Merge branch 'master' into parse-concentration

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 54.4.1
+current_version = 54.4.8
 commit = True
 tag = True
 tag_name = v{new_version}

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "54.4.1"
+__version__ = "54.4.8"

cg/constants/housekeeper_tags.py

@@ -194,4 +194,17 @@ class BalsamicProtectedTags:
         ["gisaid-log"],
         ["gisaid-csv"],
     ],
+    str(Pipeline.RNAFUSION): [
+        [AnalysisTag.FUSION, AnalysisTag.ARRIBA],
+        [AnalysisTag.FUSION, AnalysisTag.STARFUSION],
+        [AnalysisTag.FUSION, AnalysisTag.FUSIONCATCHER],
+        [AnalysisTag.FUSIONINSPECTOR],
+        [AnalysisTag.FUSIONREPORT, AnalysisTag.RESEARCH],
+        [AnalysisTag.FUSIONINSPECTOR_HTML, AnalysisTag.RESEARCH],
+        [AnalysisTag.ARRIBA_VISUALIZATION, AnalysisTag.RESEARCH],
+        [AnalysisTag.MULTIQC_HTML, AnalysisTag.RNA],
+        [HK_DELIVERY_REPORT_TAG],
+        [AnalysisTag.VCF_FUSION],
+        [AnalysisTag.GENE_COUNTS],
+    ],
 }

cg/io/gzip.py

@@ -0,0 +1,8 @@
+import gzip
+from pathlib import Path
+
+
+def read_gzip_first_line(file_path: Path) -> str:
+    """Return first line of gzip file."""
+    with gzip.open(file_path) as file:
+        return file.readline().decode()

cg/meta/archive/archive.py

@@ -9,7 +9,7 @@
 from cg.constants import SequencingFileTag
 from cg.constants.archiving import ArchiveLocations
 from cg.exc import ArchiveJobFailedError
-from cg.meta.archive.ddn_dataflow import DDNDataFlowClient
+from cg.meta.archive.ddn.ddn_data_flow_client import DDNDataFlowClient
 from cg.meta.archive.models import ArchiveHandler, FileAndSample, SampleAndDestination
 from cg.models.cg_config import DataFlowConfig
 from cg.store import Store

cg/meta/archive/ddn/constants.py

@@ -0,0 +1,51 @@
+from enum import StrEnum
+
+OSTYPE: str = "Unix/MacOS"
+ROOT_TO_TRIM: str = "/home"
+
+DESTINATION_ATTRIBUTE: str = "destination"
+SOURCE_ATTRIBUTE: str = "source"
+
+
+class DataflowEndpoints(StrEnum):
+    """Enum containing all DDN dataflow endpoints used."""
+
+    ARCHIVE_FILES = "files/archive"
+    DELETE_FILE = "files/delete"
+    GET_AUTH_TOKEN = "auth/token"
+    REFRESH_AUTH_TOKEN = "auth/token/refresh"
+    RETRIEVE_FILES = "files/retrieve"
+    GET_JOB_STATUS = "activity/jobs/"
+
+
+class JobStatus(StrEnum):
+    """Enum for the different job statuses which can be returned via Miria."""
+
+    CANCELED = "Canceled"
+    COMPLETED = "Completed"
+    DENIED = "Denied"
+    CREATION_IN_PROGRESS = "Creation in progress"
+    IN_QUEUE = "In Queue"
+    INVALID_LICENSE = "Invalid license"
+    ON_VALIDATION = "On validation"
+    REFUSED = "Refused"
+    RUNNING = "Running"
+    SUSPENDED = "Suspended"
+    TERMINATED_ON_ERROR = "Terminated on error"
+    TERMINATED_ON_WARNING = "Terminated on warning"
+
+
+FAILED_JOB_STATUSES: list[str] = [
+    JobStatus.CANCELED,
+    JobStatus.DENIED,
+    JobStatus.INVALID_LICENSE,
+    JobStatus.REFUSED,
+    JobStatus.TERMINATED_ON_ERROR,
+    JobStatus.TERMINATED_ON_WARNING,
+]
+ONGOING_JOB_STATUSES: list[str] = [
+    JobStatus.CREATION_IN_PROGRESS,
+    JobStatus.IN_QUEUE,
+    JobStatus.ON_VALIDATION,
+    JobStatus.RUNNING,
+]

cg/meta/archive/ddn_dataflow.py → cg/meta/archive/ddn/ddn_data_flow_client.py

@@ -1,265 +1,37 @@
 """Module for archiving and retrieving folders via DDN Dataflow."""
 import logging
 from datetime import datetime
-from enum import StrEnum
 from pathlib import Path
 from urllib.parse import urljoin
 
