From d5280c25f4ba7653c1c75c444c29e9d0a56a3123 Mon Sep 17 00:00:00 2001 From: Nathan Thorpe Date: Wed, 21 May 2025 16:24:17 -0700 Subject: [PATCH 1/4] add example for tags and bump api client --- cirro/services/dataset.py | 5 +- poetry.lock | 817 ++++++++++++++++++++------------------ pyproject.toml | 4 +- 3 files changed, 425 insertions(+), 401 deletions(-) diff --git a/cirro/services/dataset.py b/cirro/services/dataset.py index 10076c40..68ad10e3 100644 --- a/cirro/services/dataset.py +++ b/cirro/services/dataset.py @@ -93,7 +93,7 @@ def create(self, project_id: str, upload_request: UploadDatasetRequest) -> Uploa ID of the created dataset and the path to upload files ```python - from cirro_api_client.v1.models import UploadDatasetRequest + from cirro_api_client.v1.models import UploadDatasetRequest, Tag from cirro.cirro_client import CirroApi cirro = CirroApi() @@ -101,7 +101,8 @@ def create(self, project_id: str, upload_request: UploadDatasetRequest) -> Uploa name="Name of new dataset", process_id="paired_dnaseq", expected_files=["read_1.fastq.gz", "read_2.fastq.gz"], - description="Description of the dataset" + description="Description of the dataset", + tags=[Tag(value="tag1"), Tag(value="tag2")] ) cirro.datasets.create("project-id", request) ``` diff --git a/poetry.lock b/poetry.lock index 3b5ad433..37841b2a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -471,14 +471,14 @@ files = [ [[package]] name = "cirro-api-client" -version = "1.0.1" +version = "1.0.2" description = "A client library for accessing Cirro" optional = false python-versions = "<4.0,>=3.8" groups = ["main"] files = [ - {file = "cirro_api_client-1.0.1-py3-none-any.whl", hash = "sha256:0fccfcd5bf05b7868047a462ded9541cc73874ca27cfa35f2c19498376c02155"}, - {file = "cirro_api_client-1.0.1.tar.gz", hash = "sha256:bfe898cb5fc5057fdb186490830710a5a1e7d551c7ca6e6ddf0c419e8e3f2bd6"}, + {file = "cirro_api_client-1.0.2-py3-none-any.whl", hash = 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@@ packages = [{include = "cirro"}] [tool.poetry.dependencies] python = ">3.9.0,<3.9.1 || >3.9.1,<4.0" attrs = ">=21.3.0" -cirro_api_client = "1.0.1" +cirro_api_client = "1.0.2" click = "^8.1.3" boto3 = "~=1.37" questionary = "^2.0.1" From b25700b91357c3c7da91239a0239670df8992d90 Mon Sep 17 00:00:00 2001 From: Nathan Thorpe Date: Wed, 21 May 2025 16:25:35 -0700 Subject: [PATCH 2/4] add example for import dataset --- cirro/services/dataset.py | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/cirro/services/dataset.py b/cirro/services/dataset.py index 68ad10e3..b0237b14 100644 --- a/cirro/services/dataset.py +++ b/cirro/services/dataset.py @@ -78,6 +78,20 @@ def import_public(self, project_id: str, import_request: ImportDataRequest) -> C Returns: ID of the created dataset + + ```python + from cirro_api_client.v1.models import ImportDataRequest, Tag + from cirro.cirro_client import CirroApi + + cirro = CirroApi() + request = ImportDataRequest( + name="Imported dataset", + description="Description of the dataset", + public_ids=["SRR123456", "SRR123457"], + tags=[Tag(value="tag1")] + ) + cirro.datasets.create("project-id", request) + ``` """ return import_public_dataset.sync(project_id=project_id, client=self._api_client, body=import_request) From fe52219112072108e337c12998408a3bbc446b58 Mon Sep 17 00:00:00 2001 From: Nathan Thorpe Date: Wed, 21 May 2025 16:42:32 -0700 Subject: [PATCH 3/4] add to sdk --- cirro/sdk/project.py | 13 ++++++++++--- cirro/services/dataset.py | 2 +- poetry.lock | 8 ++++---- pyproject.toml | 2 +- 4 files changed, 16 insertions(+), 9 deletions(-) diff --git a/cirro/sdk/project.py b/cirro/sdk/project.py index 8042867d..792810c3 100644 --- a/cirro/sdk/project.py +++ b/cirro/sdk/project.py @@ -2,7 +2,7 @@ from time import sleep from typing import List, Union -from cirro_api_client.v1.models import Project, UploadDatasetRequest, Dataset, Sample +from cirro_api_client.v1.models import