Unverified Commit a41a0989 authored by mvdbeek's avatar mvdbeek
Browse files

Allow setting auto_decompress property in staging interface 

This allows defining inputs such as
```
     Drosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz:
       class: File
       location: https://zenodo.org/record/6457007/files/Drosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz
       filetype: gtf
       decompress: true
```

without needing to know what the server side default of auto_compress
is.
parent 85df98a7

lib/galaxy/tool_util/client/staging.py

+4 −0
Original line number Diff line number Diff line
@@ -40,6 +40,7 @@ LOAD_TOOLS_FROM_PATH = True 
DEFAULT_USE_FETCH_API = True

DEFAULT_FILE_TYPE = "auto"

DEFAULT_DBKEY = "?"

DEFAULT_DECOMPRESS = False





class StagingInterface(metaclass=abc.ABCMeta):
@@ -104,6 +105,7 @@ class StagingInterface(metaclass=abc.ABCMeta): 
                    file_type=file_type,

                    dbkey=dbkey,

                    to_posix_lines=to_posix_lines,

                    decompress=upload_target.properties.get("decompress") or DEFAULT_DECOMPRESS,

                )

                name = _file_path_to_name(file_path)

                if file_path is not None:
@@ -333,6 +335,8 @@ def _fetch_payload(history_id, file_type=DEFAULT_FILE_TYPE, dbkey=DEFAULT_DBKEY, 
            element[arg] = kwd[arg]

    if "file_name" in kwd:

        element["name"] = kwd["file_name"]

    if "decompress" in kwd:

        element["auto_decompress"] = kwd["decompress"]

    target = {

        "destination": {"type": "hdas"},

        "elements": [element],

lib/galaxy/tool_util/cwl/util.py

+2 −0
Original line number Diff line number Diff line
@@ -232,6 +232,8 @@ def galactic_job_json( 
            kwd["tags"] = value.get("tags")

        if "dbkey" in value:

            kwd["dbkey"] = value.get("dbkey")

        if "decompress" in value:

            kwd["decompress"] = value["decompress"]

        if composite_data_raw:

            composite_data = []

            for entry in composite_data_raw:

lib/galaxy_test/api/test_tools_upload.py

+34 −0
Original line number Diff line number Diff line
@@ -280,6 +280,40 @@ class TestToolsUpload(ApiTestCase): 
        details = self.dataset_populator.get_history_dataset_details(history_id=history_id, dataset=dataset)

        assert details["genome_build"] == "hg19"



    @skip_if_github_down

    def test_stage_fetch_decompress_true(self, history_id: str) -> None:

        job = {

            "input1": {

                "class": "File",

                "format": "fasta",

                "location": "https://github.com/galaxyproject/galaxy/blob/dev/test-data/1.fasta.gz?raw=true",

                "decompress": True,

            }

        }

        inputs, datasets = stage_inputs(

            self.galaxy_interactor, history_id, job, use_path_paste=False, to_posix_lines=False

        )

        dataset = datasets[0]

        content = self.dataset_populator.get_history_dataset_content(history_id=history_id, dataset=dataset)

        assert content.startswith(">hg17")



    @skip_if_github_down

    def test_stage_fetch_decompress_false(self, history_id: str) -> None:

        job = {

            "input1": {

                "class": "File",

                "format": "fasta",

                "location": "https://github.com/galaxyproject/galaxy/blob/dev/test-data/1.fasta.gz?raw=true",

                "decompress": False,

            }

        }

        inputs, datasets = stage_inputs(

            self.galaxy_interactor, history_id, job, use_path_paste=False, to_posix_lines=False

        )

        dataset = datasets[0]

        content = self.dataset_populator.get_history_dataset_content(history_id=history_id, dataset=dataset)

        assert not content.startswith(">hg17")



    @skip_if_github_down

    def test_upload_multiple_mixed_success(self, history_id):

        destination = {"type": "hdas"}