nci-cidc-schemas 0.28.2__tar.gz → 0.28.3__tar.gz

{nci_cidc_schemas-0.28.2/nci_cidc_schemas.egg-info → nci_cidc_schemas-0.28.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_schemas
-Version: 0.28.2
+Version: 0.28.3
 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-0.28.2 → nci_cidc_schemas-0.28.3}/cidc_schemas/__init__.py

@@ -2,4 +2,4 @@
 
 __author__ = """NCI"""
 __email__ = "nci-cidc-tools-admin@mail.nih.gov"
-__version__ = "0.28.2"
+__version__ = "0.28.3"

{nci_cidc_schemas-0.28.2 → nci_cidc_schemas-0.28.3}/cidc_schemas/prism/constants.py

@@ -28,6 +28,7 @@ SUPPORTED_ASSAYS = [
     "mihc",
     "scrnaseq",
     "visium",
+    "nulisa",
 ]
 
 SUPPORTED_SHIPPING_MANIFESTS = [
@@ -143,6 +144,7 @@ ASSAY_TO_FILEPATH: Dict[str, str] = {
             "scrnaseq_analysis",
             "visium",
             "visium_analysis",
+            "nulisa",
         ]
     },
 }

{nci_cidc_schemas-0.28.2 → nci_cidc_schemas-0.28.3}/cidc_schemas/schemas/assays/components/available_assays.json

@@ -167,6 +167,17 @@
         "$ref": "assays/microbiome_assay.json"
       },
       "mergeStrategy": "append"
+    },
+    "nulisa": {
+      "type": "array",
+      "description": "NULISA",
+      "items": {
+        "$ref": "assays/nulisa_assay.json"
+      },
+      "mergeStrategy": "arrayMergeById",
+      "mergeOptions": {
+        "idRef": "batch_id"
+      }
     }
   }
 }

nci_cidc_schemas-0.28.3/cidc_schemas/schemas/assays/components/nulisa_input.json

@@ -0,0 +1,46 @@
+{
+  "$schema": "metaschema/strict_meta_schema.json#",
+  "$id": "nulisa_input",
+  "title": "NULISA Input Files and Data",
+  "type": "object",
+  "description": "NULISA assay input files and data",
+  "inheritableBase": true,
+  "properties": {
+    "ic_median": {
+      "description": "Percentage sample IC reads relative to the median (within +/- 40% of the plate median)",
+      "type": "number"
+    },
+    "detectability": {
+      "description": "Percentage of targets with reads above the Limit of Detection (LOD) (Minimum threshold = plasma-90%, serum-90%, csf-70%, other-0%)",
+      "type": "number"
+    },
+    "ic_reads": {
+      "description": "Number of Internal Control (IC) reads within a sample (Minimum threshold = 1,000)",
+      "type": "integer"
+    },
+    "qc_status": {
+      "description": "Status",
+      "type": "string",
+      "enum": [
+        "warning",
+        "passed",
+        "NA"
+      ]
+    },
+    "reads": {
+      "description": "Number of reads within a sample (Minimum threshold = 500,000)",
+      "type": "integer"
+    },
+    "auto_well_position": {
+      "description": "Auto well position label",
+      "type": "string"
+    }
+  },
+  "required": [
+    "ic_median",
+    "ic_reads",
+    "qc_status",
+    "reads",
+    "auto_well_position"
+  ]
+}