 from housekeeper.store.models import File
-from pydantic import BaseModel, Field
-from requests.models import Response
+from requests import Response
 
 from cg.constants.constants import APIMethods
 from cg.exc import ArchiveJobFailedError, DdnDataflowAuthenticationError
 from cg.io.controller import APIRequest
-from cg.meta.archive.models import (
-    ArchiveHandler,
-    FileAndSample,
-    FileTransferData,
-    SampleAndDestination,
+from cg.meta.archive.ddn.constants import (
+    DESTINATION_ATTRIBUTE,
+    FAILED_JOB_STATUSES,
+    SOURCE_ATTRIBUTE,
+    DataflowEndpoints,
+    JobStatus,
 )
+from cg.meta.archive.ddn.models import (
+    AuthPayload,
+    AuthToken,
+    DeleteFilePayload,
+    GetJobStatusPayload,
+    GetJobStatusResponse,
+    MiriaObject,
+    RefreshPayload,
+    TransferPayload,
+)
+from cg.meta.archive.models import ArchiveHandler, FileAndSample, SampleAndDestination
 from cg.models.cg_config import DataFlowConfig
-from cg.store.models import Sample
 
 LOG = logging.getLogger(__name__)
 
-OSTYPE: str = "Unix/MacOS"
-ROOT_TO_TRIM: str = "/home"
-
-DESTINATION_ATTRIBUTE: str = "destination"
-SOURCE_ATTRIBUTE: str = "source"
-
-
-def get_request_log(headers: dict, body: dict):
-    return "Sending request with headers: \n" + f"{headers} \n" + "and body: \n" + f"{body}"
-
-
-class DataflowEndpoints(StrEnum):
-    """Enum containing all DDN dataflow endpoints used."""
-
-    ARCHIVE_FILES = "files/archive"
-    DELETE_FILE = "files/delete"
-    GET_AUTH_TOKEN = "auth/token"
-    REFRESH_AUTH_TOKEN = "auth/token/refresh"
-    RETRIEVE_FILES = "files/retrieve"
-    GET_JOB_STATUS = "activity/jobs/"
-
-
-class JobStatus(StrEnum):
-    """Enum for the different job statuses which can be returned via Miria."""
-
-    CANCELED = "Canceled"
-    COMPLETED = "Completed"
-    DENIED = "Denied"
-    CREATION_IN_PROGRESS = "Creation in progress"
-    IN_QUEUE = "In Queue"
-    INVALID_LICENSE = "Invalid license"
-    ON_VALIDATION = "On validation"
-    REFUSED = "Refused"
-    RUNNING = "Running"
-    SUSPENDED = "Suspended"
-    TERMINATED_ON_ERROR = "Terminated on error"
-    TERMINATED_ON_WARNING = "Terminated on warning"
-
-
-FAILED_JOB_STATUSES: list[str] = [
-    JobStatus.CANCELED,
-    JobStatus.DENIED,
-    JobStatus.INVALID_LICENSE,
-    JobStatus.REFUSED,
-    JobStatus.TERMINATED_ON_ERROR,
-    JobStatus.TERMINATED_ON_WARNING,
-]
-ONGOING_JOB_STATUSES: list[str] = [
-    JobStatus.CREATION_IN_PROGRESS,
-    JobStatus.IN_QUEUE,
-    JobStatus.ON_VALIDATION,
-    JobStatus.RUNNING,
-]
-
-
-class MiriaObject(FileTransferData):
-    """Model for representing a singular object transfer."""
-
-    _metadata = None
-    destination: str
-    source: str
-
-    @classmethod
-    def create_from_file_and_sample(
-        cls, file: File, sample: Sample, is_archiving: bool = True
-    ) -> "MiriaObject":
-        """Instantiates the class from a File and Sample object."""
-        if is_archiving:
-            return cls(destination=sample.internal_id, source=file.full_path)
-        return cls(destination=file.full_path, source=sample.internal_id)
-
-    @classmethod
-    def create_from_sample_and_destination(
-        cls, sample_and_destination: SampleAndDestination
-    ) -> "MiriaObject":
-        """Instantiates the class from a SampleAndDestination object,
-        i.e. when we want to fetch a folder containing all spring files for said sample."""
-        return cls(
-            destination=sample_and_destination.destination,
-            source=sample_and_destination.sample.internal_id,
-        )
-
-    def trim_path(self, attribute_to_trim: str):
-        """Trims the given attribute (source or destination) from its root directory."""
-        setattr(
-            self,
-            attribute_to_trim,
-            f"/{Path(getattr(self, attribute_to_trim)).relative_to(ROOT_TO_TRIM)}",
-        )
-
-    def add_repositories(self, source_prefix: str, destination_prefix: str):
-        """Prepends the given repositories to the source and destination paths."""
-        self.source: str = source_prefix + self.source
-        self.destination: str = destination_prefix + self.destination
-
-
-class TransferPayload(BaseModel):
-    """Model for representing a Dataflow transfer task."""
-
-    files_to_transfer: list[MiriaObject]
-    osType: str = OSTYPE
-    createFolder: bool = True
-    settings: list[dict] = []
-
-    def trim_paths(self, attribute_to_trim: str):
-        """Trims the source path from its root directory for all objects in the transfer."""
