nci-cidc-schemas 0.27.18__tar.gz → 0.27.20__tar.gz

{nci_cidc_schemas-0.27.18/nci_cidc_schemas.egg-info → nci_cidc_schemas-0.27.20}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_schemas
-Version: 0.27.18
+Version: 0.27.20
 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-0.27.18 → nci_cidc_schemas-0.27.20}/cidc_schemas/__init__.py

@@ -2,4 +2,4 @@
 
 __author__ = """NCI"""
 __email__ = "nci-cidc-tools-admin@mail.nih.gov"
-__version__ = "0.27.18"
+__version__ = "0.27.20"

{nci_cidc_schemas-0.27.18 → nci_cidc_schemas-0.27.20}/cidc_schemas/prism/core.py

@@ -18,6 +18,7 @@ from .merger import PRISM_MERGE_STRATEGIES, MergeCollisionException
 from ..util import get_logger
 from jsonmerge import Merger
 from jsonpointer import EndOfList, JsonPointer, JsonPointerException, resolve_pointer
+from datetime import date
 
 from .constants import SUPPORTED_TEMPLATES
 
@@ -533,4 +534,25 @@ def prismify(
     else:
         root_ct_obj = template_root_obj
 
+    # Adding additional fields during manifest ingestion
+    if "shipments" in root_ct_obj:
+        if len(root_ct_obj["shipments"]) != 1:
+            raise Exception("Can only process one manifest at a time")
+        root_ct_obj["shipments"][0]["upload_type"] = template.type
+        root_ct_obj["shipments"][0]["date_ingested"] = date.today().strftime("%Y-%m-%d")
+        manifest = root_ct_obj["shipments"][0]
+        for participant in root_ct_obj["participants"]:
+            for sample in participant["samples"]:
+                fields = [
+                    "manifest_id",
+                    "upload_type",
+                    "assay_type",
+                    "ship_to_name",
+                    "ship_from_name",
+                    "date_ingested",
+                ]
+                for field in fields:
+                    if field in manifest:
+                        sample[field] = manifest[field]
+
     return root_ct_obj, collected_files, errors_so_far

{nci_cidc_schemas-0.27.18 → nci_cidc_schemas-0.27.20}/cidc_schemas/schemas/sample.json

@@ -537,6 +537,30 @@
         "intended_assay": {
             "type": "string",
             "description": "The assay that this sample is expected to be used as input for."
+        },
+        "manifest_id": {
+            "type": "string",
+            "description": "Id of the manifest"
+        },
+        "upload_type": {
+            "type": "string",
+            "description": "Type of manifest"
+        },
+        "date_ingested": {
+            "type": "string",
+            "description": "Date CIDC ingested the sample/manifest"
+        },
+        "assay_type": {
+            "type": "string",
+            "description": "Assay type of sample"
+        },
+        "ship_to_name": {
+            "type": "string",
+            "description": "Recipient of sample"
+        },
+        "ship_from_name": {
+            "type": "string",
+            "description": "Sender of sample"
         }
     },
     "additionalProperties": false,

{nci_cidc_schemas-0.27.18 → nci_cidc_schemas-0.27.20}/cidc_schemas/schemas/shipping_core.json

@@ -42,20 +42,27 @@
       "enum": [
         "Olink",
         "WES",
+        "BD Rhapsody",
+        "GeoMx",
         "RNAseq",
         "IHC",
         "CyTOF",
         "H&E",
         "ELISA",
+        "EVP",
         "mIF",
         "mIHC",
+        "MALDI Glycan",
         "TCRseq",
         "ATACseq",
         "ctDNA",
         "Microbiome",
         "Nanostring",
+        "NULISA",
         "MIBI",
-        "scRNA-Seq"
+        "scRNA-Seq",
+        "snRNA-Seq",
+        "Visium"
       ]
     },
     "courier": {
@@ -174,6 +181,14 @@
     "receiving_party": {
       "description": "Site where sample was shipped to be assayed.",
       "type": "string"
+    },
+    "upload_type": {
+      "description": "The type of manifest being uploaded",
+      "type": "string"
+    },
+    "date_ingested": {
+      "description": "The date CIDC ingests the manifest",
+      "type": "string"
     }
   }
 }

