{"action":"created","issue":{"url":"https://api.github.com/repos/genepattern/genepattern-python/issues/1","repository_url":"https://api.github.com/repos/genepattern/genepattern-python","labels_url":"https://api.github.com/repos/genepattern/genepattern-python/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/genepattern/genepattern-python/issues/1/comments","events_url":"https://api.github.com/repos/genepattern/genepattern-python/issues/1/events","html_url":"https://github.com/genepattern/genepattern-python/issues/1","id":169759069,"number":1,"title":"Uploaded file names + how to call stderr from job?","user":{"login":"olgabot","id":806256,"avatar_url":"https://avatars.githubusercontent.com/u/806256?v=3","gravatar_id":"","url":"https://api.github.com/users/olgabot","html_url":"https://github.com/olgabot","followers_url":"https://api.github.com/users/olgabot/followers","following_url":"https://api.github.com/users/olgabot/following{/other_user}","gists_url":"https://api.github.com/users/olgabot/gists{/gist_id}","starred_url":"https://api.github.com/users/olgabot/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/olgabot/subscriptions","organizations_url":"https://api.github.com/users/olgabot/orgs","repos_url":"https://api.github.com/users/olgabot/repos","events_url":"https://api.github.com/users/olgabot/events{/privacy}","received_events_url":"https://api.github.com/users/olgabot/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"tmtabor","id":9056964,"avatar_url":"https://avatars.githubusercontent.com/u/9056964?v=3","gravatar_id":"","url":"https://api.github.com/users/tmtabor","html_url":"https://github.com/tmtabor","followers_url":"https://api.github.com/users/tmtabor/followers","following_url":"https://api.github.com/users/tmtabor/following{/other_user}","gists_url":"https://api.github.com/users/tmtabor/gists{/gist_id}","starred_url":"https://api.github.com/users/tmtabor/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tmtabor/subscriptions","organizations_url":"https://api.github.com/users/tmtabor/orgs","repos_url":"https://api.github.com/users/tmtabor/repos","events_url":"https://api.github.com/users/tmtabor/events{/privacy}","received_events_url":"https://api.github.com/users/tmtabor/received_events","type":"User","site_admin":false},"assignees":[{"login":"tmtabor","id":9056964,"avatar_url":"https://avatars.githubusercontent.com/u/9056964?v=3","gravatar_id":"","url":"https://api.github.com/users/tmtabor","html_url":"https://github.com/tmtabor","followers_url":"https://api.github.com/users/tmtabor/followers","following_url":"https://api.github.com/users/tmtabor/following{/other_user}","gists_url":"https://api.github.com/users/tmtabor/gists{/gist_id}","starred_url":"https://api.github.com/users/tmtabor/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tmtabor/subscriptions","organizations_url":"https://api.github.com/users/tmtabor/orgs","repos_url":"https://api.github.com/users/tmtabor/repos","events_url":"https://api.github.com/users/tmtabor/events{/privacy}","received_events_url":"https://api.github.com/users/tmtabor/received_events","type":"User","site_admin":false}],"milestone":null,"comments":8,"created_at":"2016-08-06T18:15:38Z","updated_at":"2016-08-22T17:42:30Z","closed_at":null,"body":"Hello, I'm trying to run ssGSEA using `genepattern-python` and am having trouble understanding what to upload, how to use the uploaded file name, and how to get the stderr from the job.\r\n\r\n### Question 1: How do you reference the uploaded files when submitting GenePattern Jobs?\r\n\r\n[Here](https://gist.github.com/f09a4ef0535f5ea326340b3869bf0f71) is a notebook where I've created some `.gmt` and `.gct` files, upload them to GenePattern, reference them in a `gene.sets.database.list.file` for ssGSEA, and call `ssGSEA`. Since I have multiple gene sets I want to reference, I created a file with newline-separated urls of the uploaded files (`uploaded_file.get_url()`). Is this correct? I get this message in the `stderr.txt`:\r\n\r\n```\r\nError in file(con, \"r\") : cannot open the connection\r\nCalls: ssGSEA.projection.cmdline\r\nExecution halted\r\n```\r\n\r\nBut I don't know *which* file it can't open... and I thought I uploaded everything already!\r\n\r\nand `gp_execution_log.txt` says this:\r\n\r\n```\r\n# Created: Fri Aug 05 18:46:43 EDT 2016 by obot\r\n# Job: 1333723    server:  https://genepattern.broadinstitute.org/gp/\r\n# Module: ssGSEAProjection urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00270:7\r\n# Parameters: \r\n#    input.gct.file = autism_brain_rnaseq_v2_expression.gct   https://genepattern.broadinstitute.org/gp/users/obot/tmp/run2516524705743219998.tmp/autism_brain_rnaseq_v2_expression.gct\r\n#    output.file.prefix = \r\n#    gene.sets.database = c1.all.v5.1.symbols.gmt [Positional]\r\n#    gene.sets.database.file = \r\n#    gene.sets.database.list.file = all_gene_sets.txt   https://genepattern.broadinstitute.org/gp/users/obot/tmp/run4732359326197085757.tmp/all_gene_sets.txt\r\n#    gene.symbol.column = Column 1\r\n#    gene.set.selection = ALL\r\n#    sample.normalization.method = rank\r\n#    weighting.exponent = 0.75\r\n#    min.gene.set.size = 10\r\n#    combine.mode = combine.add\r\n```\r\n\r\n### Question 2: How to programmatically get the `stderr` from a job?\r\n\r\nI can see the submitted jobs in the GenePattern sidebar:\r\n\r\n![image](https://cloud.githubusercontent.com/assets/806256/17458461/3a33caa4-5bc6-11e6-85aa-1be639d1d9fe.png)\r\n\r\nBut getting the stderr is too many clicks for me. Is there a way to do this automatically? `ssgseaprojection_job.get_info()` doesn't seem to return anything..\r\n \r\nEDIT: added notebook link"},"comment":{"url":"https://api.github.com/repos/genepattern/genepattern-python/issues/comments/241491268","html_url":"https://github.com/genepattern/genepattern-python/issues/1#issuecomment-241491268","issue_url":"https://api.github.com/repos/genepattern/genepattern-python/issues/1","id":241491268,"user":{"login":"tmtabor","id":9056964,"avatar_url":"https://avatars.githubusercontent.com/u/9056964?v=3","gravatar_id":"","url":"https://api.github.com/users/tmtabor","html_url":"https://github.com/tmtabor","followers_url":"https://api.github.com/users/tmtabor/followers","following_url":"https://api.github.com/users/tmtabor/following{/other_user}","gists_url":"https://api.github.com/users/tmtabor/gists{/gist_id}","starred_url":"https://api.github.com/users/tmtabor/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tmtabor/subscriptions","organizations_url":"https://api.github.com/users/tmtabor/orgs","repos_url":"https://api.github.com/users/tmtabor/repos","events_url":"https://api.github.com/users/tmtabor/events{/privacy}","received_events_url":"https://api.github.com/users/tmtabor/received_events","type":"User","site_admin":false},"created_at":"2016-08-22T17:42:30Z","updated_at":"2016-08-22T17:42:30Z","body":"Sorry for the delay. To keep you in the loop: to fix this issue I'm going to need to talk to our queueing system expert, but he's been on vacation and gets back Wednesday. So we will hopefully have a fix in place later this week."}}
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