nci-cidc-schemas 0.27.5__py2.py3-none-any.whl → 0.27.7__py2.py3-none-any.whl

cidc_schemas/__init__.py

@@ -2,4 +2,4 @@
 
 __author__ = """NCI"""
 __email__ = "nci-cidc-tools-admin@mail.nih.gov"
-__version__ = "0.27.05"
+__version__ = "0.27.07"

cidc_schemas/schemas/sample.json

@@ -168,16 +168,30 @@
             "description": "Indicates the specimen source of the sample shipped. Example: Na Heparin blood draw aliquots (2 of three), FFPE block #52",
             "type": "string",
             "enum": [
-                "Blood Draw",
-                "Excision",
+                "Fine Needle Aspiration",
+                "Phlebotomy",
+                "Bone Marrow Aspiration",
+                "Bone Marrow Core Biopsy",
                 "Core Biopsy",
-                "Punch Biopsy",
                 "Endoscopic Biopsy",
-                "Bone Marrow Core Biopsy",
-                "Bone Marrow Aspirate",
+                "Surgical Excision",
+                "Fine Needle Aspiration",
                 "Lumbar Puncture",
-                "Aspirate",
-                "Fine-Needle Aspiration",
+                "FFPE Block Punch Biopsy",
+                "Skin Biopsy",
+                "Apheresis",
+                "Bone Biopsy",
+                "Bronchoalveolar Lavage",
+                "Buccal Swab",
+                "Leukapheresis",
+                "Mid Stream Urine Collection",
+                "Peritoneal Lavage",
+                "Peritoneal Paracentesis",
+                "Pleural Thoracentesis",
+                "Saliva Collection",
+                "Stool Collection",
+                "Surgical Incision",
+                "Urine Voiding",
                 "Not Reported",
                 "Other"
             ]

