From: Fábio Madeira Date: Fri, 26 May 2017 16:59:20 +0000 (+0100) Subject: JWS-119 & JWS-116 Fixed the location of the documentation pages. Also fixed the relat... X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=eb7b65a41fb6bc51ef10eb42ebfb5f25e09153b4;p=jabaws.git JWS-119 & JWS-116 Fixed the location of the documentation pages. Also fixed the relative paths throughout the RST files and RTD template. --- diff --git a/docs/v_2_2_0/_themes/sphinx_rtd_theme/breadcrumbs.html b/docs/v_2_2_0/_themes/sphinx_rtd_theme/breadcrumbs.html index 360f552..6bceed9 100755 --- a/docs/v_2_2_0/_themes/sphinx_rtd_theme/breadcrumbs.html +++ b/docs/v_2_2_0/_themes/sphinx_rtd_theme/breadcrumbs.html @@ -62,7 +62,7 @@ {{ _('View page source') }} {% elif show_source and has_source and sourcename %} - Return to the JABAWS homepage + Return to the JABAWS homepage {% endif %} {% endif %} diff --git a/docs/v_2_2_0/_themes/sphinx_rtd_theme/footer.html b/docs/v_2_2_0/_themes/sphinx_rtd_theme/footer.html index ddba32b..af71c74 100755 --- a/docs/v_2_2_0/_themes/sphinx_rtd_theme/footer.html +++ b/docs/v_2_2_0/_themes/sphinx_rtd_theme/footer.html @@ -13,7 +13,7 @@
-

