nci-cidc-schemas 0.28.2__tar.gz → 0.28.4__tar.gz

{nci_cidc_schemas-0.28.2/nci_cidc_schemas.egg-info → nci_cidc_schemas-0.28.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_schemas
-Version: 0.28.2
+Version: 0.28.4
 Summary: The CIDC data model and tools for working with it.
 Home-page: https://github.com/NCI-CIDC/cidc-schemas
 Author: NCI
@@ -131,11 +131,17 @@ python3 -m cidc_schemas.cli [args]
 
 In order to create a new assay type, your best bet is to just search for an existing assay and copy it.
 
-Preferably, look at visium and copy exactly what it does. Make changes in the assay schema and template for your
+Preferably, look at scrnaseq and copy exactly what it does. Make changes in the assay schema and template for your
 particular assay and/or analysis schema.
 
-There are a lot of gotchas and hidden parsing going on behind the scenes. Listing them all would be hard, so this is the best
-practical advice.
+Once you update and update the version of this repo, update api-gae. You should only need to copy what scrnaseq
+did in api-gae in order for files to show up on the portal. Make sure to update the api-gae version. Update the api-gae version used
+in cloud-functions.
+
+Finally, make sure to update the cli tool to include the new assay.
+
+There are a lot of gotchas and hidden parsing going on behind the scenes. Listing them all would be hard, so the
+practical advice is to follow an existing working template.
 
 Be sure to regenerate the docs after creating your schema, so the new schema is added to the reference docs.
 

{nci_cidc_schemas-0.28.2 → nci_cidc_schemas-0.28.4}/README.md

@@ -90,11 +90,17 @@ python3 -m cidc_schemas.cli [args]
 
 In order to create a new assay type, your best bet is to just search for an existing assay and copy it.
 
-Preferably, look at visium and copy exactly what it does. Make changes in the assay schema and template for your
+Preferably, look at scrnaseq and copy exactly what it does. Make changes in the assay schema and template for your
 particular assay and/or analysis schema.
 
-There are a lot of gotchas and hidden parsing going on behind the scenes. Listing them all would be hard, so this is the best
-practical advice.
+Once you update and update the version of this repo, update api-gae. You should only need to copy what scrnaseq
+did in api-gae in order for files to show up on the portal. Make sure to update the api-gae version. Update the api-gae version used
+in cloud-functions.
+
+Finally, make sure to update the cli tool to include the new assay.
+
+There are a lot of gotchas and hidden parsing going on behind the scenes. Listing them all would be hard, so the
+practical advice is to follow an existing working template.
 
 Be sure to regenerate the docs after creating your schema, so the new schema is added to the reference docs.
 

{nci_cidc_schemas-0.28.2 → nci_cidc_schemas-0.28.4}/cidc_schemas/__init__.py

@@ -2,4 +2,4 @@
 
 __author__ = """NCI"""
 __email__ = "nci-cidc-tools-admin@mail.nih.gov"
-__version__ = "0.28.2"
+__version__ = "0.28.4"

{nci_cidc_schemas-0.28.2 → nci_cidc_schemas-0.28.4}/cidc_schemas/prism/constants.py

@@ -28,6 +28,8 @@ SUPPORTED_ASSAYS = [
     "mihc",
     "scrnaseq",
     "visium",
+    "nulisa",
+    "maldi_glycan",
 ]
 
 SUPPORTED_SHIPPING_MANIFESTS = [
@@ -143,6 +145,8 @@ ASSAY_TO_FILEPATH: Dict[str, str] = {
             "scrnaseq_analysis",
             "visium",
             "visium_analysis",
+            "nulisa",
+            "maldi_glycan",
         ]
     },
 }

nci_cidc_schemas-0.28.4/cidc_schemas/schemas/artifacts/artifact_ibd.json

@@ -0,0 +1,51 @@
+{
+  "$schema": "metaschema/strict_meta_schema.json#",
+  "$id": "ibd_artifact",
+  "title": "IBD Artifact",
+  "type": "object",
+  "description": "Information about a IBD file.",
+  "additionalProperties": false,
+  "properties": {
+    "data_format": {
+      "description": "Data format.",
+      "const": "IBD"
+    },
+    "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-0.28.4/cidc_schemas/schemas/artifacts/artifact_imzml.json

@@ -0,0 +1,51 @@
+{
+  "$schema": "metaschema/strict_meta_schema.json#",
+  "$id": "imzml_artifact",
+  "title": "IMZML Artifact",
+  "type": "object",
+  "description": "Information about an IMZML file.",
+  "additionalProperties": false,
+  "properties": {
+    "data_format": {
+      "description": "Data format.",
+      "const": "IMZML"
+    },
+    "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-0.28.2 → nci_cidc_schemas-0.28.4}/cidc_schemas/schemas/assays/components/available_assays.json

