nci-cidc-schemas 0.28.7__py2.py3-none-any.whl → 0.28.13__py2.py3-none-any.whl

cidc_schemas/schemas/templates/analyses/scrnaseq_analysis_template.json

@@ -16,62 +16,66 @@
             "type": "string",
             "allow_empty": true
           },
-          "batch id": {
+          "CIMAC Batch ID": {
             "merge_pointer": "0/batch_id",
             "type_ref": "assays/scrnaseq_assay.json#properties/batch_id"
           },
+          "CIDC Submission ID": {
+            "merge_pointer": "0/optional_id",
+            "type_ref": "assays/scrnaseq_assay.json#properties/optional_id"
+          },
           "samples metadata csv": {
             "merge_pointer": "0/samples_metadata_csv",
             "type_ref": "assays/components/local_file.json#properties/file_path",
-            "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{batch id}/samples_metadata.csv",
+            "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{cimac batch id}/samples_metadata.csv",
             "is_artifact": 1
           },
           "config yaml": {
             "merge_pointer": "0/config_yaml",
             "type_ref": "assays/components/local_file.json#properties/file_path",
-            "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{batch id}/config.yaml",
+            "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{cimac batch id}/config.yaml",
             "is_artifact": 1
           },
           "r package versions": {
             "merge_pointer": "0/r_package_versions",
             "type_ref": "assays/components/local_file.json#properties/file_path",
-            "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{batch id}/R_package_versions.csv",
+            "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{cimac batch id}/R_package_versions.csv",
             "is_artifact": 1
           },
           "integration rds": {
             "merge_pointer": "0/integration_rds",
             "type_ref": "assays/components/local_file.json#properties/file_path",
-            "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{batch id}/integration.rds",
+            "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{cimac batch id}/integration.rds",
             "is_artifact": 1
           },
           "integration heatmap plots": {
             "merge_pointer": "0/integration_heatmap_plots",
             "type_ref": "assays/components/local_file.json#properties/file_path",
-            "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{batch id}/integration_heatmap_plots.zip",
+            "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{cimac batch id}/integration_heatmap_plots.zip",
             "is_artifact": 1
           },
           "integration markers zip": {
             "merge_pointer": "0/integration_markers_zip",
             "type_ref": "assays/components/local_file.json#properties/file_path",
-            "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{batch id}/integration_markers.zip",
+            "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{cimac batch id}/integration_markers.zip",
             "is_artifact": 1
           },
           "integration split percent plots": {
             "merge_pointer": "0/integration_split_percent_plots",
             "type_ref": "assays/components/local_file.json#properties/file_path",
-            "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{batch id}/integration_split_percent_plots.zip",
+            "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{cimac batch id}/integration_split_percent_plots.zip",
             "is_artifact": 1
           },
           "integration split umap plots": {
             "merge_pointer": "0/integration_split_umap_plots",
             "type_ref": "assays/components/local_file.json#properties/file_path",
-            "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{batch id}/integration_split_umap_plots.zip",
+            "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{cimac batch id}/integration_split_umap_plots.zip",
             "is_artifact": 1
           },
           "integration umap plots": {
             "merge_pointer": "0/integration_umap_plots",
             "type_ref": "assays/components/local_file.json#properties/file_path",
-            "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{batch id}/integration_umap_plots.zip",
+            "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{cimac batch id}/integration_umap_plots.zip",
             "is_artifact": 1
           }
         },
@@ -85,126 +89,126 @@
                 {
                   "parse_through": "lambda id: f'{folder or \"\"}clustering/{id}_clustering.rds'",
                   "merge_pointer": "0/clustering_rds",
-                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{batch id}/{cimac id}/clustering.rds",