cidc_schemas/schemas/templates/analyses/wes_analysis_template.json

@@ -293,63 +293,63 @@
                             "type_ref": "sample.json#properties/cimac_id",
                             "process_as": [
                                 {
-                                    "parse_through": "lambda id: f'{folder or \"\"}analysis/align/{id}/{id}.sorted.dedup.bam'",
+                                    "parse_through": "lambda normal_id, run_id: f'{folder or \"\"}analysis/align/{run_id}/{normal_id}.sorted.dedup.bam'",
                                     "merge_pointer": "/normal/alignment/align_sorted_dedup",
                                     "gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/normal/{normal cimac id}/sorted.dedup.bam",
                                     "type_ref": "assays/components/local_file.json#properties/file_path",
                                     "is_artifact": 1
                                 },
                                 {
-                                    "parse_through": "lambda id: f'{folder or \"\"}analysis/align/{id}/{id}.sorted.dedup.bam.bai'",
+                                    "parse_through": "lambda normal_id, run_id: f'{folder or \"\"}analysis/align/{run_id}/{normal_id}.sorted.dedup.bam.bai'",
                                     "merge_pointer": "/normal/alignment/align_sorted_dedup_index",
                                     "gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/normal/{normal cimac id}/sorted.dedup.bam.bai",
                                     "type_ref": "assays/components/local_file.json#properties/file_path",
                                     "is_artifact": 1
                                 },
                                 {
-                                    "parse_through": "lambda id: f'{folder or \"\"}analysis/align/{id}/{id}_recalibrated.bam'",
+                                    "parse_through": "lambda normal_id, run_id: f'{folder or \"\"}analysis/align/{run_id}/{normal_id}_recalibrated.bam'",
                                     "merge_pointer": "/normal/alignment/align_recalibrated",
                                     "gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/normal/{normal cimac id}/recalibrated.bam",
                                     "type_ref": "assays/components/local_file.json#properties/file_path",
                                     "is_artifact": 1
                                 },
                                 {
-                                    "parse_through": "lambda id: f'{folder or \"\"}analysis/align/{id}/{id}_recalibrated.bam.bai'",
+                                    "parse_through": "lambda normal_id, run_id: f'{folder or \"\"}analysis/align/{run_id}/{normal_id}_recalibrated.bam.bai'",
                                     "merge_pointer": "/normal/alignment/align_recalibrated_index",
                                     "gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/normal/{normal cimac id}/recalibrated.bam.bai",
                                     "type_ref": "assays/components/local_file.json#properties/file_path",
                                     "is_artifact": 1
                                 },
                                 {
-                                    "parse_through": "lambda id: f'{folder or \"\"}analysis/germline/{id}/{id}_haplotyper.output.vcf'",
+                                    "parse_through": "lambda normal_id, run_id: f'{folder or \"\"}analysis/germline/{run_id}/{normal_id}_haplotyper.output.vcf'",
                                     "merge_pointer": "/normal/germline/haplotyper_output",
                                     "gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/normal/{normal cimac id}/haplotyper_output.vcf",
                                     "type_ref": "assays/components/local_file.json#properties/file_path",
                                     "is_artifact": 1
                                 },
                                 {
-                                    "parse_through": "lambda id: f'{folder or \"\"}analysis/germline/{id}/{id}_haplotyper.targets.vcf.gz'",
+                                    "parse_through": "lambda normal_id, run_id: f'{folder or \"\"}analysis/germline/{run_id}/{normal_id}_haplotyper.targets.vcf.gz'",
                                     "merge_pointer": "/normal/germline/haplotyper_targets",
                                     "gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/normal/{normal cimac id}/haplotyper_targets.vcf.gz",
                                     "type_ref": "assays/components/local_file.json#properties/file_path",
                                     "is_artifact": 1
                                 },
                                 {
-                                    "parse_through": "lambda id: f'{folder or \"\"}analysis/hlahd/{id}/result/{id}_final.result.txt'",
+                                    "parse_through": "lambda normal_id, run_id: f'{folder or \"\"}analysis/hlahd/{run_id}/result/{normal_id}_final.result.txt'",
                                     "merge_pointer": "/normal/hla/hla_final_result",
                                     "gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/normal/{normal cimac id}/hla_final_result.txt",
                                     "type_ref": "assays/components/local_file.json#properties/file_path",
                                     "is_artifact": 1
                                 },
                                 {
-                                    "parse_through": "lambda id: f'{folder or \"\"}analysis/optitype/{id}/{id}_result.tsv'",
+                                    "parse_through": "lambda normal_id, run_id: f'{folder or \"\"}analysis/optitype/{run_id}/{normal_id}_result.tsv'",
                                     "merge_pointer": "/normal/hla/optitype_result",
                                     "gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/normal/{normal cimac id}/optitype_result.tsv",
                                     "type_ref": "assays/components/local_file.json#properties/file_path",
                                     "is_artifact": 1
                                 },
                                 {
-                                    "parse_through": "lambda id: f'{folder or \"\"}analysis/xhla/{id}/report-{id}-hla.json'",
+                                    "parse_through": "lambda normal_id, run_id: f'{folder or \"\"}analysis/xhla/{run_id}/report-{normal_id}-hla.json'",
                                     "merge_pointer": "/normal/hla/xhla_report_hla",
                                     "gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/normal/{normal cimac id}/xhla_report_hla.json",
                                     "type_ref": "assays/components/local_file.json#properties/file_path",

cidc_schemas/template.py

@@ -750,7 +750,7 @@ class _FieldDef(NamedTuple):
 
         if self.parse_through:
             try:
-                raw_val = eval(self.parse_through, format_context, {})(raw_val)
+                raw_val = self._eval_lambda_expression(raw_val, format_context)
 
             # catching everything, because of eval
             except Exception as e:
@@ -786,6 +786,41 @@ class _FieldDef(NamedTuple):
         else:
             return [AtomicChange(self.merge_pointer, val)], files
 
