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POM.xml version update
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GuilhemSempere committed Aug 22, 2024
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2 changes: 1 addition & 1 deletion pom.xml
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<modelVersion>4.0.0</modelVersion>
<properties>
<project.version>2.8-RELEASE</project.version>
<project.version>2.9-snapshot</project.version>
<endorsed.dir>${project.build.directory}/endorsed</endorsed.dir>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<bundle.dir>${project.build.directory}/bundles</bundle.dir>
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63 changes: 40 additions & 23 deletions src/main/webapp/docs/gigwa_docs.html
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<BR>
<P
STYLE="margin-top: 0.17in; margin-bottom: 0in; line-height: 100%; page-break-inside: avoid; page-break-after: avoid">
<FONT COLOR="#2e74b5"><FONT FACE="Arial, sans-serif"><FONT
<FONT COLOR="#2e74B6"><FONT FACE="Arial, sans-serif"><FONT
SIZE=4 class='title1'>A/ USER DOCUMENTATION</FONT></FONT></FONT>
</P>
<P STYLE="margin-bottom: 0.14in">
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<LI>
<P
STYLE="margin-top: 0.03in; margin-bottom: 0in; line-height: 100%; page-break-inside: avoid; page-break-after: avoid">
<FONT COLOR="#2e74b5"><FONT FACE="Arial, sans-serif"><FONT SIZE=3 class='title2'>A1/ IMPORTING DATA</FONT></FONT></FONT>
<FONT COLOR="#2e74B6"><FONT FACE="Arial, sans-serif"><FONT SIZE=3 class='title2'>A1/ IMPORTING DATA</FONT></FONT></FONT>
</P>
<P STYLE="margin-bottom: 0.14in">Choosing "Manage data" then "Import data" from the main horizontal menu leads to a page dedicated to data imports, split in two sections accessible via tabs named "Genotype import" and "Metadata import".
</P>
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<P STYLE="margin-bottom: 0in; line-height: 100%">By specifying an absolute path on the webserver filesystem (convenient for administrators managing a production instance used as data portal);
</P>
<LI>
<P STYLE="margin-bottom: 0in; line-height: 100%">By uploading files from the client computer (with an adjustable size limit: see section B7.2);
<P STYLE="margin-bottom: 0in; line-height: 100%">By uploading files from the client computer (with an adjustable size limit: see section B8.2);
</P>
<LI>
<P STYLE="margin-bottom: 0in; line-height: 100%">By providing an http URL, linking either to data files or to a BrAPI v1.1 base-url.
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<UL>
<LI>
<P STYLE="margin-top: 0.03in; margin-bottom: 0in; line-height: 100%; page-break-inside: avoid; page-break-after: avoid">
<FONT COLOR="#2e74b5"><FONT FACE="Arial, sans-serif"><FONT SIZE=3 class='title2'>A2/ WORKING WITH GENOTYPING DATA</FONT></FONT></FONT>
<FONT COLOR="#2e74B6"><FONT FACE="Arial, sans-serif"><FONT SIZE=3 class='title2'>A2/ WORKING WITH GENOTYPING DATA</FONT></FONT></FONT>
</P>
<P STYLE="margin-bottom: 0.14in">From the home page, select a database and a project. Note the presence of an "Enable browse
and export" checkbox that toggles between a mode where only variant counts are displayed, and one where users may browse,
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<LI>
<P
STYLE="margin-top: 0.03in; margin-bottom: 0in; line-height: 100%; page-break-inside: avoid; page-break-after: avoid">
<FONT COLOR="#2e74b5"><FONT FACE="Arial, sans-serif"><FONT
<FONT COLOR="#2e74B6"><FONT FACE="Arial, sans-serif"><FONT
SIZE=3 class='title2'>A3/ WORKING WITH REST APIs (for advanced users)</FONT></FONT></FONT>
</P>
<P STYLE="margin-bottom: 0.14in">Any data imported into Gigwa is
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</P>
<P
STYLE="margin-top: 0.17in; margin-bottom: 0in; line-height: 100%; page-break-inside: avoid; page-break-after: avoid">
<FONT COLOR="#2e74b5"><FONT FACE="Arial, sans-serif"><FONT
<FONT COLOR="#2e74B6"><FONT FACE="Arial, sans-serif"><FONT
SIZE=4 class='title1'>B/ ADMINISTRATOR DOCUMENTATION</FONT></FONT></FONT>
</P>
<P LANG="fr-FR" STYLE="margin-bottom: 0.14in">
<SPAN LANG="en-US">By default, a fresh instance of Gigwa comes