JABAWS 2.2 +

JABAWS 2.2 {%- if show_copyright %} {%- if hasdoc('copyright') %} {% trans path=pathto('copyright'), copyright=copyright|e %}© Copyright {{ copyright }}.{% endtrans %} diff --git a/docs/v_2_2_0/advanced.rst b/docs/v_2_2_0/advanced.rst index e636c8a..46eba95 100644 --- a/docs/v_2_2_0/advanced.rst +++ b/docs/v_2_2_0/advanced.rst @@ -463,8 +463,8 @@ JABAWS War File Content .. links .. _war file content table: advanced.html#jabaws_war_file_content -.. _dm_javadoc: ../dm_javadoc/index.html -.. _full_javadoc: ../full_javadoc/index.html +.. _dm_javadoc: dm_javadoc/index.html +.. _full_javadoc: full_javadoc/index.html .. _prog_docs: http://www.compbio.dundee.ac.uk/jabaws/prog_docs/ .. _test JABAWS: advanced.html#testing-the-jabaws-server .. _deploying on Tomcat tips: war.html diff --git a/docs/v_2_2_0/develop.rst b/docs/v_2_2_0/develop.rst index d29c25d..998f37a 100644 --- a/docs/v_2_2_0/develop.rst +++ b/docs/v_2_2_0/develop.rst @@ -615,14 +615,14 @@ If you made any changes to the data model and would like to generate a complete .. links .. _Git-tracker: https://source.jalview.org/crucible/changelog/jabaws -.. _Data Model JavaDoc: ../dm_javadoc/index.html -.. _Complete JavaDoc: ../full_javadoc/index.html +.. _Data Model JavaDoc: dm_javadoc/index.html +.. _Complete JavaDoc: full_javadoc/index.html .. _JavaDoc: http://www.compbio.dundee.ac.uk/jabaws/full_javadoc/index.html .. _Test Results: http://www.compbio.dundee.ac.uk/user/www-jws2/tests/index.html .. _TestNG: http://testng.org/doc/index.html .. _Apache Ant: http://ant.apache.org/ -.. _download page: download.jsp -.. _JABAWS CLI client: download.jsp#client +.. _download page: ../download.jsp +.. _JABAWS CLI client: ../download.jsp#client .. _first aligning sequences example: develop.html#aligning-sequences .. _JAX-WS: http://jax-ws.java.net/ .. _WS-I: http://www.ws-i.org/ diff --git a/docs/v_2_2_0/generate_manual.sh b/docs/v_2_2_0/generate_manual.sh index 07cd59a..517e557 100755 --- a/docs/v_2_2_0/generate_manual.sh +++ b/docs/v_2_2_0/generate_manual.sh @@ -4,8 +4,8 @@ rm -rf _build # generating the html pages make html -mkdir ../website/docs/v_2_2_0/ -cp -r _build/html/* ../../website/docs/v_2_2_0/ +mkdir ../website/docs/ +cp -r _build/html/* ../../website/docs/ # extra for testing #mkdir ../../jabaws-2.2-dev/docs #cp -r _build/html/* ../../jabaws-2.2-dev/docs/ @@ -35,13 +35,10 @@ rm -rf _build # } # add the note. -# Note: Some of the hyper-links found in this pdf might not work properly. - # # \begin{sphinxadmonition}{note}{Note:} -# # Some of the links might not work properly in the pdf version... +# # Some of the hyper-links found in this pdf might not work properly. # # \end{sphinxadmonition} -# cp _build/latex/JABAWS.pdf ../../jabaws-2.2-dev/docs/jabaws_manual.pdf -# cp _build/latex/JABAWS.pdf ../../website/docs/v_2_2_0/jabaws_manual.pdf +# cp _build/latex/JABAWS.pdf ../../website/docs/jabaws_manual.pdf # rm -rf _build # for multiple versions of this manual we need to implement some solution diff --git a/docs/v_2_2_0/va.rst b/docs/v_2_2_0/va.rst index b5f3de4..374898d 100644 --- a/docs/v_2_2_0/va.rst +++ b/docs/v_2_2_0/va.rst @@ -3,7 +3,7 @@ Virtual Appliance (VA) The JABAWS Virtual Appliance is a way to run a JABAWS server locally, without the need to connect to the internet or configure JABAWS. What the appliance provides is a 'virtual server machine' (or more simply - *virtual machine* or *VM*), running an installation of the JABAWS Web Application Archive (WAR) on `TurnKey Linux`_ 12.1 (Standlone Tomcat). Once this has started up, it displays a message indicating the IP address of the JABAWS server, allowing any JABAWS client (such as Jalview or the JABAWS command line client) to connect to it. -You can run the appliance with freely available program such as `VMware Player`_, but you will need to install it first. We have tested the JABAWS appliance with VMware Player v 3.1.2 on Windows and Linux, and VMware Fusion on Mac. However, you are not limited to these virtualization systems and can use the JABAWS Appliance with any other virtualization platform. You can use `VMware OVF`_ tool to prepare JABAWS image for a different virtualization platform e.g. `VirtualBox`_. +You can run the appliance with freely available program such as `VMware Player`_, but you will need to install it first. We have tested the JABAWS appliance with VMware Player v 3.1.2 on Windows and Linux, and VMware Fusion on Mac. However, you are not limited to these virtualization systems and can use the JABAWS Appliance with any other virtualization platform. You can use `VMware OVF`_ tool to prepare JABAWS image for a different virtualization platform e.g. `VirtualBox`_. `VirtualBox`_ can also use the ``jabaws*.vmdk`` directly as an *existing preconfigured virtual hard disk file*, when creating a new Linux 2.4 / 3.x / 4.x 64-bit VM. .. note:: The appliance best suits users who would like to use the JABAWS web-services locally. This might be because they do not want to access systems over an internet, or just want to keep their data private. It is also the recommended option for users who want to install JABAWS on Windows, which does not support all the bioinformatics programs that JABAWS can run. @@ -21,7 +21,7 @@ Installing The free `VMware Player`_ can be used to run the JABAWS services from the Windows and Linux host operating systems. `VMware Fusion`_, a commercial VMware product, offers virtual machine support for Mac. -To run the JABAWS server on VMware player, unpack the JABAWS VM into one of the folders on your local hard drive. Open VMware Player, click "Open Virtual Machine" and point the Player to the location of the JABAWS, then choose the ``JABAWS*.vmx`` file to open an appliance. +To run the JABAWS server on VMware player, unpack the JABAWS VM into one of the folders on your local hard drive. Open VMware Player, click "Open Virtual Machine" and point the Player to the location of the JABAWS, then choose the ``jabaws*.vmx`` file to open an appliance. When you play the machine for the first time the Player might ask you whether "This virtual machine may have been moved or copied.", say that you have copied it. That is all. diff --git a/website/docs/v_2_2_0/_images/VMware_booted.png b/website/docs/_images/VMware_booted.png similarity index 100% rename from website/docs/v_2_2_0/_images/VMware_booted.png rename to website/docs/_images/VMware_booted.png diff --git a/website/docs/v_2_2_0/_images/VMware_cpu.png b/website/docs/_images/VMware_cpu.png similarity index 100% rename from website/docs/v_2_2_0/_images/VMware_cpu.png rename to website/docs/_images/VMware_cpu.png diff --git a/website/docs/v_2_2_0/_images/aligment.png b/website/docs/_images/aligment.png similarity index 100% rename from website/docs/v_2_2_0/_images/aligment.png rename to website/docs/_images/aligment.png diff --git a/website/docs/v_2_2_0/_images/folder-small.png b/website/docs/_images/folder-small.png similarity index 100% rename from website/docs/v_2_2_0/_images/folder-small.png rename to website/docs/_images/folder-small.png diff --git a/website/docs/v_2_2_0/_images/usage_statistics_details.gif b/website/docs/_images/usage_statistics_details.gif similarity index 100% rename from website/docs/v_2_2_0/_images/usage_statistics_details.gif rename to website/docs/_images/usage_statistics_details.gif diff --git a/website/docs/v_2_2_0/_images/usage_statistics_job_details.gif b/website/docs/_images/usage_statistics_job_details.gif similarity index 100% rename from website/docs/v_2_2_0/_images/usage_statistics_job_details.gif rename to website/docs/_images/usage_statistics_job_details.gif diff --git a/website/docs/v_2_2_0/_images/usage_statistics_main.gif b/website/docs/_images/usage_statistics_main.gif similarity index 100% rename from website/docs/v_2_2_0/_images/usage_statistics_main.gif rename to website/docs/_images/usage_statistics_main.gif diff --git a/website/docs/v_2_2_0/_images/usage_statistics_month.gif b/website/docs/_images/usage_statistics_month.gif similarity index 100% rename from website/docs/v_2_2_0/_images/usage_statistics_month.gif rename to website/docs/_images/usage_statistics_month.gif diff --git a/website/docs/v_2_2_0/_images/vm_welcome_screen.png b/website/docs/_images/vm_welcome_screen.png similarity index 100% rename from website/docs/v_2_2_0/_images/vm_welcome_screen.png rename to website/docs/_images/vm_welcome_screen.png diff --git a/website/docs/v_2_2_0/_images/ws-structure.png b/website/docs/_images/ws-structure.png similarity index 100% rename from website/docs/v_2_2_0/_images/ws-structure.png rename to website/docs/_images/ws-structure.png diff --git a/website/docs/v_2_2_0/_sources/advanced.rst.txt b/website/docs/_sources/advanced.rst.txt similarity index 99% rename from website/docs/v_2_2_0/_sources/advanced.rst.txt rename to website/docs/_sources/advanced.rst.txt index e636c8a..46eba95 100644 --- a/website/docs/v_2_2_0/_sources/advanced.rst.txt +++ b/website/docs/_sources/advanced.rst.txt @@ -463,8 +463,8 @@ JABAWS War File Content .. links .. _war file content table: advanced.html#jabaws_war_file_content -.. _dm_javadoc: ../dm_javadoc/index.html -.. _full_javadoc: ../full_javadoc/index.html +.. _dm_javadoc: dm_javadoc/index.html +.. _full_javadoc: full_javadoc/index.html .. _prog_docs: http://www.compbio.dundee.ac.uk/jabaws/prog_docs/ .. _test JABAWS: advanced.html#testing-the-jabaws-server .. _deploying on Tomcat tips: war.html diff --git a/website/docs/v_2_2_0/_sources/changelog.rst.txt b/website/docs/_sources/changelog.rst.txt similarity index 100% rename from website/docs/v_2_2_0/_sources/changelog.rst.txt rename to website/docs/_sources/changelog.rst.txt diff --git a/website/docs/v_2_2_0/_sources/citations.rst.txt b/website/docs/_sources/citations.rst.txt similarity index 100% rename from website/docs/v_2_2_0/_sources/citations.rst.txt rename to website/docs/_sources/citations.rst.txt diff --git a/website/docs/v_2_2_0/_sources/client.rst.txt b/website/docs/_sources/client.rst.txt similarity index 100% rename from website/docs/v_2_2_0/_sources/client.rst.txt rename to website/docs/_sources/client.rst.txt diff --git a/website/docs/v_2_2_0/_sources/develop.rst.txt b/website/docs/_sources/develop.rst.txt similarity index 99% rename from website/docs/v_2_2_0/_sources/develop.rst.txt rename to website/docs/_sources/develop.rst.txt index d29c25d..998f37a 100644 --- a/website/docs/v_2_2_0/_sources/develop.rst.txt +++ b/website/docs/_sources/develop.rst.txt @@ -615,14 +615,14 @@ If you made any changes to the data model and would like to generate a complete .. links .. _Git-tracker: https://source.jalview.org/crucible/changelog/jabaws -.. _Data Model JavaDoc: ../dm_javadoc/index.html -.. _Complete JavaDoc: ../full_javadoc/index.html +.. _Data Model JavaDoc: dm_javadoc/index.html +.. _Complete JavaDoc: full_javadoc/index.html .. _JavaDoc: http://www.compbio.dundee.ac.uk/jabaws/full_javadoc/index.html .. _Test Results: http://www.compbio.dundee.ac.uk/user/www-jws2/tests/index.html .. _TestNG: http://testng.org/doc/index.html .. _Apache Ant: http://ant.apache.org/ -.. _download page: download.jsp -.. _JABAWS CLI client: download.jsp#client +.. _download page: ../download.jsp +.. _JABAWS CLI client: ../download.jsp#client .. _first aligning sequences example: develop.html#aligning-sequences .. _JAX-WS: http://jax-ws.java.net/ .. _WS-I: http://www.ws-i.org/ diff --git a/website/docs/v_2_2_0/_sources/getting_started.rst.txt b/website/docs/_sources/getting_started.rst.txt similarity index 100% rename from website/docs/v_2_2_0/_sources/getting_started.rst.txt rename to website/docs/_sources/getting_started.rst.txt diff --git a/website/docs/v_2_2_0/_sources/included_tools.rst.txt b/website/docs/_sources/included_tools.rst.txt similarity index 100% rename from website/docs/v_2_2_0/_sources/included_tools.rst.txt rename to website/docs/_sources/included_tools.rst.txt diff --git a/website/docs/v_2_2_0/_sources/index.rst.txt b/website/docs/_sources/index.rst.txt similarity index 100% rename from website/docs/v_2_2_0/_sources/index.rst.txt rename to website/docs/_sources/index.rst.txt diff --git a/website/docs/v_2_2_0/_sources/stats.rst.txt b/website/docs/_sources/stats.rst.txt similarity index 100% rename from website/docs/v_2_2_0/_sources/stats.rst.txt rename to website/docs/_sources/stats.rst.txt diff --git a/website/docs/v_2_2_0/_sources/va.rst.txt b/website/docs/_sources/va.rst.txt similarity index 96% rename from website/docs/v_2_2_0/_sources/va.rst.txt rename to website/docs/_sources/va.rst.txt index b5f3de4..374898d 100644 --- a/website/docs/v_2_2_0/_sources/va.rst.txt +++ b/website/docs/_sources/va.rst.txt @@ -3,7 +3,7 @@ Virtual Appliance (VA) The JABAWS Virtual Appliance is a way to run a JABAWS server locally, without the need to connect to the internet or configure JABAWS. What the appliance provides is a 'virtual server machine' (or more simply - *virtual machine* or *VM*), running an installation of the JABAWS Web Application Archive (WAR) on `TurnKey Linux`_ 12.1 (Standlone Tomcat). Once this has started up, it displays a message indicating the IP address of the JABAWS server, allowing any JABAWS client (such as Jalview or the JABAWS command line client) to connect to it. -You can run the appliance with freely available program such as `VMware Player`_, but you will need to install it first. We have tested the JABAWS appliance with VMware Player v 3.1.2 on Windows and Linux, and VMware Fusion on Mac. However, you are not limited to these virtualization systems and can use the JABAWS Appliance with any other virtualization platform. You can use `VMware OVF`_ tool to prepare JABAWS image for a different virtualization platform e.g. `VirtualBox`_. +You can run the appliance with freely available program such as `VMware Player`_, but you will need to install it first. We have tested the JABAWS appliance with VMware Player v 3.1.2 on Windows and Linux, and VMware Fusion on Mac. However, you are not limited to these virtualization systems and can use the JABAWS Appliance with any other virtualization platform. You can use `VMware OVF`_ tool to prepare JABAWS image for a different virtualization platform e.g. `VirtualBox`_. `VirtualBox`_ can also use the ``jabaws*.vmdk`` directly as an *existing preconfigured virtual hard disk file*, when creating a new Linux 2.4 / 3.x / 4.x 64-bit VM. .. note:: The appliance best suits users who would like to use the JABAWS web-services locally. This might be because they do not want to access systems over an internet, or just want to keep their data private. It is also the recommended option for users who want to install JABAWS on Windows, which does not support all the bioinformatics programs that JABAWS can run. @@ -21,7 +21,7 @@ Installing The free `VMware Player`_ can be used to run the JABAWS services from the Windows and Linux host operating systems. `VMware Fusion`_, a commercial VMware product, offers virtual machine support for Mac. -To run the JABAWS server on VMware player, unpack the JABAWS VM into one of the folders on your local hard drive. Open VMware Player, click "Open Virtual Machine" and point the Player to the location of the JABAWS, then choose the ``JABAWS*.vmx`` file to open an appliance. +To run the JABAWS server on VMware player, unpack the JABAWS VM into one of the folders on your local hard drive. Open VMware Player, click "Open Virtual Machine" and point the Player to the location of the JABAWS, then choose the ``jabaws*.vmx`` file to open an appliance. When you play the machine for the first time the Player might ask you whether "This virtual machine may have been moved or copied.", say that you have copied it. That is all. diff --git a/website/docs/v_2_2_0/_sources/war.rst.txt b/website/docs/_sources/war.rst.txt similarity index 100% rename from website/docs/v_2_2_0/_sources/war.rst.txt rename to website/docs/_sources/war.rst.txt diff --git a/website/docs/v_2_2_0/_static/ajax-loader.gif b/website/docs/_static/ajax-loader.gif similarity index 100% rename from website/docs/v_2_2_0/_static/ajax-loader.gif rename to website/docs/_static/ajax-loader.gif diff --git a/website/docs/v_2_2_0/_static/basic.css b/website/docs/_static/basic.css similarity index 100% rename from website/docs/v_2_2_0/_static/basic.css rename to website/docs/_static/basic.css diff --git a/website/docs/v_2_2_0/_static/comment-bright.png b/website/docs/_static/comment-bright.png similarity index 100% rename from website/docs/v_2_2_0/_static/comment-bright.png rename to website/docs/_static/comment-bright.png diff --git a/website/docs/v_2_2_0/_static/comment-close.png b/website/docs/_static/comment-close.png similarity index 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diff --git a/website/docs/v_2_2_0/_static/js/theme.js b/website/docs/_static/js/theme.js similarity index 100% rename from website/docs/v_2_2_0/_static/js/theme.js rename to website/docs/_static/js/theme.js diff --git a/website/docs/v_2_2_0/_static/minus.png b/website/docs/_static/minus.png similarity index 100% rename from website/docs/v_2_2_0/_static/minus.png rename to website/docs/_static/minus.png diff --git a/website/docs/v_2_2_0/_static/plus.png b/website/docs/_static/plus.png similarity index 100% rename from website/docs/v_2_2_0/_static/plus.png rename to website/docs/_static/plus.png diff --git a/website/docs/v_2_2_0/_static/pygments.css b/website/docs/_static/pygments.css similarity index 100% rename from website/docs/v_2_2_0/_static/pygments.css rename to website/docs/_static/pygments.css diff --git a/website/docs/v_2_2_0/_static/searchtools.js b/website/docs/_static/searchtools.js similarity index 100% rename from website/docs/v_2_2_0/_static/searchtools.js rename to website/docs/_static/searchtools.js diff --git a/website/docs/v_2_2_0/_static/underscore-1.3.1.js b/website/docs/_static/underscore-1.3.1.js similarity index 100% rename from website/docs/v_2_2_0/_static/underscore-1.3.1.js rename to website/docs/_static/underscore-1.3.1.js diff --git a/website/docs/v_2_2_0/_static/underscore.js b/website/docs/_static/underscore.js similarity index 100% rename from website/docs/v_2_2_0/_static/underscore.js rename to website/docs/_static/underscore.js diff --git a/website/docs/v_2_2_0/_static/up-pressed.png b/website/docs/_static/up-pressed.png similarity index 100% rename from website/docs/v_2_2_0/_static/up-pressed.png rename to website/docs/_static/up-pressed.png diff --git a/website/docs/v_2_2_0/_static/up.png b/website/docs/_static/up.png similarity index 100% rename from website/docs/v_2_2_0/_static/up.png rename to website/docs/_static/up.png diff --git a/website/docs/v_2_2_0/_static/websupport.js b/website/docs/_static/websupport.js similarity index 100% rename from website/docs/v_2_2_0/_static/websupport.js rename to website/docs/_static/websupport.js diff --git a/website/docs/v_2_2_0/advanced.html b/website/docs/advanced.html similarity index 99% rename from website/docs/v_2_2_0/advanced.html rename to website/docs/advanced.html index 36fbc72..6966c9b 100644 --- a/website/docs/v_2_2_0/advanced.html +++ b/website/docs/advanced.html @@ -176,7 +176,7 @@ - Return to the JABAWS homepage + Return to the JABAWS homepage @@ -541,10 +541,10 @@ After you have completed the editing your configuration may look like this:

