fixed dataset containing no fileset

PolusAI · Apr 23, 2024 · 30d5f2b · 30d5f2b
1 parent 98ac45f
commit 30d5f2b
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Showing 8 changed files with 175 additions and 130 deletions.
diff --git a/...mero-download-tool/examples/idr0019-test/22_lines_HC_EGF_200145913/B2_f0_z0_t0_c0.ome.tif b/...mero-download-tool/examples/idr0019-test/22_lines_HC_EGF_200145913/B2_f0_z0_t0_c0.ome.tif
diff --git a/...mero-download-tool/examples/idr0019-test/22_lines_HC_EGF_200145913/B2_f0_z0_t0_c1.ome.tif b/...mero-download-tool/examples/idr0019-test/22_lines_HC_EGF_200145913/B2_f0_z0_t0_c1.ome.tif
diff --git a/...mero-download-tool/examples/idr0019-test/22_lines_HC_EGF_200145913/B2_f0_z0_t0_c2.ome.tif b/...mero-download-tool/examples/idr0019-test/22_lines_HC_EGF_200145913/B2_f0_z0_t0_c2.ome.tif
diff --git a/utils/omero-download-tool/plugin.json b/utils/omero-download-tool/plugin.json
@@ -41,9 +41,9 @@
       "required": "False"
     },
     {
-      "name": "id",
+      "name": "objectId",
       "type": "integer",
-      "title": "id",
+      "title": "objectId",
       "description": "Identifier of the object to be downloaded.",
       "required": "False"
     },
@@ -79,9 +79,9 @@
       "required": "False"
     },
     {
-      "key": "inputs.id",
+      "key": "inputs.objectId",
       "type": "integer",
-      "title": "id",
+      "title": "objectId",
       "description": "Identifier of the object to be downloaded.",
       "required": "False"
     },

diff --git a/utils/omero-download-tool/run-plugin.sh b/utils/omero-download-tool/run-plugin.sh
@@ -7,7 +7,7 @@ echo ${datapath}
 # Inputs
 out_dir=${datapath}/out
 dataType="well"
-id=1084
+objectId=1084
 
 
 # #Show the help options
@@ -17,5 +17,5 @@ docker run -v ${datapath}:${datapath} \
             polusai/omero-download-tool:${version} \
             --dataType ${dataType} \
             --name ${name} \
-            --id ${name} \
+            --objectId ${name} \
             --outDir ${out_dir}
diff --git a/utils/omero-download-tool/src/polus/images/utils/omero_download/omero_download.py b/utils/omero-download-tool/src/polus/images/utils/omero_download/omero_download.py
diff --git a/utils/omero-download-tool/tests/conftest.py b/utils/omero-download-tool/tests/conftest.py
@@ -9,6 +9,7 @@
 from typing import Union
 
 import pytest
+from polus.images.utils.omero_download.omero_download import DATATYPE
 
 
 def pytest_addoption(parser: pytest.Parser) -> None:
@@ -37,7 +38,11 @@ def output_directory() -> Union[str, Path]:
 
 @pytest.fixture(
     params=[
-        ("well", None, 1084),
+        (DATATYPE.WELL, None, 1084),
+        (DATATYPE.DATASET, "211129_pyomero", None),
+        (DATATYPE.SCREEN, "Inae_timeseries", None),
+        (DATATYPE.PROJECT, "NCI_IMS", None),
+        (DATATYPE.PLATE, None, 60),
     ],
 )
 def get_params(request: pytest.FixtureRequest) -> pytest.FixtureRequest:

diff --git a/utils/omero-download-tool/tests/test_omero_download.py b/utils/omero-download-tool/tests/test_omero_download.py
@@ -22,7 +22,6 @@ def test_omero_download(
         out_dir=output_directory,
     )
     model.get_data()
-
     assert any(output_directory.iterdir()) is True
 
     clean_directories()