phc-ingestion 0.10.13__py3-none-any.whl → 0.10.15__py3-none-any.whl

ingestion/caris/util/ihc.py

@@ -121,9 +121,16 @@ def get_ihc_results(data, log) -> list[dict]:
                         )
                         trigger = True
                 if test_results.get("stainPercent"):
-                    if np.isnan(test_results["stainPercent"]) == False:
+                    try:
+                        stain_percent = float(test_results["stainPercent"])
+                        if np.isnan(stain_percent) == False:
+                            log.warning(
+                                f'IHC test {test_results["biomarkerName"]} has an unexpected pattern for "stainPercent": value of "{test_results["stainPercent"]}" was given when None was expected'
+                            )
+                            trigger = True
+                    except (ValueError, TypeError):
                         log.warning(
-                            f'IHC test {test_results["biomarkerName"]} has an unexpected pattern for "stainPercent": value of "{test_results["stainPercent"]}" was given when None was expected'
+                            f'IHC test {test_results["biomarkerName"]} has an invalid value for "stainPercent": "{test_results["stainPercent"]}"'
                         )
                         trigger = True
 
@@ -193,9 +200,16 @@ def get_ihc_results(data, log) -> list[dict]:
                     )
                     trigger = True
             if test_results.get("stainPercent"):
-                if np.isnan(test_results["stainPercent"]) == False:
+                try:
+                    stain_percent = float(test_results["stainPercent"])
+                    if not np.isnan(stain_percent):
+                        log.warning(
+                            f'IHC test {test_results["biomarkerName"]} has an unexpected pattern for "stainPercent": value of "{test_results["stainPercent"]}" was given when None was expected'
+                        )
+                        trigger = True
+                except (ValueError, TypeError):
                     log.warning(
-                        f'IHC test {test_results["biomarkerName"]} has an unexpected pattern for "stainPercent": value of "{test_results["stainPercent"]}" was given when None was expected'
+                        f'IHC test {test_results["biomarkerName"]} has an invalid value for "stainPercent": "{test_results["stainPercent"]}"'
                     )
                     trigger = True
             if test_results.get("threshold"):

ingestion/nebula/manifest_assembler.py

@@ -154,7 +154,7 @@ class ManifestAssembler:
         except Exception as e:
             return None
 
-    def __extract_report_date(self) -> dict[str, str]:
+    def __extract_collection_date(self) -> dict[str, str]:
         in_file = self.vcf_file_path
         with gzip.open(in_file, "rt") if in_file.endswith(".gz") else open(in_file, "r") as f:
             headers = read_headers(f)
@@ -173,7 +173,7 @@ class ManifestAssembler:
                 report_date = epoch_time or date_string
                 if report_date:
                     return {
-                        "reportDate": report_date.astimezone(tz=timezone.utc)
+                        "collDate": report_date.astimezone(tz=timezone.utc)
                         .isoformat(timespec="milliseconds")
                         .replace("+00:00", "Z")
                     }
@@ -204,7 +204,7 @@ class ManifestAssembler:
         return {
             "name": "Nebula",
             "indexedDate": datetime.now().strftime("%Y-%m-%d"),
-            **self.__extract_report_date(),
+            **self.__extract_collection_date(),
             "reference": "GRCh38",
             "patientId": patient.get("id"),
             "mrn": self.__extract_elation_mrn(patient),

{phc_ingestion-0.10.13.dist-info → phc_ingestion-0.10.15.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phc-ingestion
-Version: 0.10.13
+Version: 0.10.15
 Summary: Functions for LifeOmic PHC genomic ingestions
 License: MIT
 Author-email: LifeOmic Development <development@lifeomic.com>

