genelastic 0.9.0__py3-none-any.whl → 0.10.0__py3-none-any.whl

genelastic/common/cli.py

@@ -66,17 +66,10 @@ def add_es_connection_args(parser: argparse.ArgumentParser) -> None:
     Arguments are added to the parser by using its reference.
     """
     parser.add_argument(
-        "--es-host",
-        dest="es_host",
-        default="localhost",
-        help="Address of Elasticsearch host.",
-    )
-    parser.add_argument(
-        "--es-port",
-        type=int,
-        default=9200,
-        dest="es_port",
-        help="Elasticsearch port.",
+        "--es-url",
+        dest="es_url",
+        default="https://localhost:9200/",
+        help="URL of the Elasticsearch host.",
     )
     parser.add_argument(
         "--es-usr", dest="es_usr", default="elastic", help="Elasticsearch user."

genelastic/import_data/cli/cli_check.py

@@ -96,13 +96,12 @@ def main() -> None:
     configure_logging(args.verbose)
 
     logger.info(
-        "Connecting to Elasticsearch at https://%s:%s ...",
-        args.es_host,
-        args.es_port,
+        "Connecting to Elasticsearch at %s...",
+        args.es_url,
     )
 
     es = ElasticQueryConn(
-        f"https://{args.es_host}:{args.es_port}",
+        args.es_url,
         args.es_cert_fp,
         args.es_index_prefix,
         basic_auth=(args.es_usr, args.es_pwd),

genelastic/import_data/cli/import_data.py

@@ -234,10 +234,9 @@ def main() -> None:
     logger.debug("LOGGERS: %s", logging.root.manager.loggerDict)
 
     # Open connection to ES
-    addr = f"https://{args.es_host}:{args.es_port}"
-    logger.info("Connecting to Elasticsearch at %s...", addr)
+    logger.info("Connecting to Elasticsearch at %s...", args.es_url)
     es_import_conn = ElasticImportConn(
-        addr,
+        args.es_url,
         args.es_cert_fp,
         args.es_index_prefix,
         args.dryrun,

genelastic/import_data/cli/info.py

@@ -209,10 +209,9 @@ def main() -> None:
     configure_logging(args.verbose)
     logger.debug("Arguments: %s", args)
 
-    addr = f"https://{args.es_host}:{args.es_port}"
-    logger.info("Connecting to Elasticsearch at %s...", addr)
+    logger.info("Connecting to Elasticsearch at %s...", args.es_url)
     es_query_conn = ElasticQueryConn(
-        addr,
+        args.es_url,
         args.es_cert_fp,
         args.es_index_prefix,
         basic_auth=(args.es_usr, args.es_pwd),

genelastic/import_data/cli/integrity.py

@@ -366,10 +366,9 @@ def main() -> None:
     wet_processes_index = f"{args.es_index_prefix}-wet_processes"
     bi_processes_index = f"{args.es_index_prefix}-bi_processes"
 
-    addr = f"https://{args.es_host}:{args.es_port}"
-    logger.info("Connecting to Elasticsearch at %s...", addr)
+    logger.info("Connecting to Elasticsearch at %s...", args.es_url)
     es_query_conn = ElasticQueryConn(
-        addr,
+        args.es_url,
         args.es_cert_fp,
         args.es_index_prefix,
         args.dryrun,

genelastic/import_data/importers/importer_base.py

@@ -72,7 +72,12 @@ class BaseImporter(ABC, Generic[T]):
         """Load and parse raw data from the file."""
 
     def _validate(self, data: T) -> None:
-        """Validate the data structure (optional)."""
+        """Validate the data structure (optional).
+
+        Note: Do not implement for streaming-based importers (generators).
+        Generators should not be consumed here; validate per-record in
+        ``_transform`` if needed.
+        """
 
     @abstractmethod
     def _transform(self, data: T) -> Iterable[dict[str, Any]]:

genelastic/import_data/importers/importer_types.py

@@ -77,15 +77,26 @@ class VCFImporter(BaseImporter[Iterable[_Record]]):
         :raises ImporterError: If the file could not be opened, decoded or is empty.
         """
         try:
-            yield from vcf.Reader(
+            # StopIteration can come from two sources:
+            # 1. vcf.Reader() constructor if file is empty
+            # (unhandled in header parsing)
+            # 2. next() if file has valid headers but no variant records
+            reader = vcf.Reader(
                 filename=str(self._data_file.path), encoding="utf-8"
             )
+            first_record = next(reader)
         except StopIteration:
-            msg = f"VCF file '{self._data_file.path}' is empty."
+            msg = (
+                f"VCF file '{self._data_file.path}' is empty or "
+                f"contains no variant records."
+            )
             raise ImporterError(msg) from None
         except (OSError, UnicodeDecodeError) as e:
             raise ImporterError(e) from None
 
