From 1e0f9288094c29859161994caf70b9485153f1b3 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Fri, 20 Sep 2024 10:25:03 -0400
Subject: [PATCH 1/2] Jupyter Interactive Tool 1.0.1/24.07

---
 .../interactive/interactivetool_jupyter_notebook_1.0.0.xml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/tools/interactive/interactivetool_jupyter_notebook_1.0.0.xml b/tools/interactive/interactivetool_jupyter_notebook_1.0.0.xml
index 5b5e91e16144..8c249e289af2 100644
--- a/tools/interactive/interactivetool_jupyter_notebook_1.0.0.xml
+++ b/tools/interactive/interactivetool_jupyter_notebook_1.0.0.xml
@@ -1,7 +1,10 @@
-<tool id="interactive_tool_jupyter_notebook" tool_type="interactive" name="Interactive JupyterLab Notebook" version="1.0.0" profile="22.01">
+<tool id="interactive_tool_jupyter_notebook" tool_type="interactive" name="Interactive JupyterLab Notebook" version="1.0.1" profile="23.0">
     <requirements>
-        <container type="docker">quay.io/bgruening/docker-jupyter-notebook:2021-03-05</container>
+        <container type="docker">quay.io/bgruening/docker-jupyter-notebook:24.07</container>
     </requirements>
+    <required_files>
+        <include path="default_notebook.ipynb"/>
+    </required_files>
     <entry_points>
         <entry_point name="JupyTool interactive tool" label="jupytool" requires_domain="False" requires_path_in_url="True">
             <port>8888</port>

From 615bd1971805ad04132502bd5ae05dad31526f6e Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Tue, 1 Oct 2024 12:21:29 -0400
Subject: [PATCH 2/2] Keep Jupyter 1.0.1 IT as a separate tool

---
 lib/galaxy/config/sample/tool_conf.xml.sample |   1 +
 ...interactivetool_jupyter_notebook_1.0.0.xml |   4 +-
 ...interactivetool_jupyter_notebook_1.0.1.xml | 271 ++++++++++++++++++
 3 files changed, 274 insertions(+), 2 deletions(-)
 create mode 100644 tools/interactive/interactivetool_jupyter_notebook_1.0.1.xml

diff --git a/lib/galaxy/config/sample/tool_conf.xml.sample b/lib/galaxy/config/sample/tool_conf.xml.sample
index 841f054b93d0..7ddcec93af91 100644
--- a/lib/galaxy/config/sample/tool_conf.xml.sample
+++ b/lib/galaxy/config/sample/tool_conf.xml.sample
@@ -140,6 +140,7 @@
     <tool file="interactive/interactivetool_ethercalc.xml" />
     <tool file="interactive/interactivetool_guacamole_desktop.xml" />
     <tool file="interactive/interactivetool_hicbrowser.xml" />
+    <tool file="interactive/interactivetool_jupyter_notebook_1.0.1.xml" />
     <tool file="interactive/interactivetool_jupyter_notebook_1.0.0.xml" />
     <tool file="interactive/interactivetool_jupyter_notebook.xml" />
     <tool file="interactive/interactivetool_neo4j.xml" />
diff --git a/tools/interactive/interactivetool_jupyter_notebook_1.0.0.xml b/tools/interactive/interactivetool_jupyter_notebook_1.0.0.xml
index 8c249e289af2..870ecd19fd28 100644
--- a/tools/interactive/interactivetool_jupyter_notebook_1.0.0.xml
+++ b/tools/interactive/interactivetool_jupyter_notebook_1.0.0.xml
@@ -1,6 +1,6 @@
-<tool id="interactive_tool_jupyter_notebook" tool_type="interactive" name="Interactive JupyterLab Notebook" version="1.0.1" profile="23.0">
+<tool id="interactive_tool_jupyter_notebook" tool_type="interactive" name="Interactive JupyterLab Notebook" version="1.0.0" profile="22.01">
     <requirements>
-        <container type="docker">quay.io/bgruening/docker-jupyter-notebook:24.07</container>
+        <container type="docker">quay.io/bgruening/docker-jupyter-notebook:2021-03-05</container>
     </requirements>
     <required_files>
         <include path="default_notebook.ipynb"/>
diff --git a/tools/interactive/interactivetool_jupyter_notebook_1.0.1.xml b/tools/interactive/interactivetool_jupyter_notebook_1.0.1.xml
new file mode 100644
index 000000000000..8c249e289af2
--- /dev/null
+++ b/tools/interactive/interactivetool_jupyter_notebook_1.0.1.xml
@@ -0,0 +1,271 @@
+<tool id="interactive_tool_jupyter_notebook" tool_type="interactive" name="Interactive JupyterLab Notebook" version="1.0.1" profile="23.0">
+    <requirements>
+        <container type="docker">quay.io/bgruening/docker-jupyter-notebook:24.07</container>
+    </requirements>
+    <required_files>
+        <include path="default_notebook.ipynb"/>
+    </required_files>
+    <entry_points>
+        <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>
+    </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_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"/>
+        <configfile name="staging_script" filename="staging_script.py"><![CDATA[
+import json, os, shutil
+import os.path
+galaxy_inputs = "galaxy_inputs.json"
