jabaws

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Friday 02 Jun 2017
4:41 pm

Jim Procter

4:40 pm

Jim Procter

this looks like the same pattern of scheduler settings as in ServiceStatus - if you wanted to be more Java-ish, you'd have a generic ScheduledEventAttribute class that manipulated a given servlet c...

this looks like the same pattern of scheduler settings as in ServiceStatus - if you wanted to be more Java-ish, you'd have a generic ScheduledEventAttribute class that manipulated a given servlet context's attributes to create/update these stats

4:31 pm

Jim Procter

  • More
  • CR-2
  • started review
JWS-121: Service status and usage statistics show cached results for faster loads
JWS-121: Service status and usage statistics show cached results for faster loads
Thursday 02 Feb 2017
5:16 pm

Fábio Madeira

I guess Geoff only wants updated looks here, so I guess this could be an improvement as well.

I guess Geoff only wants updated looks here, so I guess this could be an improvement as well.

5:14 pm

Fábio Madeira

So Geoff does not want JPred to included in the next release. My understanding is that if Jabaws 2.1 includes a previous version of Jpred, it should be removed...

So Geoff does not want JPred to included in the next release. My understanding is that if Jabaws 2.1 includes a previous version of Jpred, it should be removed...

4:24 pm

Fábio Madeira

Thanks Jim Procter! Gonna read it and get my way around. Also, I am going to remove the file, was more to see whether the pushing was working...

Thanks Jim Procter! Gonna read it and get my way around. Also, I am going to remove the file, was more to see whether the pushing was working...

3:57 pm

Jim Procter

  • More
  • CR-1
  • finished reviewing
3:57 pm

Jim Procter

Rather than create cryptic .txt files in the jabaws source repository (where they will stay forever), I suggest you instead use the JWS Jira project. We have some (now slightly out of date) notes ...

Rather than create cryptic .txt files in the jabaws source repository (where they will stay forever), I suggest you instead use the JWS Jira project.

We have some (now slightly out of date) notes on how the jalview team does this on the wiki. The take home message, however, is that before you start coding, or whatever, use the issue tracker to decide what to code/write/fix, and log your progress. You may even discover issues that you wanted to fix that have already been lodged by someone else !

Remember: If it doesn't happen on the bug tracker, then it hasn't happened yet

No, really.

For more info see: https://wiki.jalview.org/index.php/Development#Pick_something_to_work_on_from_issues.jalview.org

3:36 pm

Jim Procter

I suspect an epic is called for here, since there will be a number of issues for each tool

I suspect an epic is called for here, since there will be a number of issues for each tool

3:36 pm

Jim Procter

Again, this should be a new, separate issue.

Again, this should be a new, separate issue.

3:34 pm

Jim Procter

Suggest you create an epic to collect issues for improving the stats page (or create a component and a series of issues tagged to it)

Suggest you create an epic to collect issues for improving the stats page (or create a component and a series of issues tagged to it)

3:33 pm

Jim Procter

Is this for downloading JABAWS ? Again, you should create an 'Improvement' on the JWS project to tag this - since it goes into the release notes for the updated version

Is this for downloading JABAWS ?

Again, you should create an 'Improvement' on the JWS project to tag this - since it goes into the release notes for the updated version

3:32 pm

Jim Procter

Suggest you create a task for this

Suggest you create a task for this

3:30 pm

Jim Procter

  • More
  • CR-1
  • started review
Added a new document for logging the goals and todos (work in progress)
Added a new document for logging the goals and todos (work in progress)
Monday 04 Jun 2012
5:08 pm

jprocter <jprocter@compbio.dundee.ac.uk>

Merge branch 'JWS-27-jronn' into JABAWS_Release_2_0

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5:06 pm

jprocter <jprocter@compbio.dundee.ac.uk>

JWS-27 replaced JRonn with patched biojava 3.0.4 version which runs correctly for large sets of sequences in multithreaded mode