/ help pages, index.html is the starting page -dm_javadoc +dm_javadoc JavaDoc for the JABAWS Data Model -full_javadoc +full_javadoc JavaDoc for the complete JABAWS prog_docs @@ -576,7 +576,7 @@ After you have completed the editing your configuration may look like this:

-

JABAWS 2.2 +

JABAWS 2.2 © Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Daniel Barton, Fábio Madeira, Alexey Drozdetskiy, Suzanne Duce and Geoff Barton.

diff --git a/website/docs/v_2_2_0/changelog.html b/website/docs/changelog.html similarity index 99% rename from website/docs/v_2_2_0/changelog.html rename to website/docs/changelog.html index ec1262c..6c5e640 100644 --- a/website/docs/v_2_2_0/changelog.html +++ b/website/docs/changelog.html @@ -158,7 +158,7 @@ - Return to the JABAWS homepage + Return to the JABAWS homepage @@ -271,7 +271,7 @@
-

JABAWS 2.2 +

JABAWS 2.2 © Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Daniel Barton, Fábio Madeira, Alexey Drozdetskiy, Suzanne Duce and Geoff Barton.

diff --git a/website/docs/v_2_2_0/citations.html b/website/docs/citations.html similarity index 98% rename from website/docs/v_2_2_0/citations.html rename to website/docs/citations.html index 1174473..8b9dabc 100644 --- a/website/docs/v_2_2_0/citations.html +++ b/website/docs/citations.html @@ -153,7 +153,7 @@ - Return to the JABAWS homepage + Return to the JABAWS homepage @@ -197,7 +197,7 @@
-

JABAWS 2.2 +

JABAWS 2.2 © Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Daniel Barton, Fábio Madeira, Alexey Drozdetskiy, Suzanne Duce and Geoff Barton.

diff --git a/website/docs/v_2_2_0/client.html b/website/docs/client.html similarity index 99% rename from website/docs/v_2_2_0/client.html rename to website/docs/client.html index a2c7b11..47f4574 100644 --- a/website/docs/v_2_2_0/client.html +++ b/website/docs/client.html @@ -158,7 +158,7 @@ - Return to the JABAWS homepage + Return to the JABAWS homepage @@ -272,7 +272,7 @@ Please note that -r and -f options cannot be used together. Alignment is done wi
-

JABAWS 2.2 +

JABAWS 2.2 © Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Daniel Barton, Fábio Madeira, Alexey Drozdetskiy, Suzanne Duce and Geoff Barton.

diff --git a/website/docs/v_2_2_0/develop.html b/website/docs/develop.html similarity index 98% rename from website/docs/v_2_2_0/develop.html rename to website/docs/develop.html index ec79d44..8be0fdd 100644 --- a/website/docs/v_2_2_0/develop.html +++ b/website/docs/develop.html @@ -178,7 +178,7 @@ - Return to the JABAWS homepage + Return to the JABAWS homepage @@ -207,8 +207,8 @@

The API¶

-

Data Model JavaDoc - read this if your are coding against JABA Web Services

-

Complete JavaDoc - for developers who want to use JABAWS framework and use Engines and Executables directly

+

Data Model JavaDoc - read this if your are coding against JABA Web Services

+

Complete JavaDoc - for developers who want to use JABAWS framework and use Engines and Executables directly

@@ -338,12 +338,12 @@ JABAWS uses TestNG for testing. There is a TestNG plugin available for Eclipse w

Additional utility libraries that this client depend upon is the compbio-util-1.3.jar and compbio-annotation-1.0.jar.

-

Please refer to a Data Model JavaDoc for a detailed description of each class and its methods.

+

Please refer to a Data Model JavaDoc for a detailed description of each class and its methods.

Connecting to JABAWS¶

-

For a complete working example of JABAWS command line client please see compbio.ws.client.Jws2Client class. JABAWS command line client source code is available from the download page. Please note that for now all the examples are in Java, other languages will follow if there is sufficient demand.

+

For a complete working example of JABAWS command line client please see compbio.ws.client.Jws2Client class. JABAWS command line client source code is available from the download page. Please note that for now all the examples are in Java, other languages will follow if there is sufficient demand.

Download a binary JABAWS client. Add the client to the class path. The following code excerpt will connect your program to Clustal web service deployed in the University of Dundee.

import java.net.URL;
 import javax.xml.namespace.QName;
@@ -456,7 +456,7 @@ Methods and classes mentioned in the excerpt are available from the JABAWS clien

A complete client example¶

-

Finally, a complete example of the program that connects to JABAWS Clustal service and aligns sequences using one of the Clustal web service presets. All you need for this to work is a JABAWS CLI client. Please make sure that the client is in the Java class path before running this example.

