Merge pull request #4737 from xgaia/askomics-ie

AskOmics Interactive Environment

config/plugins/interactive_environments/askomics/config/allowed_images.yml.sample

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+# This file lists acceptable images to allow runing.
+#
+# This allows you, the admin, to create multiple flavours
+# for your users to run. E.g. maybe you need a geosciences flavour,
+# you can create the image based on our default image and add the
+# appropriate `apt-get/pip install` statements.
+---
+-
+    image: askomics/askomics-ie
+    description: |
+        AskOmics, a visual SPARQL query builder

config/plugins/interactive_environments/askomics/config/askomics.ini.sample

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+[main]
+# Unused
+
+[docker]
+# Command to launch docker container. For example `sudo docker` or `docker-lxc`.
+# If you need to use a command like `sg` you can do that here, just be sure to
+# wrap all of the docker portion in single quotes. E.g. `sg 'docker' 'docker {docker_args}'`
+#
+# It is recommended that you use command_inject if you need to inject
+# additional parameters. This command string is re-used for a `docker inspect`
+# command and will likely cause errors if it is extensively modified, past the
+# usual group/sudo changes.
+#command = docker {docker_args}
+
+# The image argument was moved to "allowed_images.yml.sample"
+
+# Additional arguments that are passed to the `docker run` command.
+#command_inject = --sig-proxy=true -e DEBUG=false
+
+# URL to access the Galaxy API with from the spawn Docker containter, if empty
+# this falls back to galaxy.ini's galaxy_infrastructure_url and finally to the
+# Docker host of the spawned container if that is also not set.
+#galaxy_url =
+
+# The Docker hostname. It can be useful to run the Docker daemon on a different
+# host than Galaxy.
+#docker_hostname = localhost
+
+# Try to set the tempdirectory to world execute - this can fix the issue
+# where 'sudo docker' is not able to mount the folder otherwise.
+# "finalize namespace chdir to /import permission denied"
+#wx_tempdir = False
+
+# Overwride the IE tempdirectory. This can be useful if you regular tempdir is
+# located on an NFS share, which does not work well as Docker volume. In this case
+# you can have a shared sshfs share which you can use as temporary directory to
+# share data between the IE and Galaxy.
+#docker_galaxy_temp_dir = None
+
+# If your Docker container exposes more then one port, Galaxy needs to know to
+# which ports it needs to connect. With this option you can specify the port number
+# inside your container to which Galaxy should connect the UI.
+docker_connect_port = 6543

config/plugins/interactive_environments/askomics/config/askomics.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE interactive_environment SYSTEM "../../interactive_environments.dtd">
+<interactive_environment name="AskOmics">
+    <data_sources>
+        <data_source>
+            <model_class>HistoryDatasetAssociation</model_class>
+            <test type="isinstance" test_attr="datatype" result_type="datatype">tabular.Tabular</test>
+            <test type="isinstance" test_attr="datatype" result_type="datatype">tabular.gff</test>
+            <test type="isinstance" test_attr="datatype" result_type="datatype">tabular.gff3</test>
+            <test type="isinstance" test_attr="datatype" result_type="datatype">tabular.bed</test>
+            <to_param param_attr="id">dataset_id</to_param>
+        </data_source>
+    </data_sources>
+    <params>
+        <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
+    </params>
+    <entry_point entry_point_type="mako">askomics.mako</entry_point>
+</interactive_environment>

config/plugins/interactive_environments/askomics/static/js/askomics.js

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+var IES = window.IES;
+
+function load_askomics(url){
+    $( document ).ready(function() {
+        IES.test_ie_availability(url, function(){
+            IES.append_notebook(url);
+        });
+    });
+}

config/plugins/interactive_environments/askomics/templates/askomics.mako

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+<%namespace name="ie" file="ie.mako" />
+<%
+import random
+import string
+# Sets ID and sets up a lot of other variables
+ie_request.load_deploy_config()
+
+# get an API key for AskOmics
+askomics_api_key = ie_request.notebook_pw
+
+# Get ids of selected datasets
+additional_ids = trans.request.params.get('additional_dataset_ids', None)
+if not additional_ids:
+    additional_ids = str(trans.security.encode_id( hda.id ) )
+else:
+    additional_ids += "," + trans.security.encode_id( hda.id )
+
+# Launch the IE. This builds and runs the docker command in the background.
+ie_request.launch(
+    additional_ids=additional_ids if ie_request.use_volumes else None,
+    env_override={
+        'ASKO_load_url': 'http://localhost:6543',
+        'ASKOMICS_API_KEY': askomics_api_key,
+        'ASKO_files_dir': '/tmp/askomics-ie',
+        'VIRT_Parameters_NumberOfBuffers': 10000,  # see https://github.com/xgaia/askomics-docker-compose/tree/master/virtuoso#virtuoso for this values
+        'VIRT_Parameters_MaxDirtyBuffers': 6000
+    }
+)
+
+# Only once the container is launched can we template our URLs. The ie_request
+# doesn't have all of the information needed until the container is running.
+url = ie_request.url_template('${PROXY_URL}/login_api_gie?key=' + askomics_api_key)
+%>
+<html>
+<head>
+${ ie.load_default_js() }
+</head>
+<body>
+<script type="text/javascript">
+${ ie.default_javascript_variables() }
+var url = '${ url }';
+${ ie.plugin_require_config() }
+requirejs(['galaxy.interactive_environments', 'plugin/askomics'], function(IES){
+    window.IES = IES;
+    load_askomics(url);
+});
+</script>
+<div id="main" width="100%" height="100%">
+</div>
+</body>
+</html>