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Merge branch 'release_16.04' into dev

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This commit is contained in:
Dannon Baker
2016-07-08 15:58:57 -04:00
parent 77f547ed89 05c063b13a
commit a74a23764c
14 changed files with 49 additions and 49 deletions
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client/galaxy/scripts/mvc/dataset/data.js
+6 -3
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@@ -64,7 +64,7 @@ var TabularDataset = Dataset.extend({
defaults: _.extend({}, Dataset.prototype.defaults, {
chunk_url: null,
first_data_chunk: null,
chunk_index: -1,
offset: 0,
at_eof: false
}),
@@ -72,7 +72,9 @@ var TabularDataset = Dataset.extend({
Dataset.prototype.initialize.call(this);
// If first data chunk is available, next chunk is 1.
this.attributes.chunk_index = (this.attributes.first_data_chunk ? 1 : 0);
if (this.attributes.first_data_chunk){
this.attributes.offset = this.attributes.first_data_chunk.offset;
}
this.attributes.chunk_url = Galaxy.root + 'dataset/display?dataset_id=' + this.id;
this.attributes.url_viz = Galaxy.root + 'visualization';
},
@@ -90,12 +92,13 @@ var TabularDataset = Dataset.extend({
var self = this,
next_chunk = $.Deferred();
$.getJSON(this.attributes.chunk_url, {
chunk: self.attributes.chunk_index++
offset: self.attributes.offset
}).success(function(chunk) {
var rval;
if (chunk.ck_data !== '') {
// Found chunk.
rval = chunk;
self.attributes.offset = chunk.offset;
}
else {
// At EOF.
lib/galaxy/datatypes/binary.py
+1 -1
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@@ -73,7 +73,7 @@ class Binary( data.Data ):
"""Returns the mime type of the datatype"""
return 'application/octet-stream'
def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, size=None, offset=None, **kwd):
def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, **kwd):
trans.response.set_content_type(dataset.get_mime())
trans.log_event( "Display dataset id: %s" % str( dataset.id ) )
trans.response.headers['Content-Length'] = int( os.stat( dataset.file_name ).st_size )
lib/galaxy/datatypes/data.py
+1 -1
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@@ -312,7 +312,7 @@ class Data( object ):
trans.response.headers["Content-Disposition"] = 'attachment; filename="Galaxy%s-[%s].%s"' % (dataset.hid, fname, to_ext)
return open( dataset.file_name )
def display_data(self, trans, data, preview=False, filename=None, to_ext=None, size=None, offset=None, **kwd):
def display_data(self, trans, data, preview=False, filename=None, to_ext=None, **kwd):
""" Old display method, for transition - though still used by API and
test framework. Datatypes should be very careful if overridding this
method and this interface between datatypes and Galaxy will likely
lib/galaxy/datatypes/molecules.py
+1 -1
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@@ -393,7 +393,7 @@ class OBFS(Binary):
return "OpenBabel Fastsearch Index"
def display_data(self, trans, data, preview=False, filename=None,
to_ext=None, size=None, offset=None, **kwd):
to_ext=None, **kwd):
"""Apparently an old display method, but still gets called.
This allows us to format the data shown in the central pane via the "eye" icon.
lib/galaxy/datatypes/tabular.py
+14 -22
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@@ -58,31 +58,23 @@ class TabularData( data.Text ):
except:
return False
def get_chunk(self, trans, dataset, chunk):
ck_index = int(chunk)
f = open(dataset.file_name)
initial_offset = (ck_index * trans.app.config.display_chunk_size)
f.seek(initial_offset)
# If we aren't at the start of the file, seek to next newline. Do this better eventually.
if f.tell() != 0:
cursor = f.read(1)
while cursor and cursor != '\n':
def get_chunk(self, trans, dataset, offset=0, ck_size=None):
with open(dataset.file_name) as f:
f.seek(offset)
ck_data = f.read(ck_size or trans.app.config.display_chunk_size)
if ck_data and ck_data[-1] != '\n':
cursor = f.read(1)
read_start_offset = f.tell()
