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Merge pull request #4178 from zipho/neo_datatype
Neostore Zip datatype support
This commit is contained in:
John Chilton
@@ -620,6 +620,9 @@
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<datatype extension="mothur.sff.flow" type="galaxy.datatypes.mothur:SffFlow" display_in_upload="true"/>
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<datatype extension="mothur.count_table" type="galaxy.datatypes.mothur:CountTable" display_in_upload="true"/>
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<datatype extension="neostore" type="galaxy.datatypes.neo4j:Neo4jDB" mimetype="text/html" display_in_upload="false"/>
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<datatype extension="neostore.zip" type="galaxy.datatypes.neo4j:Neo4jDBzip" display_in_upload="true">
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<converter file="neostorezip_to_neostore_converter.xml" target_datatype="neostore"/>
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</datatype>
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<datatype extension="trackhub" type="galaxy.datatypes.tracks:UCSCTrackHub" display_in_upload="true">
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<display file="ucsc/trackhub.xml" />
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</datatype>
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@@ -824,5 +827,6 @@
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<sniffer type="galaxy.datatypes.binary:OxliStopTags"/>
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<sniffer type="galaxy.datatypes.binary:OxliSubset"/>
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<sniffer type="galaxy.datatypes.binary:OxliGraphLabels"/>
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<sniffer type="galaxy.datatypes.neo4j:Neo4jDBzip"/>
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</sniffers>
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</datatypes>
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@@ -0,0 +1,14 @@
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<tool id="CONVERTER_neostorezip_to_neostore" name="Convert neostore.zip files to neostore" version="1.0.0" hidden="true">
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<command><![CDATA[
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unzip '${input1.extra_files_path}/neostore_file.zip' -d '${output1.files_path}' > $output1
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]]>
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</command>
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<inputs>
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<param format="neostore.zip" name="input1" type="data" label="Choose neostore database file"/>
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</inputs>
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<outputs>
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<data format="neostore" name="output1"/>
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</outputs>
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<help>
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</help>
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</tool>
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@@ -8,6 +8,7 @@ import sys
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from galaxy.datatypes.data import Data
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from galaxy.datatypes.images import Html
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from galaxy.datatypes.metadata import MetadataElement
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from galaxy.util import FILENAME_VALID_CHARS
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gal_Log = logging.getLogger(__name__)
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@@ -26,6 +27,7 @@ class Neo4j(Html):
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This is called only at upload to write the html file
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cannot rename the datasets here - they come with the default unfortunately
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"""
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# self.regenerate_primary_file(dataset)
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rval = [
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'<html><head><title>Files for Composite Dataset (%s)</title></head><p/>\
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This composite dataset is composed of the following files:<p/><ul>' % (
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@@ -34,7 +36,8 @@ class Neo4j(Html):
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opt_text = ''
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if composite_file.optional:
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opt_text = ' (optional)'
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rval.append('<li><a href="%s">%s</a>%s' % (composite_name, composite_name, opt_text))
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rval.append('<li><a href="%s">%s</a>%s' %
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(composite_name, composite_name, opt_text))
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rval.append('</ul></html>')
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return "\n".join(rval)
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@@ -68,22 +71,27 @@ class Neo4j(Html):
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trans.log_event("Display dataset id: %s" % str(data.id))
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# the target directory name
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neo4j_dir_name = '/dataset_{}_files/neo4jdb'.format(data.dataset.id)
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dir_name = str(os.path.dirname(trans.app.object_store.get_filename(data.dataset))) + neo4j_dir_name
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neo4j_dir_name = '/dataset_{}_files'.format(
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data.dataset.id)
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dir_name = str(os.path.dirname(
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trans.app.object_store.get_filename(data.dataset))) + neo4j_dir_name
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# generate unique filename for this dataset
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fname = ''.join(c in FILENAME_VALID_CHARS and c or '_' for c in data.name)[0:150]
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fname = ''.join(
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c in FILENAME_VALID_CHARS and c or '_' for c in data.name)[0:150]
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# zip the target directory (dir_name) using the fname
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shutil.make_archive(fname, 'zip', dir_name)
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download_zip = fname + '.zip'
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# setup headers for the download
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trans.response.headers['Content-Length'] = int(os.stat(download_zip).st_size)
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trans.response.headers['Content-Length'] = int(
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os.stat(download_zip).st_size)
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# force octet-stream so Safari doesn't append mime extensions to filename
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trans.response.set_content_type("application/octet-stream")
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trans.response.headers["Content-Disposition"] = 'attachment; filename="Galaxy%s-[%s].%s"' % \
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(data.hid, download_zip, "zip")
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(data.hid,
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download_zip, "zip")
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return open(download_zip)
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@@ -97,39 +105,74 @@ class Neo4jDB(Neo4j, Data):
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Data.__init__(self, **kwd)
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self.add_composite_file('neostore', is_binary=True)
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self.add_composite_file('neostore.id', is_binary=True)
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self.add_composite_file('neostore.counts.db.a', is_binary=True)
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self.add_composite_file('neostore.counts.db.b', is_binary=True)
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self.add_composite_file('neostore.counts.db.a', optional=True, is_binary=True)
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self.add_composite_file('neostore.counts.db.b', optional=True, is_binary=True)
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self.add_composite_file('neostore.labeltokenstore.db', is_binary=True)
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self.add_composite_file('neostore.labeltokenstore.db.id', is_binary=True)
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self.add_composite_file('neostore.labeltokenstore.db.names', is_binary=True)
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self.add_composite_file('neostore.labeltokenstore.db.names.id', is_binary=True)
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self.add_composite_file(
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'neostore.labeltokenstore.db.id', is_binary=True)
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self.add_composite_file(
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'neostore.labeltokenstore.db.names', is_binary=True)
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self.add_composite_file(
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'neostore.labeltokenstore.db.names.id', is_binary=True)
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self.add_composite_file('neostore.nodestore.db', is_binary=True)
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self.add_composite_file('neostore.nodestore.db.id', is_binary=True)
