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ga4gh/ga4gh-server
|
ga4gh/server/datamodel/obo_parser.py
|
OBOReader._add_to_ref
|
def _add_to_ref(self, rec_curr, line, lnum):
"""Add new fields to the current reference."""
# Written by DV Klopfenstein
# Examples of record lines containing ':' include:
# id: GO:0000002
# name: mitochondrial genome maintenance
# namespace: biological_process
# def: "The maintenance of ...
# is_a: GO:0007005 ! mitochondrion organization
mtch = re.match(r'^(\S+):\s*(\S.*)$', line)
if mtch:
field_name = mtch.group(1)
field_value = mtch.group(2)
if field_name == "id":
self._chk_none(rec_curr.id, lnum)
rec_curr.id = field_value
elif field_name == "alt_id":
rec_curr.alt_ids.append(field_value)
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self._chk_none(rec_curr.name, lnum)
rec_curr.name = field_value
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self._chk_none(rec_curr.namespace, lnum)
rec_curr.namespace = field_value
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rec_curr._parents.append(field_value.split()[0])
elif field_name == "is_obsolete" and field_value == "true":
rec_curr.is_obsolete = True
elif field_name in self.optional_attrs:
self.update_rec(rec_curr, field_name, field_value)
else:
self._die("UNEXPECTED FIELD CONTENT: {L}\n".format(L=line), lnum)
|
python
|
def _add_to_ref(self, rec_curr, line, lnum):
"""Add new fields to the current reference."""
# Written by DV Klopfenstein
# Examples of record lines containing ':' include:
# id: GO:0000002
# name: mitochondrial genome maintenance
# namespace: biological_process
# def: "The maintenance of ...
# is_a: GO:0007005 ! mitochondrion organization
mtch = re.match(r'^(\S+):\s*(\S.*)$', line)
if mtch:
field_name = mtch.group(1)
field_value = mtch.group(2)
if field_name == "id":
self._chk_none(rec_curr.id, lnum)
rec_curr.id = field_value
elif field_name == "alt_id":
rec_curr.alt_ids.append(field_value)
elif field_name == "name":
self._chk_none(rec_curr.name, lnum)
rec_curr.name = field_value
elif field_name == "namespace":
self._chk_none(rec_curr.namespace, lnum)
rec_curr.namespace = field_value
elif field_name == "is_a":
rec_curr._parents.append(field_value.split()[0])
elif field_name == "is_obsolete" and field_value == "true":
rec_curr.is_obsolete = True
elif field_name in self.optional_attrs:
self.update_rec(rec_curr, field_name, field_value)
else:
self._die("UNEXPECTED FIELD CONTENT: {L}\n".format(L=line), lnum)
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train
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https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datamodel/obo_parser.py#L130-L161
|
ga4gh/ga4gh-server
|
ga4gh/server/datamodel/obo_parser.py
|
OBOReader.update_rec
|
def update_rec(self, rec, name, value):
"""Update current GOTerm with optional record."""
# 'def' is a reserved word in python, do not use it as a Class attr.
if name == "def":
name = "defn"
# If we have a relationship, then we will split this into a further
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if hasattr(rec, name):
if name not in self.attrs_scalar:
if name not in self.attrs_nested:
getattr(rec, name).add(value)
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self._add_nested(rec, name, value)
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raise Exception("ATTR({NAME}) ALREADY SET({VAL})".format(
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else: # Initialize new GOTerm attr
if name in self.attrs_scalar:
setattr(rec, name, value)
elif name not in self.attrs_nested:
setattr(rec, name, set([value]))
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name = '_{:s}'.format(name)
setattr(rec, name, defaultdict(list))
self._add_nested(rec, name, value)
|
python
|
def update_rec(self, rec, name, value):
"""Update current GOTerm with optional record."""
# 'def' is a reserved word in python, do not use it as a Class attr.
if name == "def":
name = "defn"
# If we have a relationship, then we will split this into a further
# dictionary.
if hasattr(rec, name):
if name not in self.attrs_scalar:
if name not in self.attrs_nested:
getattr(rec, name).add(value)
else:
self._add_nested(rec, name, value)
else:
raise Exception("ATTR({NAME}) ALREADY SET({VAL})".format(
NAME=name, VAL=getattr(rec, name)))
else: # Initialize new GOTerm attr
if name in self.attrs_scalar:
setattr(rec, name, value)
elif name not in self.attrs_nested:
setattr(rec, name, set([value]))
else:
name = '_{:s}'.format(name)
setattr(rec, name, defaultdict(list))
self._add_nested(rec, name, value)
|
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Update current GOTerm with optional record.
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[
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datamodel/obo_parser.py#L163-L189
|
ga4gh/ga4gh-server
|
ga4gh/server/datamodel/obo_parser.py
|
OBOReader._add_to_typedef
|
def _add_to_typedef(self, typedef_curr, line, lnum):
"""Add new fields to the current typedef."""
mtch = re.match(r'^(\S+):\s*(\S.*)$', line)
if mtch:
field_name = mtch.group(1)
field_value = mtch.group(2).split('!')[0].rstrip()
if field_name == "id":
self._chk_none(typedef_curr.id, lnum)
typedef_curr.id = field_value
elif field_name == "name":
self._chk_none(typedef_curr.name, lnum)
typedef_curr.name = field_value
elif field_name == "transitive_over":
typedef_curr.transitive_over.append(field_value)
elif field_name == "inverse_of":
self._chk_none(typedef_curr.inverse_of, lnum)
typedef_curr.inverse_of = field_value
# Note: there are other tags that aren't imported here.
else:
self._die("UNEXPECTED FIELD CONTENT: {L}\n".format(L=line), lnum)
|
python
|
def _add_to_typedef(self, typedef_curr, line, lnum):
"""Add new fields to the current typedef."""
mtch = re.match(r'^(\S+):\s*(\S.*)$', line)
if mtch:
field_name = mtch.group(1)
field_value = mtch.group(2).split('!')[0].rstrip()
if field_name == "id":
self._chk_none(typedef_curr.id, lnum)
typedef_curr.id = field_value
elif field_name == "name":
self._chk_none(typedef_curr.name, lnum)
typedef_curr.name = field_value
elif field_name == "transitive_over":
typedef_curr.transitive_over.append(field_value)
elif field_name == "inverse_of":
self._chk_none(typedef_curr.inverse_of, lnum)
typedef_curr.inverse_of = field_value
# Note: there are other tags that aren't imported here.
else:
self._die("UNEXPECTED FIELD CONTENT: {L}\n".format(L=line), lnum)
|
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Add new fields to the current typedef.
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[
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] |
train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datamodel/obo_parser.py#L191-L211
|
ga4gh/ga4gh-server
|
ga4gh/server/datamodel/obo_parser.py
|
OBOReader._add_nested
|
def _add_nested(self, rec, name, value):
"""Adds a term's nested attributes."""
