nci-cidc-schemas 0.28.6__py2.py3-none-any.whl → 0.28.8__py2.py3-none-any.whl

cidc_schemas/__init__.py

@@ -2,4 +2,4 @@
 
 __author__ = """NCI"""
 __email__ = "nci-cidc-tools-admin@mail.nih.gov"
-__version__ = "0.28.6"
+__version__ = "0.28.8"

cidc_schemas/schemas/assays/hande_assay.json

@@ -27,6 +27,10 @@
             {
               "$comment": "Path to the H & E image in JPG format.",
               "$ref": "artifacts/artifact_jpg.json"
+            },
+            {
+              "$comment": "Path to the H & E image in OME-TIFF format.",
+              "$ref": "artifacts/artifact_jpg.json"
             }
           ]
         },
@@ -41,6 +45,10 @@
             {
               "$comment": "Path to the H & E annotated image in JPG format.",
               "$ref": "artifacts/artifact_jpg.json"
+            },
+            {
+              "$comment": "Path to the H & E annotated image in OME-TIFF format.",
+              "$ref": "artifacts/artifact_jpg.json"
             }
           ]
         }

cidc_schemas/schemas/assays/wes_assay.json

@@ -72,12 +72,25 @@
       "sequencing_protocol": {
           "description": "Protocol and version used for the sequencing.",
           "type": "string",
-          "enum": ["Express Somatic Human WES (Deep Coverage) v1.1", "Somatic Human WES v6", "TWIST Custom Panel PN 101042", "TWIST"]
+          "enum": [
+            "Express Somatic Human WES (Deep Coverage) v1.1",
+            "Somatic Human WES v4",
+            "Somatic Human WES v6",
+            "TWIST Custom Panel PN 101042",
+            "TWIST"
+          ]
       },
       "bait_set": {
           "description": "Bait set ID.",
           "type": "string",
-          "enum": ["whole_exome_illumina_coding_v1","broad_custom_exome_v1","TWIST Dana Farber Custom Panel", "TWIST Custom Panel PN 101042", "TWIST Clin Research Exome PN 104033"]
+          "enum": [
+            "whole_exome_illumina_coding_v1",
+            "broad_custom_exome_v1",
+            "TWIST Dana Farber Custom Panel",
+            "TWIST Custom Panel PN 101042",
+            "TWIST Clin Research Exome PN 104033",
+            "Agilent SS Human All Exon V4"
+          ]
       },
       "read_length": {
           "description": "Number of cycles for each sequencing read.",

cidc_schemas/schemas/templates/assays/hande_template.json

@@ -27,7 +27,7 @@
                           "do_not_merge": true,
                           "allow_empty": true,
                           "type": "string",
-                          "enum": ["svs", "jpg"]
+                          "enum": ["svs", "jpg", "ome.tiff"]
                       },
                       "image file": {
                         "merge_pointer": "0/files/image_file",
@@ -41,7 +41,7 @@
                         "do_not_merge": true,
                         "allow_empty": true,
                         "type": "string",
-                        "enum": ["svs", "jpg"]
+                        "enum": ["svs", "jpg", "ome.tiff"]
                     },
                       "annotated image": {
                           "merge_pointer": "0/files/annotated_image",

{nci_cidc_schemas-0.28.6.dist-info → nci_cidc_schemas-0.28.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_schemas
-Version: 0.28.6
+Version: 0.28.8
 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-0.28.6.dist-info → nci_cidc_schemas-0.28.8.dist-info}/RECORD

