id}/{cimac id}/assignment.csv",
+                            "gcs_uri_format": "{protocol identifier}/cytof_analysis/{assay run id}/{cimac batch id}/{cimac id}/assignment.csv",
                             "is_artifact": 1
                         },
                         "compartment": {
                             "merge_pointer": "0/output_files/compartment",
                             "type_ref": "assays/components/local_file.json#properties/file_path",
-                            "gcs_uri_format": "{protocol identifier}/cytof_analysis/{assay run id}/{batch id}/{cimac id}/compartment.csv",
+                            "gcs_uri_format": "{protocol identifier}/cytof_analysis/{assay run id}/{cimac batch id}/{cimac id}/compartment.csv",
                             "is_artifact": 1
                         },
                         "profiling": {
                             "merge_pointer": "0/output_files/profiling",
                             "type_ref": "assays/components/local_file.json#properties/file_path",
-                            "gcs_uri_format": "{protocol identifier}/cytof_analysis/{assay run id}/{batch id}/{cimac id}/profiling.csv",
+                            "gcs_uri_format": "{protocol identifier}/cytof_analysis/{assay run id}/{cimac batch id}/{cimac id}/profiling.csv",
                             "is_artifact": 1
                         },
                         "cell counts assignment": {
                             "merge_pointer": "0/output_files/cell_counts_assignment",
                             "type_ref": "assays/components/local_file.json#properties/file_path",
-                            "gcs_uri_format": "{protocol identifier}/cytof_analysis/{assay run id}/{batch id}/{cimac id}/cell_counts_assignment.csv",
+                            "gcs_uri_format": "{protocol identifier}/cytof_analysis/{assay run id}/{cimac batch id}/{cimac id}/cell_counts_assignment.csv",
                             "is_artifact": 1
                         },
                         "cell counts compartment": {
                             "merge_pointer": "0/output_files/cell_counts_compartment",
                             "type_ref": "assays/components/local_file.json#properties/file_path",
-                            "gcs_uri_format": "{protocol identifier}/cytof_analysis/{assay run id}/{batch id}/{cimac id}/cell_counts_compartment.csv",
+                            "gcs_uri_format": "{protocol identifier}/cytof_analysis/{assay run id}/{cimac batch id}/{cimac id}/cell_counts_compartment.csv",
                             "is_artifact": 1
                         },
                         "cell counts profiling": {
                             "merge_pointer": "0/output_files/cell_counts_profiling",
                             "type_ref": "assays/components/local_file.json#properties/file_path",
-                            "gcs_uri_format": "{protocol identifier}/cytof_analysis/{assay run id}/{batch id}/{cimac id}/cell_counts_profiling.csv",
+                            "gcs_uri_format": "{protocol identifier}/cytof_analysis/{assay run id}/{cimac batch id}/{cimac id}/cell_counts_profiling.csv",
                             "is_artifact": 1
                         }
                     }
@@ -108,4 +112,4 @@
             }
         }
     }
-}
+}

cidc_schemas/schemas/templates/analyses/rna_level1_analysis_template.json

@@ -11,6 +11,14 @@
                         "merge_pointer": "2/protocol_identifier",
                         "type_ref": "clinical_trial.json#properties/protocol_identifier"
                     },
+                    "CIMAC Batch ID": {
+                        "merge_pointer": "0/batch_id",
+                        "type_ref": "assays/rna_assay-v0.json#properties/batch_id"
+                    },
+                    "CIDC Submission ID": {
+                        "merge_pointer": "0/optional_id",
+                        "type_ref": "assays/rna_assay-v0.json#properties/optional_id"
+                    },
                     "folder": {
                         "do_not_merge": true,
                         "type": "string",
@@ -220,4 +228,4 @@
             }
         }
     }
-}
+}