{nci_cidc_schemas-0.27.18 → nci_cidc_schemas-0.27.20/nci_cidc_schemas.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_schemas
-Version: 0.27.18
+Version: 0.27.20
 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-0.27.18 → nci_cidc_schemas-0.27.20}/tests/prism/cidc_test_data/manifest_data.py

@@ -9,6 +9,7 @@ from .utils import (
     LocalFileUploadEntry,
     PrismTestData,
 )
+from datetime import date
 
 manifest_data_generators = []
 
@@ -21,12 +22,15 @@ def manifest_data_generator(f):
 @manifest_data_generator
 def plasma() -> PrismTestData:
     upload_type = "plasma"
+    current_date = date.today().strftime("%Y-%m-%d")
     prismify_args = get_prismify_args(upload_type)
     prismify_patch = {
         "protocol_identifier": "test_prism_trial_id",
         "shipments": [
             {
                 "manifest_id": "test_prism_trial_id_PLASMA",
+                "upload_type": "plasma",
+                "date_ingested": current_date,
                 "assay_priority": "4",
                 "assay_type": "Olink",
                 "receiving_party": "MSSM_Gnjatic",
@@ -59,23 +63,21 @@ def plasma() -> PrismTestData:
             {
                 "samples": [
                     {
-                        "shipping_entry_number": 1,
                         "cimac_id": "CTTTP01A1.00",
-                        "surgical_pathology_report_id": "test_encrypted('Surgical pathology report 1')",
-                        "clinical_report_id": "test_encrypted('clinical report 1')",
+                        "upload_type": "plasma",
+                        "manifest_id": "test_prism_trial_id_PLASMA",
+                        "assay_type": "Olink",
+                        "date_ingested": current_date,
+                        "ship_to_name": "Marie",
+                        "ship_from_name": "Jared",
                         "collection_event_name": "Baseline",
-                        "diagnosis_verification": "Local pathology review was not consistent",
-                        "site_description": "ADRENAL GLANDS",
-                        "topography_code": "C00.2",
-                        "topography_description": "External lower lip",
-                        "histology_behavior": "8003/3",
-                        "histology_behavior_description": "Neoplasm, malignant",
                         "parent_sample_id": "test_encrypted('TTTPP1A1')",
                         "processed_sample_id": "test_encrypted('BIOBANK 1A1')",
-                        "processed_sample_quantity": 5,
+                        "processed_sample_quantity": 5.0,
                         "box_number": "1",
                         "sample_location": "A1",
                         "type_of_sample": "Whole Blood",
+                        "type_of_primary_container": "Bag",
                         "sample_collection_procedure": "Core Biopsy",
                         "processed_sample_type": "Bone Marrow Film",
                         "processed_sample_volume": 1.0,
@@ -91,11 +93,16 @@ def plasma() -> PrismTestData:
                         "comments": "Comment",
                     },
                     {
-                        "shipping_entry_number": 2,
                         "collection_event_name": "Baseline",
                         "parent_sample_id": "test_encrypted('TTTPP1A2')",
                         "processed_sample_id": "test_encrypted('BIOBANK 1A2')",
                         "cimac_id": "CTTTP01A2.00",
+                        "upload_type": "plasma",
+                        "manifest_id": "test_prism_trial_id_PLASMA",
+                        "assay_type": "Olink",
+                        "date_ingested": current_date,
+                        "ship_to_name": "Marie",
+                        "ship_from_name": "Jared",
                         "box_number": "1",
                         "sample_location": "A2",
                         "type_of_sample": "Whole Blood",
@@ -116,11 +123,16 @@ def plasma() -> PrismTestData:
                         "comments": "No comment",
                     },
                     {
-                        "shipping_entry_number": 3,
