nci-cidc-api-modules 1.2.41__tar.gz → 1.2.43__tar.gz

{nci_cidc_api_modules-1.2.41/nci_cidc_api_modules.egg-info → nci_cidc_api_modules-1.2.43}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.41
+Version: 1.2.43
 Summary: SQLAlchemy data models and configuration tools used in the NCI CIDC API
 Home-page: https://github.com/NCI-CIDC/cidc-api-gae
 License: MIT license
@@ -41,7 +41,7 @@ Requires-Dist: opentelemetry-instrumentation-requests>=0.59b0
 Requires-Dist: opentelemetry-instrumentation-sqlalchemy>=0.59b0
 Requires-Dist: opentelemetry-exporter-gcp-trace>=1.11.0
 Requires-Dist: opentelemetry-propagator-gcp>=1.11.0
-Requires-Dist: nci-cidc-schemas==0.28.10
+Requires-Dist: nci-cidc-schemas==0.28.11
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page

nci_cidc_api_modules-1.2.43/cidc_api/__init__.py

@@ -0,0 +1 @@
+__version__ = "1.2.43"

{nci_cidc_api_modules-1.2.41 → nci_cidc_api_modules-1.2.43}/cidc_api/models/db/stage1/stem_cell_transplant_orm.py

@@ -18,7 +18,7 @@ class StemCellTransplantORM(BaseORM):
     treatment_id: Mapped[int] = mapped_column(ForeignKey("stage1.treatment.treatment_id", ondelete="CASCADE"))
 
     stem_cell_donor_type: Mapped[StemCellDonorType]
-    allogeneic_donor_type: Mapped[AllogeneicDonorType]
+    allogeneic_donor_type: Mapped[AllogeneicDonorType | None]
     stem_cell_source: Mapped[StemCellSource]
     days_to_transplant: Mapped[NonNegativeInt]
     conditioning_regimen_type: Mapped[ConditioningRegimenType | None]

{nci_cidc_api_modules-1.2.41 → nci_cidc_api_modules-1.2.43}/cidc_api/models/db/stage2/stem_cell_transplant_orm.py

@@ -18,7 +18,7 @@ class StemCellTransplantORM(BaseORM):
     treatment_id: Mapped[int] = mapped_column(ForeignKey("stage2.treatment.treatment_id", ondelete="CASCADE"))
 
     stem_cell_donor_type: Mapped[StemCellDonorType]
-    allogeneic_donor_type: Mapped[AllogeneicDonorType]
+    allogeneic_donor_type: Mapped[AllogeneicDonorType | None]
     stem_cell_source: Mapped[StemCellSource]
     days_to_transplant: Mapped[NonNegativeInt]
     conditioning_regimen_type: Mapped[ConditioningRegimenType | None]

{nci_cidc_api_modules-1.2.41 → nci_cidc_api_modules-1.2.43}/cidc_api/models/files/facets.py

@@ -376,6 +376,10 @@ assay_facets: Facets = {
         "Channels": FacetConfig(["/maldi_glycan/channels.csv", "Channels csv file for MALDI Glycan run"]),
         "Tiff Zip": FacetConfig(["/maldi_glycan/tiff.zip", "Tiff zip for MALDI Glycan run"]),
     },
+    "TCRseq RNA": {
+        "Alpha Results": FacetConfig(["/tcrseq_rna/alpha.csv"]),
+        "Beta Results": FacetConfig(["/tcrseq_rna/beta.csv"]),
+    },
     "mIHC": {
         "Samples Report": FacetConfig(["/mihc/sample_report.csv"], "Samples report for mIHC run"),
         "Multitiffs": FacetConfig(["/mihc/multitiffs.tar.gz"], "Multi Tiffs file from mIHC run"),

{nci_cidc_api_modules-1.2.41 → nci_cidc_api_modules-1.2.43}/cidc_api/models/models.py

@@ -28,6 +28,7 @@ __all__ = [
     "JobFileCategories",
     "CategoryDataElements",
     "ValidationConfigs",
+    "MASTER_APPENDIX_A",
     "TRIAL_APPENDIX_A",
     "TRIAL_APPENDIX_A_CELL_THAT_ENDS_THE_HEADER",
     "REQUEST_LETTER",
@@ -3262,6 +3263,7 @@ def upload_manifest_json(
     return manifest_upload.id
 
 
+MASTER_APPENDIX_A = "master_appendix_a"
 TRIAL_APPENDIX_A = "trial_appendix_a"
 REQUEST_LETTER = "request_letter"
 DETAILED_VALIDATION = "detailed_validation"
@@ -3361,6 +3363,16 @@ class PreprocessedFiles(CommonColumns):
         query = cls.add_job_filter(query, job_id)
         return query.all()
 
+    @classmethod
+    @with_default_session
+    def get_latest_current_file(
+        cls, file_category: str, job_id: int = None, session: Session = None
+    ) -> Optional["PreprocessedFiles"]:
+        """Return the latest 'current' file for the given category and job_id. Returns None if no file exists."""
+        query = session.query(cls).filter_by(file_category=file_category, status="current")
+        query = cls.add_job_filter(query, job_id)
+        return query.order_by(cls.version.desc()).first()
+
     @classmethod
     @with_default_session
     def get_file_by_category_and_version(

{nci_cidc_api_modules-1.2.41 → nci_cidc_api_modules-1.2.43}/cidc_api/models/types.py

