odm-processors-sdk 1.65.0__py3-none-any.whl

odm_processors_sdk/transformations/api.py

@@ -0,0 +1,176 @@
+import odm_api
+from . import client
+
+
+def data_import() -> (
+    odm_api.api.data_import_via_direct_file_upload_api.DataImportViaDirectFileUploadApi
+):
+    """
+    Get an instance of the Data Import Jobs API.
+    """
+    c = client.get()
+    return odm_api.api.data_import_via_direct_file_upload_api.DataImportViaDirectFileUploadApi(
+        c
+    )
+
+
+def job_operations() -> odm_api.api.job_operations_api.JobOperationsApi:
+    """
+    Get an instance of the Job Operations API.
+    """
+    c = client.get()
+    return odm_api.api.job_operations_api.JobOperationsApi(c)
+
+
+def file() -> odm_api.api.files_as_curator_api.FilesAsCuratorApi:
+    """
+    Get an instance of the Files As Curator API.
+    """
+    c = client.get()
+    return odm_api.api.files_as_curator_api.FilesAsCuratorApi(c)
+
+
+def sample() -> odm_api.api.sample_spo_tas_curator_api.SampleSPoTAsCuratorApi:
+    """
+    Get an instance of the SampleSPoT As Curator API.
+    """
+    c = client.get()
+    return odm_api.api.sample_spo_tas_curator_api.SampleSPoTAsCuratorApi(c)
+
+
+def library() -> odm_api.api.library_spo_tas_curator_api.LibrarySPoTAsCuratorApi:
+    """
+    Get an instance of the LibrarySPoT As Curator API.
+    """
+    c = client.get()
+    return odm_api.api.library_spo_tas_curator_api.LibrarySPoTAsCuratorApi(c)
+
+
+def preparation() -> (
+    odm_api.api.preparation_spo_tas_curator_api.PreparationSPoTAsCuratorApi
+):
+    """
+    Get an instance of the PreparationSPoT As Curator API.
+    """
+    c = client.get()
+    return odm_api.api.preparation_spo_tas_curator_api.PreparationSPoTAsCuratorApi(c)
+
+
+def cells() -> odm_api.api.cells_as_curator_api.CellsAsCuratorApi:
+    """
+    Get an instance of the Cells As Curator API.
+    """
+    c = client.get()
+    return odm_api.api.cells_as_curator_api.CellsAsCuratorApi(c)
+
+
+def expression() -> (
+    odm_api.api.expression_spo_tas_curator_api.ExpressionSPoTAsCuratorApi
+):
+    """
+    Get an instance of the ExpressionSPoT As Curator API.
+    """
+    c = client.get()
+    return odm_api.api.expression_spo_tas_curator_api.ExpressionSPoTAsCuratorApi(c)
+
+
+def study_integration() -> (
+    odm_api.api.study_integration_as_curator_api.StudyIntegrationAsCuratorApi
+):
+    """
+    Get an instance of the Study Integration As Curator API.
+    """
+    c = client.get()
+    return odm_api.api.study_integration_as_curator_api.StudyIntegrationAsCuratorApi(c)
+
+
+def sample_integration() -> (
+    odm_api.api.sample_integration_as_curator_api.SampleIntegrationAsCuratorApi
+):
+    """
+    Get an instance of the Sample Integration As Curator API.
+    """
+    c = client.get()
+    return odm_api.api.sample_integration_as_curator_api.SampleIntegrationAsCuratorApi(
+        c
+    )
+
+
+def library_integration() -> (
+    odm_api.api.library_integration_as_curator_api.LibraryIntegrationAsCuratorApi
+):
+    """
+    Get an instance of the Library Integration As Curator API.
+    """
+    c = client.get()
+    return (
+        odm_api.api.library_integration_as_curator_api.LibraryIntegrationAsCuratorApi(c)
+    )
+
+
+def preparation_integration() -> (
+    odm_api.api.preparation_integration_as_curator_api.PreparationIntegrationAsCuratorApi
+):
+    """
+    Get an instance of the Preparation Integration As Curator API.
+    """
+    c = client.get()
+    return odm_api.api.preparation_integration_as_curator_api.PreparationIntegrationAsCuratorApi(
+        c
+    )
+
+
+def cell_integration() -> (
+    odm_api.api.cell_integration_as_curator_api.CellIntegrationAsCuratorApi
+):
+    """
+    Get an instance of the Cell Integration As Curator API.
+    """
+    c = client.get()
+    return odm_api.api.cell_integration_as_curator_api.CellIntegrationAsCuratorApi(c)
+
+
+def expression_integration() -> (
+    odm_api.api.expression_integration_as_curator_api.ExpressionIntegrationAsCuratorApi
+):
+    """
+    Get an instance of the Expression Integration As Curator API.
+    """
+    c = client.get()
+    return odm_api.api.expression_integration_as_curator_api.ExpressionIntegrationAsCuratorApi(
+        c
+    )
+
+
+def variant_integration() -> (
+    odm_api.api.variant_integration_as_curator_api.VariantIntegrationAsCuratorApi
+):
+    """
+    Get an instance of the Variant Integration As Curator API.
+    """
+    c = client.get()
+    return (
+        odm_api.api.variant_integration_as_curator_api.VariantIntegrationAsCuratorApi(c)
+    )
+
+
+def flow_cytometry_facs_integration() -> (
+    odm_api.api.flow_cytometry_facs_integration_as_curator_api.FlowCytometryFACSIntegrationAsCuratorApi
+):
+    """
+    Get an instance of the Flow Cytometry FACS Integration As Curator API.
+    """
+    c = client.get()
+    return odm_api.api.flow_cytometry_facs_integration_as_curator_api.FlowCytometryFACSIntegrationAsCuratorApi(
+        c
+    )
+
+
+def omics_queries() -> (
+    odm_api.api.omics_queries_as_curator_api.OmicsQueriesAsCuratorApi
+):
+    """
+    Get an instance of the Omics Queries As Curator API.
+    """
+    c = client.get()
+    return odm_api.api.omics_queries_as_curator_api.OmicsQueriesAsCuratorApi(c)