                         "collection_event_name": "Baseline",
                         "parent_sample_id": "test_encrypted('TTTPP1A3')",
                         "processed_sample_id": "test_encrypted('BIOBANK 1A3')",
                         "cimac_id": "CTTTP01A3.00",
+                        "upload_type": "plasma",
+                        "manifest_id": "test_prism_trial_id_PLASMA",
+                        "assay_type": "Olink",
+                        "date_ingested": current_date,
+                        "ship_to_name": "Marie",
+                        "ship_from_name": "Jared",
                         "box_number": "1",
                         "sample_location": "A3",
                         "type_of_sample": "Whole Blood",
@@ -143,19 +155,21 @@ def plasma() -> PrismTestData:
                 ],
                 "participant_id": "test_encrypted('TTTP01')",
                 "cimac_participant_id": "CTTTP01",
-                "gender": "Female",
-                "race": "Asian",
-                "ethnicity": "Hispanic or Latino",
                 "cohort_name": "Arm_Z",
             },
             {
                 "samples": [
                     {
-                        "shipping_entry_number": 4,
                         "collection_event_name": "Baseline",
                         "parent_sample_id": "test_encrypted('TTTPP2A1')",
                         "processed_sample_id": "test_encrypted('BIOBANK 2A1')",
                         "cimac_id": "CTTTP02A1.00",
+                        "upload_type": "plasma",
+                        "manifest_id": "test_prism_trial_id_PLASMA",
+                        "assay_type": "Olink",
+                        "date_ingested": current_date,
+                        "ship_to_name": "Marie",
+                        "ship_from_name": "Jared",
                         "box_number": "1",
                         "sample_location": "A4",
                         "type_of_sample": "Whole Blood",
@@ -179,6 +193,12 @@ def plasma() -> PrismTestData:
                         "parent_sample_id": "test_encrypted('TTTPP2A2')",
                         "processed_sample_id": "test_encrypted('BIOBANK 2A2')",
                         "cimac_id": "CTTTP02A2.00",
+                        "upload_type": "plasma",
+                        "manifest_id": "test_prism_trial_id_PLASMA",
+                        "assay_type": "Olink",
+                        "date_ingested": current_date,
+                        "ship_to_name": "Marie",
+                        "ship_from_name": "Jared",
                         "box_number": "1",
                         "sample_location": "A5",
                         "type_of_sample": "Whole Blood",
@@ -202,6 +222,12 @@ def plasma() -> PrismTestData:
                         "parent_sample_id": "test_encrypted('TTTPP2A3')",
                         "processed_sample_id": "test_encrypted('BIOBANK 2A3')",
                         "cimac_id": "CTTTP02A3.00",
+                        "upload_type": "plasma",
+                        "manifest_id": "test_prism_trial_id_PLASMA",
+                        "assay_type": "Olink",
+                        "date_ingested": current_date,
+                        "ship_to_name": "Marie",
+                        "ship_from_name": "Jared",
                         "box_number": "1",
                         "sample_location": "A6",
                         "type_of_sample": "Whole Blood",

{nci_cidc_schemas-0.27.18 → nci_cidc_schemas-0.27.20}/tests/prism/test_cidc_data_model.py

@@ -59,10 +59,10 @@ def test_gcs_uri_format(prism_test: PrismTestData):
         assert ue.gs_key.startswith(f"{prot_id}/{assay}")
 
 
-@pytest.mark.skip(
-    reason="Uses Manifest template(s) that are intended to go away with CSMS integration."
-)
 def test_prismify(prism_test: PrismTestData, monkeypatch):
+    # TODO: make tests work for all manifest types. It was a lot of work to make one work
+    if prism_test.upload_type != "plasma":
+        pytest.skip("Manifest tests not set up yet")
     monkeypatch.setattr(
         "cidc_schemas.prism.core._encrypt", lambda x: f"test_encrypted({str(x)!r})"
     )