From fc2644033b34d3ee5130562c41fdb1b5a991946e Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Wed, 9 Jun 2021 13:49:03 +0200
Subject: [PATCH 1/6] allow multiple inputs in jupyter IT

+ fix a bug with saving notebooks on exit that had non-default name
+ remove the confusion with naming notebooks after inputs
---
 .../interactivetool_jupyter_notebook.xml      | 69 +++++++++++--------
 1 file changed, 39 insertions(+), 30 deletions(-)

diff --git a/tools/interactive/interactivetool_jupyter_notebook.xml b/tools/interactive/interactivetool_jupyter_notebook.xml
index 8c4af7ccbc6..7c19b386717 100644
--- a/tools/interactive/interactivetool_jupyter_notebook.xml
+++ b/tools/interactive/interactivetool_jupyter_notebook.xml
@@ -16,38 +16,47 @@
         <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 &&
+#import re
+#import random
+#import string
+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}' &&
+#set $cleaned_names = []
+#for $file in $input
+    #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($file.element_identifier))
+    ## prevent overwriting data with a randomized suffix
+    #if $cleaned_name in $cleaned_names:
+        #set $cleaned_name = $cleaned_name + '_' + ''.join(random.choice(string.ascii_lowercase) for _ in range(3))
+    #end if
+    #set $cleaned_names += [$cleaned_name]
+    ln -sf '$file' './jupyter/data/${cleaned_name}' &&
+#end for
 
-        ## change into the directory where the notebooks are located
-        cd ./jupyter/ &&
-        export HOME=/home/jovyan/ &&
-        export PATH=/home/jovyan/.local/bin:\$PATH &&
+## change into the directory where the notebooks are located
+cd ./jupyter/ &&
+export HOME=/home/jovyan/ &&
+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 --NotebookApp.shutdown_button=True &&
-            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 $mode.run_it:
-                jupyter nbconvert --to notebook --execute --output ./ipython_galaxy_notebook.ipynb --allow-errors  ./*.ipynb &&
-            #else:
-                jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
-            #end if
-            cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook'
-        #end if
+#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 --NotebookApp.shutdown_button=True &&
+    cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook'
+#else:
+    #set $noteboook_name = re.sub('[^\w\-\.]', '_', str($mode.ipynb.element_identifier))
+    cp '$mode.ipynb' ./${noteboook_name}.ipynb &&
+    jupyter trust ./${noteboook_name}.ipynb &&
+    #if $mode.run_it:
+        jupyter nbconvert --to notebook --execute --output ./ipython_galaxy_notebook.ipynb --allow-errors  ./*.ipynb &&
+        #set $noteboook_name = 'ipython_galaxy_notebook'
+    #else:
+        jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
+    #end if
+    cp ./${noteboook_name}.ipynb '$jupyter_notebook'
+#end if
     ]]>
     </command>
     <inputs>
@@ -64,7 +73,7 @@
                     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"/>
+        <param name="input" multiple="true" type="data" optional="true" label="Include data into the environment"/>
 
     </inputs>
     <outputs>

From 26a7bcf89c27f718b06879f3db5f7ee6901ab6ad Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Wed, 9 Jun 2021 13:50:35 +0200
Subject: [PATCH 2/6] bump version

---
 tools/interactive/interactivetool_jupyter_notebook.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/interactive/interactivetool_jupyter_notebook.xml b/tools/interactive/interactivetool_jupyter_notebook.xml
index 7c19b386717..5f03e496a52 100644
--- a/tools/interactive/interactivetool_jupyter_notebook.xml
+++ b/tools/interactive/interactivetool_jupyter_notebook.xml
@@ -1,4 +1,4 @@
-<tool id="interactive_tool_jupyter_notebook" tool_type="interactive" name="Interactive Jupyter Notebook" version="0.1">
+<tool id="interactive_tool_jupyter_notebook" tool_type="interactive" name="Interactive Jupyter Notebook" version="0.2">
     <requirements>
         <container type="docker">quay.io/bgruening/docker-jupyter-notebook:ie2</container>
     </requirements>

From 0b1bad89582d4d8fae8cfb722b7ecf32f8c20c9e Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Wed, 9 Jun 2021 13:57:32 +0200
Subject: [PATCH 3/6] respect the cheetah style

