presigned URL in score-client

Question

[Javier]

Hi, I'm working on a project that uses data from ICGC. I'm downloading CRAM files from 2 cohorts. At the moment I download them, there are no problems, but since the last maintenance, the same command I used doesn't work. im using the new object ids and downloaded the newest version of the Score client, and yet it doesn't work.

This is the last error that stops me:

ERROR: Command error: Could not parse presigned URL - missing expected expiry date parameters
Please check the log for detailed error messages

Checking the logs, there's this:

2024-06-28 17:49:47,515 [main] ERROR b.o.s.c.ClientMain - Unknown error: 
java.lang.IllegalArgumentException: Could not parse presigned URL - missing expected expiry date parameters
    at bio.overture.score.client.util.AzurePresignedUrlValidator.extractExpiryDate(AzurePresignedUrlValidator.java:52)
    at bio.overture.score.client.util.PresignedUrlValidator.extractExpiryDate(PresignedUrlValidator.java:67)
    at bio.overture.score.client.util.PresignedUrlValidator.getExpiry(PresignedUrlValidator.java:57)
    at bio.overture.score.client.util.PresignedUrlValidator.isUrlExpired(PresignedUrlValidator.java:43)
    at bio.overture.score.client.util.PresignedUrlValidator.isUrlExpired(PresignedUrlValidator.java:39)
    at bio.overture.score.client.download.DownloadStateStore.getProgress(DownloadStateStore.java:97)
    at bio.overture.score.client.download.DownloadService.resumeIfPossible(DownloadService.java:155)
    at bio.overture.score.client.download.DownloadService.download(DownloadService.java:118)
    at bio.overture.score.client.command.DownloadCommand.downloadObjects(DownloadCommand.java:258)
    at bio.overture.score.client.command.DownloadCommand.execute(DownloadCommand.java:161)
    at bio.overture.score.client.ClientMain.run(ClientMain.java:147)
    at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:779)
    at org.springframework.boot.SpringApplication.callRunners(SpringApplication.java:763)
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:318)
    at org.springframework.boot.builder.SpringApplicationBuilder.run(SpringApplicationBuilder.java:139)
    at bio.overture.score.client.ClientMain.main(ClientMain.java:122)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:568)
    at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:47)
    at org.springframework.boot.loader.Launcher.launch(Launcher.java:86)
    at org.springframework.boot.loader.Launcher.launch(Launcher.java:50)
    at org.springframework.boot.loader.JarLauncher.main(JarLauncher.java:51)

Apparently, this is a problem related to AWS, but I didn't use it the first time and I tried it on another computer and it gives me the same problem. Is this problem on my end at all, or a bug from ICGC?

[GenoMax]

This sounds like a SCORe client problem. Strangely many of the ICGC pages are not working for me. The SCORe client link on this page is also coming up with a 404 error: https://song-docs.readthedocs.io/en/develop/score-client.html

Your best bet may be to contact ICGC support.

[Javier]

Thanks a lot for the fast answer. I had another question that I forgot to ask: Have you ever tried the slice CRAM option? (to get just a section of the genome) Because it has never worked for me; the output always contains just the header but none of the information.