OMERO.openlink

An OMERO.web app and script for sharing data and prepare data for web download via curl (included in the newer Windows 10 builds).

You can generate URL's for specific data for batch web download via curl and to share data with other collaborates that are not in your group or member of your OMERO system. All operations are available in OMERO.web.

Features

• Create coded URL for html page with read only URL links to your data
• You can add data to an existing page
• You can delete whole pages
• Fast batch download for all data of one openlink area with curl (skip already downloaded files, compressed for transfer)

OMERO.openlink is composed of two components:

Create_OpenLink.py (generation) A server side script that generates soft links to your data and creates a curl file for batch download of this data. You can share only your own data or the data of a non-private group if you are the owner of this group (the owner of the data will be informed by mail).

NOTE: If you prefer another download manager, you can change the generated commands in the Python script.

omero-openlink (visualization) An OMERO.web plugin that lists the links to generated areas of softlinks via the nginx server. Provides the corresponding curl command to start the download in a shell. With the plugin the areas can also be deleted via OMERO.web.

Requirements:

• OMERO.web 5.6.0 or newer
• nginx server configurations

Installing

This section assumes that an OMERO.web is already installed and you will use the nginx server to provide the data links.

Prerequisite:

Variable OPENLINK_DIR: You have to define a directory on your OMERO.server (here /path/to/open_link_dir), where your nginx server has access. The system user omero-server requires read and write access to this directory for link generation. If you want to use the plugin, omero-web also needs read and write access. Please specify the full path to this directory under OPENLINK_DIR.

Variable SERVER_NAME: The url alias of your OMERO.web server without leading http://.

Variable NGINX_LOCATION: The location defined in the nginx configuration. Leave empty if you don't use the nginx feature.

Installation Create_OpenLink.py:

Download Create_OpenLink.py located in omero-openlink/omero_openlink/scripts/omero/ and open it to add your specifications under the configuration section:

#-------------------------------------------------
#------------ Configuration ----------------------
#-------------------------------------------------

# Directory for links that the nginx server also has access to
OPENLINK_DIR= "/path/to/open_link_dir"

# name of nginx website
SERVER_NAME = "omero-data.myfacility.com"

# name of nginx location
NGINX_LOCATION= '/openlink'

# email originator
ADMIN_EMAIL = "myemail@yourfacilitydomain"

# length of hash string used in the openlink url
LENGTH_HASH = 12
#--------------------------------------------------

Upload the script Create_OpenLink.py to OMERO.server ( howto)

Installation Plugin omero-openlink:

Download omero-openlink to your OMERO.web system. Go to omero-openlink and install the plugin using pip:

$ cd omero-openlink
$ pip install -e .

Add OpenLink app to your installed web apps:

$ omero config append omero.web.apps '"omero_openlink"'

Display the OpenLink pane in the right pane

$ omero config append omero.web.ui.right_plugins '["OpenLink", "omero_openlink/webclient_plugins/right_plugin.openlink.js.html", "openlink_tab"]'

Configuration settings (with omero config set):

• omero.web.openlink.dir OPENLINK_DIR
• omero.web.openlink.servername SERVER_NAME/NGINX_LOCATION

Examples for configuration settings (values see also script configuration section):

$omero config set omero.web.openlink.dir '"/path/to/open_link_dir"'
$omero config set omero.web.openlink.servername '"omero-data.myfacility.com/openlink"'

Nginx configuration:

Add a new location to your nginx configuration file (etc/nginx/conf.d/omeroweb.conf):

location  /openlink {
        proxy_read_timeout 36000;  # 10 hours
        limit_rate 10000M;  # 10 GByte
        gzip on;
        gzip_min_length 10240;
        disable_symlinks off;  # enable symlinks
        autoindex on;
        autoindex_format html; # html, xml, json, or jsonp
        autoindex_exact_size off; # on off
        autoindex_localtime on; # on off  (UTC)
        alias OPENLINK_DIR/;  # the links will be created here
}

Or create a new website for nginx by create a new file (e.g. openlink.conf) in /etc/nginx/conf.d/ with:

server {
    listen 80;
    server_name SERVER_NAME;  # url alias to this nginx site

    location /openlink {

        proxy_read_timeout 36000;  # 10 hours
        limit_rate 10000M;  # 10 GByte
        gzip on;
        gzip_min_length 10240;
        disable_symlinks off;  # enable symlinks
        autoindex on;
        autoindex_format html; # html, xml, json, or jsonp
        autoindex_exact_size off; # on off
        autoindex_localtime on; # on off  (UTC)
        alias OPENLINK_DIR/;  # the links will be created here
    }
}

The name of the location, in this example /openlink, is the value you must use to specify the value for NGINX_LOCATION.

Place an index.html file with the following content in the top level directory of your OPENLINK_DIR to protect downloads from other users:

<!DOCTYPE html>
<html lang="de">
<head>
    <meta charset="utf-8" />
    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
    <title>Omero Openlink</title>
</head>
<body>

<a href=OMERO_URL>Please go first to the Omero-System to create Openlinks!</a>

</body>
</html>

Reload your system and restart the OMERO server:

$ omero admin restart

Validation

Validation of configuration in Create_OpenLink.py:

In order to check whether the values for x have been entered correctly, please test the link that was entered in the log file under URL and also check the entered url's in the batch_download.curl that is available there.

Validation of configuration omero-openlink:

There is a debug output available for the plugin. Go to subdirectory omero_openlink of the installation directory of omero-openlink

$ cd omero-openlink/omero_openlink

open the urls.py and delete the leading # in the line

#url(r'^debugoutput/$',views.debugoutput,name='debugoutput'),

After restarting the web server, find the debug output for your Openlink plugin by replacing webclient by oemro_openlink/debugoutput in the URL of the omero.web (for example: https://server.openmicroscopy.org/webclient -> https://server.openmicroscopy.org/omero_openlink/debugoutput). This output shows you:

• what is defined under OPENLINK_DIR, SERVER_NAME
• check if OPENLINK_DIR is accessible
• check permission of OPENLINK_DIR for omero-web user
• overview of OpenLink Areas of currently logged-in user

License

OMERO.openlink is released under the AGPL. Any additional material in this repository (images, presentations, etc.) is available for use with attribution under the Creative Commons Attribution 4.0 International (CC BY 4.0) license.