@@ -167,6 +167,29 @@
         "$ref": "assays/microbiome_assay.json"
       },
       "mergeStrategy": "append"
+    },
+    "nulisa": {
+      "type": "array",
+      "description": "NULISA",
+      "items": {
+        "$ref": "assays/nulisa_assay.json"
+      },
+      "mergeStrategy": "arrayMergeById",
+      "mergeOptions": {
+        "idRef": "batch_id"
+      }
+    },
+    "maldi_glycan": {
+      "type": "array",
+      "description": "MALDI Glycan",
+      "items": {
+        "$ref": "assays/maldi_glycan_assay.json"
+      },
+      "mergeStrategy": "arrayMergeById",
+      "mergeOptions": {
+        "idRef": "batch_id"
+      }
     }
+
   }
 }

nci_cidc_schemas-0.28.4/cidc_schemas/schemas/assays/components/maldi_glycan_input.json

@@ -0,0 +1,28 @@
+{
+  "$schema": "metaschema/strict_meta_schema.json#",
+  "$id": "maldi_glycan_input",
+  "title": "MALDI Glycan Input Files and Data",
+  "type": "object",
+  "description": "MALDI Glycan assay input files and data",
+  "inheritableBase": true,
+  "properties": {
+    "ibd_file": {
+      "$ref": "artifacts/artifact_ibd.json"
+    },
+    "imzml_file": {
+      "$ref": "artifacts/artifact_imzml.json"
+    },
+    "channels_csv": {
+      "$ref": "artifacts/artifact_csv.json"
+    },
+    "tiff_zip": {
+      "$ref": "artifacts/artifact_zip.json"
+    }
+  },
+  "required": [
+    "ibd_file",
+    "imzml_file",
+    "channels_csv",
+    "tiff_zip"
+  ]
+}

nci_cidc_schemas-0.28.4/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-0.28.4/cidc_schemas/schemas/assays/maldi_glycan_assay.json

@@ -0,0 +1,68 @@
+{
+    "$schema": "metaschema/strict_meta_schema.json#",
+    "$id": "maldi_glycan_assay",
+    "title": "MALDI Glycan Assay",
+    "type": "object",
+    "$comment": "description used in docs/index.html and docs/assays.maldi_glycan.html",
+    "description": "MALDI Glycan assay",
+    "additionalProperties": false,
+    "definitions": {
+        "record": {
+            "type": "object",
+            "mergeStrategy": "objectMerge",
+            "description": "A single data record from a MALDI Glycan assay.",
+            "additionalProperties": false,
+            "required": [
+                "cimac_id",
+                "details"
+            ],
+            "properties": {
+                "cimac_id": {
+                    "description": "Id of an sample within this clinical trial, that this assay record is based upon.",
+                    "$ref": "sample.json#properties/cimac_id"
+                },
+                "details": {
+                    "$ref": "assays/components/maldi_glycan_input.json"
+                }
+            }
+        }
+    },
+    "properties": {
+        "assay_creator": {
+            "$ref": "assays/components/assay_core.json#properties/assay_creator"
+        },
+        "batch_id": {
+            "description": "Batch identification number. Unique to every upload.",
+            "type": "string"
+        },
+        "molecular_assignments_file": {
+            "$ref": "artifacts/artifact_tsv.json"
+        },
+        "metadata_tsv": {"$ref": "artifacts/artifact_tsv.json"},
+
+        "antibodies": {
+            "type": "array",
+            "items": {
+                "$ref": "assays/components/mibi_antibody.json"
+            },
+            "mergeStrategy": "arrayMergeById",
+            "mergeOptions": {
+                "idRef": "antibody"
+            }
+        },
+        "records": {
+            "type": "array",
+            "description": "A single data record from a MALDI Glycan assay.",
+            "items": {
+                "$ref": "assays/maldi_glycan_assay.json#definitions/record"
+            },
+            "mergeStrategy": "append"
+        }
+    },
+    "required": [
+        "assay_creator",
+        "batch_id",
+        "molecular_assignments_file",
+        "records"
+    ]
+}

nci_cidc_schemas-0.28.4/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-0.28.2 → nci_cidc_schemas-0.28.4}/cidc_schemas/schemas/shipping_core.json

@@ -58,6 +58,7 @@
         "ctDNA",
         "Microbiome",
         "Nanostring",
+        "MALDI Glycan",
         "NULISA",
         "MIBI",
         "scRNAseq",

nci_cidc_schemas-0.28.4/cidc_schemas/schemas/templates/assays/maldi_glycan_template.json

