nci-cidc-schemas 0.26.23__py2.py3-none-any.whl → 0.26.25__py2.py3-none-any.whl

cidc_schemas/__init__.py

@@ -2,4 +2,4 @@
 
 __author__ = """NCI"""
 __email__ = "nci-cidc-tools-admin@mail.nih.gov"
-__version__ = "0.26.23"
+__version__ = "0.26.25"

cidc_schemas/schemas/assays/hande_assay.json

@@ -29,6 +29,20 @@
               "$ref": "artifacts/artifact_jpg.json"
             }
           ]
+        },
+        "annotated_image": {
+          "inheritableBase": true,
+          "mergeStrategy": "objectMerge",
+          "anyOf": [
+            {
+              "$comment": "Path to the H & E annotated image in SVS format.",
+              "$ref": "artifacts/artifact_image.json"
+            },
+            {
+              "$comment": "Path to the H & E annotated image in JPG format.",
+              "$ref": "artifacts/artifact_jpg.json"
+            }
+          ]
         }
       },
       "required": ["image_file"]

cidc_schemas/schemas/shipping_core.json

@@ -52,7 +52,8 @@
         "TCRseq",
         "ATACseq",
         "ctDNA",
-        "Microbiome"
+        "Microbiome",
+        "Nanostring"
       ]
     },
     "courier": {

cidc_schemas/schemas/templates/assays/hande_template.json

@@ -34,7 +34,13 @@
                           "gcs_uri_format": "{protocol identifier}/hande/{cimac id}/image_file.{file type}",
                           "type_ref": "assays/components/local_file.json#properties/file_path"
                       },
-
+                      "annotated image": {
+                          "merge_pointer": "0/files/annotated_image",
+                          "is_artifact": 1,
+                          "gcs_uri_format": "{protocol identifier}/hande/{cimac id}/annotated_image.{file type}",
+                          "type_ref": "assays/components/local_file.json#properties/file_path",
+                          "allow_empty": true
+                      },
                       "tumor tissue (% total area)": {
                         "merge_pointer": "0/tumor_tissue_percentage",
                         "type_ref": "assays/hande_assay.json#definitions/record/properties/tumor_tissue_percentage",

cidc_schemas/unprism.py

@@ -203,6 +203,8 @@ def _olink_derivation(context: DeriveFilesContext) -> DeriveFilesResult:
                 0
             ]
 
+            # TODO: Not all Olink batch NPX files contain LOD column (see LuTK02 olink Batch2 for example).
+            # Rewrite to make it optional.
             df.columns = pd.MultiIndex.from_tuples(
                 [
                     (

{nci_cidc_schemas-0.26.23.dist-info → nci_cidc_schemas-0.26.25.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nci-cidc-schemas
-Version: 0.26.23
+Version: 0.26.25
 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-0.26.23.dist-info → nci_cidc_schemas-0.26.25.dist-info}/RECORD

