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fábio madeira <fmmarquesmadeira@dundee.ac.uk> in jabaws

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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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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JWS-116 & JWS-109 Fixed the version number, month and number of jobs performes in the jabaws description.

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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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JWS-112 Updated AACon to version 1.1.

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

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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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JWS-114 Fixed what the default for local and cluster should (also considering people not running jabaws in Dundee)

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JWS-116 Minor changes to the bash script used to generate the docs with Sphinx

JWS-109 Added a release date to the website

JWS-109 Updated the download page with the link to the new turnkey linux

JWS-116 New build with previous changes to the source files in the docs

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JWS-116 Added a release date to the website to the changelog

JWS-116 Updated the VA pages with the new passwords and turnkey versions

JWS-112 Updated the versions the tool versions that are shown in the ServiceStatus page

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JWS-114 Bumping varied config files and jetbrains xmls. Also adding some java classes that are generated during the compilation.

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JWS-116 Added entries for the jabaws docs source files to the build.xml

JWS-117 Compiled all tools with ./compilebin.sh and some were missing related files.

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JWS-109 Fixed the links in the navbar header and footer to match the new documentation pages.

JWS-109 General improvements and further fixes to typos and proofreading.

JWS-116 Moved the boostrap’ed manual pages to a temporary dir. The documentation pages are now generated with Sphinx.

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