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ome / omero-insight

Gradle project containing insight java client for OMERO
https://www.openmicroscopy.org/omero/
GNU General Public License v2.0
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Harmony image format with http links fails to import #376

Open dominikl opened 1 year ago

dominikl commented 1 year ago

See https://forum.image.sc/t/bioformats-importer-in-fiji-resolves-http-urls-to-tiffs-when-importing-image-index-file-but-omero-importer-does-not/83530 .

imagesc-bot commented 1 year ago

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/bioformats-importer-in-fiji-resolves-http-urls-to-tiffs-when-importing-image-index-file-but-omero-importer-does-not/83530/2

dgault commented 1 year ago

The full stack trace using the latest Insight client (version 5.8.1):

java.io.FileNotFoundException: http:/(hostname removed)/ODA/Images/C/c64431a8-f4be-4668-a36b-d43cc4969ab7/109-41-610-410-42-124-47-811.tiff (No such file or directory)
at java.base/java.io.FileInputStream.open0(Native Method)
at java.base/java.io.FileInputStream.open(FileInputStream.java:219)
at java.base/java.io.FileInputStream.(FileInputStream.java:157)
at ome.formats.importer.transfers.UploadFileTransfer.transfer(UploadFileTransfer.java:54)
at ome.formats.importer.ImportLibrary.uploadFile(ImportLibrary.java:531)
at org.openmicroscopy.shoola.env.data.OMEROGateway.importImageFile(OMEROGateway.java:5825)
at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1233)
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:103)
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:49)
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:127)
at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
at java.base/java.lang.Thread.run(Thread.java:829)

at org.openmicroscopy.shoola.env.data.OMEROGateway.importImageFile(OMEROGateway.java:5857)
at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1233)
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:103)
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:49)
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:127)
at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
at java.base/java.lang.Thread.run(Thread.java:829)
Caused by: java.io.FileNotFoundException: http:/(hostname removed)/ODA/Images/C/c64431a8-f4be-4668-a36b-d43cc4969ab7/109-41-610-410-42-124-47-811.tiff (No such file or directory)
at java.base/java.io.FileInputStream.open0(Native Method)
at java.base/java.io.FileInputStream.open(FileInputStream.java:219)
at java.base/java.io.FileInputStream.(FileInputStream.java:157)
at ome.formats.importer.transfers.UploadFileTransfer.transfer(UploadFileTransfer.java:54)
at ome.formats.importer.ImportLibrary.uploadFile(ImportLibrary.java:531)
at org.openmicroscopy.shoola.env.data.OMEROGateway.importImageFile(OMEROGateway.java:5825)
… 11 more
jburel commented 1 year ago

CLI import also does not allow to import data from a URL