+

Finally, a complete example of the program that connects to JABAWS Clustal service and aligns sequences using one of the Clustal web service presets. All you need for this to work is a JABAWS CLI client. Please make sure that the client is in the Java class path before running this example.

import java.io.ByteArrayInputStream;
 import java.io.FileNotFoundException;
 import java.io.IOException;
@@ -588,7 +588,7 @@ Methods and classes mentioned in the excerpt are available from the JABAWS clien
 }
-

For a more detailed description of all available types and their functions please refer to the Data Model JavaDoc.

+

For a more detailed description of all available types and their functions please refer to the Data Model JavaDoc.

@@ -689,7 +689,7 @@ Methods and classes mentioned in the excerpt are available from the JABAWS clien
-

JABAWS 2.2 +

JABAWS 2.2 © Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Daniel Barton, Fábio Madeira, Alexey Drozdetskiy, Suzanne Duce and Geoff Barton.

diff --git a/website/docs/v_2_2_0/genindex.html b/website/docs/genindex.html similarity index 99% rename from website/docs/v_2_2_0/genindex.html rename to website/docs/genindex.html index 1cd0fe8..a5513cc 100644 --- a/website/docs/v_2_2_0/genindex.html +++ b/website/docs/genindex.html @@ -181,7 +181,7 @@
-

JABAWS 2.2 +

JABAWS 2.2 © Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Daniel Barton, Fábio Madeira, Alexey Drozdetskiy, Suzanne Duce and Geoff Barton.

diff --git a/website/docs/v_2_2_0/getting_started.html b/website/docs/getting_started.html similarity index 99% rename from website/docs/v_2_2_0/getting_started.html rename to website/docs/getting_started.html index 980b555..bfa3f37 100644 --- a/website/docs/v_2_2_0/getting_started.html +++ b/website/docs/getting_started.html @@ -163,7 +163,7 @@ - Return to the JABAWS homepage + Return to the JABAWS homepage @@ -327,7 +327,7 @@
-

JABAWS 2.2 +

JABAWS 2.2 © Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Daniel Barton, Fábio Madeira, Alexey Drozdetskiy, Suzanne Duce and Geoff Barton.

diff --git a/website/docs/v_2_2_0/included_tools.html b/website/docs/included_tools.html similarity index 98% rename from website/docs/v_2_2_0/included_tools.html rename to website/docs/included_tools.html index a4d7cea..5170a1f 100644 --- a/website/docs/v_2_2_0/included_tools.html +++ b/website/docs/included_tools.html @@ -159,7 +159,7 @@ - Return to the JABAWS homepage + Return to the JABAWS homepage @@ -231,7 +231,7 @@
-

JABAWS 2.2 +

JABAWS 2.2 © Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Daniel Barton, Fábio Madeira, Alexey Drozdetskiy, Suzanne Duce and Geoff Barton.

diff --git a/website/docs/v_2_2_0/index.html b/website/docs/index.html similarity index 99% rename from website/docs/v_2_2_0/index.html rename to website/docs/index.html index a06267d..e62ca33 100644 --- a/website/docs/v_2_2_0/index.html +++ b/website/docs/index.html @@ -152,7 +152,7 @@ - Return to the JABAWS homepage + Return to the JABAWS homepage @@ -305,7 +305,7 @@
-

JABAWS 2.2 +

JABAWS 2.2 © Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Daniel Barton, Fábio Madeira, Alexey Drozdetskiy, Suzanne Duce and Geoff Barton.

diff --git a/website/docs/v_2_2_0/jabaws_manual.pdf b/website/docs/jabaws_manual.pdf similarity index 91% rename from website/docs/v_2_2_0/jabaws_manual.pdf rename to website/docs/jabaws_manual.pdf index 7ee7aef..27dd272 100644 Binary files a/website/docs/v_2_2_0/jabaws_manual.pdf and b/website/docs/jabaws_manual.pdf differ diff --git a/website/docs/v_2_2_0/objects.inv b/website/docs/objects.inv similarity index 100% rename from website/docs/v_2_2_0/objects.inv rename to website/docs/objects.inv diff --git a/website/docs/v_2_2_0/search.html b/website/docs/search.html similarity index 99% rename from website/docs/v_2_2_0/search.html rename to website/docs/search.html index c7598a5..0c2bf24 100644 --- a/website/docs/v_2_2_0/search.html +++ b/website/docs/search.html @@ -186,7 +186,7 @@
-

JABAWS 2.2 +

JABAWS 2.2 © Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Daniel Barton, Fábio Madeira, Alexey Drozdetskiy, Suzanne Duce and Geoff Barton.

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\ No newline at end of file diff --git a/website/docs/v_2_2_0/stats.html b/website/docs/stats.html similarity index 99% rename from website/docs/v_2_2_0/stats.html rename to website/docs/stats.html index 0764fe8..40e0f84 100644 --- a/website/docs/v_2_2_0/stats.html +++ b/website/docs/stats.html @@ -160,7 +160,7 @@ - Return to the JABAWS homepage + Return to the JABAWS homepage @@ -299,7 +299,7 @@ local.stat.maxruntime=6
-

JABAWS 2.2 +

JABAWS 2.2 © Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Daniel Barton, Fábio Madeira, Alexey Drozdetskiy, Suzanne Duce and Geoff Barton.