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    • binary
    /binaries/windows/bj3.0.4p-jronn.jar
    • -0
    • +4
    /binaries/windows/bj3.0.4p-jronn.jar.readme
    • -0
    • +23
    /binaries/windows/bj3.0.4p-jronn.patch
    • binary
    /binaries/windows/jronn3.1.jar
    • -1
    • +1
    /conf/Executable.properties
Friday 01 Jun 2012
12:56 pm

jprocter <jprocter@compbio.dundee.ac.uk>

Merge branch 'JWS-29' into JABAWS_Release_2_0

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12:53 pm

jprocter <jprocter@compbio.dundee.ac.uk>

JWS-29 patch fixes bug - wierd workaround since "^\\s*>" caused scanner to advance to end of file rather than start of next FASTA header

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    • -4
    • +17
    /datamodel/compbio/data/sequence/FastaReader.java
11:17 am

jprocter <jprocter@compbio.dundee.ac.uk>

test demonstrating JWS-29 assertion failure

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    • -0
    • +4
    /testsrc/compbio/data/sequence/FastaReaderTester.java
    • -1
    • +8
    /testsrc/testdata/complicated.fasta
11:08 am

jprocter <jprocter@compbio.dundee.ac.uk>

Merge branch 'JWS-36' into JABAWS_Release_2_0

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10:57 am

jprocter <jprocter@compbio.dundee.ac.uk>

JWS-36 patched Scores writer to put spaces between ranges and space separated scores

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    • -5
    • +6
    /datamodel/compbio/data/sequence/Score.java
Thursday 31 May 2012
6:31 pm

jprocter <jprocter@compbio.dundee.ac.uk>

Merge branch 'JWS-35' into JABAWS_Release_2_0

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6:27 pm

jprocter <jprocter@compbio.dundee.ac.uk>

patch fixes JWS-35

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    • -2
    • +2
    /datamodel/compbio/data/sequence/SequenceUtil.java
6:27 pm

jprocter <jprocter@compbio.dundee.ac.uk>

test for JWS-35 - check that range and first value of prediction for each method matches expected values

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    • -4
    • +40
    /testsrc/compbio/data/sequence/SequenceUtilTester.java
Tuesday 15 May 2012
4:55 pm

jprocter <jprocter@compbio.dundee.ac.uk>

remove jabaws 3 development code

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    • -98
    • +0
    /conf/temp/blastdbcmd.txt
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    • +0
    /conf/temp/jackhmmer.txt
    • -249
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    /conf/temp/psiblast.txt
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    • +0
    /engine/compbio/engine/cluster/drmaa/_DrmaaExample.java
    • -59
    • +0
    /engine/compbio/engine/cluster/drmaa/_JobStatus.java
    • -152
    • +0
    /engine/compbio/engine/cluster/dundee/_Queue.java
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    • +0
    /engine/compbio/engine/cluster/dundee/_QueueConstraints.java
    • -121
    • +0
    /engine/compbio/engine/conf/_Key.java
    • -123
    • +0
    /engine/compbio/engine/local/_TrackingExecutor.java
    • -48
    • +0
    /runner/compbio/data/_structure/JnetAnnotation.java
    • -39
    • +0
    /runner/compbio/data/_structure/JpredAnnotation.java
    • -61
    • +0
    /runner/compbio/data/_structure/JpredResult.java
    • -65
    • +0
    /runner/compbio/pipeline/_jpred/BlastBlastComparator.java
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    • +0
    /runner/compbio/pipeline/_jpred/BlastHmmerComparator.java
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    • +0
    /runner/compbio/pipeline/_jpred/BlastParser.java
  16. … 30 more files in changeset.
4:54 pm

jprocter <jprocter@compbio.dundee.ac.uk>

ensure we never check in autogenerated documentation or build artefacts

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    • -0
    • +5
    /.gitignore
4:53 pm

jprocter <jprocter@compbio.dundee.ac.uk>

fix jabaws download link

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    • -1
    • +1
    /webservices/compbio/stat/servlet/DownloadRedirector.java
Monday 12 Dec 2011
4:19 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

word order

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4814 e3abac25-378b-4346-85de-24260fe3988d

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    • -1
    • +1
    /website/index.html
2:46 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

load the driver explicitly

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4813 e3abac25-378b-4346-85de-24260fe3988d

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    • -12
    • +19
    /webservices/compbio/stat/collector/StatDB.java
Friday 09 Dec 2011
5:23 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

AMI ID update

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4809 e3abac25-378b-4346-85de-24260fe3988d

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    • -6
    • +1
    /website/man_awscloud.html