Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Blocker
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:2
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Epic Link:
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Sprint:Summer 2: 22 Jun - 3 Jul
Description
Situation: When a user clicks View in IGB for data at usegalaxy.org a url is created and the user is directed to bioviz where javascript alters the url allowing data to be streamed to IGB. Currently, when clicking View in IGB at usegalaxy.org the page responds with "This site can't be reached".
Example data: https://usegalaxy.org/u/nfreese/h/visualization-of-whole-genome-dna-methylation-data-in-igb-focus-on-a-feature
Task: Determine the problem and implement a solution so that data are sent to IGB.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1880 [ 17970 ] |
| Priority | Major [ 3 ] | Blocker [ 1 ] |
| Description |
Situation: When a user clicks View in IGB for data at usegalaxy.org a url is created and the user is directed to bioviz where javascript alters the url allowing data to be streamed to IGB. Currently, when clicking View in IGB at usegalaxy.org the page responds with "This site can't be reached".
Example data: https://usegalaxy.org/u/nfreese/h/visualization-of-whole-genome-dna-methylation-data-in-igb-focus-on-a-feature The url that is eventually created and sent to IGB looks like this as an example: http://127.0.0.1:7085/IGBControl? version=H_sapiens_Dec_2013& loadresidues=false& cyverse_data=true& feature_url_0=https://data.cyverse.org/dav-anon/iplant/home/nowlanf/SmokeTesting/H_sapiens_Dec_2013/BedGraph_HomoSapien_noName_NowlanTEST.bedGraph& sym_method_0=https://data.cyverse.org/dav-anon/iplant/home/nowlanf/SmokeTesting/H_sapiens_Dec_2013/BedGraph_HomoSapien_noName_NowlanTEST.bedGraph& sym_col_0=0x00FFFF& sym_bg_0=0x000000& sym_name_0=RefSeqCurated& query_url=https://data.cyverse.org/dav-anon/iplant/home/nowlanf/SmokeTesting/H_sapiens_Dec_2013/BedGraph_HomoSapien_noName_NowlanTEST.bedGraph& server_url=cyverse Task: Determine the problem and implement a solution so that data are sent to IGB. |
Situation: When a user clicks View in IGB for data at usegalaxy.org a url is created and the user is directed to bioviz where javascript alters the url allowing data to be streamed to IGB. Currently, when clicking View in IGB at usegalaxy.org the page responds with "This site can't be reached".
Example data: https://usegalaxy.org/u/nfreese/h/visualization-of-whole-genome-dna-methylation-data-in-igb-focus-on-a-feature Task: Determine the problem and implement a solution so that data are sent to IGB. |
https://github.com/galaxyproject/galaxy - Galaxy code base
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Problem was with redirect configuration in httpd.conf.
For fix: See commit 21b8eb3 in lorainelab/bioviz-playbooks.git.
We need to automate testing of BioViz Web site deployment – AL (me) forgot to check Galaxy connectivity.
Notes on testing:
Nowlan Freese noted:
Hitting this URL:
https://usegalaxy.org/display_application/bbd44e69cb8906b52300b547db6d5d14/igb_bam/View
When this goes to Bioviz.org, BioViz.org substitutes https for http and redirects again.
Next, BioViz modifies the URL a bit and substitutes domain localhost.
We need something that tests each part of this sequence.
Somehow we have to build some automated testing on live bioviz test sites.
Investigate "test" infrastructure in ansible.
Creating a new Jira issue to investigate building testing using ansible.
| Link | This issue relates to IGBF-2458 [ IGBF-2458 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
May be an issue with a misplaced forward slash.
This is the URL that I am currently getting that is broken:
https://www.bioviz.orggalaxy.html/?version=Arabidopsis_thaliana_TAIR10&feature_url_0=https://usegalaxy.org/display_application/bbd44e69cb8906b51371325f402dce0f/igb_bam/View/f7d0b06217bfdb8a/data/RNA_seq_Chr1_KO.bam&sym_name_0=RNA_seq_Chr1_KO&sym_method_0=https://usegalaxy.org/display_application/bbd44e69cb8906b51371325f402dce0f/igb_bam/View/f7d0b06217bfdb8a/data/RNA_seq_Chr1_KO.bam&query_url=https://usegalaxy.org/display_application/bbd44e69cb8906b51371325f402dce0f/igb_bam/View/f7d0b06217bfdb8a/data/RNA_seq_Chr1_KO.bam&server_url=galaxy
Note that there is no forward slash between org and galaxy.html, but there is a forward slash between html and ?
Moving the forward slash to the correct position seems to fix the url.
https://www.bioviz.org/galaxy.html?version=Arabidopsis_thaliana_TAIR10&feature_url_0=https://usegalaxy.org/display_application/bbd44e69cb8906b51371325f402dce0f/igb_bam/View/f7d0b06217bfdb8a/data/RNA_seq_Chr1_KO.bam&sym_name_0=RNA_seq_Chr1_KO&sym_method_0=https://usegalaxy.org/display_application/bbd44e69cb8906b51371325f402dce0f/igb_bam/View/f7d0b06217bfdb8a/data/RNA_seq_Chr1_KO.bam&query_url=https://usegalaxy.org/display_application/bbd44e69cb8906b51371325f402dce0f/igb_bam/View/f7d0b06217bfdb8a/data/RNA_seq_Chr1_KO.bam&server_url=galaxy