From 11f0099c814757c2f0984664450d0c9d3183d541 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Guilhem=20Semp=C3=A9r=C3=A9?= Date: Thu, 22 Aug 2024 18:21:04 +0200 Subject: [PATCH] POM.xml version update --- pom.xml | 2 +- src/main/webapp/docs/gigwa_docs.html | 63 ++++++++++++++++++---------- 2 files changed, 41 insertions(+), 24 deletions(-) diff --git a/pom.xml b/pom.xml index 707f8caf..3efaadbd 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ 4.0.0 - 2.8-RELEASE + 2.9-snapshot ${project.build.directory}/endorsed UTF-8 ${project.build.directory}/bundles diff --git a/src/main/webapp/docs/gigwa_docs.html b/src/main/webapp/docs/gigwa_docs.html index 14f5ca78..ebde86c1 100644 --- a/src/main/webapp/docs/gigwa_docs.html +++ b/src/main/webapp/docs/gigwa_docs.html @@ -28,7 +28,7 @@

- A/ USER DOCUMENTATION

@@ -38,7 +38,7 @@

  • - A1/ IMPORTING DATA + A1/ IMPORTING DATA

    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".

    @@ -59,7 +59,7 @@

    By specifying an absolute path on the webserver filesystem (convenient for administrators managing a production instance used as data portal);

  • -

    By uploading files from the client computer (with an adjustable size limit: see section B7.2); +

    By uploading files from the client computer (with an adjustable size limit: see section B8.2);

  • By providing an http URL, linking either to data files or to a BrAPI v1.1 base-url. @@ -138,7 +138,7 @@

    • - A2/ WORKING WITH GENOTYPING DATA + A2/ WORKING WITH GENOTYPING DATA

      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, @@ -333,7 +333,7 @@

    • - A3/ WORKING WITH REST APIs (for advanced users)

      Any data imported into Gigwa is @@ -387,7 +387,7 @@

      - B/ ADMINISTRATOR DOCUMENTATION

      @@ -395,7 +395,7 @@ with a single pre-defined administrator account (login: gigwadmin, password: nimda). It is of course strongly advised to change this password upon first connection (see section B5 below). + LANG="en-US"> (see section B6 below).


      @@ -404,7 +404,7 @@

    • - B1/ TOMCAT CONFIGURATION

      Ready-to-use bundled packages @@ -450,7 +450,7 @@

    • - B2/ APACHE CONFIGURATION

      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: @@ -465,8 +465,8 @@

    • - B3/ ENABLING PASSWORD ENCRYPTION + B3/ ENABLING PASSWORD ENCRYPTION (for "local" user accounts)

      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:

        @@ -487,8 +487,25 @@

      1. - B4/ CENTRAL AUTHENTICATION SERVICE COMPATIBILITY + B4/ PASSWORD RESET FUNCTIONALITY (for "local" user accounts) +

        +

        This feature becomes active if a valid org.springframework.mail.javamail.JavaMailSenderImpl bean is added to applicationContext-MVC.xml (see https://github.com/SouthGreenPlatform/Gigwa2/blob/master/src/main/resources/applicationContext-MVC.xml 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:

        +
          +
        • 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) +
        • When logging in, other users are encouraged to specify an e-mail address for their account +
        • 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 +
        +
    +

    +
    +

    +
      +
    • +

      + B5/ CENTRAL AUTHENTICATION SERVICE COMPATIBILITY

      Single-Sign-On is supported via the implementation of the CAS protocol. 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: @@ -510,8 +527,8 @@

    • - B5/ MANAGING DATA + B6/ MANAGING DATA

      The visibility of a database is defined @@ -571,8 +588,8 @@

    • - B6/ MANAGING USER ACCOUNTS + B7/ MANAGING USER ACCOUNTS AND PERMISSIONS

      By choosing the "Administer existing data and user permissions" link from @@ -604,8 +621,8 @@

    • - B7/ CONFIGURING ADVANCED + B8/ CONFIGURING ADVANCED SETTINGS (FOR SYSTEM ADMINISTRATORS: REQUIRES WRITE PERMISSIONS ON INSTALLED FILES)

      @@ -620,7 +637,7 @@

      B7.1/ Managing data hosts + SIZE=3>B8.1/ Managing data hosts

      Declaring MongoDB hosts is done via the WEB-INF/classes/applicationContext-data.xml file following @@ -638,7 +655,7 @@

      B7.2/ Setting configuration properties + SIZE=3>B8.2/ Setting configuration properties

      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). @@ -850,8 +867,8 @@

    • - B8/ MONGODB CACHE CONFIGURATION + B9/ MONGODB CACHE CONFIGURATION

      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 in most cases, setting it to 10 Gb is more than enough. This leaves the remaining memory available for other operations such as collection-scans, and can significantly improve performance (at least for searches).