+    def _eval_lambda_expression(self, raw_val: str, format_context: dict):
+        """
+        Evaluates a lambda expression stored in `self.parse_through`, optionally
+        passing an additional parameter if the lambda function has two parameters.
+
+        Args:
+            raw_val (str): Initial value to process.
+            format_context (dict): Dictionary providing format context.
+
+        Returns:
+            Processed value after applying the lambda function.
+        """
+        parse_lambda = self.parse_through
+        # Check for multiple lambda parameters
+        if (
+            parse_lambda.startswith("lambda ")
+            and ":" in parse_lambda
+            and "," in parse_lambda
+        ):
+            # Extract the parameter section (between "lambda " and ":")
+            colon_index = parse_lambda.find(":")
+            param_section = parse_lambda[7:colon_index].strip()
+            params = [param.strip() for param in param_section.split(",")]
+
+            # Handles up to two parameters at this time
+            if len(params) == 2:
+                # Convert underscores to spaces to match column header formatting
+                param_name = params[1].replace("_", " ")
+                extra_val = format_context.get(param_name)
+                # Evaluate the lambda function with two parameters
+                return eval(parse_lambda, format_context, {})(raw_val, extra_val)
+
+        # Evaluate the lambda function with one parameter
+        return eval(parse_lambda, format_context, {})(raw_val)
+
     ## TODO easy - split val coerce / files calc to handle exceptions separately
     ## TODO hard - files (artifact and multi) should be just coerce?
     def _calc_val_and_files(self, raw_val, format_context: dict, encrypt_fn: Callable):

{nci_cidc_schemas-0.27.5.dist-info → nci_cidc_schemas-0.27.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: nci_cidc_schemas
-Version: 0.27.5
+Version: 0.27.7
 Summary: The CIDC data model and tools for working with it.
 Home-page: https://github.com/NCI-CIDC/cidc-schemas
 Author: NCI
@@ -37,6 +37,7 @@ Dynamic: description-content-type
 Dynamic: home-page
 Dynamic: keywords
 Dynamic: license
+Dynamic: license-file
 Dynamic: requires-dist
 Dynamic: requires-python
 Dynamic: summary