@@ -113,6 +113,7 @@ AssayType = Literal[
     "snRNA-Seq",
     "Visium",
     "Olink HT",
+    "TCRseq RNA",
 ]
 
 

{nci_cidc_api_modules-1.2.41 → nci_cidc_api_modules-1.2.43}/cidc_api/shared/file_handling.py

@@ -17,14 +17,22 @@ logger = get_logger(__name__)
 
 @trace_()
 def set_current_file(
-    file: FileStorage, file_category: str, gcs_folder: str, session: Session, uploader_email: str, job_id: int = None
+    file: FileStorage,
+    file_category: str,
+    gcs_folder: str,
+    session: Session,
+    uploader_email: str,
+    job_id: int = None,
+    append_timestamp: bool = None,
 ) -> PreprocessedFiles:
     """
     Archives any existing 'current' files for the given category and job,
     then uploads the new file as the latest 'current' version.
     """
     latest_version = PreprocessedFiles.archive_current_files(file_category, job_id=job_id, session=session)
-    latest_file = create_file(file, gcs_folder, file_category, session, uploader_email, job_id, latest_version + 1)
+    latest_file = create_file(
+        file, gcs_folder, file_category, session, uploader_email, job_id, latest_version + 1, append_timestamp
+    )
     return latest_file
 
 
@@ -37,11 +45,12 @@ def create_file(
     uploader_email: str,
     job_id: int = None,
     version: int = None,
+    append_timestamp: bool = None,
 ) -> PreprocessedFiles:
     """Upload file to GCS and create corresponding metadata record in the database."""
     status = "pending" if gcs_folder.endswith("pending/") else "current"
-    # only need timestamp for current/versioned files
-    append_timestamp = status == "current"
+    # only need timestamp for current/versioned files, if not specified otherwise
+    append_timestamp = append_timestamp if append_timestamp is not None else (status == "current")
     # create file in GCS
     gcs_file_path = upload_file_to_gcs(file, GOOGLE_CLINICAL_DATA_BUCKET, gcs_folder, append_timestamp=append_timestamp)
     # create corresponding record in db

{nci_cidc_api_modules-1.2.41 → nci_cidc_api_modules-1.2.43}/cidc_api/shared/gcloud_client.py

@@ -907,6 +907,7 @@ def get_signed_url(
     bucket_name: str = GOOGLE_ACL_DATA_BUCKET,
     method: str = "GET",
     expiry_mins: int = 30,
+    use_short_filename: bool = False,
 ) -> str:
     """
     Generate a signed URL for `object_name` to give a client temporary access.
@@ -921,7 +922,11 @@ def get_signed_url(
 
     # Generate the signed URL, allowing a client to use `method` for `expiry_mins` minutes
     expiration = datetime.timedelta(minutes=expiry_mins)
-    full_filename = object_name.replace("/", "_").replace('"', "_").replace(" ", "_")
+    if use_short_filename:
+        filename = os.path.basename(object_name)
+    else:
+        # full filename with path included
+        filename = object_name.replace("/", "_").replace('"', "_").replace(" ", "_")
     other_kwargs = {}
     if os.environ.get("DEV_GOOGLE_STORAGE", None):
         other_kwargs["api_access_endpoint"] = (os.environ.get("DEV_GOOGLE_STORAGE") or "") + (
@@ -931,7 +936,7 @@ def get_signed_url(
         version="v2",
         expiration=expiration,
         method=method,
-        response_disposition=f'attachment; filename="{full_filename}"',
+        response_disposition=f'attachment; filename="{filename}"',
         **other_kwargs,
     )
     logger.info(f"generated signed URL for {object_name}: {url}")

{nci_cidc_api_modules-1.2.41 → nci_cidc_api_modules-1.2.43/nci_cidc_api_modules.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.41
+Version: 1.2.43
 Summary: SQLAlchemy data models and configuration tools used in the NCI CIDC API
 Home-page: https://github.com/NCI-CIDC/cidc-api-gae
 License: MIT license
@@ -41,7 +41,7 @@ Requires-Dist: opentelemetry-instrumentation-requests>=0.59b0
 Requires-Dist: opentelemetry-instrumentation-sqlalchemy>=0.59b0
 Requires-Dist: opentelemetry-exporter-gcp-trace>=1.11.0
 Requires-Dist: opentelemetry-propagator-gcp>=1.11.0
-Requires-Dist: nci-cidc-schemas==0.28.10
+Requires-Dist: nci-cidc-schemas==0.28.11
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page

{nci_cidc_api_modules-1.2.41 → nci_cidc_api_modules-1.2.43}/nci_cidc_api_modules.egg-info/requires.txt

@@ -32,4 +32,4 @@ opentelemetry-instrumentation-requests>=0.59b0
 opentelemetry-instrumentation-sqlalchemy>=0.59b0
 opentelemetry-exporter-gcp-trace>=1.11.0
 opentelemetry-propagator-gcp>=1.11.0
-nci-cidc-schemas==0.28.10
+nci-cidc-schemas==0.28.11

{nci_cidc_api_modules-1.2.41 → nci_cidc_api_modules-1.2.43}/requirements.modules.txt

@@ -40,4 +40,4 @@ opentelemetry-exporter-gcp-trace >= 1.11.0
 opentelemetry-propagator-gcp >= 1.11.0
 
 # cidc deps
-nci-cidc-schemas==0.28.10
+nci-cidc-schemas==0.28.11

nci_cidc_api_modules-1.2.41/cidc_api/__init__.py

@@ -1 +0,0 @@
-__version__ = "1.2.41"