odm_processors_sdk/transformations/client.py

@@ -0,0 +1,13 @@
+import os
+
+import odm_api
+
+
+def get() -> odm_api.ApiClient:
+    """
+    Create and configure an API client for ODM API.
+    """
+    c = odm_api.ApiClient.get_default()
+    c.configuration.host = os.environ["ODM_URL"]
+    c.default_headers["Genestack-API-Token"] = os.environ["GENESTACK_API_TOKEN"]
+    return c

odm_processors_sdk/transformations/configuration.py

@@ -0,0 +1,22 @@
+import json
+import os
+import logging
+
+
+def read():
+    config_path = os.environ.get("CONFIGURATION_PATH")
+
+    if not config_path:
+        logging.warning("CONFIGURATION_PATH environment variable is not set")
+        return None
+
+    try:
+        with open(config_path, "r") as file:
+            return json.load(file)
+    except FileNotFoundError:
+        logging.warning(f"Configuration file not found at: {config_path}")
+        return None
+    except json.JSONDecodeError as e:
+        raise json.JSONDecodeError(f"Invalid JSON in configuration file: {e}")
+    except Exception as e:
+        raise Exception(f"Error reading configuration file: {e}")

odm_processors_sdk/transformations/environment.py

@@ -0,0 +1,29 @@
+import os
+
+
+def input_accessions() -> list[str] | None:
+    return os.environ.get("INPUT_ACCESSIONS").split(",")
+
+
+def dry_run() -> bool | None:
+    return os.environ.get("DRY_RUN").lower() == "true"
+
+
+def image_name() -> str:
+    return os.environ.get("IMAGE_NAME")
+
+
+def image_version() -> str:
+    return os.environ.get("IMAGE_VERSION")
+
+
+def configuration_id() -> str:
+    return os.environ.get("CONFIGURATION_ID")
+
+
+def configuration_version() -> str:
+    return os.environ.get("CONFIGURATION_VERSION")
+
+
+def job_id() -> str:
+    return os.environ.get("JOB_ID")

odm_processors_sdk/transformations/logger.py

@@ -0,0 +1,25 @@
+import json
+import sys
+import warnings
+
+from loguru import logger
+
+
+def make_sink(destination):
+    def strip_text_sink(message):
+        obj = json.loads(message)
+        obj.pop("text", None)
+        destination.write(json.dumps(obj) + "\n")
+
+    return strip_text_sink
+
+
+def log():
+    logger.remove()
+    logger.add(make_sink(sys.stdout), level="INFO", serialize=True)
+    warnings.showwarning = (
+        lambda message, category, filename, lineno, *args, **kwargs: logger.warning(
+            f"{category.__name__} ({filename}:{lineno}): {message}"
+        )
+    )
+    return logger