with a single pre-defined administrator account (login: gigwadmin,
password: nimda). It is of course strongly advised to </SPAN><SPAN
LANG="en-US"><B>change this password upon first connection</B></SPAN><SPAN
LANG="en-US"> (see section B5 below).</SPAN>
LANG="en-US"> (see section B6 below).</SPAN>
</P>
<P STYLE="margin-bottom: 0.14in">
<BR>
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<LI>
<P
STYLE="margin-top: 0.03in; margin-bottom: 0in; line-height: 100%; page-break-inside: avoid; page-break-after: avoid">
<FONT COLOR="#2e74b5"><FONT FACE="Arial, sans-serif"><FONT
<FONT COLOR="#2e74B6"><FONT FACE="Arial, sans-serif"><FONT
SIZE=3 class='title2'>B1/ TOMCAT CONFIGURATION</FONT></FONT></FONT>
</P>
<P STYLE="margin-bottom: 0.14in">Ready-to-use bundled packages
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<LI>
<P
STYLE="margin-top: 0.03in; margin-bottom: 0in; line-height: 100%; page-break-inside: avoid; page-break-after: avoid">
<FONT COLOR="#2e74b5"><FONT FACE="Arial, sans-serif"><FONT
<FONT COLOR="#2e74B6"><FONT FACE="Arial, sans-serif"><FONT
SIZE=3 class='title2'>B2/ APACHE CONFIGURATION</FONT></FONT></FONT>
</P>
<P STYLE="margin-bottom: 0.14in">In production environments, Tomcat often runs behind an Apache proxy. If such is your case, you must include the following line in your VirtualHost configuration:
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<LI>
<P
STYLE="margin-top: 0.03in; margin-bottom: 0in; line-height: 100%; page-break-inside: avoid; page-break-after: avoid">
<FONT COLOR="#2e74b5"><FONT FACE="Arial, sans-serif"><FONT
SIZE=3 class='title2'>B3/ ENABLING PASSWORD ENCRYPTION</FONT></FONT></FONT>
<FONT COLOR="#2e74B6"><FONT FACE="Arial, sans-serif"><FONT
SIZE=3 class='title2'>B3/ ENABLING PASSWORD ENCRYPTION (for "local" user accounts)</FONT></FONT></FONT>
</P>
<P STYLE="margin-bottom: 0.14in">User information is stored in WEB-INF/classes/users.properties. By default, passwords are not encoded. Administrator may enable password encoding to enhance security by:</P>
<ol>
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<LI>
<P
STYLE="margin-top: 0.03in; margin-bottom: 0in; line-height: 100%; page-break-inside: avoid; page-break-after: avoid">
<FONT COLOR="#2e74b5"><FONT FACE="Arial, sans-serif"><FONT
SIZE=3 class='title2'>B4/ CENTRAL AUTHENTICATION SERVICE COMPATIBILITY</FONT></FONT></FONT>
<FONT COLOR="#2e74B6"><FONT FACE="Arial, sans-serif"><FONT
SIZE=3 class='title2'>B4/ PASSWORD RESET FUNCTIONALITY (for "local" user accounts)</FONT></FONT></FONT>
</P>
<P STYLE="margin-bottom: 0.14in">This feature becomes active if a valid <b>org.springframework.mail.javamail.JavaMailSenderImpl</b> bean is added to applicationContext-MVC.xml (see <a href="https://github.com/SouthGreenPlatform/Gigwa2/blob/master/src/main/resources/applicationContext-MVC.xml" target="_blank">https://github.com/SouthGreenPlatform/Gigwa2/blob/master/src/main/resources/applicationContext-MVC.xml</a> for an example). As of v2.9, Gigwa supports attaching an e-mail address to user accounts, which is required for this feature to be used. Please note that:</P>
<ul>
<li>User accounts whose username is actually an e-mail address are automatically updated (attached e-mail address is by default the same as their username, although they can change it, but only the one in the e-mail field will be treated a such)
<li>When logging in, other users are encouraged to specify an e-mail address for their account
<li>Any user with an e-mail address specified may use the "Lost your password?" link present on the login page to receive a secret code by e-mail, allowing him to override his current password
</ul>
</UL>
<P STYLE="margin-bottom: 0.14in">
<BR>
</P>
<UL>
<LI>
<P
STYLE="margin-top: 0.03in; margin-bottom: 0in; line-height: 100%; page-break-inside: avoid; page-break-after: avoid">
<FONT COLOR="#2e74B6"><FONT FACE="Arial, sans-serif"><FONT
SIZE=3 class='title2'>B5/ CENTRAL AUTHENTICATION SERVICE COMPATIBILITY</FONT></FONT></FONT>
</P>
<P STYLE="margin-bottom: 0.14in">Single-Sign-On is supported via the implementation of the <a href="https://apereo.github.io/cas/6.5.x/protocol/CAS-Protocol-Specification.html" target="_blank">CAS protocol</a>.