# Remove comments and split term into typedef / target term.
(typedef, target_term) = value.split('!')[0].rstrip().split(' ')
# Save the nested term.
getattr(rec, name)[typedef].append(target_term)
|
python
|
def _add_nested(self, rec, name, value):
"""Adds a term's nested attributes."""
# Remove comments and split term into typedef / target term.
(typedef, target_term) = value.split('!')[0].rstrip().split(' ')
# Save the nested term.
getattr(rec, name)[typedef].append(target_term)
|
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[
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datamodel/obo_parser.py#L213-L219
|
ga4gh/ga4gh-server
|
ga4gh/server/datamodel/obo_parser.py
|
OBOReader._init_optional_attrs
|
def _init_optional_attrs(self, optional_attrs):
"""Prepare to store data from user-desired optional fields.
Not loading these optional fields by default saves in space and speed.
But allow the possibility for saving these fields, if the user desires,
Including:
comment consider def is_class_level is_metadata_tag is_transitive
relationship replaced_by subset synonym transitive_over xref
"""
# Written by DV Klopfenstein
# Required attributes are always loaded. All others are optionally loaded.
self.attrs_req = ['id', 'alt_id', 'name', 'namespace', 'is_a', 'is_obsolete']
self.attrs_scalar = ['comment', 'defn',
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self.attrs_nested = frozenset(['relationship'])
# Allow user to specify either: 'def' or 'defn'
# 'def' is an obo field name, but 'defn' is legal Python attribute name
fnc = lambda aopt: aopt if aopt != "defn" else "def"
if optional_attrs is None:
optional_attrs = []
elif isinstance(optional_attrs, str):
optional_attrs = [fnc(optional_attrs)] if optional_attrs not in self.attrs_req else []
elif isinstance(optional_attrs, list) or isinstance(optional_attrs, set):
optional_attrs = set([fnc(f) for f in optional_attrs if f not in self.attrs_req])
else:
raise Exception("optional_attrs arg MUST BE A str, list, or set.")
self.optional_attrs = optional_attrs
|
python
|
def _init_optional_attrs(self, optional_attrs):
"""Prepare to store data from user-desired optional fields.
Not loading these optional fields by default saves in space and speed.
But allow the possibility for saving these fields, if the user desires,
Including:
comment consider def is_class_level is_metadata_tag is_transitive
relationship replaced_by subset synonym transitive_over xref
"""
# Written by DV Klopfenstein
# Required attributes are always loaded. All others are optionally loaded.
self.attrs_req = ['id', 'alt_id', 'name', 'namespace', 'is_a', 'is_obsolete']
self.attrs_scalar = ['comment', 'defn',
'is_class_level', 'is_metadata_tag',
'is_transitive', 'transitive_over']
self.attrs_nested = frozenset(['relationship'])
# Allow user to specify either: 'def' or 'defn'
# 'def' is an obo field name, but 'defn' is legal Python attribute name
fnc = lambda aopt: aopt if aopt != "defn" else "def"
if optional_attrs is None:
optional_attrs = []
elif isinstance(optional_attrs, str):
optional_attrs = [fnc(optional_attrs)] if optional_attrs not in self.attrs_req else []
elif isinstance(optional_attrs, list) or isinstance(optional_attrs, set):
optional_attrs = set([fnc(f) for f in optional_attrs if f not in self.attrs_req])
else:
raise Exception("optional_attrs arg MUST BE A str, list, or set.")
self.optional_attrs = optional_attrs
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Not loading these optional fields by default saves in space and speed.
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Including:
comment consider def is_class_level is_metadata_tag is_transitive
relationship replaced_by subset synonym transitive_over xref
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[
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datamodel/obo_parser.py#L221-L248
|
ga4gh/ga4gh-server
|
ga4gh/server/datamodel/obo_parser.py
|
OBOReader._die
|
def _die(self, msg, lnum):
"""Raise an Exception if file read is unexpected."""
raise Exception("**FATAL {FILE}({LNUM}): {MSG}\n".format(
FILE=self.obo_file, LNUM=lnum, MSG=msg))
|
python
|
def _die(self, msg, lnum):
"""Raise an Exception if file read is unexpected."""
raise Exception("**FATAL {FILE}({LNUM}): {MSG}\n".format(
FILE=self.obo_file, LNUM=lnum, MSG=msg))
|
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[
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datamodel/obo_parser.py#L251-L254
|
ga4gh/ga4gh-server
|
ga4gh/server/datamodel/obo_parser.py
|
GOTerm.write_hier_rec
|
def write_hier_rec(self, gos_printed, out=sys.stdout,
len_dash=1, max_depth=None, num_child=None, short_prt=False,
include_only=None, go_marks=None,
depth=1, dp="-"):
"""Write hierarchy for a GO Term record."""
# Added by DV Klopfenstein
GO_id = self.id
# Shortens hierarchy report by only printing the hierarchy
# for the sub-set of user-specified GO terms which are connected.
if include_only is not None and GO_id not in include_only:
return
nrp = short_prt and GO_id in gos_printed
if go_marks is not None:
out.write('{} '.format('>' if GO_id in go_marks else ' '))
if len_dash is not None:
# Default character indicating hierarchy level is '-'.
# '=' is used to indicate a hierarchical path printed in detail previously.
letter = '-' if not nrp or not self.children else '='
dp = ''.join([letter]*depth)
out.write('{DASHES:{N}} '.format(DASHES=dp, N=len_dash))
if num_child is not None:
out.write('{N:>5} '.format(N=len(self.get_all_children())))
out.write('{GO}\tL-{L:>02}\tD-{D:>02}\t{desc}\n'.format(
GO=self.id, L=self.level, D=self.depth, desc=self.name))
# Track GOs previously printed only if needed
if short_prt:
gos_printed.add(GO_id)
# Do not print hierarchy below this turn if it has already been printed
if nrp:
return
depth += 1
if max_depth is not None and depth > max_depth:
return
for p in self.children:
p.write_hier_rec(gos_printed, out, len_dash, max_depth, num_child, short_prt,
include_only, go_marks,
depth, dp)
|
python
|
def write_hier_rec(self, gos_printed, out=sys.stdout,
len_dash=1, max_depth=None, num_child=None, short_prt=False,
include_only=None, go_marks=None,
depth=1, dp="-"):
"""Write hierarchy for a GO Term record."""