+        yield first_record
+        yield from reader
+
     def _transform(self, data: Iterable[_Record]) -> Iterable[dict[str, Any]]:
         """Transform each VCF file record into a JSON document."""
         for record in data:

{genelastic-0.9.0.dist-info → genelastic-0.10.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: genelastic
-Version: 0.9.0
+Version: 0.10.0
 Summary: Generate and store genetic data into an Elasticsearch database.
 Keywords: CNRGH,genelastic,generation,storage,elasticsearch,database
 Author: CNRGH, Pierrick ROGER, Maxime BLANCHON

{genelastic-0.9.0.dist-info → genelastic-0.10.0.dist-info}/RECORD

@@ -11,7 +11,7 @@ genelastic/api/server.py,sha256=3zkxOmm5L9-phdZcmPTsFQo_Uy9tzdGKRlYyWTkxv4Q,2571
 genelastic/api/settings.py,sha256=dbKQib2QQisxvi4riwJ67iB9imu-x7ZXOcKjeXuO0rU,316
 genelastic/api/specification.yml,sha256=dRo5Ttenp5-Nu3rNs9VWXpktHf4UCgvbgkBY5MAvwW8,15659
 genelastic/common/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-genelastic/common/cli.py,sha256=1X9e3zWSOy_9i5IVWJKdro2sp6xOlukuErjGopd7ET4,4539
+genelastic/common/cli.py,sha256=czzdvij007oHgqwF8iO8kfgcCkU9PuZMDrLrdSJ2agI,4399
 genelastic/common/elastic.py,sha256=tpmHeYUMgGS6ZMdowB1h5JO9eAkcK5H4_0Z0CRS-woA,17550
 genelastic/common/exceptions.py,sha256=hl2KNGOc88Rf0zdIAtS9Y4b4lghUZmqoiSD6VSMpDs8,961
 genelastic/common/server.py,sha256=qirZaMrgvF9VHS7c8zB3-NOVzV26LonSvgKKxCh5qLE,1561
@@ -20,20 +20,20 @@ genelastic/import_data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3
 genelastic/import_data/checker.py,sha256=IbtlJ7SDFYgScu2-KuBx3RZh9B73L643p-T497wUxIA,3737
 genelastic/import_data/checker_observer.py,sha256=0BQFNqtC12rcuihTR8IYYcxTm0D4cMIX2UPFEL8HjYA,416
 genelastic/import_data/cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-genelastic/import_data/cli/cli_check.py,sha256=5_YNTAZucuHfzUasZ1coX31Jl_WWLTSw9wvRphPjO1o,3509
+genelastic/import_data/cli/cli_check.py,sha256=Xy76YYLvrPDUbk9rrWPyOqYLR0HEZ-n8OBvUwlwacPQ,3445
 genelastic/import_data/cli/gen_data.py,sha256=wCCZutbhl2yYQb3-JBgcgrtrhk72BrIDUmojv-STSVU,4071
-genelastic/import_data/cli/import_data.py,sha256=SXi_vjBKiUvpfasKzD1AUOFoivUQJefeqqRv7trx6L4,10672
-genelastic/import_data/cli/info.py,sha256=Blx402DlvAuwPT-5GiBEX1tFj3_jZm_t6H66B9CXc54,7097
-genelastic/import_data/cli/integrity.py,sha256=Hxk71nKBHStDo7ZnZOUlzw3tZgpDPzWFQokA3X-m1CQ,12915
+genelastic/import_data/cli/import_data.py,sha256=dJ-Val5vlbB1J7K0Fj7BqBEil70P9XBIrD5WCkH3Hrs,10634
+genelastic/import_data/cli/info.py,sha256=_76XDvfLoxT9ibBihy2MdfRis8D4SEU-_f9wtCWk3-I,7059
+genelastic/import_data/cli/integrity.py,sha256=zzYbGioyLu0VzJWTzGPC0zlL2Udy1l6EsP4d21xUaSU,12877
 genelastic/import_data/cli/validate.py,sha256=2pLX7hTElqY6V-Cc7VQgNBQGzQtFoTbOr_bPnoABJOc,4178
