nci-cidc-schemas 0.27.18__py2.py3-none-any.whl → 0.27.20__py2.py3-none-any.whl

cidc_schemas/__init__.py

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

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,

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.dist-info → nci_cidc_schemas-0.27.20.dist-info}/METADATA

@@ -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.dist-info → nci_cidc_schemas-0.27.20.dist-info}/RECORD

@@ -1,4 +1,4 @@
-cidc_schemas/__init__.py,sha256=xZBbp_EukH5SFvMq6iFrfayuSjiBbQGdQVv-pAc6jgY,136
+cidc_schemas/__init__.py,sha256=yi2KxIY-2AGxT7M-1FX19wNnU2g4mQGctrrjhsdwFRo,136
 cidc_schemas/cli.py,sha256=gWiktRlraNH8Q0zNUae9dohKjPwBmcY0BJwdcQ_fIic,4099
 cidc_schemas/constants.py,sha256=RULs7pGuBAVq1teXymrfbVsK23ZowJvLuZlv0KcjL-Y,698
 cidc_schemas/json_validation.py,sha256=spmPsqinib7Ns5GvWOKKa1rc7IrN_s2bqifpTKdaLVU,23288
@@ -12,7 +12,7 @@ cidc_schemas/metaschema/strict_meta_schema.json,sha256=3FiS0r2dAXgfPsruJwZYbQoQn
 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=xRxwWtux1PUed2BsdfW9-21NQzNdc05HYYcO5Q0jkEQ,2357
-cidc_schemas/prism/core.py,sha256=2WZ6e1-T88zHUYnl5PnD9pBSu-enRJBtRsf-WKc42Wk,19301
+cidc_schemas/prism/core.py,sha256=tXDCCHurvcrxfU11meH3NRAVo9niklup0dpLRoIXwPk,20242
 cidc_schemas/prism/extra_metadata.py,sha256=S9w5EGAT0xwaWMrpYluF7Y1ONsI4wFtxFD8ib6Va_fU,8567
 cidc_schemas/prism/merger.py,sha256=36CKBPVoWecHuvGp3oT9a2d4jWIkvKuS_UofKTEpMYs,13065
 cidc_schemas/prism/pipelines.py,sha256=dvZtoC7pEVgdPual_DZUTBFfgvSV7yTdk1RHwi5h6Vs,33522
@@ -20,8 +20,8 @@ cidc_schemas/schemas/aliquot.json,sha256=F24s6xGTeJl-VT6s6wvV8YtMA4O-0BsUCwtD2OE
 cidc_schemas/schemas/clinical_data.json,sha256=ubt2dqTLCbDuxuOXrBObT_xLHVSArMBx4oASFOAYEas,1474
 cidc_schemas/schemas/clinical_trial.json,sha256=aUjYgdtlRWDfULk0-apralt4-KrtjriUqt3qNTdL2Rc,4442
 cidc_schemas/schemas/participant.json,sha256=X72GQSdLqhZl_Vg8OHPqRotblIluNSmiw8N5UeM-di8,2843
-cidc_schemas/schemas/sample.json,sha256=4WnxrgJ978CybHg3bQ2JrYgi_0ih0zHyIhr1DwPuDRc,21519
-cidc_schemas/schemas/shipping_core.json,sha256=cth7FYWKEujJkWOkOHTj2QWgKPUOL0pizbzAJZ67lOs,4260
+cidc_schemas/schemas/sample.json,sha256=ljUzhe7J2WKHpLcz5XZTxIx7oRQa8uEYO-OQse5L-HA,22227
+cidc_schemas/schemas/shipping_core.json,sha256=fASyy11eM2X9q5fFc3hpwfSEGls4d4VsBZawG-VeSzI,4619
 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
@@ -158,9 +158,9 @@ cidc_schemas/schemas/templates/manifests/tissue_slide_template.json,sha256=q2GmO
 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=LpaoDXDS11NCa-Dv37N-tzEGomswQrx5fypkUcG7xJk,18956
 cidc_schemas/schemas/templates/manifests/tumor_tissue_rna_template.json,sha256=-gww6NCHbtbI5z7UmNSmKyPK3IqKCE8F6n4XwTAb_gk,18101
-nci_cidc_schemas-0.27.18.dist-info/licenses/LICENSE,sha256=zK77-w4rYCZBHAYJEGkcFuPXwKIsP7jMPZ2iQOXjzko,1072
-nci_cidc_schemas-0.27.18.dist-info/METADATA,sha256=7t-gt6qTSW6RkkcohEb00Nv3X8ywvHtPBF068Nn8GJg,4554
-nci_cidc_schemas-0.27.18.dist-info/WHEEL,sha256=egKm5cKfE6OqlHwodY8Jjp4yqZDBXgsj09UsV5ojd_U,109
-nci_cidc_schemas-0.27.18.dist-info/entry_points.txt,sha256=kSyTzXeJQrJp_2ZX0GS_NnbJR8ceQKLBSgER46PM0hs,55
-nci_cidc_schemas-0.27.18.dist-info/top_level.txt,sha256=Wwb5Cu7QrnbmSJxI2d00e3-Mir36t0jTRnSulmfhi30,13
-nci_cidc_schemas-0.27.18.dist-info/RECORD,,
+nci_cidc_schemas-0.27.20.dist-info/licenses/LICENSE,sha256=zK77-w4rYCZBHAYJEGkcFuPXwKIsP7jMPZ2iQOXjzko,1072
+nci_cidc_schemas-0.27.20.dist-info/METADATA,sha256=kVdUjaEclSr5z_sQQcGy-gax_Vz3aQZ9j0TcE0z1EH8,4554
+nci_cidc_schemas-0.27.20.dist-info/WHEEL,sha256=JNWh1Fm1UdwIQV075glCn4MVuCRs0sotJIq-J6rbxCU,109
+nci_cidc_schemas-0.27.20.dist-info/entry_points.txt,sha256=kSyTzXeJQrJp_2ZX0GS_NnbJR8ceQKLBSgER46PM0hs,55
+nci_cidc_schemas-0.27.20.dist-info/top_level.txt,sha256=Wwb5Cu7QrnbmSJxI2d00e3-Mir36t0jTRnSulmfhi30,13
+nci_cidc_schemas-0.27.20.dist-info/RECORD,,

{nci_cidc_schemas-0.27.18.dist-info → nci_cidc_schemas-0.27.20.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.8.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py2-none-any
 Tag: py3-none-any