+                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{cimac batch id}/{cimac id}/clustering.rds",
                   "type_ref": "assays/components/local_file.json#properties/file_path",
                   "is_artifact": 1
                 },
                 {
                   "parse_through": "lambda id: f'{folder or \"\"}report/{id}_report.html'",
                   "merge_pointer": "0/report_html",
-                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{batch id}/{cimac id}/report.html",
+                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{cimac batch id}/{cimac id}/report.html",
                   "type_ref": "assays/components/local_file.json#properties/file_path",
                   "is_artifact": 1
                 },
                 {
                   "parse_through": "lambda id: f'{folder or \"\"}star/{id}.Aligned.sortedByCoord.out.bam'",
                   "merge_pointer": "0/star_sorted_by_coord_bam",
-                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{batch id}/{cimac id}/star_sorted_by_cord.bam",
+                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{cimac batch id}/{cimac id}/star_sorted_by_cord.bam",
                   "type_ref": "assays/components/local_file.json#properties/file_path",
                   "is_artifact": 1
                 },
                 {
                   "parse_through": "lambda id: f'{folder or \"\"}star/{id}.Aligned.sortedByCoord.out.bam.bai'",
                   "merge_pointer": "0/star_sorted_by_coord_bam_bai",
-                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{batch id}/{cimac id}/star_sorted_by_cord.bam.bai",
+                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{cimac batch id}/{cimac id}/star_sorted_by_cord.bam.bai",
                   "type_ref": "assays/components/local_file.json#properties/file_path",
                   "is_artifact": 1
                 },
                 {
                   "parse_through": "lambda id: f'{folder or \"\"}star/{id}.Log.final.out'",
                   "merge_pointer": "0/star_log_final_out",
-                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{batch id}/{cimac id}/log_final.out",
+                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{cimac batch id}/{cimac id}/log_final.out",
                   "type_ref": "assays/components/local_file.json#properties/file_path",
                   "is_artifact": 1
                 },
                 {
                   "parse_through": "lambda id: f'{folder or \"\"}star/{id}.Log.out'",
                   "merge_pointer": "0/star_log_out",
-                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{batch id}/{cimac id}/log.out",
+                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{cimac batch id}/{cimac id}/log.out",
                   "type_ref": "assays/components/local_file.json#properties/file_path",
                   "is_artifact": 1
                 },
                 {
                   "parse_through": "lambda id: f'{folder or \"\"}star/{id}.Log.progress.out'",
                   "merge_pointer": "0/star_log_progress_out",
-                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{batch id}/{cimac id}/log_progress.out",
+                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{cimac batch id}/{cimac id}/log_progress.out",
                   "type_ref": "assays/components/local_file.json#properties/file_path",
                   "is_artifact": 1
                 },
                 {
                   "parse_through": "lambda id: f'{folder or \"\"}star/{id}.SJ.out.tab'",
                   "merge_pointer": "0/star_sj_out",
-                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{batch id}/{cimac id}/sj_out.tab",
+                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{cimac batch id}/{cimac id}/sj_out.tab",
                   "type_ref": "assays/components/local_file.json#properties/file_path",
                   "is_artifact": 1
                 },
                 {
                   "parse_through": "lambda id: f'{folder or \"\"}star/{id}.Solo.out/Barcodes.stats'",
                   "merge_pointer": "0/star_barcode_stats",
-                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{batch id}/{cimac id}/barcodes.stats",
+                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{cimac batch id}/{cimac id}/barcodes.stats",
                   "type_ref": "assays/components/local_file.json#properties/file_path",
                   "is_artifact": 1
                 },
                 {
                   "parse_through": "lambda id: f'{folder or \"\"}star/{id}.Solo.out/Gene/Features.stats'",
                   "merge_pointer": "0/star_gene_features_stats",
-                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{batch id}/{cimac id}/gene_features.stats",
