IGV fails to launch from JNLP file when data files URL contains %2B or (+) sign
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pa...@pieriandx.com
Jan 20, 2017, 3:10:05 PM1/20/17
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I have my JNLP file as below
<application-desc main-class='org.broad.igv.ui.Main'>
<argument>https://s3.amazonaws.com/filepath/main.bam?AWSAccessKeyId=wfwfw87fwffqw&Expires=1484944197&Signature=%2ByaTBb90oJRltCWMnvCoXArq3Pk%3D</argument>
<argument>Chr23:74290334-74290334</argument>
<argument>-g</argument>
<argument>hg19</argument>
</application-desc>
Now when i launch this JNLP file i see below snippet in the log files.
INFO [2017-01-20 11:53:32,422] [Main.java:439] Loading: https://s3.amazonaws.com/filepath/main.bam?AWSAccessKeyId=wfwfw87fwffqw&Expires=1484944197&Signature=+yaTBb90oJRltCWMnvCoXArq3Pk=
INFO [2017-01-20 11:53:32,603] [IGVPreferences.java:198] Overriding preference: SAM.SHOW_SOFT_CLIPPED=true
INFO [2017-01-20 11:53:33,964] [GenomeManager.java:145] Loading genome: C:\Users\Pavan\igv\genomes\hg19.genome
INFO [2017-01-20 11:53:35,518] [GenomeManager.java:192] Genome loaded. id= hg19
INFO [2017-01-20 11:53:35,633] [IGV.java:1705] Loading 2 resources.
INFO [2017-01-20 11:53:35,634] [TrackLoader.java:126] Loading resource, path https://s3.amazonaws.com/filepath/main.bam?AWSAccessKeyId=wfwfw87fwffqw&Expires=1484944197&Signature= yaTBb90oJRltCWMnvCoXArq3Pk=
INFO [2017-01-20 11:53:36,280] [HttpUtils.java:288] HEAD request failed for url: https://s3.amazonaws.com/filepath/main.bam?AWSAccessKeyId=wfwfw87fwffqw&Expires=1484944197&Signature= yaTBb90oJRltCWMnvCoXArq3Pk=
INFO [2017-01-20 11:53:39,476] [HttpUtils.java:833] Range-byte request succeeded
ERROR [2017-01-20 11:53:39,665] [TrackLoader.java:270] Read error; BinaryCodec in readmode; streamed file (filename not available)
htsjdk.samtools.util.RuntimeIOException: Read error; BinaryCodec in readmode; streamed file (filename not available)
at htsjdk.samtools.util.BinaryCodec.readBytesOrFewer(BinaryCodec.java:406)
Caused by: org.broad.igv.exceptions.HttpResponseException: Access forbidden <br>
at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:750)
at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:623)
Now here issue is It tried to decode this URL twice & in first attempt it converted %2B to + sign & then in next attempt when loading file it converted + to space.
Pleas let me know if i am doing something wrong here, its issue in the code ?
James Robinson
Jan 20, 2017, 3:12:21 PM1/20/17
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Could you attach a jnlp file that I can run as a test (no protected files)?
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James Robinson
Jan 20, 2017, 3:19:54 PM1/20/17
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I think this is what you need
https%3A%2F%2Fs3.amazonaws.com%2Ffilepath%2Fmain.bam%3FAWSAccessKeyId%3Dwfwfw87fwffqw%26Expires%3D1484944197%26Signature%3D%252ByaTBb90oJRltCWMnvCoXArq3Pk%253D
But again I would like to see the jnlp
pa...@pieriandx.com
Jan 20, 2017, 5:11:18 PM1/20/17
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PFA jnlp file with which i am able to reproduce the issue .
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James Robinson
Jan 20, 2017, 5:23:38 PM1/20/17
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I can't run that (access denied). Is this URl supposed to be encoded, or not? Its confusing with the &, which I would not expect to see in a URL encoded file. Could you give me the plain URL to that file (no encoding at all)?
Also, you can't load a bam index (.bai) file directly.
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pa...@pieriandx.com
Jan 20, 2017, 7:12:23 PM1/20/17
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Sorry about that Token was expired for that file. I created new token for few days now.
Plain URL :
Also as per :https://github.com/igvteam/igv/blob/v2.3.89/src/org/broad/igv/ui/Main.java line number : 412 we can pass indexFile
James Robinson
Jan 20, 2017, 8:36:58 PM1/20/17
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Did you try these?
https%3A%2F%2Fpdx-pavan.s3.amazonaws.com%2FIGV_Bug%2Fmain.clean.bam%3FAWSAccessKeyId%3DAKIAIK4GP43NHLYBC6LQ%26Expires%3D1493597268%26Signature%3Dy4BE9a%252BiCEave81BbC%252BqfZibhEg%253D
https%3A%2F%2Fpdx-pavan.s3.amazonaws.com%2FIGV_Bug%2Fmain.clean.bai%3FAWSAccessKeyId%3DAKIAIK4GP43NHLYBC6LQ%26Expires%3D1493597141%26Signature%3Drj9Tf0v0BTRqbyI%252Bwfq3DsSECJ0%253D
You can pass an index file, but only if preceded by the option flag
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James Robinson
Jan 20, 2017, 10:24:36 PM1/20/17
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OK, there were 2 problems. An igv bug, and your paths still were not correct. See the paths I suggested earlier, or just see the attached jnlp. Just url encode the paths, don't use "&".
The igv bug was with the index file, it was not being url decoded. I have pushed a fix, you will need to pull the latest from the v2.3x branch or wait for release 2.3.91. Apparently you are the first to try this with a URL requiring decoding, or the first to report the error anyway.
Finally, its chr23 not Chr23. Other than that, and the file paths, the jnlp was correct.
pa...@pieriandx.com
Jan 23, 2017, 10:34:56 AM1/23/17
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Thanks a lot for quick fix. I will try this out.
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