odm_processors_sdk/transformations/tmp.py

@@ -0,0 +1,14 @@
+import os
+
+import tempfile
+
+
+def directory_prefix() -> str | None:
+    return os.environ.get("TEMPORARY_DIRECTORY")
+
+
+def directory():
+    """
+    Create a temporary directory using TEMPORARY_DIRECTORY environment variable as prefix.
+    """
+    return tempfile.TemporaryDirectory(dir=directory_prefix())

odm_processors_sdk/transformations/util.py

@@ -0,0 +1,56 @@
+import time
+
+from . import api
+from . import logger
+
+log = logger.log()
+
+
+def wait_job(job_exec_id):
+    """
+    Wait for a job to complete.
+    """
+
+    while True:
+        info = api.job_operations().info(job_exec_id)
+        if info.status in ("COMPLETED", "FAILED"):
+            break
+        log.info(f"Job status: {info.status}")
+        time.sleep(15)
+    return
+
+
+# TODO: It should use stream instead of bytes
+def retrieve_attachment_content(accession: str) -> bytes:
+    """
+    Retrieve CSV content from a file with the specified accession.
+
+    Returns:
+        bytes: The content of the CSV file as bytes.
+    """
+    return api.file().get_file_as_curator(accession)
+
+
+def write_attachment_file(
+    accession: str, output_file: str, chunk_size: int = 65536
+) -> None:
+    """
+    Write the attachment content to the specified output file by chunks.
+
+    Args:
+        accession: The accession of the attachment file.
+        output_file: The path to the output file.
+        chunk_size: The chunk size to read the file in. Default is 65536 bytes (64 KB).
+    """
+    with api.file().get_file_as_curator_without_preload_content(accession) as response:
+        with open(output_file, "wb") as file:
+            while True:
+                chunk = response.read(chunk_size)
+                if not chunk:
+                    break
+                file.write(chunk)
+
+
+def find_study_accession_from_attachment_accession(accession: str) -> str:
+    study = api.study_integration().get_study_by_file_as_curator(accession)
+    return study["genestack:accession"]

odm_processors_sdk-1.65.0.dist-info/METADATA

@@ -0,0 +1,8 @@
+Metadata-Version: 2.4
+Name: odm-processors-sdk
+Version: 1.65.0
+Summary: Software development kit for all of the processors in ODM (transformations, connectors, etc.)
+Requires-Python: >=3.13
+Description-Content-Type: text/markdown
+Requires-Dist: odm-api==1.65.0
+Requires-Dist: loguru==0.7.3

odm_processors_sdk-1.65.0.dist-info/RECORD

@@ -0,0 +1,13 @@
+odm_processors_sdk/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+odm_processors_sdk/transformations/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+odm_processors_sdk/transformations/api.py,sha256=_b3GGHMdZKoe6VJhD9MyRi3IzEiLbE2RE_b0Jxs24zg,4994
+odm_processors_sdk/transformations/client.py,sha256=tai9MstMVFa9HvFoVQyQUmMPV_TqG-pjKbl17bs5Hrw,311
+odm_processors_sdk/transformations/configuration.py,sha256=RSMxJGZ8OAroutZuHo02R7PaoalkdZu5L6kS5xJ0Mwg,654
+odm_processors_sdk/transformations/environment.py,sha256=soI1OgLkGvBFx9PXJE-FudBqhzRV9KyGb2G7FP_XGlU,567
+odm_processors_sdk/transformations/logger.py,sha256=zfKZdXy2Cj2PyAQ7lOSJP7jdMmRyZ_-5MiGvqXGjwZo,589
+odm_processors_sdk/transformations/tmp.py,sha256=L8PW9olVEjCu6V_zAqLiE4j_N8yVlv8OHHTPOVVfsAA,305
+odm_processors_sdk/transformations/util.py,sha256=pkDEraAN-yNfhb_66zcQqykPJLchO38gD41RpBYXUzY,1567
+odm_processors_sdk-1.65.0.dist-info/METADATA,sha256=buPyTI0WWPSvO0xKWa8Shzm_PdkQ0XYZVSOLOnXS7Mo,290
+odm_processors_sdk-1.65.0.dist-info/WHEEL,sha256=mOdXR9C3wMVov7cSY8PY-XCzo3SmmWCHvGQr5csJoao,91
+odm_processors_sdk-1.65.0.dist-info/top_level.txt,sha256=pMgCWxFau9Si-S-jGP42_c-KBd-nP-1rq3vFJMEacoc,19
+odm_processors_sdk-1.65.0.dist-info/RECORD,,

odm_processors_sdk-1.65.0.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (84.2.1)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

odm_processors_sdk-1.65.0.dist-info/top_level.txt

@@ -0,0 +1 @@
+odm_processors_sdk