+                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{cimac batch id}/{cimac id}/gene_features.stats",
                   "type_ref": "assays/components/local_file.json#properties/file_path",
                   "is_artifact": 1
                 },
                 {
                   "parse_through": "lambda id: f'{folder or \"\"}star/{id}.Solo.out/Gene/Summary.csv'",
                   "merge_pointer": "0/star_gene_summary_csv",
-                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{batch id}/{cimac id}/gene_summary.csv",
+                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{cimac batch id}/{cimac id}/gene_summary.csv",
                   "type_ref": "assays/components/local_file.json#properties/file_path",
                   "is_artifact": 1
                 },
                 {
                   "parse_through": "lambda id: f'{folder or \"\"}star/{id}.Solo.out/Gene/UMIperCellSorted.txt'",
                   "merge_pointer": "0/star_gene_umi_per_cell_sorted",
-                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{batch id}/{cimac id}/gene_umi_per_cell_sorted.txt",
+                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{cimac batch id}/{cimac id}/gene_umi_per_cell_sorted.txt",
                   "type_ref": "assays/components/local_file.json#properties/file_path",
                   "is_artifact": 1
                 },
                 {
                   "parse_through": "lambda id: f'{folder or \"\"}star/{id}.Solo.out/Gene/filtered/features.tsv'",
                   "merge_pointer": "0/star_gene_filtered_features_tsv",
-                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{batch id}/{cimac id}/gene_filtered_features.tsv",
+                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{cimac batch id}/{cimac id}/gene_filtered_features.tsv",
                   "type_ref": "assays/components/local_file.json#properties/file_path",
                   "is_artifact": 1
                 },
                 {
                   "parse_through": "lambda id: f'{folder or \"\"}star/{id}.Solo.out/Gene/filtered/barcodes.tsv'",
                   "merge_pointer": "0/star_gene_filtered_barcodes",
-                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{batch id}/{cimac id}/gene_filtered_barcodes.tsv",
+                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{cimac batch id}/{cimac id}/gene_filtered_barcodes.tsv",
                   "type_ref": "assays/components/local_file.json#properties/file_path",
                   "is_artifact": 1
                 },
                 {
                   "parse_through": "lambda id: f'{folder or \"\"}star/{id}.Solo.out/Gene/filtered/matrix.mtx'",
                   "merge_pointer": "0/star_gene_filtered_matrix",
-                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{batch id}/{cimac id}/gene_filtered_matrix.mtx",
+                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{cimac batch id}/{cimac id}/gene_filtered_matrix.mtx",
                   "type_ref": "assays/components/local_file.json#properties/file_path",
                   "is_artifact": 1
                 },
                 {
                   "parse_through": "lambda id: f'{folder or \"\"}star/{id}.Solo.out/Gene/raw/features.tsv'",
                   "merge_pointer": "0/star_gene_raw_features_tsv",
-                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{batch id}/{cimac id}/gene_raw_features.tsv",
+                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{cimac batch id}/{cimac id}/gene_raw_features.tsv",
                   "type_ref": "assays/components/local_file.json#properties/file_path",
                   "is_artifact": 1
                 },
                 {
                   "parse_through": "lambda id: f'{folder or \"\"}star/{id}.Solo.out/Gene/raw/barcodes.tsv'",
                   "merge_pointer": "0/star_gene_raw_barcodes",
-                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{batch id}/{cimac id}/gene_raw_barcodes.tsv",
+                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{cimac batch id}/{cimac id}/gene_raw_barcodes.tsv",
                   "type_ref": "assays/components/local_file.json#properties/file_path",
                   "is_artifact": 1
                 },
                 {
                   "parse_through": "lambda id: f'{folder or \"\"}star/{id}.Solo.out/Gene/raw/matrix.mtx'",
                   "merge_pointer": "0/star_gene_raw_matrix",
-                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{batch id}/{cimac id}/gene_raw_matrix.mtx",
+                  "gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{cimac batch id}/{cimac id}/gene_raw_matrix.mtx",
                   "type_ref": "assays/components/local_file.json#properties/file_path",
                   "is_artifact": 1
                 }