@@ -1,4 +1,4 @@
-cidc_schemas/__init__.py,sha256=jQ1P_041eYuQhzzrs2KhsVI2HT7Rh7VZEDxi6hB5l3U,136
+cidc_schemas/__init__.py,sha256=y-9MdPlDGjwHr96XcMwUMdtcNRLuXB7Cku9YYjTH1jk,136
 cidc_schemas/cli.py,sha256=gWiktRlraNH8Q0zNUae9dohKjPwBmcY0BJwdcQ_fIic,4099
 cidc_schemas/constants.py,sha256=RULs7pGuBAVq1teXymrfbVsK23ZowJvLuZlv0KcjL-Y,698
 cidc_schemas/json_validation.py,sha256=h9maP1xicHmboF86DAwSp9dJzEGOF-cDysPKheloo_k,20025
@@ -6,7 +6,7 @@ cidc_schemas/migrations.py,sha256=Amg_T4cFgMzySD7yNnT_PWpqP7hwlTWGeHlI_RSXuRI,14
 cidc_schemas/template.py,sha256=P_7zS6OEuuVfofg7IF8-VSFZknjOgPWsIBytFOYuGGE,49836
 cidc_schemas/template_reader.py,sha256=xXtLRKu1y4FrPj8RgyGOmB2hlsCDXcuvMBWami2_jV8,13119
 cidc_schemas/template_writer.py,sha256=faOhvSDTp4nuPhOtVQR_J7YNnFzx-vh7oyNpFdee1mY,18236
-cidc_schemas/unprism.py,sha256=IE33ZdKxQEP1tHnt5-4BzX0dIoX5pSdOwsqQOo-px7c,13173
+cidc_schemas/unprism.py,sha256=9VIuY4ItfSnT8zTC0f4nB1KMUbK2HEPeXaq9EDAtMOA,13324
 cidc_schemas/util.py,sha256=ZCQ--ROZyXYVB034fHHmxZXb5F0G2GwzPwSfyfegtGk,4348
 cidc_schemas/metaschema/strict_meta_schema.json,sha256=3FiS0r2dAXgfPsruJwZYbQoQnHhC_yl-3mclX8gfiQU,6428
 cidc_schemas/pipeline_configs/rna_level1_analysis_config.yaml.j2,sha256=6no9sFqwzb1T61RZGD-owDt2K5R8G_fPTzflV4fOroo,2832
@@ -21,7 +21,7 @@ cidc_schemas/schemas/clinical_data.json,sha256=ubt2dqTLCbDuxuOXrBObT_xLHVSArMBx4
 cidc_schemas/schemas/clinical_trial.json,sha256=mqvpCTqWGimKA8-S4F32YMDBoHcJkawpr9iTwUgH56w,4652
 cidc_schemas/schemas/participant.json,sha256=vCtxbUfVGTjvZ8SPPNLvWJkJIBZUK2NSHpYzJgdoSaY,2991
 cidc_schemas/schemas/sample.json,sha256=TRWgxQBybtj4WjLBNZAdpoShpbDTGl8iT3FceGx2gD8,16296
-cidc_schemas/schemas/shipping_core.json,sha256=nqOK1174oFPKpMlOgXK8AL32993hWqJ5XEih2ZqJ6xA,3277
+cidc_schemas/schemas/shipping_core.json,sha256=MYnULNUnXYmOOHvF6T7oSBfMsT5f1waFdzlgdknnMD0,3299
 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
@@ -63,7 +63,7 @@ cidc_schemas/schemas/assays/ctdna_assay.json,sha256=BfQSIMC9oNrm_e1lz3juNSjA1JsK
 cidc_schemas/schemas/assays/cytof_assay.json,sha256=rf0vebcoHY_dS4wlqkoBY9rclSAE3CRdxeGLXAbhScM,3659
 cidc_schemas/schemas/assays/cytof_assay_core.json,sha256=Vwg3RmEEdCpZtDDaVAWBDCKTMnSxagsdqSJq4AiDu9w,8828
 cidc_schemas/schemas/assays/elisa_assay.json,sha256=YHeoxYmgdpefLWkBXNg60JUig2Ccqg8thWZ5M5q3hyw,2233
-cidc_schemas/schemas/assays/hande_assay.json,sha256=_Ezw2WpiGAVwF8-V2_c9_5NZyxwira7a68EaRV_rcaE,2757
+cidc_schemas/schemas/assays/hande_assay.json,sha256=IijGeekLP-5gvGF9yj9unSds7sh_xZyuGTFp7lNZrvU,3226
 cidc_schemas/schemas/assays/ihc_assay.json,sha256=lD4T8sK1yox-3ZRzSFxUhAo12MyZBgJs5D9vHnX9ccA,6697
