Add a very basic framework to the Tool Shed for creating a Galaxy flavor Docker Image that uses Bjoern Gruning's Galaxy Docker project. This is a proof-of-concept that should be enhanced if kept.

2026-09-24 16:30:27 +08:00 · 2014-07-01 21:44:49 -04:00
parent 606dff1089
commit 595d737fa8
7 changed files with 183 additions and 0 deletions
@@ -65,6 +65,8 @@ class Configuration( object ):
            self.tool_dependency_dir = None
            self.use_tool_dependencies = False
        self.update_integrated_tool_panel = False
+        # Galaxy flavor Docker Image
+        self.enable_galaxy_flavor_docker_image = string_as_bool( kwargs.get( "enable_galaxy_flavor_docker_image", "False" ) )
        self.use_remote_user = string_as_bool( kwargs.get( "use_remote_user", "False" ) )
        self.user_activation_on = kwargs.get( 'user_activation_on', None )
        self.activation_grace_period = kwargs.get( 'activation_grace_period', None )
@@ -55,6 +55,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
    datatypes_grid = repository_grids.DatatypesGrid()
    deprecated_repositories_i_own_grid = repository_grids.DeprecatedRepositoriesIOwnGrid()
    email_alerts_repository_grid = repository_grids.EmailAlertsRepositoryGrid()
+    docker_image_grid = repository_grids.DockerImageGrid()
    install_matched_repository_grid = repository_grids.InstallMatchedRepositoryGrid()
    matched_repository_grid = repository_grids.MatchedRepositoryGrid()
    my_writable_repositories_grid = repository_grids.MyWritableRepositoriesGrid()
@@ -985,6 +986,62 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
            # Do all we can to eliminate spam.
            return trans.show_error_message( "You must be logged in to contact the owner of a repository." )

+    @web.expose
+    def create_galaxy_docker_image( self, trans, **kwd ):
+        message = kwd.get( 'message', '' )
+        status = kwd.get( 'status', 'done' )
+        repository_ids = util.listify( kwd.get( 'id', '' ) )
+        if 'operation' in kwd:
+            if repository_ids:
+                operation = kwd[ 'operation' ].lower()
+                if operation == "include in docker image":
+                    repository_tups = []
+                    for repository_id in repository_ids:
+                        repository = suc.get_repository_by_id( trans.app, repository_id )
+                        repository_tups.append( ( str( repository.name ),
+                                                  str( repository.user.username ),
+                                                  str( repository.type ) ) )
+                    return trans.fill_template( "/webapps/tool_shed/repository/docker_image_repositories.mako",
+                                                id=','.join( repository_ids ),
+                                                repository_tups=repository_tups,
+                                                message=message,
+                                                status=status )
+            else:
+                # This can only occur when there is a multi-select grid with check boxes and an operation,
+                # and the user clicked the operation button without checking any of the check boxes.
+                kwd[ 'message' ] = "No items were selected."
+                kwd[ 'status' ] = 'error'
+        elif kwd.get( 'create_docker_image_button', False ):
+            tmp_image_dir = tempfile.mkdtemp( prefix="tmp-toolshed-cdidir" )
+            docker_file_name = 'Dockerfile'
+            docker_file_path = os.path.join( tmp_image_dir, docker_file_name )
+            tool_shed_url = tool_shed_url = web.url_for( '/', qualified=True )
+            repository_string = ''
+            for repository_id in repository_ids:
+                repository = suc.get_repository_by_id( trans.app, repository_id )
+                template = basic_util.SELECTED_REPOSITORIES_TEMPLATE
+                repository_template = \
+                    string.Template( template ).safe_substitute( tool_shed_url=tool_shed_url,
+                                                                 repository_owner=str( repository.user.username ) ,
+                                                                 repository_name=str( repository.name ) )
+                repository_string = '%s\n%s' % ( repository_string, repository_template )
+            template = basic_util.DOCKER_IMAGE_TEMPLATE
+            docker_image_template = \
+                string.Template( template ).safe_substitute( selected_repositories=repository_string )
+            docker_image_string = docker_image_template
+            trans.response.set_content_type( 'application/text/plain' )
+            trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s"' % docker_file_name
+            opened_file = open( docker_file_path, "w" )
+            opened_file.write( docker_image_string )
+            opened_file.close()
+            opened_file = open( docker_file_path, "r" )
+            # Make sure the file is removed from disk after the contents have been downloaded.
+            os.unlink( docker_file_path )
+            docker_file_path, docker_file_name = os.path.split( docker_file_path )
+            basic_util.remove_dir( docker_file_path )
+            return opened_file
+        return self.docker_image_grid( trans, **kwd )
+
    @web.expose
    def create_repository( self, trans, **kwd ):
        message = kwd.get( 'message', ''  )
@@ -329,6 +329,26 @@ class RepositoryGrid( grids.Grid ):
                                   .outerjoin( model.Category.table )