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self.add_composite_file('neostore.nodestore.db.labels', is_binary=True)
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self.add_composite_file('neostore.nodestore.db.labels.id', is_binary=True)
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self.add_composite_file(
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'neostore.nodestore.db.labels.id', is_binary=True)
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self.add_composite_file('neostore.propertystore.db', is_binary=True)
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self.add_composite_file('neostore.propertystore.db.id', is_binary=True)
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self.add_composite_file('neostore.propertystore.db.arrays', is_binary=True)
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self.add_composite_file('neostore.propertystore.db.arrays.id', is_binary=True)
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self.add_composite_file('neostore.propertystore.db.index', is_binary=True)
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self.add_composite_file('neostore.propertystore.db.index.id', is_binary=True)
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self.add_composite_file('neostore.propertystore.db.index.keys', is_binary=True)
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self.add_composite_file('neostore.propertystore.db.index.keys.id', is_binary=True)
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self.add_composite_file('neostore.propertystore.db.strings', is_binary=True)
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self.add_composite_file('neostore.propertystore.db.strings.id', is_binary=True)
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self.add_composite_file(
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'neostore.propertystore.db.arrays', is_binary=True)
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self.add_composite_file(
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'neostore.propertystore.db.arrays.id', is_binary=True)
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self.add_composite_file(
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'neostore.propertystore.db.index', is_binary=True)
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self.add_composite_file(
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'neostore.propertystore.db.index.id', is_binary=True)
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self.add_composite_file(
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'neostore.propertystore.db.index.keys', is_binary=True)
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self.add_composite_file(
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'neostore.propertystore.db.index.keys.id', is_binary=True)
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self.add_composite_file(
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'neostore.propertystore.db.strings', is_binary=True)
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self.add_composite_file(
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'neostore.propertystore.db.strings.id', is_binary=True)
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self.add_composite_file('neostore.relationshipgroupstore.db', is_binary=True)
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self.add_composite_file('neostore.relationshipgroupstore.db.id', is_binary=True)
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self.add_composite_file('neostore.relationshipstore.db', is_binary=True)
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self.add_composite_file('neostore.relationshipstore.db.id', is_binary=True)
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self.add_composite_file('neostore.relationshiptypestore.db.names', is_binary=True)
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self.add_composite_file('neostore.relationshiptypestore.db.names.id', is_binary=True)
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self.add_composite_file(
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'neostore.relationshipgroupstore.db', is_binary=True)
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self.add_composite_file(
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'neostore.relationshipgroupstore.db.id', is_binary=True)
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self.add_composite_file(
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'neostore.relationshipstore.db', is_binary=True)
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self.add_composite_file(
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'neostore.relationshipstore.db.id', is_binary=True)
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self.add_composite_file(
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'neostore.relationshiptypestore.db.names', is_binary=True)
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self.add_composite_file(
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'neostore.relationshiptypestore.db.names.id', is_binary=True)
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self.add_composite_file('neostore.schemastore.db', is_binary=True)
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self.add_composite_file('neostore.schemastore.db.id', is_binary=True)
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self.add_composite_file('neostore.transaction.db.0', is_binary=True)
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class Neo4jDBzip(Neo4j, Data):
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"""Class for neo4jDB database files."""
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MetadataElement(name='reference_name', default='neostore_file', desc='Reference Name',
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readonly=True, visible=True, set_in_upload=True, no_value='neostore')
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MetadataElement(name="neostore_zip", default=None, desc="Neostore zip",
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readonly=True, visible=True, set_in_upload=True, no_value=None, optional=True)
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file_ext = "neostore.zip"
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composite_type = 'auto_primary_file'
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allow_datatype_change = False
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def __init__(self, **kwd):
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Data.__init__(self, **kwd)
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self.add_composite_file('%s.zip', description='neostore zip', substitute_name_with_metadata='reference_name',
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is_binary=True)
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if __name__ == '__main__':
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import doctest
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doctest.testmod(sys.modules[__name__])
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Binary file not shown.
@@ -0,0 +1,19 @@
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<tool id="compressed_neostorezip_neostore_conversion" name="Confirm neostore.zip is converted to neostore on demand">
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<command>
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cat '$input1' > '$out_file1'
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</command>
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<inputs>
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<param name="input1" type="data" format="neostore.zip" label="Compressed Dataset"/>
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</inputs>
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<outputs>
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<data name="out_file1" format="neostore"/>
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</outputs>
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<tests>
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<test>
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<param name="input1" value="neostore.zip"/>
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<output name="out_file1" file="neostore"/>
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</test>
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</tests>
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<help>
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</help>
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</tool>
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@@ -0,0 +1,19 @@
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<tool id="compressed_neostorezip_neostore_cat" name="Confirm neostorezip is not uncompressed">
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<command>
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cat '$input1' > '$out_file1'
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</command>
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<inputs>
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<param name="input1" type="data" format="neostore.zip" label="Compressed Dataset"/>
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</inputs>
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<outputs>
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<data name="out_file1" format="neostore.zip"/>
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</outputs>
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<tests>
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<test>
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<param name="input1" value="neostore.zip"/>
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<output name="out_file1" file="neostore.zip" ftype="neostore.zip"/>
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</test>
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</tests>
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<help>
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</help>
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</tool>
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