nci_cidc_schemas-0.28.3/cidc_schemas/schemas/assays/nulisa_assay.json

@@ -0,0 +1,63 @@
+{
+    "$schema": "metaschema/strict_meta_schema.json#",
+    "$id": "nulisa_assay",
+    "title": "NULISA Assay",
+    "type": "object",
+    "$comment": "description used in docs/index.html and docs/assays.nulisa.html",
+    "description": "Nucleic acid Linked Immuno-Sandwich Assay (NULISA) assay",
+    "additionalProperties": false,
+    "definitions": {
+        "record": {
+            "type": "object",
+            "mergeStrategy": "objectMerge",
+            "description": "A single data record from a NULISA assay.",
+            "additionalProperties": false,
+            "required": [
+                "cimac_id",
+                "details"
+            ],
+            "properties": {
+                "cimac_id": {
+                    "description": "Id of an sample within this clinical trial, that this assay record is based upon.",
+                    "$ref": "sample.json#properties/cimac_id"
+                },
+                "details": {
+                    "$ref": "assays/components/nulisa_input.json"
+                }
+            }
+        }
+    },
+    "properties": {
+        "assay_creator": {
+            "$ref": "assays/components/assay_core.json#properties/assay_creator"
+        },
+        "batch_id": {
+            "description": "Batch identification number. Unique to every upload.",
+            "type": "string"
+        },
+        "npq_file": {
+            "$ref": "artifacts/artifact_csv.json"
+        },
+        "raw_counts_file": {
+            "$ref": "artifacts/artifact_csv.json"
+        },
+        "metadata_csv": {"$ref": "artifacts/artifact_csv.json"},
+
+
+        "records": {
+            "type": "array",
+            "description": "A single data record from a NULISA assay.",
+            "items": {
+                "$ref": "assays/nulisa_assay.json#definitions/record"
+            },
+            "mergeStrategy": "append"
+        }
+    },
+    "required": [
+        "assay_creator",
+        "batch_id",
+        "npq_file",
+        "raw_counts_file",
+        "records"
+    ]
+}

nci_cidc_schemas-0.28.3/cidc_schemas/schemas/templates/assays/nulisa_template.json

@@ -0,0 +1,88 @@
+{
+    "title": "NULISA assay template",
+    "description": "NULISA submission.",
+    "prism_template_root_object_schema": "assays/nulisa_assay.json",
+    "prism_template_root_object_pointer": "/assays/nulisa/0",
+    "properties":
+    {
+        "worksheets":
+        {
+            "NULISA":
+            {
+                "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/scrnaseq_assay.json#properties/assay_creator"
+                    },
+                    "batch id": {
+                        "merge_pointer": "0/batch_id",
+                        "type_ref": "assays/scrnaseq_assay.json#properties/batch_id"
+                    },
+                    "npq file": {
+                        "merge_pointer": "0/npq_file",
+                        "gcs_uri_format": "{protocol identifier}/nulisa/{batch id}/npq_file.csv",
+                        "is_artifact": 1,
+                        "type_ref": "assays/components/local_file.json#properties/file_path"
+                    },
+                    "raw counts file": {
+                        "merge_pointer": "0/raw_counts_file",
+                        "gcs_uri_format": "{protocol identifier}/nulisa/{batch id}/raw_counts_file.csv",
+                        "is_artifact": 1,
+                        "type_ref": "assays/components/local_file.json#properties/file_path"
+                    },
+                    "metadata csv": {
+                        "merge_pointer": "0/metadata_csv",
+                        "gcs_uri_format": "{protocol identifier}/nulisa/{batch id}/metadata.csv",
+                        "is_artifact": 1,
+                        "type_ref": "assays/components/local_file.json#properties/file_path",
+                        "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"
+                        },
+                        "IC Median": {
+                            "merge_pointer": "0/details/ic_median",
+                            "type": "number"
+                        },
+                        "Detectability": {
+                            "merge_pointer": "0/details/detectability",
+                            "type": "number",
+                            "allow_empty": true
+                        },
+                        "IC Reads": {
+                            "merge_pointer": "0/details/ic_reads",
+                            "type": "integer"
+                        },
+                        "QC Status": {
+                            "merge_pointer": "0/details/qc_status",
+                            "type": "string"
+                        },
+                        "Reads": {
+                            "merge_pointer": "0/details/reads",
+                            "type": "integer"
+                        },
+                        "AUTO_WELLPOSITION": {
+                            "merge_pointer": "0/details/auto_well_position",
+                            "type": "string"
+                        }
+                    }
+                }
+            }
+        }
+    }
+}

{nci_cidc_schemas-0.28.2 → nci_cidc_schemas-0.28.3/nci_cidc_schemas.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_schemas
-Version: 0.28.2
+Version: 0.28.3
 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-0.28.2 → nci_cidc_schemas-0.28.3}/nci_cidc_schemas.egg-info/SOURCES.txt

