Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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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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Sprint:Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar
Description
Situation: CyVerse allows the use of special characters, including spaces, in filenames. BioViz Connect does not handle filenames with special characters, breaking most of the right-click functionality.
Task: Handle special characters in filenames when a user clicks View in IGB and when we send requests to Terrain API.
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link |
|
| Sprint | Spring 3 : 17 Feb to 28 Feb [ 87 ] | Spring 4 : 2 Mar to 13 Mar [ 89 ] |
| Sprint | Spring 4 : 2 Mar to 13 Mar [ 89 ] | Spring 3 : 17 Feb to 28 Feb [ 87 ] |
| Sprint | Spring 3 : 17 Feb to 28 Feb [ 87 ] | Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar [ 87, 89 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Chaitanya Kintali [ chaitanya ] |
| Comment |
[ The convention for creating a bookmark for a filename with spaces within IGB is to replace spaces in the feature_url sym_method and query_url with *%2520*. The convention within the parameter sym_name is to replace spaces with *+*.
For example: stuff_!@#$%^&*_ space stuff.bedGraph needs to be encoded to work with IGB bookmarks as stuff_%21%40%2523%24%2525%255E%26*_%2520space%2520stuff.bedGraph ] |
| Comment |
[ Example file name with special characters and spaces: stuff_!@#$%^&* space _stuff.bedGraph
Working link to CyVerse file with encoding on filename: https://data.cyverse.org/dav-anon/iplant/home/nowlanf/SmokeTesting/H_sapiens_Dec_2013/stuff_!%40%23%24%25%5E%26*%20space%20_stuff.bedGraph Note: there may be slight differences in the encoding between what CyVerse needs and what IGB needs. See my previous comment for the IGB bookmarks encoding expectations. ] |
| Comment |
[ filename: stuff_!@#$%^&* space _stuff.bedGraph
local file as it appears in IGB bookmarks: stuff_%21%40%2523%24%2525%255E%26*%2520space%2520_stuff.bedGraph url that works in IGB File > Open URL (single encoded file name): https://data.cyverse.org/dav-anon/iplant/home/nowlanf/SmokeTesting/H_sapiens_Dec_2013/stuff_!%40%23%24%25%5E%26*%20space%20_stuff.bedGraph url from above as it appears in IGB bookmarks: stuff_%21%2540%2523%2524%2525%255E%2526*%2520space%2520_stuff.bedGraph url that works as an IGB bookmark (double encoded file name): https://data.cyverse.org/dav-anon/iplant/home/nowlanf/SmokeTesting/H_sapiens_Dec_2013/stuff_%21%2540%2523%2524%2525%255E%2526*%2520space%2520_stuff.bedGraph sym_name that works in IGB bookmarks (single encoded file name): stuff_!%40%23%24%25%5E%26*%20space%20_stuff.bedGraph Example BioViz Connect url with double encoded filename for feature_url, sym_method, and query_url and single encoded filename for sym_name: http://127.0.0.1:7085/IGBControl? version=?& loadresidues=false& cyverse_data=true& feature_url_0=https://data.cyverse.org/dav-anon/iplant/home/nowlanf/SmokeTesting/H_sapiens_Dec_2013/stuff_%21%2540%2523%2524%2525%255E%2526*%2520space%2520_stuff.bedGraph& sym_method_0=https://data.cyverse.org/dav-anon/iplant/home/nowlanf/SmokeTesting/H_sapiens_Dec_2013/stuff_%21%2540%2523%2524%2525%255E%2526*%2520space%2520_stuff.bedGraph& sym_col_0=0x0F0F0F& sym_bg_0=0x0FFFF0& sym_name_0=stuff_!%40%23%24%25%5E%26*%20space%20_stuff.bedGraph& query_url=https://data.cyverse.org/dav-anon/iplant/home/nowlanf/SmokeTesting/H_sapiens_Dec_2013/stuff_%21%2540%2523%2524%2525%255E%2526*%2520space%2520_stuff.bedGraph& server_url=cyverse ] |
filename: stuff_!@#$%^&* space _stuff.bedGraph
Example BioViz Connect url with double encoded filename for feature_url, sym_method, and query_url and single encoded filename for sym_name:
http://127.0.0.1:7085/IGBControl?
version=?&
loadresidues=false&
cyverse_data=true&
feature_url_0=https://data.cyverse.org/dav-anon/iplant/home/nowlanf/SmokeTesting/H_sapiens_Dec_2013/stuff_!%2540%2523%2524%2525%255E%2526*%2520space%2520_stuff.bedGraph&
sym_method_0=https://data.cyverse.org/dav-anon/iplant/home/nowlanf/SmokeTesting/H_sapiens_Dec_2013/stuff_!%2540%2523%2524%2525%255E%2526*%2520space%2520_stuff.bedGraph&
sym_col_0=0x0F0F0F&
sym_bg_0=0x0FFFF0&
sym_name_0=stuff_!%40%23%24%25%5E%26*%20space%20_stuff.bedGraph&
query_url=https://data.cyverse.org/dav-anon/iplant/home/nowlanf/SmokeTesting/H_sapiens_Dec_2013/stuff_!%2540%2523%2524%2525%255E%2526*%2520space%2520_stuff.bedGraph&
server_url=cyverse
| Description |
Situation: CyVerse allows the use of special characters, including spaces, in filenames. BioViz Connect does not handle filenames with special characters, breaking most of the right-click functionality.
Task: Handle special characters in filenames. |
Situation: CyVerse allows the use of special characters, including spaces, in filenames. BioViz Connect does not handle filenames with special characters, breaking most of the right-click functionality.
Task: Handle special characters in filenames when a user clicks View in IGB and when we send requests to Terrain API. |
Pull Request Link: https://bitbucket.org/nfreese/django-cyversedev/pull-requests/135/igbf-2275/diff
As per previous comment, The parameter 'Filepath' has been encoded twice before sending it as URL query parameter to avoid failure.
Code changes have also been done to change the way we are sending the FilePath as a query parameter in many scenarios such as Manage Link. Instead changes are made to send the FilePath as Json Body to avoid failure parsing any filename with special characters.
Moving to Needs Testing. Nowlan Freese can you please test this ticket and move it done if everything works fine.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| 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 ] |
| Assignee | Chaitanya Kintali [ chaitanya ] | Nowlan Freese [ nfreese ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
I think there might be an issue with the sym_name not being encoded. The sym_name parameter is not showing correctly in the debugger for stuff_!@#$%^&* space _stuff.bedGraph when clicking View in IGB in BioViz Connect.
Terrain functionality appears to be working correctly, the three right-panels are loading correctly.
| Assignee | Nowlan Freese [ nfreese ] | Chaitanya Kintali [ chaitanya ] |
| Status | Post-merge Testing In Progress [ 10003 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar [ 87, 89 ] | Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar [ 87, 89, 90 ] |
| Rank | Ranked higher |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Chaitanya Kintali [ chaitanya ] | Nowlan Freese [ nfreese ] |
Encoding the sym_name worked, file is loading in IGB, name is showing correctly.
Closing issue.
| Assignee | Nowlan Freese [ nfreese ] | Chaitanya Kintali [ chaitanya ] |
| 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 ] |
It looks like for BioViz Connect to work, need to double encode the filename for feature_url, sym_method, and query_url and single encode the filename for sym_name.