# Added by DV Klopfenstein
GO_id = self.id
# Shortens hierarchy report by only printing the hierarchy
# for the sub-set of user-specified GO terms which are connected.
if include_only is not None and GO_id not in include_only:
return
nrp = short_prt and GO_id in gos_printed
if go_marks is not None:
out.write('{} '.format('>' if GO_id in go_marks else ' '))
if len_dash is not None:
# Default character indicating hierarchy level is '-'.
# '=' is used to indicate a hierarchical path printed in detail previously.
letter = '-' if not nrp or not self.children else '='
dp = ''.join([letter]*depth)
out.write('{DASHES:{N}} '.format(DASHES=dp, N=len_dash))
if num_child is not None:
out.write('{N:>5} '.format(N=len(self.get_all_children())))
out.write('{GO}\tL-{L:>02}\tD-{D:>02}\t{desc}\n'.format(
GO=self.id, L=self.level, D=self.depth, desc=self.name))
# Track GOs previously printed only if needed
if short_prt:
gos_printed.add(GO_id)
# Do not print hierarchy below this turn if it has already been printed
if nrp:
return
depth += 1
if max_depth is not None and depth > max_depth:
return
for p in self.children:
p.write_hier_rec(gos_printed, out, len_dash, max_depth, num_child, short_prt,
include_only, go_marks,
depth, dp)
|
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Write hierarchy for a GO Term record.
|
[
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"GO",
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"record",
"."
] |
train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datamodel/obo_parser.py#L349-L385
|
ga4gh/ga4gh-server
|
ga4gh/server/datamodel/obo_parser.py
|
GODag.write_hier_all
|
def write_hier_all(self, out=sys.stdout,
len_dash=1, max_depth=None, num_child=None, short_prt=False):
"""Write hierarchy for all GO Terms in obo file."""
# Print: [biological_process, molecular_function, and cellular_component]
for go_id in ['GO:0008150', 'GO:0003674', 'GO:0005575']:
self.write_hier(go_id, out, len_dash, max_depth, num_child, short_prt, None)
|
python
|
def write_hier_all(self, out=sys.stdout,
len_dash=1, max_depth=None, num_child=None, short_prt=False):
"""Write hierarchy for all GO Terms in obo file."""
# Print: [biological_process, molecular_function, and cellular_component]
for go_id in ['GO:0008150', 'GO:0003674', 'GO:0005575']:
self.write_hier(go_id, out, len_dash, max_depth, num_child, short_prt, None)
|
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Write hierarchy for all GO Terms in obo file.
|
[
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datamodel/obo_parser.py#L492-L497
|
ga4gh/ga4gh-server
|
ga4gh/server/datamodel/obo_parser.py
|
GODag.write_hier
|
def write_hier(self, GO_id, out=sys.stdout,
len_dash=1, max_depth=None, num_child=None, short_prt=False,
include_only=None, go_marks=None):
"""Write hierarchy for a GO Term."""
gos_printed = set()
self[GO_id].write_hier_rec(gos_printed, out, len_dash, max_depth, num_child,
short_prt, include_only, go_marks)
|
python
|
def write_hier(self, GO_id, out=sys.stdout,
len_dash=1, max_depth=None, num_child=None, short_prt=False,
include_only=None, go_marks=None):
"""Write hierarchy for a GO Term."""
gos_printed = set()
self[GO_id].write_hier_rec(gos_printed, out, len_dash, max_depth, num_child,
short_prt, include_only, go_marks)
|
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|
[
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] |
train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datamodel/obo_parser.py#L499-L505
|
ga4gh/ga4gh-server
|
ga4gh/server/datamodel/obo_parser.py
|
GODag.paths_to_top
|
def paths_to_top(self, term):
""" Returns all possible paths to the root node
Each path includes the term given. The order of the path is
top -> bottom, i.e. it starts with the root and ends with the
given term (inclusively).
Parameters:
-----------
- term:
the id of the GO term, where the paths begin (i.e. the
accession 'GO:0003682')
Returns:
--------
- a list of lists of GO Terms
"""
# error handling consistent with original authors
if term not in self:
print("Term %s not found!" % term, file=sys.stderr)
return
def _paths_to_top_recursive(rec):
if rec.level == 0:
return [[rec]]
paths = []
for parent in rec.parents:
top_paths = _paths_to_top_recursive(parent)
for top_path in top_paths:
top_path.append(rec)
paths.append(top_path)
return paths
go_term = self[term]
return _paths_to_top_recursive(go_term)
|
python
|
def paths_to_top(self, term):
""" Returns all possible paths to the root node
Each path includes the term given. The order of the path is
top -> bottom, i.e. it starts with the root and ends with the
given term (inclusively).
Parameters:
-----------
- term:
the id of the GO term, where the paths begin (i.e. the
accession 'GO:0003682')
Returns:
--------
- a list of lists of GO Terms
"""
# error handling consistent with original authors
if term not in self:
print("Term %s not found!" % term, file=sys.stderr)
return
def _paths_to_top_recursive(rec):
if rec.level == 0:
return [[rec]]
paths = []
for parent in rec.parents:
top_paths = _paths_to_top_recursive(parent)
for top_path in top_paths:
top_path.append(rec)
paths.append(top_path)
return paths
go_term = self[term]
return _paths_to_top_recursive(go_term)
|
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Returns all possible paths to the root node
Each path includes the term given. The order of the path is
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given term (inclusively).
Parameters:
-----------
- term:
the id of the GO term, where the paths begin (i.e. the
accession 'GO:0003682')
Returns:
--------
- a list of lists of GO Terms
|
[
"Returns",
"all",
"possible",
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"to",
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] |
train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datamodel/obo_parser.py#L522-L556
|
ga4gh/ga4gh-server
|
ga4gh/server/datamodel/obo_parser.py
|
GODag.make_graph_pydot
|
def make_graph_pydot(self, recs, nodecolor,
edgecolor, dpi,
draw_parents=True, draw_children=True):
"""draw AMIGO style network, lineage containing one query record."""
import pydot
G = pydot.Dot(graph_type='digraph', dpi="{}".format(dpi)) # Directed Graph
edgeset = set()
usr_ids = [rec.id for rec in recs]
for rec in recs:
if draw_parents:
edgeset.update(rec.get_all_parent_edges())
if draw_children:
edgeset.update(rec.get_all_child_edges())
lw = self._label_wrap
rec_id_set = set([rec_id for endpts in edgeset for rec_id in endpts])
nodes = {str(ID):pydot.Node(
lw(ID).replace("GO:",""), # Node name
shape="box",
style="rounded, filled",
# Highlight query terms in plum:
fillcolor="beige" if ID not in usr_ids else "plum",
color=nodecolor)
for ID in rec_id_set}
# add nodes explicitly via add_node
for rec_id, node in nodes.items():
G.add_node(node)
for src, target in edgeset:
# default layout in graphviz is top->bottom, so we invert
# the direction and plot using dir="back"
G.add_edge(pydot.Edge(nodes[target], nodes[src],
shape="normal",
color=edgecolor,
label="is_a",
dir="back"))
return G
|
python
|
def make_graph_pydot(self, recs, nodecolor,
edgecolor, dpi,
draw_parents=True, draw_children=True):
"""draw AMIGO style network, lineage containing one query record."""
