Commit d3170b9f authored by Sveinung Gundersen's avatar Sveinung Gundersen Committed by Cage, Gregory
Browse files

Merge 'Added "requires_path_in_url" and "requires_path_in_header" attributes... 

Merge 'Added "requires_path_in_url" and "requires_path_in_header" attributes to entry points for tools. Sendoff to gx-it-proxy. Cleanup' into branch
parent e86caf56

tools/interactive/interactivetool_guacamole_desktop.xml

+1 −1
Original line number Diff line number Diff line
@@ -3,7 +3,7 @@ 
        <container type="docker">quay.io/bgruening/guacamole-desktop</container>

    </requirements>

    <entry_points>

        <entry_point name="Remote Desktop" requires_domain="True">

        <entry_point name="Remote Desktop" requires_domain="False" requires_path_in_url="False">

            <port>8080</port>

            <url><![CDATA[?username=user&password=password]]></url>

        </entry_point>

tools/interactive/interactivetool_jupyter_notebook_1.0.0.xml

+3 −1
Original line number Diff line number Diff line
@@ -3,7 +3,7 @@ 
        <container type="docker">quay.io/bgruening/docker-jupyter-notebook:2021-03-05</container>

    </requirements>

    <entry_points>

        <entry_point name="JupyTool interactive tool" requires_domain="True">

        <entry_point name="JupyTool interactive tool" label="jupytool" requires_domain="False" requires_path_in_url="True">

            <port>8888</port>

            <url>ipython/lab</url>

        </entry_point>
@@ -14,6 +14,7 @@ 
        <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>

        <environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>

        <environment_variable name="API_KEY" inject="api_key"/>

        <environment_variable name="EP_PATH" inject="entry_point_path_for_label">jupytool</environment_variable>

    </environment_variables>

    <configfiles>

        <inputs name="inputs" filename="galaxy_inputs.json" data_style="staging_path_and_source_path"/>
@@ -80,6 +81,7 @@ except FileNotFoundError: 
        export GALAXY_WORKING_DIR=`pwd` &&

        mkdir -p ./jupyter/outputs/collection &&

        mkdir -p ./jupyter/galaxy_inputs &&

        export PROXY_PREFIX=\${EP_PATH%/ipython*} &&



        ## change into the directory where the notebooks are located

        cd ./jupyter/ &&

tools/interactive/interactivetool_openrefine.xml

+1 −2
Original line number Diff line number Diff line
@@ -4,7 +4,7 @@ 
        <container type="docker">ylebras/openrefine-docker</container>

    </requirements>

    <entry_points>

        <entry_point name="Openrefine visualisation" requires_domain="True">

        <entry_point name="Openrefine visualisation" requires_domain="False" requires_path_in_url="False">

            <port>3333</port>

        </entry_point>

    </entry_points>
@@ -81,4 +81,3 @@ Example input file (TAB separated):: 
]]>

    </help>

</tool>

tools/interactive/interactivetool_rstudio.xml

+1 −2
Original line number Diff line number Diff line
@@ -4,14 +4,13 @@ 
        <container type="docker">quay.io/erasche/docker-rstudio-notebook:ie2</container>

    </requirements>

    <entry_points>

        <entry_point name="RStudio" requires_domain="True">

        <entry_point name="RStudio" requires_domain="False" requires_path_in_header_named="X-RStudio-Root-Path">

            <port>8787</port>

            <url>/</url>

        </entry_point>

    </entry_points>

    <environment_variables>

        <environment_variable name="HISTORY_ID" strip="True">${__app__.security.encode_id($jupyter_notebook.history_id)}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->

        <environment_variable name="REMOTE_HOST">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->

        <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>

        <environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>

        <environment_variable name="DEBUG">true</environment_variable>

tools/interactive/interactivetool_wallace.xml

+1 −1
Original line number Diff line number Diff line
@@ -12,7 +12,7 @@ 
    <environment_variables>



        <environment_variable name="HISTORY_ID" strip="True">${__app__.security.encode_id($outfile.history_id)}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->

        <environment_variable name="REMOTE_HOST">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->

        <environment_variable name="REMOTE_HOST">$__galaxy_url__</environment_variable>

        <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>

        <environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>

        <environment_variable name="API_KEY" inject="api_key" />