cidc_schemas/schemas/templates/analyses/tcr_analysis_template.json

@@ -11,21 +11,25 @@
             "merge_pointer": "4/protocol_identifier",
             "type_ref": "clinical_trial.json#properties/protocol_identifier"
           },
-          "batch id": {
+          "CIMAC Batch ID": {
             "merge_pointer": "0/batch_id",
             "type_ref": "assays/tcr_assay.json#properties/batch_id"
           },
+          "CIDC Submission ID": {
+            "merge_pointer": "0/optional_id",
+            "type_ref": "assays/tcr_assay.json#properties/optional_id"
+          },
           "summary info": {
             "merge_pointer": "0/summary_info",
             "type_ref": "assays/components/local_file.json#properties/file_path",
-            "gcs_uri_format": "{protocol identifier}/tcr_analysis/{batch id}/summary_info.csv",
+            "gcs_uri_format": "{protocol identifier}/tcr_analysis/{cimac batch id}/summary_info.csv",
             "is_artifact": 1,
             "allow_empty": true
           },
           "report trial": {
             "merge_pointer": "0/report_trial",
             "type_ref": "assays/components/local_file.json#properties/file_path",
-            "gcs_uri_format": "{protocol identifier}/tcr_analysis/{batch id}/report_trial.tar.gz",
+            "gcs_uri_format": "{protocol identifier}/tcr_analysis/{cimac batch id}/report_trial.tar.gz",
             "is_artifact": 1
           }
         },
@@ -39,14 +43,14 @@
             "TRA Clones UMI Counts": {
               "merge_pointer": "0/tra_clone",
               "type_ref": "assays/components/local_file.json#properties/file_path",
-              "gcs_uri_format": "{protocol identifier}/tcr_analysis/{batch id}/{cimac id}/tra_clone.csv",
+              "gcs_uri_format": "{protocol identifier}/tcr_analysis/{cimac batch id}/{cimac id}/tra_clone.csv",
               "is_artifact": 1,
               "allow_empty": true
             },
             "TRB Clones UMI Counts": {
               "merge_pointer": "0/trb_clone",
               "type_ref": "assays/components/local_file.json#properties/file_path",
-              "gcs_uri_format": "{protocol identifier}/tcr_analysis/{batch id}/{cimac id}/trb_clone.csv",
+              "gcs_uri_format": "{protocol identifier}/tcr_analysis/{cimac batch id}/{cimac id}/trb_clone.csv",
               "is_artifact": 1,
               "allow_empty": true
             },