import pydot
G = pydot.Dot(graph_type='digraph', dpi="{}".format(dpi)) # Directed Graph
edgeset = set()
usr_ids = [rec.id for rec in recs]
for rec in recs:
if draw_parents:
edgeset.update(rec.get_all_parent_edges())
if draw_children:
edgeset.update(rec.get_all_child_edges())
lw = self._label_wrap
rec_id_set = set([rec_id for endpts in edgeset for rec_id in endpts])
nodes = {str(ID):pydot.Node(
lw(ID).replace("GO:",""), # Node name
shape="box",
style="rounded, filled",
# Highlight query terms in plum:
fillcolor="beige" if ID not in usr_ids else "plum",
color=nodecolor)
for ID in rec_id_set}
# add nodes explicitly via add_node
for rec_id, node in nodes.items():
G.add_node(node)
for src, target in edgeset:
# default layout in graphviz is top->bottom, so we invert
# the direction and plot using dir="back"
G.add_edge(pydot.Edge(nodes[target], nodes[src],
shape="normal",
color=edgecolor,
label="is_a",
dir="back"))
return G
|
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draw AMIGO style network, lineage containing one query record.
|
[
"draw",
"AMIGO",
"style",
"network",
"lineage",
"containing",
"one",
"query",
"record",
"."
] |
train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datamodel/obo_parser.py#L563-L601
|
ga4gh/ga4gh-server
|
ga4gh/server/sqlite_backend.py
|
sqliteRowsToDicts
|
def sqliteRowsToDicts(sqliteRows):
"""
Unpacks sqlite rows as returned by fetchall
into an array of simple dicts.
:param sqliteRows: array of rows returned from fetchall DB call
:return: array of dicts, keyed by the column names.
"""
return map(lambda r: dict(zip(r.keys(), r)), sqliteRows)
|
python
|
def sqliteRowsToDicts(sqliteRows):
"""
Unpacks sqlite rows as returned by fetchall
into an array of simple dicts.
:param sqliteRows: array of rows returned from fetchall DB call
:return: array of dicts, keyed by the column names.
"""
return map(lambda r: dict(zip(r.keys(), r)), sqliteRows)
|
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Unpacks sqlite rows as returned by fetchall
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/sqlite_backend.py#L13-L21
|
ga4gh/ga4gh-server
|
ga4gh/server/sqlite_backend.py
|
limitsSql
|
def limitsSql(startIndex=0, maxResults=0):
"""
Construct a SQL LIMIT clause
"""
if startIndex and maxResults:
return " LIMIT {}, {}".format(startIndex, maxResults)
elif startIndex:
raise Exception("startIndex was provided, but maxResults was not")
elif maxResults:
return " LIMIT {}".format(maxResults)
else:
return ""
|
python
|
def limitsSql(startIndex=0, maxResults=0):
"""
Construct a SQL LIMIT clause
"""
if startIndex and maxResults:
return " LIMIT {}, {}".format(startIndex, maxResults)
elif startIndex:
raise Exception("startIndex was provided, but maxResults was not")
elif maxResults:
return " LIMIT {}".format(maxResults)
else:
return ""
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Construct a SQL LIMIT clause
|
[
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] |
train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/sqlite_backend.py#L35-L46
|
ga4gh/ga4gh-server
|
ga4gh/server/sqlite_backend.py
|
iterativeFetch
|
def iterativeFetch(query, batchSize=default_batch_size):
"""
Returns rows of a sql fetch query on demand
"""
while True:
rows = query.fetchmany(batchSize)
if not rows:
break
rowDicts = sqliteRowsToDicts(rows)
for rowDict in rowDicts:
yield rowDict
|
python
|
def iterativeFetch(query, batchSize=default_batch_size):
"""
Returns rows of a sql fetch query on demand
"""
while True:
rows = query.fetchmany(batchSize)
if not rows:
break
rowDicts = sqliteRowsToDicts(rows)
for rowDict in rowDicts:
yield rowDict
|
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Returns rows of a sql fetch query on demand
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[
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/sqlite_backend.py#L52-L62
|
ga4gh/ga4gh-server
|
ga4gh/server/paging.py
|
_parsePageToken
|
def _parsePageToken(pageToken, numValues):
"""
Parses the specified pageToken and returns a list of the specified
number of values. Page tokens are assumed to consist of a fixed
number of integers seperated by colons. If the page token does
not conform to this specification, raise a InvalidPageToken
exception.
"""
tokens = pageToken.split(":")
if len(tokens) != numValues:
msg = "Invalid number of values in page token"
raise exceptions.BadPageTokenException(msg)
try:
values = map(int, tokens)
except ValueError:
msg = "Malformed integers in page token"
raise exceptions.BadPageTokenException(msg)
return values
|
python
|
def _parsePageToken(pageToken, numValues):
"""
Parses the specified pageToken and returns a list of the specified
number of values. Page tokens are assumed to consist of a fixed
number of integers seperated by colons. If the page token does
not conform to this specification, raise a InvalidPageToken
exception.
"""
tokens = pageToken.split(":")
if len(tokens) != numValues:
msg = "Invalid number of values in page token"
raise exceptions.BadPageTokenException(msg)
try:
values = map(int, tokens)
except ValueError:
msg = "Malformed integers in page token"
raise exceptions.BadPageTokenException(msg)
return values
|
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] |
train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/paging.py#L13-L30
|
ga4gh/ga4gh-server
|
ga4gh/server/paging.py
|
_parseIntegerArgument
|
def _parseIntegerArgument(args, key, defaultValue):
"""
Attempts to parse the specified key in the specified argument
dictionary into an integer. If the argument cannot be parsed,
raises a BadRequestIntegerException. If the key is not present,
return the specified default value.
"""
ret = defaultValue
try:
if key in args:
try:
ret = int(args[key])
except ValueError:
raise exceptions.BadRequestIntegerException(key, args[key])
except TypeError:
raise Exception((key, args))
return ret
|
python
|
def _parseIntegerArgument(args, key, defaultValue):
"""
Attempts to parse the specified key in the specified argument
dictionary into an integer. If the argument cannot be parsed,
raises a BadRequestIntegerException. If the key is not present,
return the specified default value.
"""
ret = defaultValue
try:
if key in args:
try:
ret = int(args[key])
except ValueError:
raise exceptions.BadRequestIntegerException(key, args[key])
except TypeError:
raise Exception((key, args))
return ret
|
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/paging.py#L33-L49
|
ga4gh/ga4gh-server
|
ga4gh/server/paging.py
|
IntervalIterator._initialiseIteration
|
def _initialiseIteration(self):
"""
Starts a new iteration.
"""
self._searchIterator = self._search(
self._request.start,
self._request.end if self._request.end != 0 else None)
self._currentObject = next(self._searchIterator, None)
if self._currentObject is not None:
self._nextObject = next(self._searchIterator, None)
self._searchAnchor = self._request.start
self._distanceFromAnchor = 0
firstObjectStart = self._getStart(self._currentObject)
if firstObjectStart > self._request.start:
self._searchAnchor = firstObjectStart
|
python
|
def _initialiseIteration(self):
"""
Starts a new iteration.