If your organization is using CAS, making users of your Gigwa instance able to authenticate via their institutional account is as simple as defining the following parameters in WEB-INF/classes/config.properties:
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<LI>
<P
STYLE="margin-top: 0.03in; margin-bottom: 0in; line-height: 100%; page-break-inside: avoid; page-break-after: avoid">
<FONT COLOR="#2e74b5"><FONT FACE="Arial, sans-serif"><FONT
SIZE=3 class='title2'>B5/ MANAGING DATA</FONT></FONT></FONT>
<FONT COLOR="#2e74B6"><FONT FACE="Arial, sans-serif"><FONT
SIZE=3 class='title2'>B6/ MANAGING DATA</FONT></FONT></FONT>
</P>
<P LANG="fr-FR" STYLE="margin-bottom: 0.14in">
<SPAN LANG="en-US">The visibility of a database is defined
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<LI>
<P
STYLE="margin-top: 0.03in; margin-bottom: 0in; line-height: 100%; page-break-inside: avoid; page-break-after: avoid">
<FONT COLOR="#2e74b5"><FONT FACE="Arial, sans-serif"><FONT
SIZE=3 class='title2'>B6/ MANAGING USER ACCOUNTS
<FONT COLOR="#2e74B6"><FONT FACE="Arial, sans-serif"><FONT
SIZE=3 class='title2'>B7/ MANAGING USER ACCOUNTS
AND PERMISSIONS</FONT></FONT></FONT>
</P>
<P STYLE="margin-bottom: 0.14in">By choosing the "Administer existing data and user permissions" link from
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<LI>
<P
STYLE="margin-top: 0.03in; margin-bottom: 0in; line-height: 100%; page-break-inside: avoid; page-break-after: avoid">
<FONT COLOR="#2e74b5"><FONT FACE="Arial, sans-serif"><FONT
SIZE=3 class='title2'>B7/ CONFIGURING ADVANCED
<FONT COLOR="#2e74B6"><FONT FACE="Arial, sans-serif"><FONT
SIZE=3 class='title2'>B8/ CONFIGURING ADVANCED
SETTINGS (FOR SYSTEM ADMINISTRATORS: REQUIRES WRITE PERMISSIONS
ON INSTALLED FILES)</FONT></FONT></FONT>
</P>
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<P
STYLE="margin-top: 0.03in; margin-bottom: 0in; line-height: 100%; page-break-inside: avoid; page-break-after: avoid">
<FONT COLOR="#1f4d78"><FONT FACE="Arial, sans-serif"><FONT
SIZE=3>B7.1/ Managing data hosts</FONT></FONT></FONT>
SIZE=3>B8.1/ Managing data hosts</FONT></FONT></FONT>
</P>
<P STYLE="margin-bottom: 0.14in">Declaring MongoDB hosts is done
via the WEB-INF/classes/applicationContext-data.xml file following
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<P
STYLE="margin-top: 0.03in; margin-bottom: 0in; line-height: 100%; page-break-inside: avoid; page-break-after: avoid">
<FONT COLOR="#1f4d78"><FONT FACE="Arial, sans-serif"><FONT
SIZE=3>B7.2/ Setting configuration properties</FONT></FONT></FONT>
SIZE=3>B8.2/ Setting configuration properties</FONT></FONT></FONT>
</P>
<P STYLE="margin-bottom: 0.14in">
By default, configuration parameters shall be set via the WEB-INF/classes/config.properties file. But their values may be superseeded by defining environment variables with the same name prefixed with "GIGWA." (particularly useful when using the Docker version).
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<LI>
<P
STYLE="margin-top: 0.03in; margin-bottom: 0in; line-height: 100%; page-break-inside: avoid; page-break-after: avoid">
<FONT COLOR="#2e74b5"><FONT FACE="Arial, sans-serif"><FONT
SIZE=3 class='title2'>B8/ MONGODB CACHE CONFIGURATION</FONT></FONT></FONT>
<FONT COLOR="#2e74B6"><FONT FACE="Arial, sans-serif"><FONT
SIZE=3 class='title2'>B9/ MONGODB CACHE CONFIGURATION</FONT></FONT></FONT>
</P>
<P STYLE="margin-bottom: 0.14in">In production environments with large amounts of RAM, we found it worth to tune the --wiredTigerCacheSizeGB parameter. If left unspecified, it defaults to nearly a half of the available RAM, and essentially aims at reserving memory for manipulating indexes.
As Gigwa does not make an enormous use of indexes, we found that <b>in most cases, setting it to <u>10 Gb</u> is more than enough</b>. This leaves the remaining memory available for other operations such as collection-scans, and can significantly improve performance (at least for searches).
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