cidc_schemas/schemas/templates/analyses/visium_analysis_template.json

@@ -16,10 +16,14 @@
             "type": "string",
             "allow_empty": true
           },
-          "batch id": {
+          "CIMAC Batch ID": {
             "merge_pointer": "0/batch_id",
             "type_ref": "assays/scrnaseq_assay.json#properties/batch_id"
           },
+          "CIDC Submission ID": {
+            "merge_pointer": "0/optional_id",
+            "type_ref": "assays/scrnaseq_assay.json#properties/optional_id"
+          },
           "samples metadata csv": {
             "merge_pointer": "0/samples_metadata_csv",
             "type_ref": "assays/components/local_file.json#properties/file_path",
@@ -29,19 +33,19 @@
           "config yaml": {
             "merge_pointer": "0/config_yaml",
             "type_ref": "assays/components/local_file.json#properties/file_path",
-            "gcs_uri_format": "{protocol identifier}/visium_analysis/{batch id}/config.yaml",
+            "gcs_uri_format": "{protocol identifier}/visium_analysis/{cimac batch id}/config.yaml",
             "is_artifact": 1
           },
           "r package versions": {
             "merge_pointer": "0/r_package_versions",
             "type_ref": "assays/components/local_file.json#properties/file_path",
-            "gcs_uri_format": "{protocol identifier}/visium_analysis/{batch id}/R_package_versions.csv",
+            "gcs_uri_format": "{protocol identifier}/visium_analysis/{cimac batch id}/R_package_versions.csv",
             "is_artifact": 1
           },
           "merged rds": {
             "merge_pointer": "0/merged_rds",
             "type_ref": "assays/components/local_file.json#properties/file_path",
-            "gcs_uri_format": "{protocol identifier}/visium_analysis/{batch id}/merged.rds",
+            "gcs_uri_format": "{protocol identifier}/visium_analysis/{cimac batch id}/merged.rds",
             "is_artifact": 1
           }
         },
@@ -55,21 +59,21 @@
                 {
                   "parse_through": "lambda id: f'{folder or \"\"}spatial_variable_features/{id}_spatial_variable_features.rds'",
                   "merge_pointer": "0/spatial_variable_features_rds",
-                  "gcs_uri_format": "{protocol identifier}/visium_analysis/{batch id}/{cimac id}/spatial_variable_features.rds",
+                  "gcs_uri_format": "{protocol identifier}/visium_analysis/{cimac batch id}/{cimac id}/spatial_variable_features.rds",
                   "type_ref": "assays/components/local_file.json#properties/file_path",
                   "is_artifact": 1
                 },
                 {
                   "parse_through": "lambda id: f'{folder or \"\"}report/{id}_report.html'",
                   "merge_pointer": "0/report_html",
-                  "gcs_uri_format": "{protocol identifier}/visium_analysis/{batch id}/{cimac id}/report.html",
+                  "gcs_uri_format": "{protocol identifier}/visium_analysis/{cimac batch id}/{cimac id}/report.html",
                   "type_ref": "assays/components/local_file.json#properties/file_path",
                   "is_artifact": 1
                 },
                 {
                   "parse_through": "lambda id: f'{folder or \"\"}{id}_spaceranger.zip'",
                   "merge_pointer": "0/visium_spaceranger_output_zip",
-                  "gcs_uri_format": "{protocol identifier}/visium_analysis/{batch id}/{cimac id}/visium_spaceranger_output.zip",
+                  "gcs_uri_format": "{protocol identifier}/visium_analysis/{cimac batch id}/{cimac id}/visium_spaceranger_output.zip",
                   "type_ref": "assays/components/local_file.json#properties/file_path",
                   "is_artifact": 1
                 }

cidc_schemas/schemas/templates/analyses/wes_analysis_template.json

@@ -11,6 +11,14 @@
                         "merge_pointer": "2/protocol_identifier",
                         "type_ref": "clinical_trial.json#properties/protocol_identifier"
                     },
+                    "CIMAC Batch ID": {
+                        "merge_pointer": "0/batch_id",
+                        "type_ref": "assays/wes_assay.json#properties/batch_id"
+                    },
+                    "CIDC Submission ID": {
+                        "merge_pointer": "0/optional_id",
+                        "type_ref": "assays/wes_assay.json#properties/optional_id"
+                    },
                     "folder": {
                         "do_not_merge": true,
                         "type": "string",
@@ -451,4 +459,4 @@
             }
         }
     }
-}
+}

cidc_schemas/schemas/templates/analyses/wes_tumor_only_analysis_template.json

@@ -11,6 +11,14 @@
                         "merge_pointer": "2/protocol_identifier",
                         "type_ref": "clinical_trial.json#properties/protocol_identifier"
                     },
+                    "CIMAC Batch ID": {
+                        "merge_pointer": "0/batch_id",
+                        "type_ref": "assays/wes_assay.json#properties/batch_id"
+                    },
+                    "CIDC Submission ID": {
+                        "merge_pointer": "0/optional_id",
+                        "type_ref": "assays/wes_assay.json#properties/optional_id"
+                    },
                     "folder": {
                         "do_not_merge": true,
                         "type": "string",
@@ -221,4 +229,4 @@
             }
         }
     }
-}
+}

cidc_schemas/schemas/templates/assays/atacseq_fastq_template.json

@@ -12,10 +12,14 @@
             "merge_pointer": "3/protocol_identifier",
             "type_ref": "clinical_trial.json#properties/protocol_identifier"
           },
-          "batch id": {
+          "CIMAC Batch ID": {
             "merge_pointer": "0/batch_id",
             "type_ref": "assays/atacseq_assay.json#properties/batch_id"
-        },
+          },
+          "CIDC Submission ID": {
+            "merge_pointer": "0/optional_id",
+            "type_ref": "assays/atacseq_assay.json#properties/optional_id"
+          },
           "assay creator": {
             "merge_pointer": "0/assay_creator",
             "type_ref": "assays/components/assay_core.json#properties/assay_creator"

cidc_schemas/schemas/templates/assays/clinical_data_template.json

@@ -15,6 +15,14 @@
                     "assay creator": {
                         "merge_pointer": "0/assay_creator",
                         "type_ref": "assays/components/assay_core.json#properties/assay_creator"
+                    },
+                    "CIMAC Batch ID": {
+                        "merge_pointer": "0/batch_id",
+                        "type_ref": "clinical_data.json#properties/batch_id"
+                    },
+                    "CIDC Submission ID": {
+                        "merge_pointer": "0/optional_id",
+                        "type_ref": "clinical_data.json#properties/optional_id"
                     }
                 },
                 "data_columns": {

cidc_schemas/schemas/templates/assays/ctdna_template.json

@@ -12,10 +12,14 @@
             "merge_pointer": "3/protocol_identifier",
             "type_ref": "clinical_trial.json#properties/protocol_identifier"
           },
-          "batch id": {
+          "CIMAC Batch ID": {
             "merge_pointer": "0/batch_id",
             "type_ref": "assays/ctdna_assay.json#properties/batch_id"
           },
+          "CIDC Submission ID": {
+            "merge_pointer": "0/optional_id",
+            "type_ref": "assays/ctdna_assay.json#properties/optional_id"
+          },
           "assay creator": {
             "merge_pointer": "0/assay_creator",
             "type_ref": "assays/components/assay_core.json#properties/assay_creator"
@@ -23,7 +27,7 @@
           "summary plots": {
               "merge_pointer": "0/summary_plots",
               "type_ref": "assays/components/local_file.json#properties/file_path",
-              "gcs_uri_format": "{protocol identifier}/ctdna/{batch id}/summary_plots.pdf",
+              "gcs_uri_format": "{protocol identifier}/ctdna/{cimac batch id}/summary_plots.pdf",
               "is_artifact": 1
           }
         },
@@ -35,13 +39,13 @@
             },
             "demultiplexed bam": {
               "merge_pointer": "0/demultiplexed_bam",
-              "gcs_uri_format": "{protocol identifier}/ctdna/{batch id}/{cimac id}/demultiplexed.bam",
+              "gcs_uri_format": "{protocol identifier}/ctdna/{cimac batch id}/{cimac id}/demultiplexed.bam",
               "is_artifact": 1,
               "type_ref": "assays/components/local_file.json#properties/file_path"
             },
             "demultiplexed bam index": {
               "merge_pointer": "0/demultiplexed_bam_index",
-              "gcs_uri_format": "{protocol identifier}/ctdna/{batch id}/{cimac id}/demultiplexed.bam.bai",
+              "gcs_uri_format": "{protocol identifier}/ctdna/{cimac batch id}/{cimac id}/demultiplexed.bam.bai",
               "is_artifact" : 1,
               "type_ref": "assays/components/local_file.json#properties/file_path"
             },
@@ -49,13 +53,13 @@
                 "merge_pointer": "0/genome-wide_plots",
                 "type_ref": "assays/components/local_file.json#properties/file_path",
                 "is_artifact": 1,
-                "gcs_uri_format": "{protocol identifier}/ctdna/{batch id}/{cimac id}/genome-wide_plots.pdf"
+                "gcs_uri_format": "{protocol identifier}/ctdna/{cimac batch id}/{cimac id}/genome-wide_plots.pdf"
             },
             "bias qc plots": {
                 "merge_pointer": "0/bias_qc_plots",
                 "type_ref": "assays/components/local_file.json#properties/file_path",
                 "is_artifact": 1,
-                "gcs_uri_format": "{protocol identifier}/ctdna/{batch id}/{cimac id}/bias_qc_plots.pdf"
+                "gcs_uri_format": "{protocol identifier}/ctdna/{cimac batch id}/{cimac id}/bias_qc_plots.pdf"
             },
             "fraction cna subclonal": {
                 "merge_pointer": "0/fraction_cna_subclonal",
@@ -74,13 +78,13 @@
                 "merge_pointer": "0/optimal_solution",
                 "type_ref": "assays/components/local_file.json#properties/file_path",
                 "is_artifact": 1,
-                "gcs_uri_format": "{protocol identifier}/ctdna/{batch id}/{cimac id}/optimal_solution.zip"
+                "gcs_uri_format": "{protocol identifier}/ctdna/{cimac batch id}/{cimac id}/optimal_solution.zip"
             },
             "other solutions": {
                 "merge_pointer": "0/other_solutions",
                 "type_ref": "assays/components/local_file.json#properties/file_path",
                 "is_artifact": 1,
-                "gcs_uri_format": "{protocol identifier}/ctdna/{batch id}/{cimac id}/other_solutions.zip"
+                "gcs_uri_format": "{protocol identifier}/ctdna/{cimac batch id}/{cimac id}/other_solutions.zip"
             },
             "tumor ploidy": {
                 "merge_pointer": "0/tumor_ploidy",
@@ -99,21 +103,21 @@
                 "merge_pointer": "0/on_premise_corrected_depth_file",
                 "type_ref": "assays/components/local_file.json#properties/file_path",
                 "is_artifact": 1,
-                "gcs_uri_format": "{protocol identifier}/ctdna/{batch id}/{cimac id}/OnPrem.correctedDepth.txt",
+                "gcs_uri_format": "{protocol identifier}/ctdna/{cimac batch id}/{cimac id}/OnPrem.correctedDepth.txt",
                 "allow_empty": true
             },
             "on premise parameters file": {
                 "merge_pointer": "0/on_premise_parameters_file",
                 "type_ref": "assays/components/local_file.json#properties/file_path",
                 "is_artifact": 1,
-                "gcs_uri_format": "{protocol identifier}/ctdna/{batch id}/{cimac id}/OnPrem.params.txt",
+                "gcs_uri_format": "{protocol identifier}/ctdna/{cimac batch id}/{cimac id}/OnPrem.params.txt",
                 "allow_empty": true
             },
             "on premise rdata file": {
                 "merge_pointer": "0/on_premise_rdata_file",
                 "type_ref": "assays/components/local_file.json#properties/file_path",
                 "is_artifact": 1,
-                "gcs_uri_format": "{protocol identifier}/ctdna/{batch id}/{cimac id}/OnPrem.RData",
+                "gcs_uri_format": "{protocol identifier}/ctdna/{cimac batch id}/{cimac id}/OnPrem.RData",
                 "allow_empty": true
             },
             "comments": {

