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 We have some (now slightly out of date) notes ...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We have some (now slightly out of date) notes on how the jalview team does this on the wiki.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)
Wednesday 23 Oct 2013
4:49 pm

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

modify .gitignore to current JABAWS git structure

Options
    • -8
    • +6
    /.gitignore
1:23 pm

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Changes to text on the website

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    • -2
    • +2
    /website/contacts.html
    • -9
    • +9
    /website/index.html
    • -2
    • +2
    /website/jabaws_funding.html
    • -3
    • +3
    /website/man_about.html
    • -1
    • +1
    /website/man_awscloud.html
    • -1
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    /website/man_awscloud_bs.html
    • -1
    • +1
    /website/man_awscloud_ec2.html
    • -2
    • +2
    /website/man_client.html
    • -11
    • +53
    /website/man_configuration.html
    • -36
    • +93
    /website/man_dev.html
    • -4
    • +4
    /website/man_server_dev.html
    • -1
    • +1
    /website/man_servervm.html
    • -3
    • +1
    /website/man_serverwar.html
    • -2
    • +2
    /website/man_stats.html
    • -2
    • +2
    /website/manual_qs_amazon.html
  16. … 4 more files in changeset.
Monday 14 Oct 2013
3:26 pm

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Add an old jpred.pl script

Options
    • -0
    • +1401
    /binaries/src/jpred/jpred_old.pl
3:26 pm

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Fix problems with tests

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    • -223
    • +198
    /testsrc/compbio/engine/conf/RunnerConfigMarshallerTester.java
    • -146
    • +135
    /testsrc/compbio/metadata/OptionMarshallerTester.java
    • -117
    • +78
    /testsrc/compbio/metadata/RunnerConfigTester.java
3:20 pm

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Re-design jpred.pl input options: no -seq for a file with 1 FASTA record only.

Options
    • -29
    • +53
    /binaries/src/jpred/jpred.pl
    • -28
    • +3
    /conf/settings/JpredParameters.xml
    • -32
    • +3
    /conf/settings/JpredPresets.xml
    • -0
    • +1
    /runner/compbio/runner/predictors/Jpred.java
10:58 am

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Define path to UNIREF database in conf/Executable.properties

Options
    • -1
    • +7
    /conf/Executable.properties
    • -5
    • +9
    /runner/compbio/runner/predictors/Jpred.java
    • -1
    • +1
    /webservices/compbio/ws/client/Jws2Client.java
10:56 am

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Diable printing environmental variables in procInput.txt

Options
    • -0
    • +3
    /engine/compbio/engine/local/ExecutableWrapper.java
10:56 am

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Remove difinition of UNIREF for JABAWS from jpred.pl

Options
    • -6
    • +1
    /binaries/src/jpred/jpred.pl
Friday 04 Oct 2013
3:20 pm

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Merge branch 'develop' of https://source.jalview.org/git/jabaws into develop

Options
3:20 pm

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Update information on Jabaws VA

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    • -34
    • +34
    /website/man_servervm.html
    • -0
    • +9
    /website/ws.css
3:20 pm

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Fix bug with DB checking in jpred.pl

Options
    • -2
    • +4
    /binaries/src/jpred/jpred.pl
3:19 pm

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Comment code for future options

Options
    • -1
    • +6
    /webservices/compbio/ws/client/Jws2Client.java
1:39 pm

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

JWS-17 regression error - remove unnecessary throws statement

Options
    • -1
    • +1
    /datamodel/compbio/metadata/Parameter.java
1:16 pm

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

JWS-68 parameters cannot take multiple option names (this should have been caught via configuration file validation - see JWS-73)

Options
    • -2
    • +0
    /conf/settings/GLprobsParameters.xml
    • -2
    • +0
    /conf/settings/MSAprobsParameters.xml
Thursday 03 Oct 2013
1:33 pm

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Slightly changed JSP page

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    • -3
    • +3
    /statpages/ServicesStatus.jsp
1:13 pm

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Fix wrong error message

Options
    • -13
    • +8
    /runner/compbio/runner/conservation/AACon.java