---
 .../interactivetool_jupyter_notebook.xml      | 76 +++++++++----------
 1 file changed, 38 insertions(+), 38 deletions(-)

diff --git a/tools/interactive/interactivetool_jupyter_notebook.xml b/tools/interactive/interactivetool_jupyter_notebook.xml
index 5f03e496a52..c7453f06f0d 100644
--- a/tools/interactive/interactivetool_jupyter_notebook.xml
+++ b/tools/interactive/interactivetool_jupyter_notebook.xml
@@ -16,47 +16,47 @@
         <environment_variable name="API_KEY" inject="api_key" />
     </environment_variables>
     <command detect_errors="aggressive"><![CDATA[
-#import re
-#import random
-#import string
-export GALAXY_WORKING_DIR=`pwd` &&
-mkdir -p ./jupyter/outputs/ &&
-mkdir -p ./jupyter/data &&
+        #import re
+        #import random
+        #import string
+        export GALAXY_WORKING_DIR=`pwd` &&
+        mkdir -p ./jupyter/outputs/ &&
+        mkdir -p ./jupyter/data &&
 
-#set $cleaned_names = []
-#for $file in $input
-    #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($file.element_identifier))
-    ## prevent overwriting data with a randomized suffix
-    #if $cleaned_name in $cleaned_names:
-        #set $cleaned_name = $cleaned_name + '_' + ''.join(random.choice(string.ascii_lowercase) for _ in range(3))
-    #end if
-    #set $cleaned_names += [$cleaned_name]
-    ln -sf '$file' './jupyter/data/${cleaned_name}' &&
-#end for
+        #set $cleaned_names = []
+        #for $file in $input
+            #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($file.element_identifier))
+            ## prevent overwriting data with a randomized suffix
+            #if $cleaned_name in $cleaned_names:
+                #set $cleaned_name = $cleaned_name + '_' + ''.join(random.choice(string.ascii_lowercase) for _ in range(3))
+            #end if
+            #set $cleaned_names += [$cleaned_name]
+            ln -sf '$file' './jupyter/data/${cleaned_name}' &&
+        #end for
 
-## change into the directory where the notebooks are located
-cd ./jupyter/ &&
-export HOME=/home/jovyan/ &&
-export PATH=/home/jovyan/.local/bin:\$PATH &&
+        ## change into the directory where the notebooks are located
+        cd ./jupyter/ &&
+        export HOME=/home/jovyan/ &&
+        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 --NotebookApp.shutdown_button=True &&
-    cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook'
-#else:
-    #set $noteboook_name = re.sub('[^\w\-\.]', '_', str($mode.ipynb.element_identifier))
-    cp '$mode.ipynb' ./${noteboook_name}.ipynb &&
-    jupyter trust ./${noteboook_name}.ipynb &&
-    #if $mode.run_it:
-        jupyter nbconvert --to notebook --execute --output ./ipython_galaxy_notebook.ipynb --allow-errors  ./*.ipynb &&
-        #set $noteboook_name = 'ipython_galaxy_notebook'
-    #else:
-        jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
-    #end if
-    cp ./${noteboook_name}.ipynb '$jupyter_notebook'
-#end if
+        #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 --NotebookApp.shutdown_button=True &&
+            cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook'
+        #else:
+            #set $noteboook_name = re.sub('[^\w\-\.]', '_', str($mode.ipynb.element_identifier))
+            cp '$mode.ipynb' ./${noteboook_name}.ipynb &&
+            jupyter trust ./${noteboook_name}.ipynb &&
+            #if $mode.run_it:
+                jupyter nbconvert --to notebook --execute --output ./ipython_galaxy_notebook.ipynb --allow-errors  ./*.ipynb &&
+                #set $noteboook_name = 'ipython_galaxy_notebook'
+            #else:
+                jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
+            #end if
+            cp ./${noteboook_name}.ipynb '$jupyter_notebook'
+        #end if
     ]]>
     </command>
     <inputs>

From 54dd806c26a562fc0d2c4ae5873a23be22fd8c28 Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Wed, 9 Jun 2021 14:24:01 +0200
Subject: [PATCH 4/6] Apply suggestions from code review

include file ext with a name, allow spaces in input datasets and notebook names

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
---
 tools/interactive/interactivetool_jupyter_notebook.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/interactive/interactivetool_jupyter_notebook.xml b/tools/interactive/interactivetool_jupyter_notebook.xml
index c7453f06f0d..6a9873b54b0 100644
--- a/tools/interactive/interactivetool_jupyter_notebook.xml
+++ b/tools/interactive/interactivetool_jupyter_notebook.xml
@@ -25,13 +25,13 @@
 
         #set $cleaned_names = []
         #for $file in $input
-            #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($file.element_identifier))
+            #set $cleaned_name = re.sub('[^\w\-\.\s]', '_', str($file.element_identifier))
             ## prevent overwriting data with a randomized suffix
             #if $cleaned_name in $cleaned_names:
                 #set $cleaned_name = $cleaned_name + '_' + ''.join(random.choice(string.ascii_lowercase) for _ in range(3))
             #end if
             #set $cleaned_names += [$cleaned_name]
-            ln -sf '$file' './jupyter/data/${cleaned_name}' &&
+            ln -sf '$file' './jupyter/data/${cleaned_name}.${file.ext}' && 
         #end for
 