{nci_cidc_schemas-0.27.5.dist-info → nci_cidc_schemas-0.27.7.dist-info}/RECORD

@@ -1,9 +1,9 @@
-cidc_schemas/__init__.py,sha256=w0RHYY0QLsASP0wZvu13m7fmrw-CT9Agsp-OvVUyDps,136
+cidc_schemas/__init__.py,sha256=mvfYCHhm5U-KWTKUo-eKgnaUr-hEKtBAG7AzeTc-MKU,136
 cidc_schemas/cli.py,sha256=gWiktRlraNH8Q0zNUae9dohKjPwBmcY0BJwdcQ_fIic,4099
 cidc_schemas/constants.py,sha256=RULs7pGuBAVq1teXymrfbVsK23ZowJvLuZlv0KcjL-Y,698
 cidc_schemas/json_validation.py,sha256=nHkSfTmBN7EeTrZVdbb8h6A64lWrJe5z0AIHiIy-YB0,22552
 cidc_schemas/migrations.py,sha256=Amg_T4cFgMzySD7yNnT_PWpqP7hwlTWGeHlI_RSXuRI,14766
-cidc_schemas/template.py,sha256=0QZNtH9bIzr3felvsoyShtBq0TX2t1-OVkrQQ3gs8TM,49891
+cidc_schemas/template.py,sha256=uvQNbkvusMq9D_1cnUMxT7j7Rf-iqq7o5nuZUhCaXY0,51428
 cidc_schemas/template_reader.py,sha256=xXtLRKu1y4FrPj8RgyGOmB2hlsCDXcuvMBWami2_jV8,13119
 cidc_schemas/template_writer.py,sha256=faOhvSDTp4nuPhOtVQR_J7YNnFzx-vh7oyNpFdee1mY,18236
 cidc_schemas/unprism.py,sha256=TOD3CSGkgNnTtT-OeCCE3Ihlam84lr8XGOmtdSy2lL8,13545
@@ -20,7 +20,7 @@ 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=g1rDphM20AcuPmEgRTRLFCqQLAKhVoYiYguTCKVeX5k,20797
+cidc_schemas/schemas/sample.json,sha256=8SFYwnvc3MzLblLEXMiBxn5wrwZNsPAyYjsoU-v75jo,21341
 cidc_schemas/schemas/shipping_core.json,sha256=OGdcdoFJXoKacD_FoSukX6SXJvcgFXTnWPko9VqOD5o,4234
 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
@@ -123,7 +123,7 @@ cidc_schemas/schemas/templates/analyses/atacseq_analysis_template.json,sha256=7v
 cidc_schemas/schemas/templates/analyses/cytof_analysis_template.json,sha256=d6qOGbYXXx1c8rb-saM4D_tMuK8n4ydbyW9_xaW6xhk,6381
 cidc_schemas/schemas/templates/analyses/rna_level1_analysis_template.json,sha256=vMHXSQNZz8sFxwiBUnRXb5o08GxgbKZjMu8ZPjNn4TI,15944
 cidc_schemas/schemas/templates/analyses/tcr_analysis_template.json,sha256=ai5KUp6q5GGTxDybOHBaseOnvQCVqIRh4SurETz5Vx0,3054
-cidc_schemas/schemas/templates/analyses/wes_analysis_template.json,sha256=wp0Iop9V8zpy8pM7JGBRhGzF6QoNs743Z5K89IQA7PA,35063
+cidc_schemas/schemas/templates/analyses/wes_analysis_template.json,sha256=kvnbC6nYrwqfGKfvHwZs1d4rePW_BOLzV6oRvrMkiD4,35297
 cidc_schemas/schemas/templates/analyses/wes_tumor_only_analysis_template.json,sha256=hhWA6mBPVBIM9QFg0C7CkimD9fcFXXtFSSkvo0lvnro,16264
 cidc_schemas/schemas/templates/assays/atacseq_fastq_template.json,sha256=7WygawkxnhFu5xBAuIhSOBD8TwCqDgINjC-HIYeCf4Q,3928
 cidc_schemas/schemas/templates/assays/clinical_data_template.json,sha256=1luQXzyqbAKKiNVwVQFeZ4dwzVpnTeGAropzd_mYmx4,2193
@@ -154,9 +154,9 @@ cidc_schemas/schemas/templates/manifests/tissue_slide_template.json,sha256=jwyXO
 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=eoX_YIl1HfQXiL7Q6ybIuOLs85Nbn7EylJ8dzXKiMZw,18674
 cidc_schemas/schemas/templates/manifests/tumor_tissue_rna_template.json,sha256=HK2Q2VQcDhP8FZDZapk04Qx2-Tji9dCMH1UpkVhU3Vs,17819
-nci_cidc_schemas-0.27.5.dist-info/LICENSE,sha256=zK77-w4rYCZBHAYJEGkcFuPXwKIsP7jMPZ2iQOXjzko,1072
-nci_cidc_schemas-0.27.5.dist-info/METADATA,sha256=eLvg5aQSTvaaZbb7qPcRSmXMvcK86h5q-G6I3ZT5ykc,4531
-nci_cidc_schemas-0.27.5.dist-info/WHEEL,sha256=SrDKpSbFN1G94qcmBqS9nyHcDMp9cUS9OC06hC0G3G0,109
-nci_cidc_schemas-0.27.5.dist-info/entry_points.txt,sha256=kSyTzXeJQrJp_2ZX0GS_NnbJR8ceQKLBSgER46PM0hs,55
-nci_cidc_schemas-0.27.5.dist-info/top_level.txt,sha256=Wwb5Cu7QrnbmSJxI2d00e3-Mir36t0jTRnSulmfhi30,13
-nci_cidc_schemas-0.27.5.dist-info/RECORD,,
+nci_cidc_schemas-0.27.7.dist-info/licenses/LICENSE,sha256=zK77-w4rYCZBHAYJEGkcFuPXwKIsP7jMPZ2iQOXjzko,1072
+nci_cidc_schemas-0.27.7.dist-info/METADATA,sha256=8TAQGFz61x4X7-SSENzJWG2I1xx2-XDGj-RmDT7wHkw,4553
+nci_cidc_schemas-0.27.7.dist-info/WHEEL,sha256=hLAVbN_1g7qXnG_3sY9erV0tsmek_RdDpqqJkhwSgEY,109
+nci_cidc_schemas-0.27.7.dist-info/entry_points.txt,sha256=kSyTzXeJQrJp_2ZX0GS_NnbJR8ceQKLBSgER46PM0hs,55
+nci_cidc_schemas-0.27.7.dist-info/top_level.txt,sha256=Wwb5Cu7QrnbmSJxI2d00e3-Mir36t0jTRnSulmfhi30,13
+nci_cidc_schemas-0.27.7.dist-info/RECORD,,

{nci_cidc_schemas-0.27.5.dist-info → nci_cidc_schemas-0.27.7.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (76.0.0)
+Generator: setuptools (78.0.1)
 Root-Is-Purelib: true
 Tag: py2-none-any
 Tag: py3-none-any