galaxy/test/unit/webapps/api/test_fetch_schema.py

from copy import deepcopy
from json import dumps

import yaml

from galaxy.schema.fetch_data import (
    FetchDataPayload,
    FileDataElement,
    FtpImportElement,
    NestedElement,
    PastedDataElement,
    UrlDataElement,
)

HISTORY_ID = "378807ae895b74ff"
example_payload = {
    "targets": [
        {
            "destination": {"type": "hdas"},
            "elements": [
                {
                    "src": "pasted",
                    "paste_content": "abcdef",
                    "name": None,
                    "dbkey": "?",
                    "ext": "auto",
                    "space_to_tab": False,
                    "to_posix_lines": True,
                },
                {"src": "url", "url": "https://github.com/bla.txt"},
                {"src": "files", "name": "uploaded file"},
            ],
        }
    ],
    "auto_decompress": True,
    "files": [],
    "history_id": HISTORY_ID,
}
items_payload = {
    "targets": [
        {
            "destination": {"type": "hdas"},
            "items": [
                {
                    "src": "url",
                    "url": "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/html_file.txt",
                },
            ],
        }
    ],
    "history_id": HISTORY_ID,
}

nested_collection_payload = {
    "targets": [
        {
            "destination": {"type": "hdca"},
            "elements": [{"name": "samp1", "elements": [{"src": "files", "dbkey": "hg19", "info": "my cool bed"}]}],
            "collection_type": "list:list",
            "name": "Test upload",
        }
    ],
    "history_id": HISTORY_ID,
}

ftp_hdca_target = {
    "elements_from": "directory",
    "src": "ftp_import",
    "ftp_path": "subdir",
    "collection_type": "list",
}

recursive_archive_payload = {
    "history_id": "70583a56914a26f9",
    "targets": [
        {
            "destination": {"type": "library", "name": "My Cool Library"},
            "items_from": "archive",
            "src": "path",
            "path": "/Users/mvandenb/src/metadata_embed/test-data/testdir1.zip",
        }
    ],
}


nested_element_regression_payload = {
    "history_id": "c369577e3c21d7b7",
    "targets": [
        {
            "destination": {"type": "hdca"},
            "elements": [
                {
                    "name": "a",
                    "elements": [
                        {
                            "name": "a",
                            "elements": [
                                {
                                    "url": "https://example.com",
                                    "src": "url",
                                    "dbkey": "?",
                                    "ext": "auto",
                                    "name": "forward",
                                },
                                {
                                    "url": "https://example.com",
                                    "src": "url",
                                    "dbkey": "?",
                                    "ext": "auto",
                                    "name": "reverse",
                                },
                            ],
                            "collection_type": "paired",
                        },
                    ],
                    "collection_type": "list:paired",
                },
            ],
            "collection_type": "list:list:paired",
            "name": "a",
        }
    ],
    "auto_decompress": True,
}

library_payload = yaml.safe_load(
    """
destination:
  type: library
  name: "Cool Training Library"
  description: "A longer description."
  synopsis: "Optional - does anyone ever set this?"
items:
  - name: "Test Folder 1"
    description: "Description of what is in Test Folder 1"  # Only populated with new API.
    items:
      - url: https://raw.githubusercontent.com/eteriSokhoyan/test-data/master/cliques-high-representatives.fa
        src: url
        ext: fasta
        info: "A cool longer description."  # Only populated with new API.
        dbkey: "hg19"  # Only populated with new API.
  - name: "Test data segmentation-fold"
    items:
      - url: https://raw.githubusercontent.com/yhoogstrate/segmentation-fold/55d0bb28b01e613844ca35cf21fa41379fd72770/scripts/energy-estimation-utility/tests/test-data/workflow-test_cd-box_kturns.xml
        name: workflow-test_cd-box_kturns.xml  # Only populated with new API.
        info: Downloaded from https://raw.githubusercontent.com/yhoogstrate/segmentation-fold/55d0bb28b01e613844ca35cf21fa41379fd72770/scripts/energy-estimation-utility/tests/test-data/workflow-test_cd-box_kturns.xml
        src: url
        ext: xml

"""
)


def test_fetch_data_schema():
    payload = FetchDataPayload(**example_payload)
    elements = payload.targets[0].items  # type: ignore[union-attr]  # alias doesn't type check properly
    assert len(elements) == 3
    assert isinstance(elements[0], PastedDataElement)
    assert isinstance(elements[1], UrlDataElement)
    assert isinstance(elements[2], FileDataElement)


def test_data_items():
    FetchDataPayload(**items_payload)


def test_nested_collection():
    payload = FetchDataPayload(**nested_collection_payload)
    collection_element = payload.targets[0].items[0]  # type: ignore[union-attr]  # alias doesn't type check properly
    assert isinstance(collection_element, NestedElement)
    assert isinstance(collection_element.items[0], FileDataElement)


def test_ftp_hdca_target():
    FtpImportElement(**ftp_hdca_target)


def test_recursive_archive():
    FetchDataPayload(**recursive_archive_payload)


def test_recursive_archive_form_like_data():
    payload = deepcopy(recursive_archive_payload)
    payload["targets"] = dumps(payload["targets"])
    FetchDataPayload(**payload)


def test_nested_element_regression():
    FetchDataPayload(**nested_element_regression_payload)


def test_library_payload():
    FetchDataPayload(targets=[library_payload], history_id=HISTORY_ID)