diff --git a/website/docs/v_2_2_0/_sources/man/advanced.rst.txt b/website/docs/v_2_2_0/_sources/man/advanced.rst.txt deleted file mode 100644 index 9c1f36e..0000000 --- a/website/docs/v_2_2_0/_sources/man/advanced.rst.txt +++ /dev/null @@ -1,471 +0,0 @@ -Advanced Usage -============== - -JABAWS web services are WS-I basic profile compliant, which means they can be accessed using any programming language or system that can utilize standard SOAP web services. The Web Service Definition Language (WSDL) for each service is published on the JABAWS home page, and you can use this to automatically generate service bindings for your program. If you use Java you may wish to use our client package to access JABAWS. This package is based on the autogenerated source code produced by wsimport, which is the Java tool for creating web service bindings. In addition, this offers some additional methods that simplify working with JABAWS. For more information please refer to the data model javadoc. - - ------------- - -.. _jabaws_wsdl: - -Valid WSDL ----------- - -**Multiple sequence alignment services** - -* ClustalOWS - http://www.compbio.dundee.ac.uk/jabaws/ClustalOWS?wsdl -* ClustalWS - http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl -* MuscleWS - http://www.compbio.dundee.ac.uk/jabaws/MuscleWS?wsdl -* MafftWS - http://www.compbio.dundee.ac.uk/jabaws/MafftWS?wsdl -* TcoffeeWS - http://www.compbio.dundee.ac.uk/jabaws/TcoffeeWS?wsdl -* ProbconsWS - http://www.compbio.dundee.ac.uk/jabaws/ProbconsWS?wsdl -* MSAprobsWS - http://www.compbio.dundee.ac.uk/jabaws/MSAprobsWS?wsdl -* GLprobsWS - http://www.compbio.dundee.ac.uk/jabaws/GLprobsWS?wsdl - -**Protein disorder prediction services** - -* IUPredWS - http://www.compbio.dundee.ac.uk/jabaws/IUPredWS?wsdl -* GlobPlotWS - http://www.compbio.dundee.ac.uk/jabaws/GlobPlotWS?wsdl -* DisemblWS - http://www.compbio.dundee.ac.uk/jabaws/DisemblWS?wsdl -* JronnWS - http://www.compbio.dundee.ac.uk/jabaws/JronnWS?wsdl - -**Amino acid conservation service** - -* AAConWS - http://www.compbio.dundee.ac.uk/jabaws/AAConWS?wsdl - -**RNA Secondary Structure Prediction** - -* RNAalifoldWS - http://www.compbio.dundee.ac.uk/jabaws/RNAalifoldWS?wsdl - - -Please replace http://www.compbio.dundee.ac.uk/ with your JABAWS instance host name, and jabaws with your JABAWS context name to access your local version of JABAWS web services. For example http://localhost:8080/jabaws would be a valid URL for the default Apache-Tomcat installation and jabaws.war file deployment. - - ------------- - -.. _jabaws_config: - -JABAWS Configuration --------------------- - -There are three parts of the system you can configure. The local and the cluster engines, and the paths to the individual executables for each engine. These settings are stored in configuration files within the web application directory (for an overview, then take a look at the war file content table) [link]. - -Initially, JABAWS is configured with only the local engine enabled, with job output written to directory called "jobsout" within the web application itself. This means that JABAWS will work out of the box, but may not be suitable for serving a whole lab or a university. - - ------------- - -.. _jabaws_config_le: - -Local Engine Configuration -~~~~~~~~~~~~~~~~~~~~~~~~~~ - -The Local execution engine configuration is defined in the properties file ``conf/Engine.local.properties``. The supported configuration settings are: - -``engine.local.enable=true`` - enable or disable local engine, valid values true | false - -``local.tmp.directory=D:\\clusterengine\\testoutput`` - a directory to use for temporary files storage, optional, defaults to java temporary directory - -``engine.local.thread.number=4`` - Number of threads for tasks execution (valid values between 1 and 2x cpu. Where x is a number of cores available in the system). Optional defaults to the number of cores for core number <=4 and number of cores-1 for greater core numbers. - -If the local engine going to be heavily loaded (which is often the case if you do not have a cluster) it is a good idea to increase the amount of memory available for the web application server. If you are using Apache-Tomcat, then you can define its memory settings in the JAVA_OPTS environment variable. To specify which JVM to use for Apache-Tomcat, put the full path to the JRE installation in the JAVA_HOME environment variable. (We would recommend using Sun Java Virtual Machine (JVM) in preference to Open JDK). Below is an example of code which can be added to ``/bin/setenv.sh`` script to define which JVM to use and a memory settings for Tomcat server. Tomcat server startup script (``catalina.sh``) will execute ``setenv.sh`` on each server start automatically. - -.. code:: bash - - export JAVA_HOME=/homes/ws-dev2/jdk1.6.0_17/ - export JAVA_OPTS="-server -Xincgc -Xms512m -Xmx1024m" - - ------------- - -.. _jabaws_config_ce: - -Cluster Engine Configuration -~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -Supported configuration settings: - -``engine.cluster.enable=true`` - enable or disable local engine true | false, defaults to false - -``cluster.tmp.directory=/homes/clustengine/testoutput`` - a directory to use for temporary files storage. The value must be an absolute path to the temporary directory. This is required. The value must be different from what is defined for local engine. This directory must be accessible from all cluster nodes. - -For the cluster engine to work, the SGE_ROOT and LD_LIBRARY_PATH environment variables have to be defined. They tell the cluster engine where to find DRMAA libraries. These variables should be defined when the web application server starts up, e.g. - -.. code:: bash - - SGE_ROOT=/gridware/sge - LD_LIBRARY_PATH=/gridware/sge/lib/lx24-amd64 - -Finally, do not forget to configure executables for the cluster execution, they may be the same as for the local execution but may be different. Please refer to the executable configuration section for further details. - - ------------- - -.. _jabaws_config_ec: - -Executable Configuration -~~~~~~~~~~~~~~~~~~~~~~~~ - -All the executable programs are configured in conf/Executable.properties file. Each executable is configured with a number of options. They are: - -.. code:: bash - - local.X.bin.windows= - local.X.bin= - cluster.X.bin= - X.bin.env= - X.--aamatrix.path= - X.presets.file= - X.parameters.file= - X.limits.file= - X.cluster.settings= - -Where X any of the bioinformatics tools available (e.g. clustalw, muscle, mafft, probcons, t-coffee, etc.). - -Default JABAWS configuration includes path to local executables to be run by the local engine only, all cluster related settings are commented out, but they are there for you as examples. Cluster engine is disabled by default. To configure executable for cluster execution uncomment the X.cluster settings and change them appropriately. - -By default limits are set well in excess of what you may want to offer to the users outside your lab, to make sure that the tasks are never rejected. The default limit is 100000 sequences of 100000 letters on average for all of the JABA web services. You can adjust the limits according to your needs by editing ``conf/settings/Limit.xml`` files. -After you have completed the editing your configuration may look like this: - -.. code:: bash - - local.mafft.bin=binaries/mafft - cluster.mafft.bin=/homes/cengine/mafft - mafft.bin.env=MAFFT_BINARIES#/homes/cengine/mafft;FASTA_4_MAFFT#/bin/fasta34; - mafft.--aamatrix.path=binaries/matrices - mafft.presets.file=conf/settings/MafftPresets.xml - mafft.parameters.file=conf/settings/MafftParameters.xml - mafft.limits.file=conf/settings/MafftLimits.xml - mafft.cluster.settings=-q bigmem.q -l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M - -Please not that relative paths must only be specified for the files that reside inside web application directory, all other paths must be supplied as absolute! - -Furthermore, you should avoid using environment variables within the paths or options - since these will not be evaluated correctly. Instead, please explicitly specify the absolute path to anything normally evaluated from an environment variable at execution time. - -If you are using JABAWS to submit jobs to the cluster (with cluster engine enabled), executables must be available from all cluster nodes the task can be sent to, also paths to the executables on the cluster e.g. ``cluster..bin`` must be absolute. - -Executables can be located anywhere in your system, they do not have to reside on the server as long as the web application server can access and execute them. - -Cluster settings are treated as a black box, the system will just pass whatever is specified in this line directly to the cluster submission library. This is how DRMAA itself treats this settings. More exactly DRMAA ``JobTemplate.setNativeSpecification()`` function will be called. - -For further details and examples of configuration please refer to the ``Executable.properties`` file supplied with JABAWS. - - ------------- - -.. _jabaws_config_env_exe: - -Defining Environment Variables for Executables -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - - -Environment variables can be defined in property - -.. code:: bash - - x.bin.env - -Where x is one of thw executables supported by JABAWS. Several environment variables can be specified in the same line. For example. - -.. code:: bash - - mafft.bin.env=MAFFT_BINARIES#/homes/cengine/mafft;FASTA_4_MAFFT#/bin/fasta34; - -The example above defines two environment variables with names ``MAFFT-BINARIES`` and ``FASTA_4_MAFFT`` and values ``/homes/cengine/mafft and /bin/fasta34`` respectively. Semicolon is used as a separator between different environment variables whereas hash is used as a separator for name and value of the variable. - - ------------- - -.. _jabaws_config_env_mafft: - -Configure JABAWS to Work with Mafft -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - - -If you use default configuration you do not need to read any further. The default configuration will work for you without any changes, however, if you want to install Mafft yourself then there is a couple of more steps to do. - -Mafft executable needs to know the location of other files supplied with Mafft. In addition some Mafft functions depends on the fasta executable, which is not supplied with Mafft, but is a separate package. Mafft needs to know the location of fasta34 executable. - -To let Mafft know where the other files from its package are, change the value of MAFFT-BINARIES environment variables. To let Mafft know where is the fasta34 executable set the value of FASTA_4_MAFFT environment variable to point to a location of fasta34 program. The latter can be added to the PATH variable instead. If you are using executables supplied with JABAWS, the path to Mafft binaries would be like ``/binaries/src/mafft/binaries`` and the path to fasta34 binary would be ``/binaries/src/fasta34/fasta34``. You can specify the location of Mafft binaries as well as fasta34 program elsewhere by providing an absolute path to them. All these settings are defined in ``conf/Executable.properties`` file. - - ------------- - -.. _jabaws_config_env_limit: - -Limiting the size of the job accepted by JABAWS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -JABAWS can be configured to reject excessively large tasks. This is useful if you operate JABAWS service for many users. By defining a maximum allowed task size you can provide an even service for all users and prevents waste of resources on the tasks too large to complete successfully. You can define the maximum number of sequences and the