@@ -105,6 +105,7 @@ cidc_schemas/schemas/assays/mif_assay.json
 cidc_schemas/schemas/assays/mihc_assay.json
 cidc_schemas/schemas/assays/misc_data.json
 cidc_schemas/schemas/assays/nanostring_assay.json
+cidc_schemas/schemas/assays/nulisa_assay.json
 cidc_schemas/schemas/assays/olink_assay.json
 cidc_schemas/schemas/assays/rna_assay-v0.json
 cidc_schemas/schemas/assays/rna_assay.json
@@ -138,6 +139,7 @@ cidc_schemas/schemas/assays/components/mihc_input.json
 cidc_schemas/schemas/assays/components/multiple_local_files.json
 cidc_schemas/schemas/assays/components/ngs_assay_core.json
 cidc_schemas/schemas/assays/components/ngs_assay_record.json
+cidc_schemas/schemas/assays/components/nulisa_input.json
 cidc_schemas/schemas/assays/components/reads_core.json
 cidc_schemas/schemas/assays/components/reads_with_index.json
 cidc_schemas/schemas/assays/components/scrnaseq_input.json
@@ -182,6 +184,7 @@ cidc_schemas/schemas/templates/assays/mif_template.json
 cidc_schemas/schemas/templates/assays/mihc_template.json
 cidc_schemas/schemas/templates/assays/misc_data_template.json
 cidc_schemas/schemas/templates/assays/nanostring_template.json
+cidc_schemas/schemas/templates/assays/nulisa_template.json
 cidc_schemas/schemas/templates/assays/olink_template.json
 cidc_schemas/schemas/templates/assays/rna_bam_template.json
 cidc_schemas/schemas/templates/assays/rna_fastq_template.json

{nci_cidc_schemas-0.28.2 → nci_cidc_schemas-0.28.3}/tests/prism/cidc_test_data/assay_data.py

@@ -3793,6 +3793,96 @@ def scrnaseq() -> PrismTestData:
     )
 
 
+@assay_data_generator
+def nulisa() -> PrismTestData:
+    upload_type = "nulisa"
+    prismify_args = get_prismify_args(upload_type)
+    prismify_patch = {
+        "protocol_identifier": "test_prism_trial_id",
+        "assays": {
+            "nulisa": [
+                {
+                    "assay_creator": "DFCI",
+                    "batch_id": "test_batch",
+                    "npq_file": {
+                        "upload_placeholder": "d658b480-ed78-4717-b622-3e2112"
+                    },
+                    "raw_counts_file": {
+                        "upload_placeholder": "d658b480-ed78-4717-b622-3e1122"
+                    },
+                    "metadata_csv": {
+                        "upload_placeholder": "d658b480-ed78-4717-b622-3ea112"
+                    },
+                    "records": [
+                        {
+                            "cimac_id": "CTTTPP121.01",
+                            "details": {
+                                "ic_median": 92.2,
+                                "detectability": 88.3,
+                                "ic_reads": 9402,
+                                "qc_status": "warning",
+                                "reads": 36221,
+                                "auto_well_position": "A5",
+                            },
+                        },
+                        {
+                            "cimac_id": "CTTTPP122.01",
+                            "details": {
+                                "ic_median": -57.3,
+                                "ic_reads": 132444,
+                                "qc_status": "NA",
+                                "reads": 777777,
+                                "auto_well_position": "B82",
+                            },
+                        },
+                    ],
+                }
+            ]
+        },
+    }
+    upload_entries = [
+        LocalFileUploadEntry(
+            local_path="npq.csv",
+            upload_placeholder="d658b480-ed78-4717-b622-3e2112",
+            gs_key="test_prism_trial_id/nulisa/test_batch/npq.csv",
+            metadata_availability=False,
+            allow_empty=False,
+        ),
+        LocalFileUploadEntry(
+            local_path="raw.csv",
+            upload_placeholder="d658b480-ed78-4717-b622-3e1122",
+            gs_key="test_prism_trial_id/nulisa/test_batch/raw_counts_file.csv",
+            metadata_availability=False,
+            allow_empty=False,
+        ),
+        LocalFileUploadEntry(
+            local_path="metadata.csv",
+            upload_placeholder="d658b480-ed78-4717-b622-3ea112",
+            gs_key="test_prism_trial_id/nulisa/test_batch/metadata.csv",
+            metadata_availability=False,
+            allow_empty=False,
+        ),
+    ]
+
+    cimac_ids = [
+        record["cimac_id"]
+        for batch in prismify_patch["assays"]["nulisa"]
+        for record in batch["records"]
+    ]
+    base_trial = get_test_trial(cimac_ids)
+
+    target_trial = copy_dict_with_branch(base_trial, prismify_patch, "assays")
+
+    return PrismTestData(
+        upload_type,
+        prismify_args,
+        prismify_patch,
+        upload_entries,
+        base_trial,
+        target_trial,
+    )
+
+
 @assay_data_generator
 def visium() -> PrismTestData:
     upload_type = "visium"