 cidc_schemas/schemas/assays/mibi_assay.json,sha256=gxUdCKzsNpL5FB8muT8Gq-3cqbOTGiOax-kFjI4myCA,4187
 cidc_schemas/schemas/assays/microbiome_assay.json,sha256=4eSEKRylf86yLV7QKCIlMzzjj_XHKMfQpA0njLHBs00,2078
@@ -125,7 +125,7 @@ cidc_schemas/schemas/templates/assays/clinical_data_template.json,sha256=1luQXzy
 cidc_schemas/schemas/templates/assays/ctdna_template.json,sha256=XUGwEULvSLgtDvJUloz8BA1AHS_rRtziphV4ll34tus,4919
 cidc_schemas/schemas/templates/assays/cytof_template.json,sha256=YGaLt7DKsz32o3na8NDs-bXteVnAPMiF1hLH643f6kY,13328
 cidc_schemas/schemas/templates/assays/elisa_template.json,sha256=Q8cv5ZpaRZUfvr6e4PC4uvMqhhaDGLdvVMN_s8Uiajw,2259
-cidc_schemas/schemas/templates/assays/hande_template.json,sha256=EqzfxA2goWFIs2m2r5VLfZvH4CHWOeGKKF3kroP8paQ,3512
+cidc_schemas/schemas/templates/assays/hande_template.json,sha256=4nCLANA-QfIPySl2Ugl6el1ou6lVZxk1RV4B9BAFbO4,3949
 cidc_schemas/schemas/templates/assays/ihc_template.json,sha256=lOSP6v24FMk-WN7Za4IYQkM94R-1TEvrnllRopEEYa4,7341
 cidc_schemas/schemas/templates/assays/mibi_template.json,sha256=wy-LeCZRVYpvkpD7S04GZgL6P8ZvtoGroIzzijpti6M,8984
 cidc_schemas/schemas/templates/assays/microbiome_template.json,sha256=2qaTB8W-tG6NhbSJ3KAEIacp1E4g-cFBGMOMc5zTafo,3578
@@ -149,9 +149,9 @@ cidc_schemas/schemas/templates/manifests/tissue_slide_template.json,sha256=sFPyt
 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=D4ICMeHQgKXFDwaMOqrcLcUEF-dYGalagGYDUFAploU,13276
 cidc_schemas/schemas/templates/manifests/tumor_tissue_rna_template.json,sha256=MpJTjoaTdIlNBAIIxSfmItVevA5BXnajqu_jaEXxBmo,12568
-nci_cidc_schemas-0.26.23.dist-info/LICENSE,sha256=zK77-w4rYCZBHAYJEGkcFuPXwKIsP7jMPZ2iQOXjzko,1072
-nci_cidc_schemas-0.26.23.dist-info/METADATA,sha256=oJjZglq_F_5Xw49Nhzjsn3rRbB_OKao_eLlR2HRbXnI,4484
-nci_cidc_schemas-0.26.23.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
-nci_cidc_schemas-0.26.23.dist-info/entry_points.txt,sha256=kSyTzXeJQrJp_2ZX0GS_NnbJR8ceQKLBSgER46PM0hs,55
-nci_cidc_schemas-0.26.23.dist-info/top_level.txt,sha256=Wwb5Cu7QrnbmSJxI2d00e3-Mir36t0jTRnSulmfhi30,13
-nci_cidc_schemas-0.26.23.dist-info/RECORD,,
+nci_cidc_schemas-0.26.25.dist-info/LICENSE,sha256=zK77-w4rYCZBHAYJEGkcFuPXwKIsP7jMPZ2iQOXjzko,1072
+nci_cidc_schemas-0.26.25.dist-info/METADATA,sha256=TLwJ-WLx3iySLrA8AhfyifoIkgWF1lpMCRU_OVOHbPA,4484
+nci_cidc_schemas-0.26.25.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
+nci_cidc_schemas-0.26.25.dist-info/entry_points.txt,sha256=kSyTzXeJQrJp_2ZX0GS_NnbJR8ceQKLBSgER46PM0hs,55
+nci_cidc_schemas-0.26.25.dist-info/top_level.txt,sha256=Wwb5Cu7QrnbmSJxI2d00e3-Mir36t0jTRnSulmfhi30,13
+nci_cidc_schemas-0.26.25.dist-info/RECORD,,