cirro.sdk.reference

 1from typing import List
 2
 3from cirro_api_client.v1.models import Reference
 4
 5from cirro.cirro_client import CirroApi
 6from cirro.models.file import File
 7from cirro.sdk.asset import DataPortalAssets, DataPortalAsset
 8from cirro.sdk.file import DataPortalFile
 9
10
11class DataPortalReference(DataPortalAsset):
12    """
13    Reference data object containing files which can be used for analysis in a particular project.
14    """
15    def __init__(self, ref: Reference, project_id: str, client: CirroApi):
16        """
17        Instantiate by listing the references which have been added to a particular project
18        ```python
19        from cirro import DataPortal()
20        portal = DataPortal()
21        project = portal.get_project_by_name("Project Name")
22        references = project.list_references()
23        ```
24        """
25        self._data = ref
26        self._files = [
27            DataPortalFile(File.from_file_entry(f, project_id), client) for f in ref.files
28        ]
29
30    @property
31    def files(self) -> List[DataPortalFile]:
32        """File(s) contained in the reference"""
33        return self._files
34
35    @property
36    def name(self) -> str:
37        """Reference name"""
38        return self._data.name
39
40    @property
41    def type(self) -> str:
42        """Type of reference data (e.g. genome_fasta)"""
43        return self._data.type
44
45    @property
46    def absolute_path(self):
47        if len(self._files) == 0:
48            return None
49        return self._files[0].absolute_path
50
51    def __str__(self):
52        return self.name
53
54
55class DataPortalReferences(DataPortalAssets[DataPortalReference]):
56    """Collection of DataPortalReference objects."""
57    asset_name = "reference"
58
59    def get_by_id(self, _id: str) -> DataPortalReference:
60        raise NotImplementedError("Filtering by ID is not supported, use get_by_name")