@@ -0,0 +1,139 @@
+{
+    "title": "MALDI Glycan assay template",
+    "description": "MALDI Glycan submission.",
+    "prism_template_root_object_schema": "assays/maldi_glycan_assay.json",
+    "prism_template_root_object_pointer": "/assays/maldi_glycan/0",
+    "properties": {
+        "worksheets": {
+            "MALDI Glycan": {
+                "prism_data_object_pointer": "/records/-",
+                "preamble_rows": {
+                    "protocol identifier": {
+                        "merge_pointer": "3/protocol_identifier",
+                        "type_ref": "clinical_trial.json#properties/protocol_identifier"
+                    },
+                    "batch id": {
+                        "merge_pointer": "0/batch_id",
+                        "type_ref": "assays/mibi_assay.json#properties/batch_id"
+                    },
+                    "assay creator": {
+                        "merge_pointer": "0/assay_creator",
+                        "type_ref": "assays/components/assay_core.json#properties/assay_creator"
+                    },
+                    "molecular assignments file": {
+                        "merge_pointer": "0/molecular_assignments_file",
+                        "gcs_uri_format": "{protocol identifier}/maldi_glyacn/{batch id}/molecular_assignments.tsv",
+                        "is_artifact": 1,
+                        "type_ref": "assays/components/local_file.json#properties/file_path"
+                    },
+                    "metadata tsv": {
+                        "merge_pointer": "0/metadata_tsv",
+                        "gcs_uri_format": "{protocol identifier}/maldi_glycan/{batch id}/metadata.tsv",
+                        "is_artifact": 1,
+                        "type_ref": "assays/components/local_file.json#properties/file_path",
+                        "allow_empty": true
+                    }
+                },
+                "data_columns": {
+                    "Samples": {
+                        "cimac id": {
+                            "merge_pointer": "0/cimac_id",
+                            "type_ref": "sample.json#properties/cimac_id"
+                        },
+                        "ibd file": {
+                            "merge_pointer": "0/details/ibd_file",
+                            "is_artifact": 1,
+                            "gcs_uri_format": "{protocol identifier}/maldi_glyacn/{batch id}/{cimac id}/ibd_file.ibd",
+                            "type_ref": "assays/components/local_file.json#properties/file_path"
+                        },
+                        "imzml file": {
+                            "merge_pointer": "0/details/imzml_file",
+                            "is_artifact": 1,
+                            "gcs_uri_format": "{protocol identifier}/maldi_glyacn/{batch id}/{cimac id}/imzml_file.imzml",
+                            "type_ref": "assays/components/local_file.json#properties/file_path"
+                        },
+                        "channels csv": {
+                            "merge_pointer": "0/details/channels_csv",
+                            "is_artifact": 1,
+                            "gcs_uri_format": "{protocol identifier}/maldi_glyacn/{batch id}/{cimac id}/channels.csv",
+                            "type_ref": "assays/components/local_file.json#properties/file_path"
+                        },
+                        "tiff zip": {
+                            "merge_pointer": "0/details/tiff_zip",
+                            "is_artifact": 1,
+                            "gcs_uri_format": "{protocol identifier}/maldi_glyacn/{batch id}/{cimac id}/tiff.zip",
+                            "type_ref": "assays/components/local_file.json#properties/file_path"
+                        }
+                    }
+                }
+            },
+            "Antibodies": {
+                "prism_data_object_pointer": "/antibodies/-",
+                "data_columns":
+                {
+                    "Antibodies":
+                    {
+                        "Channel id": {
+                            "merge_pointer": "0/channel_id",
+                            "type_ref": "assays/components/mibi_antibody.json#properties/channel_id"
+                        },
+                        "Antibody name": {
+                            "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",
+                            "allow_empty": true
+                        },
+                        "Uniprot accession number": {
+                            "merge_pointer": "0/uniprot_accession_number",
+                            "type_ref": "assays/components/mibi_antibody.json#properties/uniprot_accession_number",
+                            "allow_empty": true
+                        },
+                        "Lot number": {
+                            "merge_pointer": "0/lot_num",
+                            "type_ref": "assays/components/antibody.json#properties/lot_num",
+                            "allow_empty": true
+                        },
+                        "Dilution": {
+                            "merge_pointer": "0/dilution",
+                            "type_ref": "assays/components/mibi_antibody.json#properties/dilution",
+                            "allow_empty": true
+                        },
+                        "Concentration value": {
+                            "merge_pointer": "0/concentration_value",
+                            "type_ref": "assays/components/mibi_antibody.json#properties/concentration_value",
+                            "allow_empty": true
+                        },
+                        "Concentration units": {
+                            "merge_pointer": "0/concentration_units",
+                            "type_ref": "assays/components/mibi_antibody.json#properties/concentration_units",
+                            "allow_empty": true
+                        },
+                        "Conjugated catalog number": {
+                            "merge_pointer": "0/cat_num",
+                            "type_ref": "assays/components/antibody.json#properties/cat_num",
+                            "allow_empty": true
+                        },
+                        "Conjugated tag": {
+                            "merge_pointer": "0/conjugated_tag",
+                            "type_ref": "assays/components/mibi_antibody.json#properties/conjugated_tag",
+                            "allow_empty": true
+                        }
+                    }
+                }
+            }
+        }
+    }
+}

nci_cidc_schemas-0.28.4/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"
+                        }
+                    }
+                }
+            }
+        }
+    }
+}