galaxyproject/admins

Hi there. Any tips on why put() and get() are not available in jupyterlab notebook?

Using this tool wrapper:

<tool id="interactive_tool_jupyter_notebook" tool_type="interactive" name="General Jupyter Notebook" version="0.1">
  <description>Default empty notebook, reuse a previous one, or upload a new</description>
  <requirements>
    <container type="docker">quay.io/bgruening/docker-jupyter-notebook:2021-03-05</container>
  </requirements>
    <entry_points>
        <entry_point name="Jupyter Interactive Tool" requires_domain="True">
            <port>8888</port>
            <url>lab</url>
        </entry_point>
    </entry_points>
    <environment_variables>
        <environment_variable name="HISTORY_ID">$__history_id__</environment_variable>
        <environment_variable name="REMOTE_HOST">$__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" />
    </environment_variables>
    <command detect_errors="aggressive"><![CDATA[
        #import re
        export GALAXY_WORKING_DIR=`pwd` &&
        mkdir -p ./jupyter/outputs/ &&
        mkdir -p ./jupyter/data &&

        #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier))
        ln -sf '$input' './jupyter/data/${cleaned_name}' &&

        ## change into the directory where the notebooks are located
        cd ./jupyter/ &&
        export PATH=/home/jovyan/.local/bin:\$PATH &&

        #if $mode.mode_select == 'scratch':
            ## copy default notebook
            cp '$__tool_directory__/default_notebook.ipynb' ./ipython_galaxy_notebook.ipynb &&
            jupyter trust ./ipython_galaxy_notebook.ipynb &&
            jupyter lab --allow-root --no-browser  --ServerApp.token=''  &&
            cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook'

        #else:
            #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier))
            cp '$mode.ipynb' ./${cleaned_name}.ipynb &&
            jupyter trust ./${cleaned_name}.ipynb &&

            #if $mode.run_it:
                jupyter nbconvert --to notebook --execute --output ./ipython_galaxy_notebook.ipynb --allow-errors  ./*.ipynb &&
            #else:
                jupyter lab --allow-root --no-browser  --ServerApp.token='' &&
            #end if
            cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook' 

        #end if
    ]]>
    </command>
    <inputs>

        <conditional name="mode">
            <param name="mode_select" type="select" label="Do you already have a notebook?" help="If not, no problem we will provide you with a default one.">
                <option value="scratch">Start with a fresh notebook</option>
                <option value="previous">Load a previous notebook</option>
            </param>
            <when value="scratch"/>
            <when value="previous">
                <param name="ipynb" type="data" format="ipynb" label="IPython Notebook"/>
                <param name="run_it" type="boolean" truevalue="true" falsevalue="false" label="Execute notebook and return a new one."
                    help="This option is useful in workflows when you just want to execute a notebook and not dive into the webfrontend."/>
            </when>
        </conditional>
        <param name="input" type="data" optional="true" label="Include data into the environment"/>

    </inputs>
    <outputs>
        <data name="jupyter_notebook" format="ipynb" label="Executed Notebook"></data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="mode" value="previous" />
            <param name="ipynb" value="test.ipynb" />
            <param name="run_it" value="true" />
            <output name="jupyter_notebook" file="test.ipynb" ftype="ipynb"/>
        </test>
    </tests>
    <help>
    The Jupyter Notebook is an open-source web application that allows you to create