@orcabus/platform-cdk-constructs 0.0.6 → 0.0.7-alpha.4

package/lambda/layers/orcabus_api_tools/poetry.lock

@@ -0,0 +1,273 @@
+# This file is automatically @generated by Poetry 2.1.3 and should not be changed by hand.
+
+[[package]]
+name = "certifi"
+version = "2025.4.26"
+description = "Python package for providing Mozilla's CA Bundle."
+optional = false
+python-versions = ">=3.6"
+groups = ["main"]
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+
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+description = "Cross-platform colored terminal text."
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+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
+groups = ["dev"]
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+description = "Internationalized Domain Names in Applications (IDNA)"
+optional = false
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+groups = ["main"]
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+
+[[package]]
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+description = "brain-dead simple config-ini parsing"
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+python-versions = ">=3.8"
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+[[package]]
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+version = "1.38.0"
+description = "Type annotations for boto3 SecretsManager 1.38.0 service generated with mypy-boto3-builder 8.10.1"
+optional = false
+python-versions = ">=3.8"
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+files = [
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+[[package]]
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+version = "1.38.5"
+description = "Type annotations for boto3 SSM 1.38.5 service generated with mypy-boto3-builder 8.10.1"
+optional = false
+python-versions = ">=3.8"
+groups = ["dev"]
+files = [
+    {file = "mypy_boto3_ssm-1.38.5-py3-none-any.whl", hash = "sha256:1bb0f932bee9038a53ab02781f959fc553a5d7f5e9d7cba56f998d0eb0a5878f"},
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+
+[[package]]
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+version = "25.0"
+description = "Core utilities for Python packages"
+optional = false
+python-versions = ">=3.8"
+groups = ["dev"]
+files = [
+    {file = "packaging-25.0-py3-none-any.whl", hash = "sha256:29572ef2b1f17581046b3a2227d5c611fb25ec70ca1ba8554b24b0e69331a484"},
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+[[package]]
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+description = "plugin and hook calling mechanisms for python"
+optional = false
+python-versions = ">=3.8"
+groups = ["dev"]
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+[package.extras]
+dev = ["pre-commit", "tox"]
+testing = ["pytest", "pytest-benchmark"]
+
+[[package]]
+name = "pytest"
+version = "7.4.4"
+description = "pytest: simple powerful testing with Python"
+optional = false
+python-versions = ">=3.7"
+groups = ["dev"]
+files = [
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+[package.dependencies]
+colorama = {version = "*", markers = "sys_platform == \"win32\""}
+iniconfig = "*"
+packaging = "*"
+pluggy = ">=0.12,<2.0"
+
+[package.extras]
+testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
+
+[[package]]
+name = "requests"
+version = "2.32.3"
+description = "Python HTTP for Humans."
+optional = false
+python-versions = ">=3.8"
+groups = ["main"]
+files = [
+    {file = "requests-2.32.3-py3-none-any.whl", hash = "sha256:70761cfe03c773ceb22aa2f671b4757976145175cdfca038c02654d061d6dcc6"},
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+[package.dependencies]
+certifi = ">=2017.4.17"
+charset-normalizer = ">=2,<4"
+idna = ">=2.5,<4"
+urllib3 = ">=1.21.1,<3"
+
+[package.extras]
+socks = ["PySocks (>=1.5.6,!=1.5.7)"]
+use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
+
+[[package]]
+name = "urllib3"
+version = "2.4.0"
+description = "HTTP library with thread-safe connection pooling, file post, and more."
+optional = false
+python-versions = ">=3.9"
+groups = ["main"]
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+
+[package.extras]
+brotli = ["brotli (>=1.0.9) ; platform_python_implementation == \"CPython\"", "brotlicffi (>=0.8.0) ; platform_python_implementation != \"CPython\""]
+h2 = ["h2 (>=4,<5)"]
+socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
+zstd = ["zstandard (>=0.18.0)"]
+
+[metadata]
+lock-version = "2.1"
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+content-hash = "228d869db509f06071915ccd60f82b837d6834b365f6499fbe7d7bd426e96196"