+galaxy_inputs_raw = "galaxy_inputs_raw.json"
+base_staging_path = "jupyter"
+base_data_staging_path = "galaxy_inputs"
+data_staging_path = os.path.join(base_staging_path, base_data_staging_path)
+os.makedirs(data_staging_path, exist_ok=True)
+shutil.copyfile(galaxy_inputs, os.path.join(data_staging_path, galaxy_inputs_raw))
+galaxy_input_dict = {}
+for user_input in json.load(open(galaxy_inputs, "r")).get("user_inputs", []):
+    input_values = user_input['input_type']['input_value']
+    input_name = user_input["input_name"]
+    assert input_name not in galaxy_input_dict, ValueError("Each name can only be used once, but a duplicate was found: %s" % (input_name))
+    if 'dataset' in user_input['input_type']['input_type_selector']:
+        input_values2 = []
+        if not isinstance(input_values, list):
+            input_values = [input_values]
+        for input_value_dict in input_values:
+            path, filename = os.path.split(input_value_dict['staging_path'])
+            input_value_dict2 = {"path": os.path.join(base_data_staging_path, input_name, path, filename), "metadata_files": []}
+            ## TODO: enable passing in all metadata values; ideally just handed off from original json creation
+            path = os.path.join(data_staging_path, input_name, path)
+            os.makedirs(path, exist_ok=True)
+            try:
+                os.symlink(input_value_dict['source_path'], os.path.join(path, filename))
+            except FileExistsError:
+                pass
+            for metadata_value_dict in input_value_dict['metadata_files']:
+                path, filename = os.path.split(metadata_value_dict['staging_path'])
+                input_value_dict2["metadata_files"].append(os.path.join(base_data_staging_path, input_name, path, filename))
+                path = os.path.join(data_staging_path, input_name, path)
+                os.makedirs(path, exist_ok=True)
+                try:
+                    os.symlink(metadata_value_dict['source_path'], os.path.join(path, filename))
+                except FileExistsError:
+                    pass
+            input_values2.append(input_value_dict2)
+        input_values = input_values2
+    galaxy_input_dict[input_name] = input_values
+with open(os.path.join(data_staging_path, galaxy_inputs), "w") as fh:
+    json.dump(galaxy_input_dict, fh)
+]]>
+        </configfile>
+        <configfile name="galaxy_input_startup_script"><![CDATA[
+import json, os
+from galaxy_ie_helpers import get
+from galaxy_ie_helpers import put
+from galaxy_ie_helpers import get_galaxy_connection
+HISTORY_ID = os.environ.get('HISTORY_ID', None)
+try:
+    GALAXY_INPUTS = json.load(open(os.path.join(os.environ.get("GALAXY_WORKING_DIR", ""), "jupyter", "galaxy_inputs", "galaxy_inputs.json")))
+except FileNotFoundError:
+    GALAXY_INPUTS = {}
+        ]]>
+    </configfile>
+    </configfiles>
+    <command><![CDATA[
+        python staging_script.py &&
+        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/ &&
+        export HOME=/home/jovyan/ &&
+        export PATH=/home/jovyan/.local/bin:\$PATH &&
+        cp '${galaxy_input_startup_script}' /home/jovyan/.ipython/profile_default/startup/00-load.py &&
+
+        #set $output_notebook_name = 'ipython_galaxy_notebook.ipynb'
+        #if $mode.mode_select == 'scratch':
+            ## copy default notebook
+            cp '$__tool_directory__/default_notebook.ipynb' ${output_notebook_name} &&
+            jupyter trust ${output_notebook_name} &&
+            jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
+        #else:
+            #import re
+            #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($mode.ipynb.element_identifier))
+            #if not $cleaned_name.endswith(".ipynb"):
+                #set $cleaned_name = "%s.ipynb" % $cleaned_name
+            #end if
+            cp '$mode.ipynb' '${cleaned_name}' &&
+            jupyter trust '${cleaned_name}' &&
+
+            #if $mode.run_it:
+                jupyter nbconvert --to notebook --execute --output '${output_notebook_name}' --allow-errors '${cleaned_name}' &&
+            #else:
+                #set $output_notebook_name = $cleaned_name
+                jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
+            #end if
+        #end if
+        cp '${output_notebook_name}' '$jupyter_notebook'
+    ]]>
+    </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>
+        <repeat name="user_inputs" title="User inputs">
+            <param name="input_name" type="text" value="" label="Name for parameter" optional="False" help="Required. ASCII letters and numbers only.">
