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Merge branch 'release_18.09' into dev

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Dannon Baker
2018-09-18 14:57:59 -04:00
parent ed147ee052 8462df83c9
commit 5ace7d4015
3 changed files with 93 additions and 1 deletions
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config/datatypes_conf.xml.sample
+2 -1
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@@ -135,6 +135,7 @@
</datatype>
<datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="true"/>
<datatype extension="h5" type="galaxy.datatypes.binary:H5" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="loom" type="galaxy.datatypes.binary:Loom" description="An HDF5-based Loom File" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="mz5" type="galaxy.datatypes.binary:H5" subclass="true" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="hivtrace" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="true" display_in_upload="false"/>
<datatype extension="cool" type="galaxy.datatypes.binary:Cool" mimetype="application/octet-stream" display_in_upload="true"/>
@@ -503,7 +504,6 @@
<datatype extension="cel" type="galaxy.datatypes.binary:Cel" display_in_upload="true"/>
<datatype extension="rdata" type="galaxy.datatypes.binary:RData" display_in_upload="true" description="Stored data from an R session"/>
<datatype extension="rdata.sce" type="galaxy.datatypes.binary:RData" description="Stored RDS from a SingleCellObject" subclass="true" />
<datatype extension="rdata.seurat" type="galaxy.datatypes.binary:RData" description="Stored RDS from a Seurat Object" subclass="true" />
<datatype extension="oxlicg" type="galaxy.datatypes.binary:OxliCountGraph" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="oxling" type="galaxy.datatypes.binary:OxliNodeGraph" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="oxlits" type="galaxy.datatypes.binary:OxliTagSet" mimetype="application/octet-stream" display_in_upload="true"/>
@@ -716,6 +716,7 @@
<sniffer type="galaxy.datatypes.binary:GAFASQLite"/>
<sniffer type="galaxy.datatypes.binary:SQlite"/>
<sniffer type="galaxy.datatypes.binary:Cool"/>
<sniffer type="galaxy.datatypes.binary:Loom"/>
<sniffer type="galaxy.datatypes.binary:Biom2"/>
<sniffer type="galaxy.datatypes.binary:H5"/>
<sniffer type="galaxy.datatypes.binary:Bam"/>
lib/galaxy/datatypes/binary.py
+91
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@@ -736,6 +736,97 @@ class H5(Binary):
return "Binary HDF5 file (%s)" % (nice_size(dataset.get_size()))
class Loom(H5):
"""
Class describing a Loom file: http://loompy.org/
>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('test.loom')
>>> Loom().sniff(fname)
True
>>> fname = get_test_fname('test.mz5')
>>> Loom().sniff(fname)
False
"""
file_ext = "loom"
edam_format = "format_3590"
MetadataElement(name="title", default="", desc="title", readonly=True, visible=True, no_value="")
MetadataElement(name="description", default="", desc="description", readonly=True, visible=True, no_value="")
MetadataElement(name="url", default="", desc="url", readonly=True, visible=True, no_value="")
MetadataElement(name="doi", default="", desc="doi", readonly=True, visible=True, no_value="")
MetadataElement(name="loom_spec_version", default="", desc="loom_spec_version", readonly=True, visible=True, no_value="")
MetadataElement(name="creation_date", default=None, desc="creation_date", readonly=True, visible=True, no_value=None)
MetadataElement(name="shape", default=(), desc="shape", param=metadata.ListParameter, readonly=True, visible=True, no_value=())
MetadataElement(name="layers_count", default=0, desc="layers_count", readonly=True, visible=True, no_value=0)
MetadataElement(name="layers_names", desc="layers_names", default=[], param=metadata.SelectParameter, multiple=True, readonly=True, no_value=None)
MetadataElement(name="row_attrs_count", default=0, desc="row_attrs_count", readonly=True, visible=True, no_value=0)
MetadataElement(name="row_attrs_names", desc="row_attrs_names", default=[], param=metadata.SelectParameter, multiple=True, readonly=True, no_value=None)
MetadataElement(name="col_attrs_count", default=0, desc="col_attrs_count", readonly=True, visible=True, no_value=0)
MetadataElement(name="col_attrs_names", desc="col_attrs_names", default=[], param=metadata.SelectParameter, multiple=True, readonly=True, no_value=None)
MetadataElement(name="col_graphs_count", default=0, desc="col_graphs_count", readonly=True, visible=True, no_value=0)
MetadataElement(name="col_graphs_names", desc="col_graphs_names", default=[], param=metadata.SelectParameter, multiple=True, readonly=True, no_value=None)
MetadataElement(name="row_graphs_count", default=0, desc="row_graphs_count", readonly=True, visible=True, no_value=0)
MetadataElement(name="row_graphs_names", desc="row_graphs_names", default=[], param=metadata.SelectParameter, multiple=True, readonly=True, no_value=None)
def sniff(self, filename):
if super(Loom, self).sniff(filename):
try:
with h5py.File(filename) as loom_file:
return bool(loom_file.attrs.get('LOOM_SPEC_VERSION', False))
except Exception:
return False
return False
def set_peek(self, dataset, is_multi_byte=False):
if not dataset.dataset.purged:
dataset.peek = "Binary Loom file"
dataset.blurb = nice_size(dataset.get_size())
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
def display_peek(self, dataset):
try:
return dataset.peek
except Exception:
return "Binary Loom file (%s)" % (nice_size(dataset.get_size()))
def set_meta(self, dataset, overwrite=True, **kwd):
super(Loom, self).set_meta(dataset, overwrite=overwrite, **kwd)
try:
with h5py.File(dataset.file_name) as loom_file:
dataset.metadata.title = loom_file.attrs.get('title', None)
dataset.metadata.description = loom_file.attrs.get('description', None)
dataset.metadata.url = loom_file.attrs.get('url', None)
dataset.metadata.doi = loom_file.attrs.get('doi', None)
dataset.metadata.loom_spec_version = loom_file.attrs.get('LOOM_SPEC_VERSION', None)
dataset.creation_date = loom_file.attrs.get('creation_date', None)
dataset.metadata.shape = tuple(loom_file['matrix'].shape)
tmp = list(loom_file['layers'].keys())
dataset.metadata.layers_count = len(tmp)
dataset.metadata.layers_names = tmp
tmp = list(loom_file['row_attrs'].keys())
dataset.metadata.row_attrs_count = len(tmp)
dataset.metadata.row_attrs_names = tmp
tmp = list(loom_file['col_attrs'].keys())
dataset.metadata.col_attrs_count = len(tmp)
dataset.metadata.col_attrs_names = tmp
tmp = list(loom_file['col_graphs'].keys())
dataset.metadata.col_graphs_count = len(tmp)
dataset.metadata.col_graphs_names = tmp
tmp = list(loom_file['row_graphs'].keys())
dataset.metadata.row_graphs_count = len(tmp)
dataset.metadata.row_graphs_names = tmp
except Exception as e:
log.warning('%s, set_meta Exception: %s', self, e)
class GmxBinary(Binary):
"""
Base class for GROMACS binary files - xtc, trr, cpt
lib/galaxy/datatypes/test/test.loom
BIN
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