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Allow creation of subdirectories on export

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This commit is contained in:
mvdbeek
2021-05-27 17:21:01 +02:00
parent 1593e91c27
commit f5d05fb545
2 changed files with 16 additions and 7 deletions
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lib/galaxy/util/__init__.py
+9 -4
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@@ -1067,14 +1067,19 @@ def unicodify(value, encoding=DEFAULT_ENCODING, error='replace', strip_null=Fals
return value
def filesystem_safe_string(s, max_len, truncation_chars='..'):
def filesystem_safe_string(s, max_len, truncation_chars='..', strip_leading_dot=True, invalid_chars=('/',), replacement_char='_'):
"""
Strip leading dots, unicode null chars, replace `/` with `_`, truncate at 255 characters.
Strip unicode null chars, truncate at 255 characters.
Optionally replace additional ``invalid_chars`` with `replacement_char` .
This is probably only safe on linux / osx.
Defaults are probably only safe on linux / osx.
Needs further escaping if used in shell commands
"""
sanitized_string = unicodify(s, strip_null=True).lstrip('.').replace('/', '_')
sanitized_string = unicodify(s, strip_null=True)
if strip_leading_dot:
sanitized_string = sanitized_string.lstrip('.')
for invalid_char in invalid_chars:
sanitized_string = sanitized_string.replace(invalid_char, replacement_char)
if len(sanitized_string) > max_len:
sanitized_string = sanitized_string[:max_len - len(truncation_chars)]
sanitized_string = f"{sanitized_string}{truncation_chars}"
tools/data_export/export_remote.xml
+7 -3
View File
@@ -19,7 +19,7 @@ python '$__tool_directory__/export_remote.py'
#if $export_type.export_type_selector == "datasets_auto":
#set $fileconfig = json.dumps([{"real_data_path": str(infile), "name": infile.name_and_ext_filesystem_safe} for infile in $infiles])
#else
#set $fileconfig = json.dumps([{"real_data_path": str(dataset["infile"]), "name": filesystem_safe_string(str(dataset["name"]), 255)} for dataset in $export_type.datasets])
#set $fileconfig = json.dumps([{"real_data_path": str(dataset["infile"]), "name": filesystem_safe_string(str(dataset["name"]), 255, invalid_chars=())} for dataset in $export_type.datasets])
#end if
$fileconfig
</configfile>
@@ -28,16 +28,20 @@ $fileconfig
<conditional name="export_type">
<param name="export_type_selector" type="select" label="What would you like to export?">
<option value="datasets_auto" selected="True">Datasets using their Galaxy name and extension.</option>
<option value="collection_auto">Dataset Collections using their name, structure and extension</option>
<option value="datasets_named">Datasets using specified name.</option>
<!-- Allow more options - e.g. HTML, collections preserving their structure... -->
</param>
<when value="datasets_auto">
<param name="infiles" type="data" format="txt,binary" multiple="true" label="Choose your datasets"/>
<param name="infiles" type="data" format="txt,binary" multiple="true" label="Choose your datasets" help="Datasets must have unique names"/>
</when>
<when value="collection_auto">
<param name="incollection" type="data_collection" format="txt,binary" label="Choose your dataset collection" help="Dataset collection will be exported. Collections will become folders and datasets will be files"/>
</when>
<when value="datasets_named">
<repeat name="datasets" title="Dataset">
<param type="data" name="infile" label="Input dataset" />
<param type="text" name="name" label="Name">
<param type="text" name="name" label="Enter file name" help="To create a file named &quot;f1.txt&quot; in directory named &quot;dir1&quot; enter &quot;dir1/f1.txt&quot;">
<!-- 🔥 turn off sanitizer, so unicode strings can be used. Is sanitized in configfile -->
<sanitizer sanitize="false"></sanitizer>
<validator type="length" min="1" max="255"/>