{phc_ingestion-0.10.13.dist-info → phc_ingestion-0.10.15.dist-info}/RECORD

@@ -5,7 +5,7 @@ ingestion/caris/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hS
 ingestion/caris/util/cnv.py,sha256=Nrc0aoG2k4tmrqHb69hAuXr0adDZIVVJRRjf9_sO91E,4441
 ingestion/caris/util/detect_genome_ref.py,sha256=MpiPa71QmlO3MWvjxPzNdbEHyOhorOcpQWWlwE5BO4c,1640
 ingestion/caris/util/hla.py,sha256=X_t6ngBRvmdG3m4I2_KnPFeWn3BaH-3IWHtOvDbS32A,770
-ingestion/caris/util/ihc.py,sha256=vegxudxHj7tLihrXGbEx_ptwkSsu3YCCB1nZVwoiYXg,12312
+ingestion/caris/util/ihc.py,sha256=1XfFJjvQq9E45cdPX4EPrg2VkXABxbMJP_BOgzA8z7g,13091
 ingestion/caris/util/interpretation.py,sha256=CghNurqeVA5VTBBorU8-ZTN-PVNPnR8wrmTwKCH3568,555
 ingestion/caris/util/json.py,sha256=aifO1hnZwNSS-ZtY20otyGbfIoc23w9HMWJ5D56lhFo,5020
 ingestion/caris/util/metadata.py,sha256=a6NToMtGtIRrlMd3CQwq4IRjGGmIiBA9JFwsATjNEoQ,10287
@@ -28,7 +28,7 @@ ingestion/generic/process.py,sha256=ZaVnZ_gx9faDUsuresI1A0oCegTa-dPQT7DBFMeZGyY,
 ingestion/generic/utils.py,sha256=1MEIru7uq38IjUdL8lcHqDH0oTki9uWrz1f2e-pmRoU,2814
 ingestion/nebula/__init__.py,sha256=VauK-rup_N8ZXVohx3HYqHX_PE_WoPyMUhdv2R7al4o,45
 ingestion/nebula/constants.py,sha256=thKqSwemdaAwAmKvF4FEVI9l1Ph5ergsnMlx6nWte7E,357
-ingestion/nebula/manifest_assembler.py,sha256=4lVZGiUc8DBkxb2W6zWOoX3azJf0VUMWYC20-T7wDNA,7989
+ingestion/nebula/manifest_assembler.py,sha256=kcRSy6pixHkuVEK9QSoM-i6ZdLWMSYXw39eKGHvam34,7995
 ingestion/nebula/process.py,sha256=N9OuipynGV_XgEL3nO5I_-di1tk9szOy8LqsyNTw0E0,2323
 ingestion/nextgen/__init__.py,sha256=7LQ-h_Bvc5P1QcHMdzsqi1Qm4fTJn04-ozar2ty9wSc,59
 ingestion/nextgen/process.py,sha256=5Z0RfclwTAYZruGDiLPutjPCYFh1DJpoWY9dnttghT4,3993
@@ -59,6 +59,6 @@ ingestion/vcf_standardization/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQe
 ingestion/vcf_standardization/util/af_helpers.py,sha256=dpTzoeIQVeBRt0ETF3a9rp5ojZqznHg4x_hCZ8OPcOg,1061
 ingestion/vcf_standardization/util/dp_helpers.py,sha256=Nq8oLOLObu4_pv16qwwgpALRlUoJVCULrd9cFOD-eoI,823
 ingestion/vcf_standardization/util/read_write.py,sha256=x3Pf6Dq8tmolblbCS5CrNmrcHS3FGfqBSFpFgvFGC4g,2526
-phc_ingestion-0.10.13.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
-phc_ingestion-0.10.13.dist-info/METADATA,sha256=7CQQcYy4OIzsmQ-0mv5ZiO1KV9npZF62M61s2633IS0,678
-phc_ingestion-0.10.13.dist-info/RECORD,,
+phc_ingestion-0.10.15.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
+phc_ingestion-0.10.15.dist-info/METADATA,sha256=WKlso7yXse4-3pnboF_klLG79ocyMFhai3l0HLZ0xHA,678
+phc_ingestion-0.10.15.dist-info/RECORD,,