package/lambda/layers/orcabus_api_tools/pyproject.toml

@@ -0,0 +1,27 @@
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.poetry]
+name = "orcabus_api_tools"
+version = "1.0.0"
+description = "A collection of secondary-level functions to use to interact with the OrcaBus"
+license = "GPL-3.0-or-later"
+authors = [
+    "Alexis Lucattini"
+]
+homepage = "https://github.com/orcabus/platform-cdk-constructs"
+repository = "https://github.com/orcabus/platform-cdk-constructs"
+
+[tool.poetry.dependencies]
+python = "^3.12, <3.13"
+requests = "^2.31.0"
+
+[tool.poetry.group.dev]
+optional = true
+
+[tool.poetry.group.dev.dependencies]
+pytest = "^7.0.0"  # For testing only
+# For typehinting only, not required at runtime
+mypy-boto3-ssm = "^1.34"
+mypy-boto3-secretsmanager = "^1.34"

package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/fastq/__init__.py

@@ -0,0 +1,172 @@
+#!/usr/bin/env python3
+
+# Standard imports
+from typing import Dict, Optional
+
+# Local imports
+from .globals import FASTQ_SUBDOMAIN_NAME
+from ..utils.requests_helpers import (
+    get_request_response_results, get_url, patch_request, get_request, post_request
+)
+
+
+# Get url for the subdomain
+def get_fastq_url(endpoint: str) -> str:
+    """
+    Get the URL for the FastQ subdomain endpoint.
+    :param endpoint: The specific API endpoint for the FastQ subdomain.
+    :return: The full URL for the FastQ subdomain endpoint.
+    """
+    return get_url(
+        endpoint=endpoint,
+        subdomain=FASTQ_SUBDOMAIN_NAME,
+    )
+
+
+# Wrappers
+def get_fastq_request(
+        endpoint: str,
+        params: Optional[Dict] = None,
+):
+    return get_request(
+        url=get_fastq_url(endpoint),
+        params=params
+    )
+
+
+def get_fastq_request_response_results(
+        endpoint: str,
+        params: Optional[Dict] = None,
+):
+    return get_request_response_results(
+        url=get_fastq_url(endpoint),
+        params=params
+    )
+
+
+def fastq_patch_request(
+    endpoint: str,
+    params: Optional[Dict] = None,
+):
+    return patch_request(
+        url=get_fastq_url(endpoint),
+        params=params
+    )
+
+
+def fastq_post_request(
+    endpoint: str,
+    params: Optional[Dict] = None,
+):
+    return post_request(
+        url=get_fastq_url(endpoint),
+        params=params
+    )
+
+
+
+# Expose the functions
+
+# Create
+from .create_helpers import (
+    create_fastq_set_object,
+    create_fastq_list_row_object
+)
+
+# Job
+from .job_helpers import (
+    run_qc_stats,
+    run_ntsm,
+    run_file_compression_stats
+)
+
+# Query
+from .query_helpers import (
+    get_fastq,
+    get_fastq_set,
+    get_fastqs,
+    get_fastq_sets,
+    get_fastqs_in_instrument_run_id,
+    get_fastqs_in_library,
+    get_fastqs_batched,
+    get_fastqs_in_library_list,
+    get_fastqs_in_libraries_and_instrument_run_id,
+    get_fastqs_in_sample,
+    get_fastqs_in_sample_list,
+    get_fastqs_in_subject,
+    get_fastqs_in_individual,
+    get_fastqs_in_project,
+    get_fastq_list_rows_in_fastq_set,
+    get_fastq_jobs,
+)
+
+# Updaters
+from .update_helpers import (
+    add_qc_stats,
+    add_read_count,
+    add_file_compression_information,
+    add_ntsm_storage_object,
+    add_read_set,
+    detach_read_set,
+    validate_fastq,
+    invalidate_fastq,
+    link_fastq_list_row_to_fastq_set,
+    unlink_fastq_list_row_from_fastq_set,
+    allow_additional_fastqs_to_fastq_set,
+    disallow_additional_fastqs_to_fastq_set,
+    set_is_current_fastq_set,
+    set_is_not_current_fastq_set,
+)
+
+# Workflow
+from .workflow_helpers import (
+    to_fastq_list_row,
+    to_fastq_list_rows
+)
+
+
+__all__ = [
+    # Create
+    "create_fastq_set_object",
+    "create_fastq_list_row_object",
+    # Job
+    "run_qc_stats",
+    "run_ntsm",
+    "run_file_compression_stats",
+    # Query
+    "get_fastq",
+    "get_fastq_set",
+    "get_fastqs",
+    "get_fastq_sets",
+    "get_fastqs_in_instrument_run_id",
+    "get_fastqs_in_library",
+    "get_fastqs_batched",
+    "get_fastqs_in_library_list",
+    "get_fastqs_in_libraries_and_instrument_run_id",
+    "get_fastqs_in_sample",
+    "get_fastqs_in_sample_list",
+    "get_fastqs_in_subject",
+    "get_fastqs_in_individual",
+    "get_fastqs_in_project",
+    "get_fastq_list_rows_in_fastq_set",
+    "get_fastq_jobs",
+    # Updaters
+    "add_qc_stats",
+    "add_read_count",
+    "add_file_compression_information",
+    "add_ntsm_storage_object",
+    "add_read_set",
+    "detach_read_set",
+    "validate_fastq",
+    "invalidate_fastq",
+    "link_fastq_list_row_to_fastq_set",
+    "unlink_fastq_list_row_from_fastq_set",
+    "allow_additional_fastqs_to_fastq_set",
+    "disallow_additional_fastqs_to_fastq_set",
+    "set_is_current_fastq_set",
+    "set_is_not_current_fastq_set",
+    # Workflow
+    "to_fastq_list_row",
+    "to_fastq_list_rows",
+]
+

