Open d-v-b opened 1 year ago
tischi
commented
1 year ago Dear @d-v-b ,
Thank you for reporting this!
This seems like some S3 error: Caused by: org.apache.http.HttpException: s3 protocol is not supported
Not sure what is going on...
@constantinpape can you maybe try opening the above data set using some python API to see if that works?
d-v-b
commented
1 year ago Is it possible that your plugin does not support urls formatted with the s3:// protocol? As a user I would find this a bit surprising, since s3:// is the standard protocol string for accessing stuff on s3, and the plugin says it supports s3... I tried again with the http:// url for that same resource (http://janelia-cosem-datasets.s3.amazonaws.com/jrc_hela-2/jrc_hela-2.zarr/em/fibsem-uint16/), and got the following error content:
For reference, neuroglancer handles both the s3 and http versions of the url correctly.
tischi
commented
1 year ago Ok, thanks for letting us know! We will look into it! I am not sure when I will find the time (our main developer of this code unfortunately left us)... Please ping me again if it is urgent for you..
Attempting to load the following dataset from s3 (
s3://janelia-cosem-datasets/jrc_hela-2/jrc_hela-2.zarr/em/fibsem-uint16/) causes the ome-zarr bdv plugin to fail. Unfortunately the plugin doesn't record the full exception traceback, but here's what appeared:traceback
``` (Fiji Is Just) ImageJ 2.9.0/1.53t; Java 1.8.0_322 [64-bit]; Mac OS X 10.16; 100MB of 2868MB (3%) java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw exception at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:308) at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:166) at ij.IJ.runPlugIn(IJ.java) at ij.Executer.runCommand(Executer.java:152) at ij.Executer.run(Executer.java:70) at java.lang.Thread.run(Thread.java:750) Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw exception at java.util.concurrent.FutureTask.report(FutureTask.java:122) at java.util.concurrent.FutureTask.get(FutureTask.java:192) at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:304) ... 5 more Caused by: java.lang.RuntimeException: Module threw exception at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63) at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) ... 1 more Caused by: com.amazonaws.SdkClientException: Unable to execute HTTP request: null at com.amazonaws.http.AmazonHttpClient$RequestExecutor.handleRetryableException(AmazonHttpClient.java:1207) at com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeHelper(AmazonHttpClient.java:1153) at com.amazonaws.http.AmazonHttpClient$RequestExecutor.doExecute(AmazonHttpClient.java:802) at com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeWithTimer(AmazonHttpClient.java:770) at com.amazonaws.http.AmazonHttpClient$RequestExecutor.execute(AmazonHttpClient.java:744) at com.amazonaws.http.AmazonHttpClient$RequestExecutor.access$500(AmazonHttpClient.java:704) at com.amazonaws.http.AmazonHttpClient$RequestExecutionBuilderImpl.execute(AmazonHttpClient.java:686) at com.amazonaws.http.AmazonHttpClient.execute(AmazonHttpClient.java:550) at com.amazonaws.http.AmazonHttpClient.execute(AmazonHttpClient.java:530) at com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:5062) at com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:5008) at com.amazonaws.services.s3.AmazonS3Client.headBucket(AmazonS3Client.java:1416) at org.embl.mobie.io.util.S3Utils.getS3Client(S3Utils.java:78) at org.embl.mobie.io.ome.zarr.loaders.N5S3OMEZarrImageLoader$N5S3ZarrReaderCreator.create(N5S3OMEZarrImageLoader.java:93) at org.embl.mobie.io.ome.zarr.loaders.N5S3OMEZarrImageLoader.The multiscale metadata for that dataset is here:
.zattrs
```json { "multiscales": [ { "axes": [ { "name": "z", "type": "space", "unit": "nanometer" }, { "name": "y", "type": "space", "unit": "nanometer" }, { "name": "x", "type": "space", "unit": "nanometer" } ], "coordinateTransformations": [ { "scale": [ 1.0, 1.0, 1.0 ], "type": "scale" } ], "datasets": [ { "coordinateTransformations": [ { "scale": [ 5.24, 4.0, 4.0 ], "type": "scale" }, { "translation": [ 0.0, 0.0, 0.0 ], "type": "translation" } ], "path": "s0" }, { "coordinateTransformations": [ { "scale": [ 10.48, 8.0, 8.0 ], "type": "scale" }, { "translation": [ 2.62, 2.0, 2.0 ], "type": "translation" } ], "path": "s1" }, { "coordinateTransformations": [ { "scale": [ 20.960000000000004, 16.0, 16.0 ], "type": "scale" }, { "translation": [ 7.86, 6.0, 6.0 ], "type": "translation" } ], "path": "s2" }, { "coordinateTransformations": [ { "scale": [ 41.92, 32.0, 32.0 ], "type": "scale" }, { "translation": [ 18.340000000000003, 14.0, 14.0 ], "type": "translation" } ], "path": "s3" }, { "coordinateTransformations": [ { "scale": [ 83.84, 64.0, 64.0 ], "type": "scale" }, { "translation": [ 39.300000000000004, 30.0, 30.0 ], "type": "translation" } ], "path": "s4" } ], "metadata": null, "name": "", "type": null, "version": "0.4" } ] } ```