maximum average sequence length that JABAWS accepts for each JABA Web Service independently. Furthermore, you can define different limits for different presets of the same web service. - -By default limits are disabled. You can enable them by editing ``conf/Executable.properties`` file. You can adjust the limits according to your needs by editing ``conf/settings/Limit.xml`` files. - - -.. _war_precompiled_bin: - -Pre-compiled binaries -~~~~~~~~~~~~~~~~~~~~~ - -.. danger:: improve this bit - - -Using a different version of the alignment program with JABAWS - -JABAWS is supplied with binaries and source code of the executables related to the version it supports. So normally you would not need to install your own executables. However, if you have a different version of an executable (e.g. an alignment program) which you prefer, you could use it as long as it supports all the functions JABAWS executable require. This could be the case with more recent executable. If the options supported by your chosen executable is different from the standard JABAWS executable, then you need to edit ExecutableNameParamaters.xml configuration file. - - -JABAWS comes with pre-compiled x86 Linux binaries, thus on such systems JABAWS should work straight out of the box. If you are in any doubts or experience problems you may want to make sure that the binaries supplied work under your OS. To do this just execute each binary, without any command line options or input files. If you see an error message complaining about missing libraries or other problems, then you probably need to recompile the binaries [link]. - -You can try the JABAWS functionality with the JABAWS test client or have a look at deploying on Tomcat [link] tips if you experience any problems. - -.. note:: You may want to enable logging, as described here [link]. - - -JABAWS's web services use command line programs to do the actual analysis, so it must have access to programs which can be executed on your platform. The native executables bundled with JABAWS for Windows (32-bit) and Linux (i386, 32-bit) should be OK for those systems. The source code for these programs is also provided so you can recompile for your own architecture [link] and exploit any optimizations that your system can provide. Alternately, if you have already got binaries on your system, then you can simply change the paths in JABAWS's configuration files [link] so these are used instead. - ------------- - -.. _war_recompile_bin: - -Recompiling binaries for your system -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -If you have a fully equipped build environment on your (POSIX-like) system, then you should be able to recompile the programs from the source distributions which are included in the JABAWS war file. A script called 'compilebin.sh' is provided to automate this task. - -1. In a terminal window, change the working directory to ``binaries/src`` -2. Execute the compilebin.sh script: - - .. code:: bash - - chmod +x compilebin.sh; compilebin.sh > compilebin.out; -3. Then run: - - .. code:: bash - - chmod +x setexecflag.sh; sh setexecflag.sh - - If any of the binaries was not recompiled, then a 'file not found' error will be raised. - -4. Finally, restart your Tomcat server (or JABAWS application only), and test JABAWS [link] to check that it can use the new binaries. - - -If you couldn't compile everything, then it may be that your system does not have all the tools required for compiling the programs. At the very least check that you have gcc, g++ and make installed in your system. If not install these packages and repeat the compilation steps again. You should also review the compilebin.sh output - which was redirected to compilebin.out, and any errors output to the terminal. Finally, try obtaining the pre compiled binaries [link] for your OS. - - ------------- - -.. _war_reusing_bin: - -Obtaining or reusing binaries -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -You could search for pre-packaged compiled executable in your system package repository or alternately, download pre-compiled binaries from each alignment program's home page. Then, either replace the executables supplied with the downloaded ones, or modify the paths defined in ``executable.properties`` as described below. -.. Below are some suggestions on where you may be able to get the binaries for your system. - -If you would like to use the binaries you already have, then you just need to let JABAWS know where they are. To do this, edit: ``conf/Executable.properties`` - -When specifying paths to executables that already exist on your system, make sure you provide an absolute path, or one relative to the JABAWS directory inside webapps. For example, the default path for clustalw is defined as ``local.clustalw.bin=binaries/src/clustalw/src/clustalw2`` Alternatively, instead of changing ``Executable.properties`` you could also replace the executables bundled with JABAWS with the ones that you have, or make symbolic links to them. Then the default configuration will work for you. More information about the Executable.properties file is given in the JABAWS Configuration page. - - ------------- - -.. _jabaws_config_lb: - -Load balancing --------------- - -If your cluster is busy and has significant waiting times, you can achieve a faster response by allowing the server machine to calculate small tasks and then reserve the cluster for bigger jobs. This works especially well if your server is a powerful machine with many CPUs. To do this you need to enable and configure both the cluster and the local engines. Once this is done decide on the maximum size of a task to be run on the server locally. Then, edit "# LocalEngineExecutionLimit #" preset in ``Limits.xml`` file accordingly. JABAWS server then will balance the load according to the following rule: If the task size is smaller than the maximum task size for local engine, and the local engine has idle threads, then it calculates task locally otherwise it submit the task to the cluster. - - ------------- - -.. _war_testing: - -Testing the JABAWS Server -------------------------- - -.. danger:: improve this bit - -Access ``/ServiceStatus`` to test all web services. Each time you access this URL, all services are tested. For production configuration we recommend prohibiting requests to this URL for non authenticated users to prevent excessive load on the server. - -Alternatively, you can use a command line client (part of the client only package) to test your JABAWS installation as described here. If you downloaded a JABAWS server package, you can use ``/WEB-INF/lib/jaba-client.jar`` to test JABAWS installation as described here. If you downloaded the source code, then you could run a number of test suites defined in the build.xml Apache Ant file. - - -First of all make sure that Tomcat server is started successfully. If this was the case, then you should see JABAWS home page when you navigate to your Tomcat JABAWS context path in your browser (e.g. at ``http://myhost.compbio.ac.uk:8080/jabaws`` => ````) - -If you see it, then it is time to make sure that web services are working too. The easiest way to do this is to access Services Status page available from the main JABAWS web page menu. - -If you need to monitor web service health automatically when the best option is to use service checker that responds with the standard HTTP status code. To access this checker use the following URL: - -**Using JABAWS service status checker** - -If you see it, then it is time to make sure that web services are working too. The easiest way to do this is to access Services Status page available from the main JABAWS web page menu. - -If you need to monitor web service health automatically when the best option is to use service checker that responds with the standard HTTP status code. To access this checker use the following URL: ``/HttpCodeResponseServiceStatus`` or alternatively ``/man_serverwar.jsp`` - -This page returns code 200, and no page context if all services are operational, 503 if one of the services have problems. You can also check each web service individually by providing the name of the web service to check at the end of the service checker URL like this: ``/HttpCodeResponseServiceStatus/ClustalWS`` - - -Upon request, the service status checker will examine the health of the ClustalWS web service only. If the service name is not valid, then the service checker will return code 400. - -**Using command line client** - -Alternatively, you should be able to use the test program which can be found in ``/WEB-INF/lib/jabaws-client.jar`` file. To run the tests type: - -.. code:: bash - - java -jar jabaws-client.jar -h= - -For example to test all JABAWS web services on host myhost.compbio.ac.uk type: - -.. code:: bash - - java -jar jabaws-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws - - -You can choose a particular web server using -s option like this java -jar jabaws-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=ClustalWS This command line assumes that java executable is in your path and jabaws-client.jar is located in the current directory. - -An example of the report testing tool produces for operating web service looks like this: - -.. code:: bash - - Connecting to service MuscleWS on http://myhost.compbio.ac.uk:8080/jabaws ... OK - Testing alignment with default parameters: - Queering job status...OK - Retrieving results...OK - Testing alignment with presets: - Aligning with preset 'Protein alignment(Fastest speed)'... OK - Aligning with preset 'Nucleotide alignment(Fastest speed)'... OK - Aligning with preset 'Huge alignments (speed-oriented)'... OK - Queering presets...OK - Queering Parameters...OK - Queering Limits...OK - Queering Local Engine Limits...OK - Check is completed service MuscleWS IS WORKING - -An example of the response of a web service which is deployed but is not operating is below: - -.. code:: bash - - Connecting to service ProbconsWS on http://localhost:8080/ws ... OK - Testing alignment with default parameters:FAILED - Service ProbconsWS IS NOT FUNCTIONAL - - -If the web server did not respond the message looks like following: - -.. code:: bash - - Connecting to service TcoffeeWS on http://localhost:8080/ws ... FAILED - - ------------- - -.. _war_logging: - -JABAWS internal logging ------------------------ - -JABAWS can be configured to log what it is doing. This comes in handy if you would like to see who is using your web services or need to chase some problems. JABAWS uses log4j to do the logging, the example of log4j configuration is bundled with JABAWS war file. You will find it in the ``/WEB-INF/classes/log4j.properties`` file. All the lines in this file are commented out. The reason why the logging is disabled by default it simple, log4j has to know the exact location of where the log files are stored. This is not known up until the deployment time. To enable the logging you need to define logDir property in the log4j.properties and uncomment section of the file which corresponds to your need. More information is given in the log4j.properties file itself. Restart the Tomcat or the JABAWS web application to apply the settings. - -After you have done this, assuming that you did not change the log4j.properties file yourself, you should see the application log file called activity.log. The file called activity.log. The amount of information logged can be adjusted using different logging levels, it is reduced in the following order of log levels TRACE, DEBUG, INFO, WARN, ERROR, FATAL. - -If you would like to know who is using your services, you might want to enable Tomcat request logging. - ------------- - -.. _war_logging_req: - -JABAWS requests logging -~~~~~~~~~~~~~~~~~~~~~~~ - -Enable Tomcat log valve. To do this uncomment the following section of /conf/server.xml configuration file. - -.. code-block:: xml - - - - -The following information will be logged: - -+--------------+------------------------------+-------------------------------+---------------+------------------------+ -| Remote IP | Date | Method server_URL protocol | HTTP status | Response size in bytes | -+==============+==============================+===============================+===============+========================+ -| 10.31.11.159 | [10/Feb/2010:16:51:32 +0000] | "POST /jws2/MafftWS HTTP/1.1" | 200 | 2067 | -+--------------+------------------------------+-------------------------------+---------------+------------------------+ - -Which can be processed in various programs for log analysis, such as WebAlizer, Analog, AWStats [links]. - - ------------- - -.. _jabaws_config_ga: - -JABAWS and Google Analytics ---------------------------- - - -JABAWS reports web services usage to our group Google Analytics (GA) account. JABAWS usage statistics are collected for funding and reporting purposes, and no private information is collected. The data sent by JABAWS is as follows: - -1. The IP address of the JABAWS server machine (the server IP can anonymized see ``conf/GA.properties`` config file) -2. The name of the web service that was called. -3. A few details of the system such as JABAWS version, java version, user language, color depth, screen resolution and character encoding. - -Google Analytics can be disabled or adjusted by removing/editing ``conf/GA.properties`` Google Analytics (GA) settings file. We would appreciate it greatly if you could leave it on! - -All calls to GA are very lightweight, completed asynchronously, create very little overhead and do not influence the server response time or performance. - - ------------- - -.. _war_contents: - -JABAWS War File Content ------------------------ - -+---------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------+ -| Directory | Content description | -+=====================+==========================================================================================================================================================+ -| conf/ contains | configuration files such as Executable.properties, Engine.local.properties, Engine.cluster.properties | -+---------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------+ -| conf/settings | Contains individual executable description files. In particular XXXParameters.xml, XXXPresets.xml, XXXLimits.xml where XXX is the name of the executable | -+---------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------+ -| ExecutionStatistics | The database for storing the execution statistics | -+---------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------+ -| statpages | Web pages for usage statistics visialization and webservices status queries | -+---------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------+ -| jobsout/ | Contains directories generated when running an individual executable. E.g. input and output files and some other task related data (optional) | -+---------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------+ -| binaries/ | Directory contains native executables - programs, windows binaries (optional) | -+---------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------+ -| binaries/src | Contains source of native executables and Linux i386 binaries | -+---------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------+ -| binaries/windows | Contains binaries for MS Windows operating system | -+---------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------+ -| binaries/matrices | Substitution matrices | -+---------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------+ -| WEB-INF | Web application descriptor | -+---------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------+ -| WEB-INF/lib | Web application libraries | -+---------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------+ -| WEB-INF/classes | log4j.properties - log configuration file (optional) | -+---------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------+ -| static | Static content such as CSS, JavaScript and Image files | -+---------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------+ - -+---------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------+ -| **Help Pages** | | -+=====================+==========================================================================================================================================================+ -| / | help pages, index.html is the starting page | -+---------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------+ -| `dm_javadoc`_ | JavaDoc for the JABAWS Data Model | -+---------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------+ -| `full_javadoc`_ | JavaDoc for the complete JABAWS | -+---------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------+ -| `prog_docs`_ | Documentation for programs that are included in JABAWS | -+---------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------+ - -.. _dm_javadoc: http://www.compbio.dundee.ac.uk/jabaws/dm_javadoc/index.html -.. _full_javadoc: http://www.compbio.dundee.ac.uk/jabaws/full_javadoc/index.html -.. _prog_docs: http://www.compbio.dundee.ac.uk/jabaws/prog_docs/ diff --git a/website/docs/v_2_2_0/_sources/man/changelog.rst.txt b/website/docs/v_2_2_0/_sources/man/changelog.rst.txt deleted file mode 100644 index 37135b7..0000000 --- a/website/docs/v_2_2_0/_sources/man/changelog.rst.txt +++ /dev/null @@ -1,90 +0,0 @@ -Changelog -========= - - -.. _v2.2: - -Version 2.2 (Released XX April 2017) ------------------------------------- - -The website and documentation were improved: - -* `Sphinx`_ is now used to generate our documentation pages. -* Documentation was updated to reflect the latest changes introduced in the project. -* Downloading the JABAWS distributions no longer require 'sign in' or 'sign up' to a user account. -* The pre-configured JABAWS Amazon Machine Image (AMI), which allowed for JABAWS to be run in the Amazon EC2 cloud, is no longer provided due to very limited use by the scientific community peers. - -The versions of several application programs provided by JABAWS were bumped to the latest available. - -* Clustal Omega was updated to version 1.2.4 -* ClustalW was updated to version 2.1 -* Mafft was updated to version 7.3.10 -* T-Coffee was updated to version 11.00.8cbe486 -* Protein secondary structure prediction with Jpred (version 3.0.3) was dropped from the list of provided services, as the use of the dedicated Jpred REST API (Jpred 4) is encouraged and recommended. This is the version that is currently provided within Jalview 2.9 or later. - -.. note:: JABAWS version 2.2 is fully backward compatible with JABAWS v1.0 and v2.0. This means all JABAWS 1.0, 2.0, 2.0.1 and 2.1 clients should also be able to use JABAWS 2.2 services. - - -.. _Sphinx: http://www.sphinx-doc.org/en/stable/ - ------------- - -.. _v2.1: - -Version 2.1 (Released 1st Oct 2013) ------------------------------------ - -Several new web services are available in this version of JABAWS: - -* Two multiple sequence aligners (MSAprobs and GLprobs), both services return the standard Alignment object -* RNAalifoldWS returns RNAStructScoreManager, which is the standard ScoreManager objects with several additional methods -* JpredWS returns the JpredAligment object, which is the standard alignment with additional methods for extracting Jpred predictions. These predictions are supplied as additional sequences in the aligment - -Some bugs have been fixed and several improvements have been done: - -* WS status servlet returns version and some additional information on each web service -* a bug with path to help in the client -* Fix two bug with the Google Analytics library: no-stop due to running thread -* GoogleAnalytics gets proper JABAWS version - ------------- - -.. _v2.0.1: - -Version 2.0.1 (Released 2nd Jul 2013) -------------------------------------- - -JABAWS 2.0.1 includes several bug fixes and minor updates for JABAWS Version 2.0. These are listed below: - -* Disembl returned swapped strings for HOTLOOPS and REM465 -* Jronn failed to process jobs with more than 3 sequences -* JABAWS could not deal with FASTA records with '>' symbols in the record identificator -* Change of parameter description for AAcon: parameters have been replaced with options for calculation methods. This allows a user to get several AAcon's conservation scores in one call -* JABAWS never cleaned up job directories. Now JABAWS deletes the job directory if it exist longer than a period defined in Engine.properties -* Default web security has been incompatible with Tomcat 7.0.31 and newer -* Documentation has been updated - ------------- - -.. _v2.0: - -Version 2 (Released 16th Dec 2011) ----------------------------------- - -Compared to JABAWS 1, JABAWS 2 offers a greater number and diversity of web services, Amazon EC2 integration and improved ease of use. - -It now contains: - -* Updates for all multiple sequence alignment services -* Four new protein disorder prediction services -* Clustal Omega multiple sequence alignment web service -* Amino acid conservation service -* Web services execution statistics visualization -* Web services status check from a web page -* VirtualBox support was dropped in favour of VMware -* New WAR package for Mac users -* Amazon Machine Image (AMI) distributive to enable users to use JABAWS on the EC2 cloud -* Improved web services client API -* Simplified WAR package installation - -.. warning:: To access the analysis web services introduced in JABAWS 2.0, clients that were designed for JABAWS v1.0 must be updated. diff --git a/website/docs/v_2_2_0/_sources/man/citations.rst.txt b/website/docs/v_2_2_0/_sources/man/citations.rst.txt deleted file mode 100644 index 2dfcfc3..0000000 --- a/website/docs/v_2_2_0/_sources/man/citations.rst.txt +++ /dev/null @@ -1,11 +0,0 @@ - -Citations -========= - -.. Note:: It is important that you cite JABAWS when you use it. Citing us helps us funding the work we do and allow us to continue to improve the project further. - -.. _citations: - -Peter V. Troshin, James B. Procter and Geoffrey J. Barton - **Java Bioinformatics Analysis Web Services for Multiple Sequence Alignment - JABAWS:MS** Bioinformatics 2011. 