+                <validator type="empty_field" message="Name is required"/>
+                <sanitizer>
+                    <valid initial="string.ascii_letters,string.digits"/>
+                </sanitizer>
+            </param>
+            <param name="description" type="text" label="Additional optional description" optional="true"/>
+            <conditional name="input_type">
+                <param name="input_type_selector" type="select" label="Choose the input type">
+                    <option value="dataset" selected="true">Dataset</option>
+                    <option value="dataset_multiple">Multiple datasets</option>
+                    <option value="dataset_collection">Dataset collection</option>
+                    <option value="dataset_collection_list">Dataset collection (list)</option>
+                    <option value="dataset_collection_paired">Dataset collection (paired)</option>
+                    <option value="dataset_collection_list_paired">Dataset collection (list:paired)</option>
+                    <option value="text">Text</option>
+                    <option value="integer">Integer</option>
+                    <option value="float">Floating point</option>
+                    <option value="boolean">Boolean</option>
+                    <option value="color">Color selector</option>
+                    <option value="dataset_optional" selected="true">Optional Dataset</option>
+                    <option value="dataset_multiple_optional">Optional Multiple datasets</option>
+                    <option value="dataset_collection_optional">Optional Dataset collection</option>
+                    <option value="dataset_collection_list_optional">Optional Dataset collection (list)</option>
+                    <option value="dataset_collection_paired_optional">Optional Dataset collection (paired)</option>
+                    <option value="dataset_collection_list_paired_optional">Optional Dataset collection (list:paired)</option>
+                    <option value="text_optional">Optional Text</option>
+                    <option value="integer_optional">Optional Integer</option>
+                    <option value="float_optional">Optional Floating point</option>
+                    <option value="boolean_optional">Optional Boolean</option>
+                    <option value="color_optional">Optional Color selector</option>
+                </param>
+                <when value="dataset">
+                    <param name="input_value" type="data" format="data" label="Select value" multiple="false" optional="false"/>
+                </when>
+                <when value="dataset_multiple">
+                    <param name="input_value" type="data" format="data" label="Select value" multiple="true" optional="false"/>
+                </when>
+                <when value="dataset_collection">
+                    <param name="input_value" type="data_collection" format="data" label="Select value" optional="false"/>
+                </when>
+                <when value="dataset_collection_list">
+                    <param name="input_value" type="data_collection" format="data" label="Select value" collection_type="list" optional="false"/>
+                </when>
+                <when value="dataset_collection_paired">
+                    <param name="input_value" type="data_collection" format="data" label="Select value" collection_type="paired" optional="false"/>
+                </when>
+                <when value="dataset_collection_list_paired">
+                    <param name="input_value" type="data_collection" format="data" label="Select value" collection_type="list:paired" optional="false"/>
+                </when>
+                <when value="text">
+                    <param name="input_value" type="text" value="" label="Select value" optional="false"/>
+                </when>
+                <when value="integer">
+                    <param name="input_value" type="integer" value="" label="Select value" optional="false"/>
+                </when>
+                <when value="float">
+                    <param name="input_value" type="float" value="" label="Select value" optional="false"/>
+                </when>
+                <when value="boolean">
+                    <param name="input_value" type="boolean" truevalue="true" falsevalue="false" label="Select value" optional="false"/>
+                </when>
+                <when value="color">
+                    <param name="input_value" type="color" label="Select value" optional="false"/>