Project, UploadDatasetRequest, Dataset, Sample, Tag from cirro.cirro_client import CirroApi from cirro.file_utils import get_files_in_directory @@ -145,7 +145,8 @@ def upload_dataset( description='', process: Union[DataPortalProcess, str] = None, upload_folder: str = None, - files: list = None + files: List[str] = None, + tags: List[str] = None, ): """ Upload a set of files to the Data Portal, creating a new dataset. @@ -158,6 +159,7 @@ def upload_dataset( process (str | DataPortalProcess): Process to run may be referenced by name, ID, or object upload_folder (str): Folder containing files to upload files (List[str]): Optional subset of files to upload from the folder + tags (List[str]): Optional list of tags to apply to the dataset """ if name is None: @@ -178,6 +180,10 @@ def upload_dataset( if files is None or len(files) == 0: raise RuntimeWarning("No files to upload, exiting") + # Normalize into Tag object + if tags is not None: + tags = [Tag(value=value) for value in tags] + # Make sure that the files match the expected pattern self._client.processes.check_dataset_files(files, process.id, upload_folder) @@ -186,7 +192,8 @@ def upload_dataset( process_id=process.id, name=name, description=description, - expected_files=files + expected_files=files, + tags=tags, ) # Get the response diff --git a/cirro/services/dataset.py b/cirro/services/dataset.py index b0237b14..f21981e3 100644 --- a/cirro/services/dataset.py +++ b/cirro/services/dataset.py @@ -90,7 +90,7 @@ def import_public(self, project_id: str, import_request: ImportDataRequest) -> C public_ids=["SRR123456", "SRR123457"], tags=[Tag(value="tag1")] ) - cirro.datasets.create("project-id", request) + cirro.datasets.import_public("project-id", request) ``` """ return import_public_dataset.sync(project_id=project_id, client=self._api_client, body=import_request) diff --git a/poetry.lock b/poetry.lock index 37841b2a..3f8974f4 100644 --- a/poetry.lock +++ b/poetry.lock @@ -471,14 +471,14 @@ files = [ [[package]] name = "cirro-api-client" -version = "1.0.2" +version = "1.0.3" description = "A client library for accessing Cirro" optional = false python-versions = "<4.0,>=3.8" groups = ["main"] files = [ - {file = "cirro_api_client-1.0.2-py3-none-any.whl", hash = "sha256:332e3110d312fc32423c9c8a3575b4fd9240db33367b39f80f5ffcb20a217f4b"}, - {file = "cirro_api_client-1.0.2.tar.gz", hash = "sha256:8374a5aef043ef640dcd6533d4ad14916cf9d0a9de25b73f39dc6e7f442f8d49"}, + {file = "cirro_api_client-1.0.3-py3-none-any.whl", hash = "sha256:435d25490f275e65a05bf20edc18a90066c4b9b627d9ed3ebd795c18ebdca133"}, + {file = "cirro_api_client-1.0.3.tar.gz", hash = "sha256:036ba2f465eb9c94b3a2c2bd1131c83a8d6acdaa9324cca3a8d88b791e0b7d83"}, ] [package.dependencies] @@ -2386,4 +2386,4 @@ pyodide = ["requests-aws4auth"] [metadata] lock-version = "2.1" python-versions = ">3.9.0,<3.9.1 || >3.9.1,<4.0" -content-hash = "c8fb4af26379c511f11fbe504c62106918b4d420cf3a9ff67a8c2462645ff54e" +content-hash = "634131856883f97cd9c9cb68157843215f669ef32c65f822c2bb6f9d9e7c3ec3" diff --git a/pyproject.toml b/pyproject.toml index d82bf0a2..c884f7f9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -11,7 +11,7 @@ packages = [{include = "cirro"}] [tool.poetry.dependencies] python = ">3.9.0,<3.9.1 || >3.9.1,<4.0" attrs = ">=21.3.0" -cirro_api_client = "1.0.2" +cirro_api_client = "1.0.3" click = "^8.1.3" boto3 = "~=1.37" questionary = "^2.0.1" From dde1e425af98f184f92d1251aa1424c9ce5674e3 Mon Sep 17 00:00:00 2001 From: Nathan Thorpe Date: Wed, 21 May 2025 16:45:20 -0700 Subject: [PATCH 4/4] --help so exit code is 0 --- .github/workflows/package.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/package.yml b/.github/workflows/package.yml index 686c7c40..41f5d269 100644 --- a/.github/workflows/package.yml +++ b/.github/workflows/package.yml @@ -33,7 +33,7 @@ jobs: - name: Test install run: | poetry install --all-extras - poetry run cirro + poetry run cirro --help - name: Build python package run: |