+class DockerImageGrid( RepositoryGrid ):
+    columns = [
+        RepositoryGrid.NameColumn( "Name",
+                                   key="name",
+                                   link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ),
+                                   attach_popup=False ),
+        RepositoryGrid.DescriptionColumn( "Synopsis",
+                                          key="description",
+                                          attach_popup=False ),
+        RepositoryGrid.UserColumn( "Owner",
+                                   model_class=model.User,
+                                   link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ),
+                                   attach_popup=False,
+                                   key="User.username" ),
+        RepositoryGrid.EmailAlertsColumn( "Alert", attach_popup=False ),
+    ]
+    operations = [ grids.GridOperation( "Include in Docker image", allow_multiple=True  ) ]
+    show_item_checkboxes = True
+
+
 class EmailAlertsRepositoryGrid( RepositoryGrid ):
    columns = [
        RepositoryGrid.NameColumn( "Name",
@@ -20,6 +20,33 @@ NO_OUTPUT_TIMEOUT = 1200.0
 MAXDIFFSIZE = 8000
 MAX_DISPLAY_SIZE = 32768

+DOCKER_IMAGE_TEMPLATE = '''
+# Galaxy Docker image
+
+FROM bgruening/galaxy-stable
+
+MAINTAINER Bjoern A. Gruning, bjoern.gruening@gmail.com
+
+RUN sed -i 's|brand.*|brand = deepTools|g' ~/galaxy-central/universe_wsgi.ini
+
+WORKDIR /galaxy-central
+
+${selected_repositories}
+
+# Mark one folder as imported from the host.
+VOLUME ["/export/"]
+
+# Expose port 80 to the host
+EXPOSE :80
+
+# Autostart script that is invoked during container start
+CMD ["/usr/bin/startup"]
+'''
+
+SELECTED_REPOSITORIES_TEMPLATE = '''
+RUN service postgresql start && service apache2 start && ./run.sh --daemon && sleep 120 && python ./scripts/api/install_tool_shed_repositories.py --api admin -l http://localhost:8080 --url ${tool_shed_url} -o ${repository_owner} --name ${repository_name} --tool-deps --repository-deps --panel-section-name 'Docker'
+'''
+
 def evaluate_template( text, install_environment ):
    """
    Substitute variables defined in XML blocks from dependencies file.  The value of the received
@@ -155,6 +155,11 @@
                        <div class="toolTitle">
                            <a target="galaxy_main" href="${h.url_for( controller='repository', action='upload_capsule' )}">Import repository capsule</a>
                        </div>
+                        %if trans.app.config.enable_galaxy_flavor_docker_image:
+                            <div class="toolTitle">
+                                <a target="galaxy_main" href="${h.url_for( controller='repository', action='create_galaxy_docker_image' )}">Create Galaxy Docker Image</a>
+                            </div>
+                        %endif
                        %if can_review_repositories:
                            <div class="toolSectionPad"></div>
                            <div class="toolSectionTitle">
@@ -216,6 +221,11 @@
                        <div class="toolTitle">
                            <a target="galaxy_main" href="${h.url_for( controller='/user', action='login' )}">Login to create a repository</a>
                        </div>
+                        %if trans.app.config.enable_galaxy_flavor_docker_image:
+                            <div class="toolTitle">
+                                <a target="galaxy_main" href="${h.url_for( controller='repository', action='create_galaxy_docker_image' )}">Create Galaxy Docker Image</a>
+                            </div>
+                        %endif
                    %endif
                %endif
            </div>
@@ -0,0 +1,64 @@
+<%namespace file="/message.mako" import="render_msg" />
+
+<%!
+   def inherit(context):
+       if context.get('use_panels'):
+           return '/webapps/tool_shed/base_panels.mako'
+       else:
+           return '/base.mako'
+%>
+
+<%inherit file="${inherit(context)}"/>
+
+<%def name="stylesheets()">
+    ${parent.stylesheets()}
+</%def>
+
+<%def name="javascripts()">
+    ${parent.javascripts()}
+</%def>
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+<div class="toolForm">
+    <div class="toolFormBody">
+        <div class="form-row">
+            <div class="warningmessage">
+                Click the <b>Create Docker Image</b> button below to create a Docker Image that will install the following repositories.
+            </div>
+            <div style="clear: both"></div>
+        </div>
+    </div>
+</div>
+<div class="toolForm">
+    <div class="toolFormTitle">Repositories for inclusion in Docker Image</div>
+        <form id="docker_image_form" name="docker_image_form" action="${h.url_for( controller='repository', action='create_galaxy_docker_image' )}" enctype="multipart/form-data" method="post">
+            <div class="form-row">
+                <input type="hidden" name="id" value="${id}" />
+            </div>
+            <div class="form-row">
+                <table class="grid">
+                    <tr>
+                        <th bgcolor="#D8D8D8">Name</th>
+                        <th bgcolor="#D8D8D8">Owner</th>
+                        <th bgcolor="#D8D8D8">Type</th>
+                    </tr>
+                    %for repository_tup in repository_tups:
+                        <% name, owner, type = repository_tup %>
+                        <tr>
+                            <td>${ name | h }</td>
+                            <td>${ owner | h }</td>
+                            <td>${ type | h }</td>
+                        </tr>
+                    %endfor
+                </table>
+            </div>
+            <div style="clear: both"></div>
+            <div class="form-row">
+                <input type="submit" class="primary-button" name="create_docker_image_button" value="Create Docker Image">
+            </div>
+        </form>
+    </div>
+</div>
@@ -90,6 +90,9 @@ sendmail_path = /usr/sbin/sendmail
 # Profiling middleware (cProfile based)
 ## use_profile = True

+# Enable creation of Galaxy flavor Docker Image
+#enable_galaxy_flavor_docker_image = False
+
 # Use the new iframe / javascript based layout
 use_new_layout = true