+                </when>
+                <when value="dataset_optional">
+                    <param name="input_value" type="data" format="data" label="Select value" multiple="false" optional="true"/>
+                </when>
+                <when value="dataset_multiple_optional">
+                    <param name="input_value" type="data" format="data" label="Select value" multiple="true" optional="true"/>
+                </when>
+                <when value="dataset_collection_optional">
+                    <param name="input_value" type="data_collection" format="data" label="Select value" optional="true"/>
+                </when>
+                <when value="dataset_collection_list_optional">
+                    <param name="input_value" type="data_collection" format="data" label="Select value" collection_type="list" optional="true"/>
+                </when>
+                <when value="dataset_collection_paired_optional">
+                    <param name="input_value" type="data_collection" format="data" label="Select value" collection_type="paired" optional="true"/>
+                </when>
+                <when value="dataset_collection_list_paired_optional">
+                    <param name="input_value" type="data_collection" format="data" label="Select value" collection_type="list:paired" optional="true"/>
+                </when>
+                <when value="text_optional">
+                    <param name="input_value" type="text" value="" label="Select value" optional="true"/>
+                </when>
+                <when value="integer_optional">
+                    <param name="input_value" type="integer" value="" label="Select value" optional="true"/>
+                </when>
+                <when value="float_optional">
+                    <param name="input_value" type="float" value="" label="Select value" optional="true"/>
+                </when>
+                <when value="boolean_optional">
+                    <param name="input_value" type="boolean" truevalue="true" falsevalue="false" label="Select value" optional="true"/>
+                </when>
+                <when value="color_optional">
+                    <param name="input_value" type="color" label="Select value" optional="true"/>
+                </when>
+            </conditional>
+        </repeat>
+    </inputs>
+    <outputs>
+        <data name="jupyter_notebook" format="ipynb" label="Executed JupyTool Notebook"/>
+        <data name="output_dataset" format="data">
+            <discover_datasets pattern="__designation_and_ext__" directory="jupyter/outputs" visible="true" assign_primary_output="true"/>
+        </data>
+        <collection name="output_collection" type="list" label="JupyTool output collection">
+            <discover_datasets pattern="__designation_and_ext__" directory="jupyter/outputs/collection" visible="false"/>
+        </collection>
+    </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>
+    Welcome to the **JupyTool**! Here you can create, run, and share custom Galaxy tools based upon Jupyter Notebooks.
+
+    The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations,
+    visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization,
+    machine learning, and much more.
+
+    Galaxy offers you to use Jupyter Notebooks directly in Galaxy accessing and interacting with Galaxy datasets as you like. A very common use-case is to
+    do the heavy lifting and data reduction steps in Galaxy and the plotting and more `interactive` part on smaller datasets in Jupyter.
+
+    You can start with a new Jupyter notebook from scratch or load an already existing one, e.g. from your colleague and execute it on your dataset.
+    You can specify any number of user-defined inputs using the repeat input, providing `name` value, selecting the type of input, and then providing values.
+
+    You can make the JupyTool reusable in a workflow, by allowing the user to specify input values for the defined input blocks.
+    Inputs can be accessed by `name` from the automatically provided `GALAXY_INPUTS` dictionary.
+    Outputs can be written automatically to the user's history by writing to the `outputs` directory for one individual file or to the `outputs/collection` directory for multiple files.
+    Using collection tools, you can parse out the individual elements from the collection, as needed.
+
+    For backwards compatibility, you can import data into the notebook via a predefined `get()` function and write results back to Galaxy with a `put()` function.
+    </help>
+</tool>