"""
self._searchIterator = self._search(
self._request.start,
self._request.end if self._request.end != 0 else None)
self._currentObject = next(self._searchIterator, None)
if self._currentObject is not None:
self._nextObject = next(self._searchIterator, None)
self._searchAnchor = self._request.start
self._distanceFromAnchor = 0
firstObjectStart = self._getStart(self._currentObject)
if firstObjectStart > self._request.start:
self._searchAnchor = firstObjectStart
|
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Starts a new iteration.
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[
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/paging.py#L83-L97
|
ga4gh/ga4gh-server
|
ga4gh/server/paging.py
|
IntervalIterator._pickUpIteration
|
def _pickUpIteration(self, searchAnchor, objectsToSkip):
"""
Picks up iteration from a previously provided page token. There are two
different phases here:
1) We are iterating over the initial set of intervals in which start
is < the search start coorindate.
2) We are iterating over the remaining intervals in which start >= to
the search start coordinate.
"""
self._searchAnchor = searchAnchor
self._distanceFromAnchor = objectsToSkip
self._searchIterator = self._search(
searchAnchor,
self._request.end if self._request.end != 0 else None)
obj = next(self._searchIterator)
if searchAnchor == self._request.start:
# This is the initial set of intervals, we just skip forward
# objectsToSkip positions
for _ in range(objectsToSkip):
obj = next(self._searchIterator)
else:
# Now, we are past this initial set of intervals.
# First, we need to skip forward over the intervals where
# start < searchAnchor, as we've seen these already.
while self._getStart(obj) < searchAnchor:
obj = next(self._searchIterator)
# Now, we skip over objectsToSkip objects such that
# start == searchAnchor
for _ in range(objectsToSkip):
if self._getStart(obj) != searchAnchor:
raise exceptions.BadPageTokenException
obj = next(self._searchIterator)
self._currentObject = obj
self._nextObject = next(self._searchIterator, None)
|
python
|
def _pickUpIteration(self, searchAnchor, objectsToSkip):
"""
Picks up iteration from a previously provided page token. There are two
different phases here:
1) We are iterating over the initial set of intervals in which start
is < the search start coorindate.
2) We are iterating over the remaining intervals in which start >= to
the search start coordinate.
"""
self._searchAnchor = searchAnchor
self._distanceFromAnchor = objectsToSkip
self._searchIterator = self._search(
searchAnchor,
self._request.end if self._request.end != 0 else None)
obj = next(self._searchIterator)
if searchAnchor == self._request.start:
# This is the initial set of intervals, we just skip forward
# objectsToSkip positions
for _ in range(objectsToSkip):
obj = next(self._searchIterator)
else:
# Now, we are past this initial set of intervals.
# First, we need to skip forward over the intervals where
# start < searchAnchor, as we've seen these already.
while self._getStart(obj) < searchAnchor:
obj = next(self._searchIterator)
# Now, we skip over objectsToSkip objects such that
# start == searchAnchor
for _ in range(objectsToSkip):
if self._getStart(obj) != searchAnchor:
raise exceptions.BadPageTokenException
obj = next(self._searchIterator)
self._currentObject = obj
self._nextObject = next(self._searchIterator, None)
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/paging.py#L99-L132
|
ga4gh/ga4gh-server
|
ga4gh/server/paging.py
|
IntervalIterator.next
|
def next(self):
"""
Returns the next (object, nextPageToken) pair.
"""
if self._currentObject is None:
raise StopIteration()
nextPageToken = None
if self._nextObject is not None:
start = self._getStart(self._nextObject)
# If start > the search anchor, move the search anchor. Otherwise,
# increment the distance from the anchor.
if start > self._searchAnchor:
self._searchAnchor = start
self._distanceFromAnchor = 0
else:
self._distanceFromAnchor += 1
nextPageToken = "{}:{}".format(
self._searchAnchor, self._distanceFromAnchor)
ret = self._extractProtocolObject(self._currentObject), nextPageToken
self._currentObject = self._nextObject
self._nextObject = next(self._searchIterator, None)
return ret
|
python
|
def next(self):
"""
Returns the next (object, nextPageToken) pair.
"""
if self._currentObject is None:
raise StopIteration()
nextPageToken = None
if self._nextObject is not None:
start = self._getStart(self._nextObject)
# If start > the search anchor, move the search anchor. Otherwise,
# increment the distance from the anchor.
if start > self._searchAnchor:
self._searchAnchor = start
self._distanceFromAnchor = 0
else:
self._distanceFromAnchor += 1
nextPageToken = "{}:{}".format(
self._searchAnchor, self._distanceFromAnchor)
ret = self._extractProtocolObject(self._currentObject), nextPageToken
self._currentObject = self._nextObject
self._nextObject = next(self._searchIterator, None)
return ret
|
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/paging.py#L134-L155
|
ga4gh/ga4gh-server
|
ga4gh/server/paging.py
|
VariantAnnotationsIntervalIterator.filterVariantAnnotation
|
def filterVariantAnnotation(self, vann):
"""
Returns true when an annotation should be included.
"""
# TODO reintroduce feature ID search
ret = False
if len(self._effects) != 0 and not vann.transcript_effects:
return False
elif len(self._effects) == 0:
return True
for teff in vann.transcript_effects:
if self.filterEffect(teff):
ret = True
return ret
|
python
|
def filterVariantAnnotation(self, vann):
"""
Returns true when an annotation should be included.
"""
# TODO reintroduce feature ID search
ret = False
if len(self._effects) != 0 and not vann.transcript_effects:
return False
elif len(self._effects) == 0:
return True
for teff in vann.transcript_effects:
if self.filterEffect(teff):
ret = True
return ret
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train
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https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/paging.py#L246-L259
|
ga4gh/ga4gh-server
|
ga4gh/server/paging.py
|
VariantAnnotationsIntervalIterator.filterEffect
|
def filterEffect(self, teff):
"""
Returns true when any of the transcript effects
are present in the request.
"""
ret = False
for effect in teff.effects:
ret = self._matchAnyEffects(effect) or ret
return ret
|
python
|
def filterEffect(self, teff):
"""
Returns true when any of the transcript effects
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"""
ret = False
for effect in teff.effects:
ret = self._matchAnyEffects(effect) or ret
return ret
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train
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https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/paging.py#L261-L269
|
ga4gh/ga4gh-server
|
ga4gh/server/paging.py
|
VariantAnnotationsIntervalIterator._checkIdEquality
|
def _checkIdEquality(self, requestedEffect, effect):
"""
Tests whether a requested effect and an effect
present in an annotation are equal.
"""
return self._idPresent(requestedEffect) and (
effect.term_id == requestedEffect.term_id)
|
python
|
def _checkIdEquality(self, requestedEffect, effect):
"""
Tests whether a requested effect and an effect
present in an annotation are equal.
"""
return self._idPresent(requestedEffect) and (
effect.term_id == requestedEffect.term_id)
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/paging.py#L271-L277
|
ga4gh/ga4gh-server
|
scripts/glue.py
|
ga4ghImportGlue
|
def ga4ghImportGlue():
"""
Call this method before importing a ga4gh module in the scripts dir.
Otherwise, you will be using the installed package instead of
the development package.
Assumes a certain directory structure.
"""
path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
sys.path.append(path)
|
python
|
def ga4ghImportGlue():
"""
Call this method before importing a ga4gh module in the scripts dir.
Otherwise, you will be using the installed package instead of
the development package.
Assumes a certain directory structure.
"""
path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
sys.path.append(path)
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/scripts/glue.py#L16-L24
|
ga4gh/ga4gh-server
|
ga4gh/server/datamodel/__init__.py
|
PysamFileHandleCache._update
|
def _update(self, dataFile, handle):
"""
Update the priority of the file handle. The element is first
removed and then added to the left of the deque.
"""
self._cache.remove((dataFile, handle))
self._add(dataFile, handle)
|
python
|
def _update(self, dataFile, handle):
"""
Update the priority of the file handle. The element is first
removed and then added to the left of the deque.
"""
self._cache.remove((dataFile, handle))
self._add(dataFile, handle)
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train
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https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datamodel/__init__.py#L50-L56
|
ga4gh/ga4gh-server
|
ga4gh/server/datamodel/__init__.py
|
PysamFileHandleCache._removeLru
|
def _removeLru(self):
"""
Remove the least recently used file handle from the cache.
The pop method removes an element from the right of the deque.
Returns the name of the file that has been removed.
"""
(dataFile, handle) = self._cache.pop()
handle.close()
return dataFile
|
python
|
def _removeLru(self):
"""
Remove the least recently used file handle from the cache.
The pop method removes an element from the right of the deque.
Returns the name of the file that has been removed.
"""
(dataFile, handle) = self._cache.pop()
handle.close()
return dataFile
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train
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https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datamodel/__init__.py#L58-L66
|
ga4gh/ga4gh-server
|
ga4gh/server/datamodel/__init__.py
|
PysamFileHandleCache.getFileHandle
|
def getFileHandle(self, dataFile, openMethod):
"""
Returns handle associated to the filename. If the file is
already opened, update its priority in the cache and return
its handle. Otherwise, open the file using openMethod, store
it in the cache and return the corresponding handle.
"""
if dataFile in self._memoTable:
handle = self._memoTable[dataFile]
self._update(dataFile, handle)
return handle
else:
try:
handle = openMethod(dataFile)
except ValueError:
raise exceptions.FileOpenFailedException(dataFile)
self._memoTable[dataFile] = handle
self._add(dataFile, handle)
if len(self._memoTable) > self._maxCacheSize:
dataFile = self._removeLru()
del self._memoTable[dataFile]
return handle
|
python
|
def getFileHandle(self, dataFile, openMethod):
"""
Returns handle associated to the filename. If the file is
already opened, update its priority in the cache and return
its handle. Otherwise, open the file using openMethod, store
it in the cache and return the corresponding handle.
"""
if dataFile in self._memoTable:
handle = self._memoTable[dataFile]
self._update(dataFile, handle)
return handle
else:
try:
handle = openMethod(dataFile)
except ValueError:
raise exceptions.FileOpenFailedException(dataFile)
self._memoTable[dataFile] = handle
self._add(dataFile, handle)
if len(self._memoTable) > self._maxCacheSize:
dataFile = self._removeLru()
del self._memoTable[dataFile]
return handle
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train
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https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datamodel/__init__.py#L68-L90
|
ga4gh/ga4gh-server
|
ga4gh/server/datamodel/__init__.py
|
CompoundId.join
|
def join(cls, splits):
"""
Join an array of ids into a compound id string
"""
segments = []
for split in splits:
segments.append('"{}",'.format(split))
if len(segments) > 0:
segments[-1] = segments[-1][:-1]
jsonString = '[{}]'.format(''.join(segments))
return jsonString
|
python
|
def join(cls, splits):
"""
Join an array of ids into a compound id string
"""
segments = []
for split in splits:
segments.append('"{}",'.format(split))
if len(segments) > 0:
segments[-1] = segments[-1][:-1]
jsonString = '[{}]'.format(''.join(segments))
return jsonString
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datamodel/__init__.py#L172-L182
|
ga4gh/ga4gh-server
|
ga4gh/server/datamodel/__init__.py
|
CompoundId.parse
|
def parse(cls, compoundIdStr):
"""
Parses the specified compoundId string and returns an instance
of this CompoundId class.
:raises: An ObjectWithIdNotFoundException if parsing fails. This is
because this method is a client-facing method, and if a malformed
identifier (under our internal rules) is provided, the response should
be that the identifier does not exist.
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if not isinstance(compoundIdStr, basestring):
raise exceptions.BadIdentifierException(compoundIdStr)
try:
deobfuscated = cls.deobfuscate(compoundIdStr)
except TypeError:
# When a string that cannot be converted to base64 is passed
# as an argument, b64decode raises a TypeError. We must treat
# this as an ID not found error.
raise exceptions.ObjectWithIdNotFoundException(compoundIdStr)
try:
encodedSplits = cls.split(deobfuscated)
splits = [cls.decode(split) for split in encodedSplits]
except (UnicodeDecodeError, ValueError):
# Sometimes base64 decoding succeeds but we're left with
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raise exceptions.ObjectWithIdNotFoundException(compoundIdStr)
# pull the differentiator out of the splits before instantiating
# the class, if the differentiator exists
fieldsLength = len(cls.fields)
if cls.differentiator is not None:
differentiatorIndex = cls.fields.index(
cls.differentiatorFieldName)
if differentiatorIndex < len(splits):
del splits[differentiatorIndex]
else:
raise exceptions.ObjectWithIdNotFoundException(
compoundIdStr)
fieldsLength -= 1
if len(splits) != fieldsLength:
raise exceptions.ObjectWithIdNotFoundException(compoundIdStr)
return cls(None, *splits)
|
python
|
def parse(cls, compoundIdStr):
"""
Parses the specified compoundId string and returns an instance
of this CompoundId class.
:raises: An ObjectWithIdNotFoundException if parsing fails. This is
because this method is a client-facing method, and if a malformed
identifier (under our internal rules) is provided, the response should
be that the identifier does not exist.
"""
if not isinstance(compoundIdStr, basestring):
raise exceptions.BadIdentifierException(compoundIdStr)
try:
deobfuscated = cls.deobfuscate(compoundIdStr)
except TypeError:
# When a string that cannot be converted to base64 is passed
# as an argument, b64decode raises a TypeError. We must treat
# this as an ID not found error.
raise exceptions.ObjectWithIdNotFoundException(compoundIdStr)
try:
encodedSplits = cls.split(deobfuscated)
splits = [cls.decode(split) for split in encodedSplits]
except (UnicodeDecodeError, ValueError):
# Sometimes base64 decoding succeeds but we're left with
# unicode gibberish. This is also and IdNotFound.
raise exceptions.ObjectWithIdNotFoundException(compoundIdStr)
# pull the differentiator out of the splits before instantiating
# the class, if the differentiator exists
fieldsLength = len(cls.fields)
if cls.differentiator is not None:
differentiatorIndex = cls.fields.index(
cls.differentiatorFieldName)
if differentiatorIndex < len(splits):
del splits[differentiatorIndex]
else:
raise exceptions.ObjectWithIdNotFoundException(
compoundIdStr)
fieldsLength -= 1
if len(splits) != fieldsLength:
raise exceptions.ObjectWithIdNotFoundException(compoundIdStr)
return cls(None, *splits)
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datamodel/__init__.py#L207-L247
|
ga4gh/ga4gh-server
|
ga4gh/server/datamodel/__init__.py
|
CompoundId.obfuscate
|
def obfuscate(cls, idStr):
"""
Mildly obfuscates the specified ID string in an easily reversible
fashion. This is not intended for security purposes, but rather to
dissuade users from depending on our internal ID structures.
"""
return unicode(base64.urlsafe_b64encode(
idStr.encode('utf-8')).replace(b'=', b''))
|
python
|
def obfuscate(cls, idStr):
"""
Mildly obfuscates the specified ID string in an easily reversible
fashion. This is not intended for security purposes, but rather to
dissuade users from depending on our internal ID structures.
"""
return unicode(base64.urlsafe_b64encode(
idStr.encode('utf-8')).replace(b'=', b''))
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train
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https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datamodel/__init__.py#L250-L257
|
ga4gh/ga4gh-server
|
ga4gh/server/datamodel/__init__.py
|
CompoundId.deobfuscate
|
def deobfuscate(cls, data):
"""
Reverses the obfuscation done by the :meth:`obfuscate` method.
If an identifier arrives without correct base64 padding this
function will append it to the end.
"""
# the str() call is necessary to convert the unicode string
# to an ascii string since the urlsafe_b64decode method
# sometimes chokes on unicode strings
return base64.urlsafe_b64decode(str((
data + b'A=='[(len(data) - 1) % 4:])))
|
python
|
def deobfuscate(cls, data):
"""
Reverses the obfuscation done by the :meth:`obfuscate` method.
If an identifier arrives without correct base64 padding this
function will append it to the end.
"""
# the str() call is necessary to convert the unicode string
# to an ascii string since the urlsafe_b64decode method
# sometimes chokes on unicode strings
return base64.urlsafe_b64decode(str((
data + b'A=='[(len(data) - 1) % 4:])))
|
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Reverses the obfuscation done by the :meth:`obfuscate` method.
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datamodel/__init__.py#L260-L270
|
ga4gh/ga4gh-server
|
ga4gh/server/datamodel/__init__.py
|
DatamodelObject.serializeAttributes
|
def serializeAttributes(self, msg):
"""
Sets the attrbutes of a message during serialization.
"""
attributes = self.getAttributes()
for key in attributes:
protocol.setAttribute(
msg.attributes.attr[key].values, attributes[key])
return msg
|
python
|
def serializeAttributes(self, msg):
"""
Sets the attrbutes of a message during serialization.
"""
attributes = self.getAttributes()
for key in attributes:
protocol.setAttribute(
msg.attributes.attr[key].values, attributes[key])
return msg
|
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datamodel/__init__.py#L539-L547
|
ga4gh/ga4gh-server
|
ga4gh/server/datamodel/__init__.py
|
DatamodelObject._scanDataFiles
|
def _scanDataFiles(self, dataDir, patterns):
"""
Scans the specified directory for files with the specified globbing
pattern and calls self._addDataFile for each. Raises an
EmptyDirException if no data files are found.
"""
numDataFiles = 0
for pattern in patterns:
scanPath = os.path.join(dataDir, pattern)
for filename in glob.glob(scanPath):
self._addDataFile(filename)
numDataFiles += 1
if numDataFiles == 0:
raise exceptions.EmptyDirException(dataDir, patterns)
|
python
|
def _scanDataFiles(self, dataDir, patterns):
"""
Scans the specified directory for files with the specified globbing
pattern and calls self._addDataFile for each. Raises an
EmptyDirException if no data files are found.
"""
numDataFiles = 0
for pattern in patterns:
scanPath = os.path.join(dataDir, pattern)
for filename in glob.glob(scanPath):
self._addDataFile(filename)
numDataFiles += 1
if numDataFiles == 0:
raise exceptions.EmptyDirException(dataDir, patterns)
|
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datamodel/__init__.py#L555-L568
|
ga4gh/ga4gh-server
|
ga4gh/server/network/__init__.py
|
getInitialPeerList
|
def getInitialPeerList(filePath, logger=None):
"""
Attempts to get a list of peers from a file specified in configuration.
This file has one URL per line and can contain newlines and comments.
# Main ga4gh node
http://1kgenomes.ga4gh.org
# Local intranet peer
https://192.168.1.1
The server will attempt to add URLs in this file to its registry at
startup and will log a warning if the file isn't found.
"""
ret = []
with open(filePath) as textFile:
ret = textFile.readlines()
if len(ret) == 0:
if logger:
logger.warn("Couldn't load the initial "
"peer list. Try adding a "
"file named 'initial_peers.txt' "
"to {}".format(os.getcwd()))
# Remove lines that start with a hash or are empty.
return filter(lambda x: x != "" and not x.find("#") != -1, ret)
|
python
|
def getInitialPeerList(filePath, logger=None):
"""
Attempts to get a list of peers from a file specified in configuration.
This file has one URL per line and can contain newlines and comments.
# Main ga4gh node
http://1kgenomes.ga4gh.org
# Local intranet peer
https://192.168.1.1
The server will attempt to add URLs in this file to its registry at
startup and will log a warning if the file isn't found.
"""
ret = []
with open(filePath) as textFile:
ret = textFile.readlines()
if len(ret) == 0:
if logger:
logger.warn("Couldn't load the initial "
"peer list. Try adding a "
"file named 'initial_peers.txt' "
"to {}".format(os.getcwd()))
# Remove lines that start with a hash or are empty.
return filter(lambda x: x != "" and not x.find("#") != -1, ret)
|
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# Main ga4gh node
http://1kgenomes.ga4gh.org
# Local intranet peer
https://192.168.1.1
The server will attempt to add URLs in this file to its registry at
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|
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] |
train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/network/__init__.py#L15-L39
|
ga4gh/ga4gh-server
|
ga4gh/server/network/__init__.py
|
insertInitialPeer
|
def insertInitialPeer(dataRepository, url, logger=None):
"""
Takes the datarepository, a url, and an optional logger and attempts
to add the peer into the repository.