27 (14): 2001-2002. doi: `10.1093/bioinformatics/btr304`_ - -.. _10.1093/bioinformatics/btr304: https://doi.org/10.1093/bioinformatics/btr304 diff --git a/website/docs/v_2_2_0/_sources/man/client.rst.txt b/website/docs/v_2_2_0/_sources/man/client.rst.txt deleted file mode 100644 index 83ddca3..0000000 --- a/website/docs/v_2_2_0/_sources/man/client.rst.txt +++ /dev/null @@ -1,106 +0,0 @@ -Command Line Client (CLI) -========================= - -A JABAWS client is a Java application that lets you run the programs for which a JABAWS server provides web services. The most basic JABAWS client is a command line application this is able to call any of the JABAWS web services on any instance of JABAWS Server available over the web. The basic client is useful if you would like to test or execute the programs provided by the JABAWS server in your own scripts, but you do not want to handle any web service specific details. The client is an open source software, so you can also use the source code to as an example how to manipulate with JABAWS web services in your own code. Jalview [link], a multiple sequence alignment and analysis application, is a good example of a graphical JABAWS client. This client uses the same functionality as the JABAWS command line (CLI) client [link], but instead allows JABAWS services to be accessed in a more user-friendly manner, through a graphical user interface. - -The command line client comes as a part of client package [link] which you are welcome to download. The command line client can be used to align sequences using any of JABAWS supported web services. The client is OS independent and supports most of the functions which can be accessed programmatically via JABAWS API [link]. Using this client you could align sequences using presets or custom parameters, please see examples of this below. Here is the list of options supported by the command line client. - - ------------- - -.. _client_installing: - -Installing ----------- - -.. danger:: update for java - -You need Java vX or higher installed in your machine to be able to run the JABAWS CLI client. -Please see the Java web site [link] for up to date instructions and downloads. - - ------------- - -.. _cli_usage: - -Usage ------ - -.. code:: bash - - java -jar jaba-client.jar - -:: - - Usage: - java -jar -h=host_and_context -s=serviceName ACTION [OPTIONS] - -h= - a full URL to the JABAWS web server including context path e.g. http://10.31.10.159:8080/ws - -s= - one of [MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS] - - - ACTIONS: - -i= - full path to fasta formatted sequence file, from which to align sequences - -parameters - lists parameters supported by web service - -presets - lists presets supported by web service - -limits - lists web services limits - Please note that if input file is specified other actions are ignored - - - OPTIONS: (only for use with -i action): - -r= - name of the preset to use - -o= - full path to the file where to write an alignment - -f= - the name of the file with the list of parameters to use. - - Please note that -r and -f options cannot be used together. Alignment is done with either preset or aparameters from the file, but not both! - - ------------- - -.. _cli_example: - -Example Usage -------------- - - -Align sequences from input.fasta file using Mafft web service with default settings, print alignment in Clustal format to console. - -.. code:: bash - - java -jar jabaws-min-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=MafftWS -i=d:\input.fasta - -Content of input.fasta file is show below (please note sequences has been trimmed for clarity) - -:: - - >Foobar - MTADGPRELLQLRAAVRHRPQDFVAWL - >Bar - MGDTTAGEMAVQRGLALHQ - >Foofriend - MTADGPRELLQLRAAV - -Align as in above example, but write output alignment in a file out.clustal, using parameters defined in prm.in file - -.. code:: bash - - java -jar jabaws-min-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=MafftWS -i=d:\input.fasta -o=d:\out.clustal -f=prm.in - -The content of the prm.in file is shown below - -:: - - --nofft - --noscore - --fastaparttree - --retree=10 - --op=2.2 - -The format of the file is the same for all JABAWS web services. Parameters are specified in exactly the same way as for native executables - alignment programs like Mafft etc. So parameters which you can use with command line version of an alignment program can be used with JABAWS. Most of the settings controlling alignment process are supported, but because any output has to be handled by JABAWS, settings controlling output are not allowed to be changed. For a list of parameters supported by a web service see the next example. In prm.in parameters are separated by the new line, and name of the parameter is separated from its value with an equals sign. This format is constant no matter which JABAWS web service is used. - -.. code:: bash - - java -jar jabaws-min-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=MafftWS -parameters - -The same client can be used to access JABAWS on different hosts. Just point the client to the host you want to use by changing the value of -h key. - -For example you used ``-h=http://myhost.compbio.ac.uk:8080/jabaws`` server, now you want to use another server to ``-h=http://mylabserver.myuni.edu``. This comes handy if your favorite server is off and you need to do the job yesterday. diff --git a/website/docs/v_2_2_0/_sources/man/develop.rst.txt b/website/docs/v_2_2_0/_sources/man/develop.rst.txt deleted file mode 100644 index ca87e99..0000000 --- a/website/docs/v_2_2_0/_sources/man/develop.rst.txt +++ /dev/null @@ -1,625 +0,0 @@ -For Developers -============== - -.. _jabaws_source: - -Source Code ------------ - -.. note:: This is an open source project. If you want to contribute or report an issue have a look at our `Git-tracker`_. - -Publicly available Git repository: http://source.jalview.org/gitweb/?p=jabaws.git - -.. code:: bash - - git clone http://source.jalview.org/git/jabaws.git - - ------------- - -.. _jabaws_api: - -The API -------- - -`Data Model JavaDoc`_ - read this if your are coding against JABA Web Services - -`Complete JavaDoc`_ - for developers who want to use JABAWS framework and use Engines and Executables directly - - -------------- - -.. _jabaws_structure: - -Structure of the project ------------------------- - -| |folder| *binaries* contains native executables e.g. clustalw -| |folder| *src* contains sources of native executables -| |folder| *windows* contains pre-compiled Windows binaries -| |folder| *compilebin.sh* the script to complile binaries -| |folder| *setexecflag.sh* the script to set executable flag for the binaries -| |folder| *conf* contains JABAWS configuration files -| |folder| *ExecutionStatistics* the database for storing collected execution statistics -| |folder| *jobsout* a default folder for temporary job directories -| |folder| *statpages* the web pages for execution statistics display -| |folder| *WEB-INF* default -| |folder| *website* contains the JABAWS web pages -| |folder| *archive* contains JABAWS packages, the WAR and JAR files -| |folder| *datamodel* contains the JABAWS datamodel -| |folder| *engine* contains the JABAWS engine - the code that abstract the execution environment and executes native binaries -| |folder| *runner* contains the JABAWS runners - thin wrappers for native binaries -| |folder| *webservices* contains the JABAWS SOAP web services -| |folder| *testsrc* contains the JABAWS unit tests - - ------------- - -.. _jabaws_code: - -The code structure ------------------- - -.. image:: ../../website/static/img/ws-structure.png - :height: 414 - :width: 282 - :scale: 95 % - :align: left - - -Each source folder depends on the upper folders for compilation. For example, the datamodel is the top level folder so it has no other dependencies on other JABAWS code. The Engine level depends on the datamodel to compile etc. The web services folder is the bottom layer and depends on all the other source code. - -So the JABAWS project is split into 4 layers. From bottom-up the first layer consists from the value classes used by all other layers of the hierarchy, in particular web services. So, to be able to use JABAWS one needs to have these classes. At the same time classes on this layer does not have any dependencies on the layers above. - -The second layer contains code for execution of the wrappers, which are the abstraction describing native executables. JABAWS can execute tasks locally that is on the same machine as JVM and on the cluster. Thus currently code on this layer contain two engines. This layer depends on the layer underneath, the data model layer, but is completely independent from the code above. - -The third layer consists of the wrappers for the native executables and classes to handle their configuration. It depends on the engines and the data model, but know nothing about the web services. - -Finally, the upper layer contains the web services, that depend on all the layers below. - -The layer isolation is archived though specially designed compilation task which is executed sequentially in several stages so that the first layer compiles before any other layers, second layer compiles after that and process continies before all the code is compiled. Any violation of the layer boundaries results in the compilation failure. Use Ant "Compile" or "Complile_with_debug" tasks to perform the staged compilation. - -A client package contains only classes from data model layer and a simple web services client. Framework package is for anyone who want to use JABAWS framework for controlling native executables in local or cluster environments. Framework exclude the web services layer. Server package contains all the code. - - ------------- - -.. _jabaws_tests: - -Running tests -------------- - -JABAWS uses TestNG [test] framework for testing. The test results for the JABAWS package offered for download can be found at: Test Results [link] -JABAWS uses TestNG for testing. There is a TestNG plugin available for Eclipse which has functionality similar to JUnit. However, no plugins are necessary to run the test cases, as testng jar is supplied with JABAWS together with an ant tasks to run the test cases. - - -Several testing groups are supported: - -* All tests ('Test') -* Cluster tests ('Run_cluster_dependent_test') -* Cluster independent tests ('All_cluster_independent_tests') -* Windows only tests ('All_cluster_independent_windows_only_tests') -* Performance and stability tests ('Long_tests') -* Re-run failed tests ('Rerun_failed_tests') -* Run custom test ('CustomTest') - -To run the tests you need to download all sources from repository [link]. Once you have done that, enter into the command line mode, change directory to the project directory and type: - -.. code:: bash - - ant -f build.xml - - -Make sure you have Apache Ant [link] installed and path to ant executable is defined in your path environmental variable. Replace test group name with the one of the names given in the list above to run required group of tests e.g for running cluster only tests use the following command: - -.. code:: bash - - ant -f build.xml Run_cluster_dependent_test - - -If you work under Linux you could use a simple script from the root folder of repository called ``runtests.sh``. This script simply contains a collection of the test commands described above and paths to java home directory and an ant executable, which you can define once for your system and then reuse. - -A handy feature of TestNG is its ability to re-run failed tests. Failed test ant file is stored in ``test-output/testng-failed.xml``. and is used in the ant task called ``Rerun_failed_tests``. So re-running failed tests requires no more work than running any other test group and could be accomplished with the command: - -.. code:: bash - - ant -f build.xml Rerun_failed_tests - - -CustomTest runs the test defined in the project root directory file called ``temp-testng-customsuite.xml``. This file is generated by TestNG plugin every time you run the test from Eclipse. Thus an easy way to run a test in a different environment is to run it from Eclipse first and then from ant using a custom test procedure. - -For cluster execution make sure that the property ``LD_LIBRARY_PATH`` defined in build.xml points to cluster engine LD libraries directory in your local system. - - ------------- - -.. _jabaws_conn_services: - -Accessing JABAWS from your program ----------------------------------- - -.. _jabaws_conn_functions: - -Web services functions overview -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - - -All JABAWS multiple sequence alignment web services comply to the same interface, thus the function described below are available from all the services. - -Functions for initiating the alignment - -.. code:: bash - - String id = align(List list) - String id = customAlign(List sequenceList, List