@@ -1,4 +1,4 @@
-cidc_schemas/__init__.py,sha256=MqX_O9l1WaMR5--rfQFEgq8IULkVHgLUbxGm7kcAT_0,135
+cidc_schemas/__init__.py,sha256=w4cwzKY6K0LtRza5GsqnV63hvlKl-XHChzgk3PPc2_I,135
 cidc_schemas/cli.py,sha256=gWiktRlraNH8Q0zNUae9dohKjPwBmcY0BJwdcQ_fIic,4099
 cidc_schemas/constants.py,sha256=RULs7pGuBAVq1teXymrfbVsK23ZowJvLuZlv0KcjL-Y,698
 cidc_schemas/json_validation.py,sha256=4UxcYrofXlDT-Lz6uiQGO1Jwz5bRs0mN_UH4p_A84ks,23262
@@ -93,7 +93,7 @@ cidc_schemas/schemas/assays/ctdna_assay.json,sha256=NjsS0htltMIN_sGoissbnkCZCQIb
 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=NhLyBiBOgeZ9woeGO4EEIod-y_Wzz6WamsP3ZNzxtS0,3192
+cidc_schemas/schemas/assays/hande_assay.json,sha256=8UYxKtDUKgBMH76UjokYNll0nmK_UAUd8wvsSClxbFc,3510
 cidc_schemas/schemas/assays/ihc_assay.json,sha256=g1WuTUrN6M3mmQL7TCURsKL442An8jlmXaxddg2Ayak,6738
 cidc_schemas/schemas/assays/maldi_glycan_assay.json,sha256=P8ejh4UiLk0Z8nKJm_cwovdtkLc2hV4OcPolFRlFfUc,2218
 cidc_schemas/schemas/assays/mibi_assay.json,sha256=0DnK6Tl_DZbzKuLcleaBYMW19OBpI3ociSqqeK0bG04,2164
@@ -113,7 +113,7 @@ cidc_schemas/schemas/assays/tcr_assay.json,sha256=lQm_f-3UUT_nqctc4ARjYNPKjpDfmf
 cidc_schemas/schemas/assays/visium_analysis.json,sha256=5WDhZy26OuAB3z8OlT19k_vMDlopj9t6S6dcEyhZ50Q,2032
 cidc_schemas/schemas/assays/visium_assay.json,sha256=iSVYjVLougLaT9YUwpPD3j2NviTRw9F6b-YshLzBRUg,2396
 cidc_schemas/schemas/assays/wes_analysis.json,sha256=4RAnkqtCj5-txc189KmwNHJaxjrtIUIbpihFrAJFeIw,2771
-cidc_schemas/schemas/assays/wes_assay.json,sha256=vk9iK8FOiT3wU_RF3PXDV6IJqvNRbteebYGF8EfalfY,3776
+cidc_schemas/schemas/assays/wes_assay.json,sha256=no2M2rMWnoXMNuptKqei_lC6TRHySbKIfwGqPqTsI2I,3990
 cidc_schemas/schemas/assays/wes_core.json,sha256=dwAe2Hi-K5G0rm_icSbFUEIhDNG7HkESYKEGhV9L7wM,12858
 cidc_schemas/schemas/assays/wes_tumor_only_analysis.json,sha256=dU3oaeBbPnEv2Xjym7ikWr5ywwolnVbWDu1Weq2m8Wg,2018
 cidc_schemas/schemas/assays/components/antibody.json,sha256=vfLxXkXIcaJ1BXeUjCaJehrRCdVrBW3gxibwrD7zzd4,960
@@ -174,7 +174,7 @@ cidc_schemas/schemas/templates/assays/clinical_data_template.json,sha256=1luQXzy
 cidc_schemas/schemas/templates/assays/ctdna_template.json,sha256=KDyOPbBh0dytlZRJVKNuaGEB8MAyq6Ls1CvI8d2wF3o,6151
 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=EtFvoEtXZelqQPYuJKRbo2127MUek6wGnMcOvMMr3Os,4391
+cidc_schemas/schemas/templates/assays/hande_template.json,sha256=fPe4V95aQyzggihs72K8HAQTdb-aqrRj90sejQkwjSY,4415
 cidc_schemas/schemas/templates/assays/ihc_template.json,sha256=lOSP6v24FMk-WN7Za4IYQkM94R-1TEvrnllRopEEYa4,7341
 cidc_schemas/schemas/templates/assays/maldi_glycan_template.json,sha256=1-QChZx5y3W3EtSL6jFYBOSiZL79ogbF_KlDUQU6-Xk,7338
 cidc_schemas/schemas/templates/assays/mibi_template.json,sha256=X9S8ZWRj0PLYgtTwodC36Fx7D6UQFCWpbx2AVQuHfbM,7787
@@ -203,9 +203,9 @@ 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-0.28.6.dist-info/licenses/LICENSE,sha256=zK77-w4rYCZBHAYJEGkcFuPXwKIsP7jMPZ2iQOXjzko,1072
-nci_cidc_schemas-0.28.6.dist-info/METADATA,sha256=PLnv1EUdE0T2i3Rd2oF1VleWwnNaKNqo-JGiFjZEY8w,5374
-nci_cidc_schemas-0.28.6.dist-info/WHEEL,sha256=JNWh1Fm1UdwIQV075glCn4MVuCRs0sotJIq-J6rbxCU,109
-nci_cidc_schemas-0.28.6.dist-info/entry_points.txt,sha256=kSyTzXeJQrJp_2ZX0GS_NnbJR8ceQKLBSgER46PM0hs,55
-nci_cidc_schemas-0.28.6.dist-info/top_level.txt,sha256=Wwb5Cu7QrnbmSJxI2d00e3-Mir36t0jTRnSulmfhi30,13
-nci_cidc_schemas-0.28.6.dist-info/RECORD,,
+nci_cidc_schemas-0.28.8.dist-info/licenses/LICENSE,sha256=zK77-w4rYCZBHAYJEGkcFuPXwKIsP7jMPZ2iQOXjzko,1072
+nci_cidc_schemas-0.28.8.dist-info/METADATA,sha256=AbhEDpCdU-n2Drg3AGV1EUaw7uxbl1yEPZZSrHQUyRA,5374
+nci_cidc_schemas-0.28.8.dist-info/WHEEL,sha256=JNWh1Fm1UdwIQV075glCn4MVuCRs0sotJIq-J6rbxCU,109
+nci_cidc_schemas-0.28.8.dist-info/entry_points.txt,sha256=kSyTzXeJQrJp_2ZX0GS_NnbJR8ceQKLBSgER46PM0hs,55
+nci_cidc_schemas-0.28.8.dist-info/top_level.txt,sha256=Wwb5Cu7QrnbmSJxI2d00e3-Mir36t0jTRnSulmfhi30,13
+nci_cidc_schemas-0.28.8.dist-info/RECORD,,