Drop URI datatype in favor of deferred

galaxyproject · Oct 31, 2024 · 25bff00 · 25bff00
1 parent e273bc8
commit 25bff00
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Showing 2 changed files with 0 additions and 51 deletions.
diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -303,9 +303,7 @@
     </datatype>
     <datatype extension="directory" type="galaxy.datatypes.data:Directory"/>
     <datatype extension="zarr" type="galaxy.datatypes.data:ZarrDirectory" />
-    <datatype extension="zarr_uri" type="galaxy.datatypes.text:ZarrRemoteUri" display_in_upload="true"/>
     <datatype extension="ome_zarr" type="galaxy.datatypes.images:OMEZarr" />
-    <datatype extension="ome_zarr_uri" type="galaxy.datatypes.text:OMEZarrRemoteUri" subclass="true" display_in_upload="true"/>
     <datatype extension="yaml" type="galaxy.datatypes.text:Yaml" display_in_upload="true" />
     <!-- Proteomics Datatypes -->
     <datatype extension="mrm" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" subclass="true"/>
@@ -1118,7 +1116,6 @@
     <sniffer type="galaxy.datatypes.qiime2:QIIME2Metadata"/>
     <sniffer type="galaxy.datatypes.qiime2:QIIME2Artifact"/>
     <sniffer type="galaxy.datatypes.qiime2:QIIME2Visualization"/>
-    <sniffer type="galaxy.datatypes.text:ZarrRemoteUri"/>
     <sniffer type="galaxy.datatypes.binary:CompressedOMEZarrZipArchive"/>
     <sniffer type="galaxy.datatypes.binary:CompressedZarrZipArchive"/>
     <sniffer type="galaxy.datatypes.binary:CompressedZipArchive"/>

diff --git a/lib/galaxy/datatypes/text.py b/lib/galaxy/datatypes/text.py
@@ -1421,51 +1421,3 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
             (lines[9].strip() == end_header and lines[10].strip() == grid_points)
             or (lines[9].strip() == end_header_spin and lines[10].strip() == grid_points_spin)
         )
-
-
-class ZarrRemoteUri(Text):
-    """Zarr remote URI
-
-    It is a text file containing a single line with the URI to a remote Zarr store.
-    The URI must NOT include the protocol (http://, https://, s3://, etc.) otherwise
-    Galaxy will try to download it as a file.
-    """
-
-    info = "Zarr remote URI"
-
-    MetadataElement(
-        name="remote_uri",
-        default=None,
-        desc="Remote URI to a Zarr store",
-        readonly=True,
-        optional=False,
-        visible=False,
-    )
-
-    def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> None:
-        with open(dataset.get_file_name()) as f:
-            uri = f.read().strip()
-            if "://" not in uri:
-                uri = f"https://{uri}"
-            dataset.metadata.remote_uri = uri
-
-    def sniff(self, filename: str) -> bool:
-        # Must have a single line and end with '.zarr'
-        with open(filename) as f:
-            lines = f.readlines()
-            return len(lines) == 1 and lines[0].strip().endswith(".zarr")
-
-    def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
-        if not dataset.dataset.purged:
-            dataset.info = self.info
-        else:
-            dataset.peek = "file does not exist"
-            dataset.blurb = "file purged from disk"
-
-
-class OMEZarrRemoteUri(ZarrRemoteUri):
-    """OME-Zarr remote URI"""
-
-    file_ext = "ome_zarr_uri"
-
-    info = "OME-Zarr remote URI"