-        for miria_file in self.files_to_transfer:
-            miria_file.trim_path(attribute_to_trim=attribute_to_trim)
-
-    def add_repositories(self, source_prefix: str, destination_prefix: str):
-        """Prepends the given repositories to the source and destination paths all objects in the
-        transfer."""
-        for miria_file in self.files_to_transfer:
-            miria_file.add_repositories(
-                source_prefix=source_prefix, destination_prefix=destination_prefix
-            )
-
-    def model_dump(self, **kwargs) -> dict:
-        """Creates a correctly structured dict to be used as the request payload."""
-        payload: dict = super().model_dump(exclude={"files_to_transfer"})
-        payload["pathInfo"] = [miria_file.model_dump() for miria_file in self.files_to_transfer]
-        payload["metadataList"] = []
-        return payload
-
-    def post_request(self, url: str, headers: dict) -> "TransferJob":
-        """Sends a request to the given url with, the given headers, and its own content as payload.
-
-        Arguments:
-            url: URL to which the POST goes to.
-            headers: Headers which are set in the request
-        Raises:
-            HTTPError if the response status is not successful.
-            ValidationError if the response does not conform to the expected response structure.
-        Returns:
-            The job ID of the launched transfer task.
-        """
-
-        LOG.info(get_request_log(headers=headers, body=self.model_dump()))
-
-        response: Response = APIRequest.api_request_from_content(
-            api_method=APIMethods.POST,
-            url=url,
-            headers=headers,
-            json=self.model_dump(),
-            verify=False,
-        )
-        response.raise_for_status()
-        return TransferJob.model_validate(response.json())
-
-
-class AuthPayload(BaseModel):
-    """Model representing the payload for an Authentication request."""
-
-    dbName: str
-    name: str
-    password: str
-    superUser: bool = False
-
-
-class RefreshPayload(BaseModel):
-    """Model representing the payload for Auth-token refresh request."""
-
-    refresh: str
-
-
-class AuthToken(BaseModel):
-    """Model representing the response fields from an access request to the Dataflow API."""
-
-    access: str
-    expire: int
-    refresh: str | None = None
-
-
-class TransferJob(BaseModel):
-    """Model representing th response fields of an archive or retrieve reqeust to the Dataflow
-    API."""
-
-    job_id: int = Field(alias="jobId")
-
-
-class GetJobStatusResponse(BaseModel):
-    """Model representing the response fields from a get_job_status post."""
-
-    job_id: int = Field(alias="id")
-    status: JobStatus
-
-
-class GetJobStatusPayload(BaseModel):
-    """Model representing the payload for a get_job_status request."""
-
-    id: int
-
-    def get_job_status(self, url: str, headers: dict) -> GetJobStatusResponse:
-        """Sends a get request to the given URL with the given headers.
-        Returns the parsed status response of the task specified in the URL.
-        Raises:
-             HTTPError if the response code is not ok.
-        """
-
-        LOG.info(get_request_log(headers=headers, body=self.model_dump()))
-
-        response: Response = APIRequest.api_request_from_content(
-            api_method=APIMethods.GET,
-            url=url,
-            headers=headers,
-            json=self.model_dump(),
-            verify=False,
-        )
-        response.raise_for_status()
-        return GetJobStatusResponse.model_validate(response.json())
-
-
-class DeleteFileResponse(BaseModel):
-    message: str
-
-
-class DeleteFilePayload(BaseModel):
-    global_path: str
-
-    def delete_file(self, url: str, headers: dict) -> DeleteFileResponse:
-        """Posts to the given URL with the given headers to delete the file or directory at the specified global path.
-        Returns the parsed response.
-        Raises:
-             HTTPError if the response code is not ok.
-        """
-        LOG.info(get_request_log(headers=headers, body=self.model_dump()))
-
-        response: Response = APIRequest.api_request_from_content(
-            api_method=APIMethods.POST,
-            url=url,
-            headers=headers,
-            json=self.model_dump(),
-            verify=False,
-        )
-        response.raise_for_status()
-        return DeleteFileResponse.model_validate(response.json())
-
 
 class DDNDataFlowClient(ArchiveHandler):
     """Class for archiving and retrieving folders via DDN Dataflow."""