package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/fastq/create_helpers.py

@@ -0,0 +1,47 @@
+#!/usr/bin/env python3
+
+"""
+Update helpers for the update script.
+
+- add_qc_stats
+- add_read_count
+- add_ntsm_storage_object / add_ntsm
+- add_fastq_pair_storage_object / add_read_set
+- detach_fastq_pair_storage_object / detach_read_set
+- validate
+- invalidate
+"""
+
+# Standard imports
+from typing import Unpack
+
+# Local imports
+from . import fastq_post_request
+from .globals import FASTQ_LIST_ROW_ENDPOINT, FASTQ_SET_ENDPOINT
+from .models import FastqListRow, FastqSet, FastqListRowCreate, FastqSetCreate
+
+
+def create_fastq_list_row_object(**kwargs: Unpack[FastqListRowCreate]) -> FastqListRow:
+    """
+    Add a fastq list row object to the database.
+    Returns the created fastq list row object
+    """
+    return FastqListRow(
+        **fastq_post_request(
+            endpoint=FASTQ_LIST_ROW_ENDPOINT,
+            params=dict(kwargs)
+        )
+    )
+
+
+def create_fastq_set_object(**kwargs: Unpack[FastqSetCreate]) -> FastqSet:
+    """
+    Add a fastq set object to the database.
+    Returns the created fastq set object
+    """
+    return FastqSet(
+        **fastq_post_request(
+            endpoint=FASTQ_SET_ENDPOINT,
+            params=dict(kwargs)
+        )
+    )

package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/fastq/globals.py

@@ -0,0 +1,13 @@
+#!/usr/bin/env python3
+
+import re
+
+# AWS PARAMETERS
+FASTQ_SUBDOMAIN_NAME = "fastq"
+
+# API ENDPOINTS
+FASTQ_LIST_ROW_ENDPOINT = "api/v1/fastq"
+FASTQ_SET_ENDPOINT = "api/v1/fastqSet"
+
+# REGEX
+ORCABUS_ULID_REGEX_MATCH = re.compile(r'^[a-z0-9]{3}\.[A-Z0-9]{26}$')

package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/fastq/job_helpers.py

@@ -0,0 +1,53 @@
+#!/usr/bin/env python3
+
+"""
+Update helpers for the update script.
+
+- run_qc_stats
+- run_ntsm
+- run_file_compression_information
+"""
+# Standard imports
+
+# Local imports
+from . import fastq_patch_request
+from .globals import FASTQ_LIST_ROW_ENDPOINT
+from .models import Job
+
+
+def run_qc_stats(fastq_id: str) -> Job:
+    """
+    Add QC stats to a fastq_id.
+
+    :param fastq_id: Fastq str
+    """
+    return Job(
+        **fastq_patch_request(
+            f"{FASTQ_LIST_ROW_ENDPOINT}/{fastq_id}:runQcStats"
+        )
+    )
+
+
+def run_ntsm(fastq_id: str) -> Job:
+    """
+    Run ntsm for a fastq_id.
+
+    :param fastq_id: Fastq str
+    """
+    return Job(
+        **fastq_patch_request(
+            f"{FASTQ_LIST_ROW_ENDPOINT}/{fastq_id}:runNtsm"
+        )
+    )
+
+def run_file_compression_stats(fastq_id: str) -> Job:
+    """
+    Run file compression stats for a fastq_id.
+
+    :param fastq_id: Fastq str
+    """
+    return Job(
+        **fastq_patch_request(
+            f"{FASTQ_LIST_ROW_ENDPOINT}/{fastq_id}:runFileCompressionInformation"
+        )
+    )