prechunk_skip = read_start_offset - initial_offset
# We subtract the prechunk skip out of the primary chunk read to avoid
# shifting the chunk tail onto a line it shouldn't have.
ck_data = f.read(trans.app.config.display_chunk_size - prechunk_skip)
cursor = f.read(1)
while cursor and ck_data[-1] != '\n':
ck_data += cursor
cursor = f.read(1)
return dumps( { 'ck_data': util.unicodify( ck_data ), 'ck_index': ck_index + 1 } )
while cursor and cursor != '\n':
ck_data += cursor
cursor = f.read(1)
last_read = f.tell()
return dumps( { 'ck_data': util.unicodify( ck_data ),
'offset': last_read } )
def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, chunk=None, **kwd):
def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, offset=None, ck_size=None, **kwd):
preview = util.string_as_bool( preview )
if chunk:
return self.get_chunk(trans, dataset, chunk)
if offset is not None:
return self.get_chunk(trans, dataset, offset, ck_size)
elif to_ext or not preview:
to_ext = to_ext or dataset.extension
return self._serve_raw(trans, dataset, to_ext)
lib/galaxy/datatypes/text.py
+6 -8
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@@ -127,19 +127,17 @@ class Ipynb( Json ):
except:
return False
def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, chunk=None, **kwd):
def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, **kwd):
config = trans.app.config
trust = getattr( config, 'trust_ipython_notebook_conversion', False )
if trust:
return self._display_data_trusted(trans, dataset, preview=preview, filename=filename, to_ext=to_ext, chunk=chunk, **kwd)
return self._display_data_trusted(trans, dataset, preview=preview, filename=filename, to_ext=to_ext, **kwd)
else:
return super(Ipynb, self).display_data( trans, dataset, preview=preview, filename=filename, to_ext=to_ext, chunk=chunk, **kwd )
return super(Ipynb, self).display_data( trans, dataset, preview=preview, filename=filename, to_ext=to_ext, **kwd )
def _display_data_trusted(self, trans, dataset, preview=False, filename=None, to_ext=None, chunk=None, **kwd):
def _display_data_trusted(self, trans, dataset, preview=False, filename=None, to_ext=None, **kwd):
preview = string_as_bool( preview )
if chunk:
return self.get_chunk(trans, dataset, chunk)
elif to_ext or not preview:
if to_ext or not preview:
return self._serve_raw(trans, dataset, to_ext)
else:
ofile_handle = tempfile.NamedTemporaryFile(delete=False)
@@ -426,7 +424,7 @@ class SnpEffDb( Text ):
# search data_dir/genome_version for files
regulation_pattern = 'regulation_(.+).bin'
# annotation files that are included in snpEff by a flag
annotations_dict = {'nextProt.bin' : '-nextprot', 'motif.bin': '-motif'}
annotations_dict = {'nextProt.bin': '-nextprot', 'motif.bin': '-motif'}
regulations = []
annotations = []
genome_version = None
lib/galaxy/webapps/galaxy/api/datasets.py
+4 -3
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@@ -278,7 +278,7 @@ class DatasetsController( BaseAPIController, UsesVisualizationMixin ):
@web.expose_api_raw_anonymous
def display( self, trans, history_content_id, history_id,
preview=False, filename=None, to_ext=None, chunk=None, raw=False, **kwd ):
preview=False, filename=None, to_ext=None, raw=False, **kwd ):
"""
GET /api/histories/{encoded_history_id}/contents/{encoded_content_id}/display
Displays history content (dataset).
@@ -297,7 +297,8 @@ class DatasetsController( BaseAPIController, UsesVisualizationMixin ):
if raw:
if filename and filename != 'index':
file_path = trans.app.object_store.get_filename( hda.dataset,
extra_dir=( 'dataset_%s_files' % hda.dataset.id ), alt_name=filename)
extra_dir=( 'dataset_%s_files' % hda.dataset.id ),
alt_name=filename)
else:
file_path = hda.file_name
rval = open( file_path )
@@ -306,7 +307,7 @@ class DatasetsController( BaseAPIController, UsesVisualizationMixin ):
display_kwd = kwd.copy()
if 'key' in display_kwd:
del display_kwd["key"]
rval = hda.datatype.display_data( trans, hda, preview, filename, to_ext, chunk, **display_kwd )
rval = hda.datatype.display_data( trans, hda, preview, filename, to_ext, **display_kwd )
except Exception as exception:
log.error( "Error getting display data for dataset (%s) from history (%s): %s",
lib/galaxy/webapps/galaxy/controllers/dataset.py
+8 -2
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@@ -232,11 +232,17 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesItemRatings, Uses
return trans.app.object_store.file_ready(data.dataset)
@web.expose
def display(self, trans, dataset_id=None, preview=False, filename=None, to_ext=None, chunk=None, **kwd):
def display(self, trans, dataset_id=None, preview=False, filename=None, to_ext=None, offset=None, ck_size=None, **kwd):
data = self._check_dataset(trans, dataset_id)
if not isinstance( data, trans.app.model.DatasetInstance ):
return data
return data.datatype.display_data(trans, data, preview, filename, to_ext, chunk, **kwd)
# Ensure offset is an integer before passing through to datatypes.
if offset:
offset = int(offset)
# Ensure ck_size is an integer before passing through to datatypes.
if ck_size:
ck_size = int(ck_size)
return data.datatype.display_data(trans, data, preview, filename, to_ext, offset=offset, ck_size=ck_size, **kwd)
@web.expose
def edit(self, trans, dataset_id=None, filename=None, hid=None, **kwd):
lib/galaxy/webapps/galaxy/controllers/tag.py
+3 -3
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@@ -128,9 +128,9 @@ class TagsController ( BaseUIController, UsesTagsMixin ):
# Create and return autocomplete data.
ac_data = "#Header|Your Tags\n"
for row in result_set:
tag = self.get_tag_handler( trans ).get_tag_by_id( trans, row[0] )
tag = self.get_tag_handler( trans ).get_tag_by_id( row[0] )
# Exclude tags that are already applied to the item.
if ( item is not None ) and ( self.get_tag_handler( trans ).item_has_tag( trans, trans.user, item, tag ) ):
if ( item is not None ) and ( self.get_tag_handler( trans ).item_has_tag( trans.user, item, tag ) ):
continue
# Add tag to autocomplete data. Use the most frequent name that user
# has employed for the tag.
@@ -146,7 +146,7 @@ class TagsController ( BaseUIController, UsesTagsMixin ):
tag_name_and_value = q.split( ":" )
tag_name = tag_name_and_value[0]
tag_value = tag_name_and_value[1]
tag = self.get_tag_handler( trans ).get_tag_by_name( trans, tag_name )
tag = self.get_tag_handler( trans ).get_tag_by_name( tag_name )
# Don't autocomplete if tag doesn't exist.
if tag is None:
return ""
static/maps/mvc/dataset/data.js.map
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static/scripts/bundled/analysis.bundled.js
+1 -1
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static/scripts/bundled/analysis.bundled.js.map
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static/scripts/bundled/libs.bundled.js.map
+1 -1
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static/scripts/mvc/dataset/data.js
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