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cytomine / Cytomine-core

Cytomine-Core is the main web server implementing the Cytomine API
http://doc.cytomine.org
Apache License 2.0
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Cytomine Core : Upload image failed #1203

Open hervekhg opened 3 years ago

hervekhg commented 3 years ago

Hi, I've installed Cytomine, all the services (core, ims, iipoff, iipcyto...) is running but when I try to upload image it's failed. image

But i can see the image on /data/images on ims containers image

Below the complete logs of ims when i try to upload a file.

2021-06-02 06:33:27,837 [http-bio-8081-exec-3] INFO storage.StorageController - Upload is made on Cytomine = http://core.cyto89.local 2021-06-02 06:33:27,837 [http-bio-8081-exec-3] INFO storage.StorageController - We use "e3c09071-c05b-466e-9218-91d12c560da6"/"5546bb94-269d-4765-b86a-37a4c3b58c45" to connect 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - tryAPIAuthentification 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - cytomineUrl=http://core.cyto89.local 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - ISPubKey="e3c09071-c05b-466e-9218-91d12c560da6" 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - ISPrivKey="5546bb94-269d-4765-b86a-37a4c3b58c45" 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - authorization=CYTOMINE e3c09071-c05b-466e-9218-91d12c560da6:OxBhLvTzry6MQ//y6tj46E2MUbc= 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - host=ims:8081 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - connection=close 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - content-length=648 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - x-request-id=6c59df8f6425cba8912ef4b51490861a 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - x-real-ip=10.96.89.4 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - x-forwarded-for=10.96.89.4 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - x-forwarded-proto=http 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - x-forwarded-host=upload.cyto89.local 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - x-forwarded-port=80 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - x-scheme=http 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - origin=http://core.cyto89.local 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - referer=http://core.cyto89.local/ 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - user-agent=Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/70.0.3538.102 Safari/537.36 Edge/18.19043 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - cache-control=max-age=0 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - accept=application/json, text/plain, / 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - accept-language=en-US,en;q=0.5 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - authorization=CYTOMINE e3c09071-c05b-466e-9218-91d12c560da6:OxBhLvTzry6MQ//y6tj46E2MUbc= 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - content-type=multipart/form-data; boundary=---------------------------7e519b1b20214 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - content-type-full=null 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - datefull=2021-06-02T06:02:20.308Z 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - accept-encoding=gzip, deflate 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - finalDate=2021-06-02T06:02:20.308Z 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - forwardURI=/upload 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - content_md5= 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - content_type= 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - date=2021-06-02T06:02:20.308Z 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - queryString=?cytomine=http://core.cyto89.local&idStorage=86 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - path=/upload 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - method=POST 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - accessKey=e3c09071-c05b-466e-9218-91d12c560da6 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - Connection Cytomine: http://core.cyto89.local "e3c09071-c05b-466e-9218-91d12c560da6" "5546bb94-269d-4765-b86a-37a4c3b58c45" 2021-06-02 06:33:27,838 [http-bio-8081-exec-3] INFO web.CytomineService - cytomine.getUser(e3c09071-c05b-466e-9218-91d12c560da6) 2021-06-02 06:33:27,839 [http-bio-8081-exec-3] INFO client.HttpClient - Connection to http://core.cyto89.local/api/user.json?publicKey=e3c09071-c05b-466e-9218-91d12c560da6 2021-06-02 06:33:50,240 [quartzScheduler_Worker-9] INFO client.Cytomine - fetchCollection=/api/deletecommand.json?domain=uploadedFile&after=1622442830240&max=0&offset=0 2021-06-02 06:33:50,240 [quartzScheduler_Worker-9] INFO client.HttpClient - Connection to http://core:8080/api/deletecommand.json?domain=uploadedFile&after=1622442830240&max=0&offset=0 2021-06-02 06:33:50,248 [quartzScheduler_Worker-9] INFO client.Cytomine - 401 2021-06-02 06:33:50,248 [quartzScheduler_Worker-9] INFO core.JobRunShell - Job GRAILS_JOBS.ims.DeleteImageFileJob threw a JobExecutionException: org.quartz.JobExecutionException: java.lang.NullPointerException [See nested exception: java.lang.NullPointerException] at grails.plugins.quartz.GrailsJobFactory$GrailsJob.execute(GrailsJobFactory.java:111) at org.quartz.core.JobRunShell.run(JobRunShell.java:202) at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:573) Caused by: java.lang.NullPointerException at be.cytomine.client.collections.Collection.size(Collection.java:66) at ims.DeleteImageFileJob.execute(DeleteImageFileJob.groovy:36) at grails.plugins.quartz.GrailsJobFactory$GrailsJob.execute(GrailsJobFactory.java:104) ... 2 more 2021-06-02 06:33:50,248 [quartzScheduler_Worker-9] ERROR listeners.ExceptionPrinterJobListener - Exception occurred in job: Grails Job org.quartz.JobExecutionException: java.lang.NullPointerException [See nested exception: java.lang.NullPointerException] at grails.plugins.quartz.GrailsJobFactory$GrailsJob.execute(GrailsJobFactory.java:111) at org.quartz.core.JobRunShell.run(JobRunShell.java:202) at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:573) Caused by: java.lang.NullPointerException at be.cytomine.client.collections.Collection.size(Collection.java:66) at ims.DeleteImageFileJob.execute(DeleteImageFileJob.groovy:36) at grails.plugins.quartz.GrailsJobFactory$GrailsJob.execute(GrailsJobFactory.java:104) ... 2 more

EKami commented 1 year ago

Looks like we are a lot of people running into this issue but never had a response from the devs. Did you manage to fix it?

geektortoise commented 1 year ago

Hello, I'm no more on this project. However, a new version of Cytomine has been released with a new Core (this one is the legacy). Does the problem still occur ?