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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>
This commit is contained in:
Martin Cech
2021-06-09 14:24:01 +02:00
committed by GitHub
co-authored by Marius van den Beek
parent 0b1bad8958
commit 54dd806c26
1 changed files with 3 additions and 3 deletions
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tools/interactive/interactivetool_jupyter_notebook.xml
+3 -3
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@@ -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: