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Add OMERO File Source Plugin #21367

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Add OMERO File Source Plugin #21367

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664580c
Adds OMERO remote file source integration
davelopez Nov 28, 2025
8c28045
Add omero-py conditional dependency
davelopez Nov 28, 2025
76e1c02
Adds OMERO user template
davelopez Nov 28, 2025
a8199b6
Exports all Z-planes as multi-page TIFF
davelopez Nov 28, 2025
8a46e6e
Refactors OMERO connection handling with context manager
davelopez Nov 28, 2025
292f6fb
Improves OMERO error handling with specific exceptions
davelopez Nov 28, 2025
8d7f3dd
Adds pagination support to OMERO file listings
davelopez Nov 28, 2025
39a5104
Adds server-side search and filtering to OMERO file source
davelopez Nov 28, 2025
c1a6d54
Handles OMERO SecurityViolation on original file download
davelopez Nov 28, 2025
e31baca
Improve OMERO template description
davelopez Nov 28, 2025
cd1df36
Remove unnecessary type ignores
davelopez Nov 28, 2025
d841037
Adds conditional import handling for OMERO file source
davelopez Nov 28, 2025
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4 changes: 4 additions & 0 deletions client/src/api/fileSources.ts
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Expand Up @@ -70,6 +70,10 @@ export const templateTypes: FileSourceTypesDetail = {
icon: faHubspot,
message: "This is a file repository plugin that connects with the Hugging Face Hub.",
},
omero: {
icon: faNetworkWired,
message: "This is a file repository plugin that connects with an OMERO server.",
},
};

export const FileSourcesValidFilters = {
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6 changes: 4 additions & 2 deletions client/src/api/schema/schema.ts
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Expand Up @@ -11882,7 +11882,8 @@ export interface components {
| "zenodo"
| "rspace"
| "dataverse"
| "huggingface";
| "huggingface"
| "omero";
/** Variables */
variables?:
| (
Expand Down Expand Up @@ -23040,7 +23041,8 @@ export interface components {
| "zenodo"
| "rspace"
| "dataverse"
| "huggingface";
| "huggingface"
| "omero";
/** Uri Root */
uri_root: string;
/**
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3 changes: 3 additions & 0 deletions lib/galaxy/dependencies/__init__.py
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Expand Up @@ -336,6 +336,9 @@ def is_redis_url(url: str) -> bool:
def check_huggingface_hub(self):
return "huggingface" in self.file_sources

def check_omero_py(self):
return "omero" in self.file_sources


def optional(config_file=None):
if not config_file:
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1 change: 1 addition & 0 deletions lib/galaxy/dependencies/conditional-requirements.txt
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Expand Up @@ -34,6 +34,7 @@ fs-basespace # type: basespace
fs-azureblob # type: azure
rspace-client>=2.6.1,<3 # type: rspace
huggingface_hub
omero-py #type: omero # Requires manual installation of additional dependencies, see https://omero.readthedocs.io/en/stable/developers/Python.html#omero-python-language-bindings

# Vault backend
hvac
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