         ## change into the directory where the notebooks are located
@@ -46,7 +46,7 @@
             jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
             cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook'
         #else:
-            #set $noteboook_name = re.sub('[^\w\-\.]', '_', str($mode.ipynb.element_identifier))
+            #set $noteboook_name = re.sub('[^\w\-\.\s]', '_', str($mode.ipynb.element_identifier))
             cp '$mode.ipynb' ./${noteboook_name}.ipynb &&
             jupyter trust ./${noteboook_name}.ipynb &&
             #if $mode.run_it:

From cd2c1a5d853d052f2e394ce1099dafa2872279b6 Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Thu, 10 Jun 2021 14:30:34 +0200
Subject: [PATCH 5/6] prefix all datasets with their index

---
 .../interactivetool_jupyter_notebook.xml         | 16 ++++------------
 1 file changed, 4 insertions(+), 12 deletions(-)

diff --git a/tools/interactive/interactivetool_jupyter_notebook.xml b/tools/interactive/interactivetool_jupyter_notebook.xml
index c7453f06f0d..0ca5732b858 100644
--- a/tools/interactive/interactivetool_jupyter_notebook.xml
+++ b/tools/interactive/interactivetool_jupyter_notebook.xml
@@ -17,21 +17,13 @@
     </environment_variables>
     <command detect_errors="aggressive"><![CDATA[
         #import re
-        #import random
-        #import string
         export GALAXY_WORKING_DIR=`pwd` &&
         mkdir -p ./jupyter/outputs/ &&
         mkdir -p ./jupyter/data &&
 
-        #set $cleaned_names = []
-        #for $file in $input
-            #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($file.element_identifier))
-            ## prevent overwriting data with a randomized suffix
-            #if $cleaned_name in $cleaned_names:
-                #set $cleaned_name = $cleaned_name + '_' + ''.join(random.choice(string.ascii_lowercase) for _ in range(3))
-            #end if
-            #set $cleaned_names += [$cleaned_name]
-            ln -sf '$file' './jupyter/data/${cleaned_name}' &&
+        #for $count, $file in enumerate($input):
+            #set $cleaned_name = str($count + 1) + '_' + re.sub('[^\w\-\.\s]', '_', str($file.element_identifier))
+            ln -sf '$file' './jupyter/data/${cleaned_name}.${file.ext}' &&
         #end for
 
         ## change into the directory where the notebooks are located
@@ -46,7 +38,7 @@
             jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
             cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook'
         #else:
-            #set $noteboook_name = re.sub('[^\w\-\.]', '_', str($mode.ipynb.element_identifier))
+            #set $noteboook_name = re.sub('[^\w\-\.\s]', '_', str($mode.ipynb.element_identifier))
             cp '$mode.ipynb' ./${noteboook_name}.ipynb &&
             jupyter trust ./${noteboook_name}.ipynb &&
             #if $mode.run_it:

From d7b1a913bc5da08daeaa4ee0bdb494ffcf3b5ad2 Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Thu, 10 Jun 2021 15:21:09 +0200
Subject: [PATCH 6/6] properly quote var expansion, since it can contain spaces
 now

---
 tools/interactive/interactivetool_jupyter_notebook.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/interactive/interactivetool_jupyter_notebook.xml b/tools/interactive/interactivetool_jupyter_notebook.xml
index 0ca5732b858..3ad598ceed0 100644
--- a/tools/interactive/interactivetool_jupyter_notebook.xml
+++ b/tools/interactive/interactivetool_jupyter_notebook.xml
@@ -39,15 +39,15 @@
             cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook'
         #else:
             #set $noteboook_name = re.sub('[^\w\-\.\s]', '_', str($mode.ipynb.element_identifier))
-            cp '$mode.ipynb' ./${noteboook_name}.ipynb &&
-            jupyter trust ./${noteboook_name}.ipynb &&
+            cp '$mode.ipynb' './${noteboook_name}.ipynb' &&
+            jupyter trust './${noteboook_name}.ipynb' &&
             #if $mode.run_it:
                 jupyter nbconvert --to notebook --execute --output ./ipython_galaxy_notebook.ipynb --allow-errors  ./*.ipynb &&
                 #set $noteboook_name = 'ipython_galaxy_notebook'
             #else:
                 jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
             #end if
-            cp ./${noteboook_name}.ipynb '$jupyter_notebook'
+            cp './${noteboook_name}.ipynb' '$jupyter_notebook'
         #end if
     ]]>
     </command>