 genelastic/import_data/collect.py,sha256=XU1JraaBuMUuM69Nr10MRanqwK-LlgC9nUIXDy3znbM,6288
 genelastic/import_data/constants.py,sha256=A1nT9dCJhfwB4D2_x1FVtwGPa0_p-zgEjNIFt5-j-9s,4659
 genelastic/import_data/import_bundle.py,sha256=uxPxn-c7EkEqhhhzKXmQqRNDBFBJVORBrkx2BaNmy5M,6683
 genelastic/import_data/import_bundle_factory.py,sha256=sQncdNtoUWzi-v4VMfWkwV_ngTymBJAO1tt8h8xqP-E,7516
 genelastic/import_data/importers/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-genelastic/import_data/importers/importer_base.py,sha256=S2KhKnOT2gP5hAfs1rKOsB1t_Tl-mGqrwRrz2adHQ7o,4131
+genelastic/import_data/importers/importer_base.py,sha256=WgeI7y0cMpCj4fAdbj61vzJ44wAktDXpSrcXgOSD-L4,4321
 genelastic/import_data/importers/importer_factory.py,sha256=9tP2EGRYxa-92wvZMzIMlwzFNj7MtOeP80zt9O5lr7s,2984
-genelastic/import_data/importers/importer_types.py,sha256=vdWJodd2u_HSeQBZLwK1xs9mTmxQqvKt7KDsoGtrc7Y,7827
+genelastic/import_data/importers/importer_types.py,sha256=4wGemKk1c6z3RvttpvIo7stX9CwsT-muDOjPr2GiKNg,8233
 genelastic/import_data/logger.py,sha256=VfoMU8ESvcohqesqEsLz_cDd3HJkublqYh_q7VnxkOA,1946
 genelastic/import_data/models/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 genelastic/import_data/models/analyses.py,sha256=AqZGVgoOd3fAoB4YCMST_SXxg6wJ-ROokZmyQu-svUM,6816
@@ -69,8 +69,8 @@ genelastic/ui/templates/layout.html,sha256=IOhrnchqOhdqyrJITyp1r6JaJAj7_Ll5_f_Kj
 genelastic/ui/templates/version.html,sha256=cP8RLUFXWuN1KkrN4vlK7v4o97PCTu92-6p_FMVpYsA,599
 genelastic/ui/templates/wet_process_detail.html,sha256=vtjmIl1o4XOt850eGuCjqN1D1PHZSQAZR-NBWjpUd0g,5906
 genelastic/ui/templates/wet_processes.html,sha256=DJKdMG6KyC6Qq3pNhdJ2LoO0rouAZgqhvpXV5tmuiBY,4929
-genelastic-0.9.0.dist-info/licenses/LICENSE,sha256=9Ip7fr8UdH7_fKYaL2LmieyBUV1xZihhhYXaU6L95iw,21779
-genelastic-0.9.0.dist-info/WHEEL,sha256=3id4o64OvRm9dUknh3mMJNcfoTRK08ua5cU6DFyVy-4,79
-genelastic-0.9.0.dist-info/entry_points.txt,sha256=ZyrFPza2Zwka9lc0lHTt56KfSqNtlE_b_I3xEXH2mJM,441
-genelastic-0.9.0.dist-info/METADATA,sha256=pjfWvmRClh7ItL9lE7URNOxyXB2XAKRRxaFtbMtah74,22010
-genelastic-0.9.0.dist-info/RECORD,,
+genelastic-0.10.0.dist-info/licenses/LICENSE,sha256=9Ip7fr8UdH7_fKYaL2LmieyBUV1xZihhhYXaU6L95iw,21779
+genelastic-0.10.0.dist-info/WHEEL,sha256=XV0cjMrO7zXhVAIyyc8aFf1VjZ33Fen4IiJk5zFlC3g,80
+genelastic-0.10.0.dist-info/entry_points.txt,sha256=ZyrFPza2Zwka9lc0lHTt56KfSqNtlE_b_I3xEXH2mJM,441
+genelastic-0.10.0.dist-info/METADATA,sha256=G7Z-M6_Rs6pTOjXpo2kjGpAT6mssQ5xR4ahfnD16DYQ,22011
+genelastic-0.10.0.dist-info/RECORD,,

{genelastic-0.9.0.dist-info → genelastic-0.10.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: uv 0.9.13
+Generator: uv 0.9.26
 Root-Is-Purelib: true
-Tag: py3-none-any
+Tag: py3-none-any