cidc_schemas/schemas/templates/assays/cytof_template.json

@@ -12,10 +12,15 @@
                         "merge_pointer": "/assay_run_id",
                         "type_ref": "assays/cytof_assay_core.json#properties/assay_run_id"
                     },
-                    "batch id": {
+                    "CIMAC Batch ID": {
                         "merge_pointer": "0/batch_id",
                         "type_ref": "assays/cytof_assay_core.json#properties/batch_id"
                     },
+                    "CIDC Submission ID": {
+                        "merge_pointer": "0/optional_id",
+                        "type_ref": "assays/cytof_assay_core.json#properties/optional_id"
+                    },
+
                     "protocol identifier": {
                         "merge_pointer": "3/protocol_identifier",
                         "type_ref": "clinical_trial.json#properties/protocol_identifier"
@@ -64,7 +69,7 @@
                     "concatenated spike in fcs filename": {
                         "merge_pointer": "0/spike_in_fcs",
                         "is_artifact" : 1,
-                        "gcs_uri_format": "{protocol identifier}/cytof/{batch id}/spike_in.fcs",
+                        "gcs_uri_format": "{protocol identifier}/cytof/{cimac batch id}/spike_in.fcs",
                         "type_ref": "assays/components/local_file.json#properties/file_path",
                         "description": "Path to a file on a User's computer. \nThis file contains the normalized & debarcoded spike-in for a batch.",
                         "allow_empty": true
@@ -72,7 +77,7 @@
                     "concatenated raw fcs filename(s)": {
                         "merge_pointer": "0/source_fcs",
                         "type_ref": "assays/components/local_file.json#properties/file_path",
-                        "gcs_uri_format": "{protocol identifier}/cytof/{batch id}/source_{num}.fcs",
+                        "gcs_uri_format": "{protocol identifier}/cytof/{cimac batch id}/source_{num}.fcs",
                         "is_artifact": "multi",
                         "allow_empty": true
                     }
@@ -217,7 +222,7 @@
                     "Debarcoding key file": {
                         "merge_pointer": "0/barcoding_key_csv",
                         "is_artifact" : 1,
-                        "gcs_uri_format": "{protocol identifier}/cytof/{batch id}/debarcoding_key.csv",
+                        "gcs_uri_format": "{protocol identifier}/cytof/{cimac batch id}/debarcoding_key.csv",
                         "type_ref": "assays/components/local_file.json#properties/file_path",
                         "description": "Path to a file on a User's computer. \nThis contains the master debarcoding key in a CSV file.",
                         "allow_empty": true

cidc_schemas/schemas/templates/assays/elisa_template.json

@@ -18,14 +18,18 @@
             "merge_pointer": "0/assay_creator",
             "type_ref": "assays/components/assay_core.json#properties/assay_creator"
           },
-          "run id": {
-            "merge_pointer": "0/assay_run_id",
-            "type_ref": "assays/elisa_assay.json#properties/assay_run_id"
+          "CIMAC Batch ID": {
+            "merge_pointer": "0/batch_id",
+            "type_ref": "assays/elisa_assay.json#properties/batch_id"
+          },
+          "CIDC Submission ID": {
+            "merge_pointer": "0/optional_id",
+            "type_ref": "assays/elisa_assay.json#properties/optional_id"
           },
           "serology file": {
             "merge_pointer": "0/assay_xlsx",
             "is_artifact" : 1,
-            "gcs_uri_format": "{protocol identifier}/elisa/{run id}/assay.xlsx",
+            "gcs_uri_format": "{protocol identifier}/elisa/{cimac batch id}/assay.xlsx",
             "type_ref": "assays/components/local_file.json#properties/file_path",
             "extra_metadata": true,
             "description": "XLSX ELISA results file name on a user's computer."

cidc_schemas/schemas/templates/assays/hande_template.json

@@ -15,6 +15,14 @@
                   "assay creator": {
                       "merge_pointer": "0/assay_creator",
                       "type_ref": "assays/components/assay_core.json#properties/assay_creator"
+                  },
+                  "CIMAC Batch ID": {
+                      "merge_pointer": "0/batch_id",
+                      "type_ref": "assays/hande_assay.json#properties/batch_id"
+                  },
+                  "CIDC Submission ID": {
+                      "merge_pointer": "0/optional_id",
+                      "type_ref": "assays/hande_assay.json#properties/optional_id"
                   }
               },
               "data_columns": {

cidc_schemas/schemas/templates/assays/ihc_template.json

@@ -16,6 +16,14 @@
                         "merge_pointer": "0/assay_creator",
                         "type_ref": "assays/components/assay_core.json#properties/assay_creator"
                     },
+                    "CIMAC Batch ID": {
+                        "merge_pointer": "0/batch_id",
+                        "type_ref": "assays/ihc_assay.json#properties/batch_id"
+                    },
+                    "CIDC Submission ID": {
+                        "merge_pointer": "0/optional_id",
+                        "type_ref": "assays/ihc_assay.json#properties/optional_id"
+                    },
                     "slide scanner model": {
                         "merge_pointer": "0/slide_scanner_model",
                         "type_ref": "assays/ihc_assay.json#properties/slide_scanner_model"