Fábio Madeira

Updated the Jabaws 2.2 reference and bumped the date

JWS-114 Bumped the version of the webservices 'JABAWS_VERSION' to 2.2.

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    /webservices/compbio/data/msa/JABAService.java
JWS-109 & JWS-116 Bumped the release date and fixed the text regarding the Elixir-UK.

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    /website/docs/_sources/changelog.rst.txt
JWS-112 Uploaded a new aacon jar, following a minor update made to AAcon's output format.

JWS-122 & JWS-116 New documentation entry with instructions on how to use the JABAWS Docker image and new built html pages.

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JWS-122 & JWS-109 Minor updates to the homepage to point out new Docker support and bump date.

JWS-122 Added a Dockerfile and some container image specific Executable.properties.

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    /docker/Executable.properties
JWS-121 Minor bug fix on the timeexec - wrong units.

JWS-109 & JWS-116 Added the new chaching as new entries to index.jsp and the docs’ changelog. Also bumped the release/update dates.

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    /website/docs/_sources/changelog.rst.txt
JWS-121 Added new refresher methods and the respective servlets and mappings entries in web.xml. These are used to update the ServletContext values as an input from the user (clickable links) that point to the new endpoints.

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    /webservices/compbio/stat/servlet/AnnualStatRefresher.java
JWS-121 & JWS-109 Service Status now gives an indication of the health of service. Fixed the links to the Service Status and Usage Statistics pages. Also removed now unecessary files.

JWS-121 Improved the AnnualStat and ServiceStatus classes so they start the scheduler in the init() method and refresh the in memory cache every X minutes. The number of minutes is defined in the Engine.local.properties config. In memory values are cached in the ServletContext.

JWS-121 Added new scheduler utility classes so that usage statistics and service status can be monitored in a cronjob-like manner. RefreshIterator implements a ScheduleIterator that runs a new task every X minutes.

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    /webservices/compbio/stat/servlet/util/RefreshIterator.java
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    /webservices/compbio/stat/servlet/util/Scheduler.java
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    /webservices/compbio/stat/servlet/util/SchedulerTask.java
JWS-110 Commented out the servlet entries for the Download redirects no longer needed.

JWS-121 & JWS-109 Improved the way the service_status.jsp and usage_statistics.jsp work to load cached htmls or to redirect on error (i.e. missing cached htmls). This is a very hacky temporary solution. The provided script can be used to refresh the cached htmls every x minutes.

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    /website/refresh_service_status.sh
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    /website/statpages/MonthlySummary.jsp
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    /website/statpages/ServicesStatus.jsp
JWS-121 & JWS-111 Adding ‘timestamp’ (string formatted date + time) to the HttpServletRequest to be used in the jsp and setting ‘timexec’ as seconds instead of millisecs.

JWS-121 Added new jsp enpoints that try loading chached service status and usage statistics pages. If not available there is a redirect to the main endpoints. Also fixed the header and footer links to match the new endpoints.

JWS-109 Some minor fixes for broken links and missing space.

JWS-119 & JWS-109 Fixed the relative paths to the documentation pages and bumped the date.

JWS-119 & JWS-116 Fixed the location of the documentation pages. Also fixed the relative paths throughout the RST files and RTD template.

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JWS-120 Fixes the exception raised by the ChunkHolder method in GenericMetadataService. This behavior was expected for services which do not support execution statistics. This solution was found in the compbio.ws.server.JronnWS.java.

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    /webservices/compbio/ws/server/IUPredWS.java
JWS-116 & JWS-109 Fixed the version number, month and number of jobs performes in the jabaws description.

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    /website/docs/v_2_2_0/jabaws_manual.pdf
JWS-116 Some minor fixes to the documentation pages and added the alignment image to the getting started pages.

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JWS-114 Updated the names of the distributives so that they match the ones used in the download pages.

JWS-116 New fixes to the documentation pages. Various fixes to the content, as well as bumped versions of aacon and dates. New citation, and pdf with full authors and contact information.

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JWS-109 New fixes and updated looks as suggested by Geoff. Added new section about elixir, fixed the top bar and added a MSA figure. Also bumped the date, and fixed the links to some of the downloads.

JWS-112 Hotfix the last t-coffee version 11. The -mode quickaln preset breaks if ’t_coffee’ is not found in $PATH. By calling t_coffee.sh instead, the problem is fixed by updating the $PATH on the flight and passing the original arguments to t_coffee.

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    /binaries/src/tcoffee/t_coffee_source/t_coffee.sh
JWS-112 Updated AACon to version 1.1.

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    /webservices/compbio/ws/client/Services.java
JWS-109 & JWS-116 Regenerated the JABAWS JavaDoc (with eclipse java 8) and moved it to docs/.

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    /website/dm_javadoc/allclasses-frame.html
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JWS-109 & JWS-116 Moved the docs (source and html built) to a new location that is based on the version.

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