"""
insertPeer = dataRepository.insertPeer
try:
peer = datamodel.peers.Peer(url)
insertPeer(peer)
except exceptions.RepoManagerException as exc:
if logger:
logger.debug(
"Peer already in registry {} {}".format(peer.getUrl(), exc))
except exceptions.BadUrlException as exc:
if logger:
logger.debug("A URL in the initial "
"peer list {} was malformed. {}".format(url), exc)
|
python
|
def insertInitialPeer(dataRepository, url, logger=None):
"""
Takes the datarepository, a url, and an optional logger and attempts
to add the peer into the repository.
"""
insertPeer = dataRepository.insertPeer
try:
peer = datamodel.peers.Peer(url)
insertPeer(peer)
except exceptions.RepoManagerException as exc:
if logger:
logger.debug(
"Peer already in registry {} {}".format(peer.getUrl(), exc))
except exceptions.BadUrlException as exc:
if logger:
logger.debug("A URL in the initial "
"peer list {} was malformed. {}".format(url), exc)
|
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/network/__init__.py#L42-L58
|
ga4gh/ga4gh-server
|
ga4gh/server/datamodel/peers.py
|
isUrl
|
def isUrl(urlString):
"""
Attempts to return whether a given URL string is valid by checking
for the presence of the URL scheme and netloc using the urlparse
module, and then using a regex.
From http://stackoverflow.com/questions/7160737/
"""
parsed = urlparse.urlparse(urlString)
urlparseValid = parsed.netloc != '' and parsed.scheme != ''
regex = re.compile(
r'^(?:http|ftp)s?://' # http:// or https://
r'(?:(?:[A-Z0-9](?:[A-Z0-9-]{0,61}[A-Z0-9])?\.)'
r'+(?:[A-Z]{2,6}\.?|[A-Z0-9-]{2,}\.?)|' # domain...
r'localhost|' # localhost...
r'\d{1,3}\.\d{1,3}\.\d{1,3}\.\d{1,3})' # ...or ip
r'(?::\d+)?' # optional port
r'(?:/?|[/?]\S+)$', re.IGNORECASE)
return regex.match(urlString) and urlparseValid
|
python
|
def isUrl(urlString):
"""
Attempts to return whether a given URL string is valid by checking
for the presence of the URL scheme and netloc using the urlparse
module, and then using a regex.
From http://stackoverflow.com/questions/7160737/
"""
parsed = urlparse.urlparse(urlString)
urlparseValid = parsed.netloc != '' and parsed.scheme != ''
regex = re.compile(
r'^(?:http|ftp)s?://' # http:// or https://
r'(?:(?:[A-Z0-9](?:[A-Z0-9-]{0,61}[A-Z0-9])?\.)'
r'+(?:[A-Z]{2,6}\.?|[A-Z0-9-]{2,}\.?)|' # domain...
r'localhost|' # localhost...
r'\d{1,3}\.\d{1,3}\.\d{1,3}\.\d{1,3})' # ...or ip
r'(?::\d+)?' # optional port
r'(?:/?|[/?]\S+)$', re.IGNORECASE)
return regex.match(urlString) and urlparseValid
|
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Attempts to return whether a given URL string is valid by checking
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From http://stackoverflow.com/questions/7160737/
|
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"."
] |
train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datamodel/peers.py#L17-L36
|
ga4gh/ga4gh-server
|
ga4gh/server/datamodel/peers.py
|
Peer.setUrl
|
def setUrl(self, url):
"""
Attempt to safely set the URL by string.
"""
if isUrl(url):
self._url = url
else:
raise exceptions.BadUrlException(url)
return self
|
python
|
def setUrl(self, url):
"""
Attempt to safely set the URL by string.
"""
if isUrl(url):
self._url = url
else:
raise exceptions.BadUrlException(url)
return self
|
[
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] |
Attempt to safely set the URL by string.
|
[
"Attempt",
"to",
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"set",
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"URL",
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"string",
"."
] |
train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datamodel/peers.py#L53-L61
|
ga4gh/ga4gh-server
|
ga4gh/server/datamodel/peers.py
|
Peer.setAttributesJson
|
def setAttributesJson(self, attributesJson):
"""
Sets the attributes dictionary from a JSON string.
"""
try:
self._attributes = json.loads(attributesJson)
except:
raise exceptions.InvalidJsonException(attributesJson)
return self
|
python
|
def setAttributesJson(self, attributesJson):
"""
Sets the attributes dictionary from a JSON string.
"""
try:
self._attributes = json.loads(attributesJson)
except:
raise exceptions.InvalidJsonException(attributesJson)
return self
|
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] |
Sets the attributes dictionary from a JSON string.
|
[
"Sets",
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"."
] |
train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datamodel/peers.py#L73-L81
|
ga4gh/ga4gh-server
|
ga4gh/server/datamodel/peers.py
|
Peer.populateFromRow
|
def populateFromRow(self, peerRecord):
"""
This method accepts a model record and sets class variables.
"""
self.setUrl(peerRecord.url) \
.setAttributesJson(peerRecord.attributes)
return self
|
python
|
def populateFromRow(self, peerRecord):
"""
This method accepts a model record and sets class variables.
"""
self.setUrl(peerRecord.url) \
.setAttributesJson(peerRecord.attributes)
return self
|
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"(",
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"attributes",
")",
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] |
This method accepts a model record and sets class variables.
|
[
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] |
train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/datamodel/peers.py#L105-L111
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend._topLevelObjectGenerator
|
def _topLevelObjectGenerator(self, request, numObjects, getByIndexMethod):
"""
Returns a generator over the results for the specified request, which
is over a set of objects of the specified size. The objects are
returned by call to the specified method, which must take a single
integer as an argument. The returned generator yields a sequence of
(object, nextPageToken) pairs, which allows this iteration to be picked
up at any point.
"""
currentIndex = 0
if request.page_token:
currentIndex, = paging._parsePageToken(
request.page_token, 1)
while currentIndex < numObjects:
object_ = getByIndexMethod(currentIndex)
currentIndex += 1
nextPageToken = None
if currentIndex < numObjects:
nextPageToken = str(currentIndex)
yield object_.toProtocolElement(), nextPageToken
|
python
|
def _topLevelObjectGenerator(self, request, numObjects, getByIndexMethod):
"""
Returns a generator over the results for the specified request, which
is over a set of objects of the specified size. The objects are
returned by call to the specified method, which must take a single
integer as an argument. The returned generator yields a sequence of
(object, nextPageToken) pairs, which allows this iteration to be picked
up at any point.
"""
currentIndex = 0
if request.page_token:
currentIndex, = paging._parsePageToken(
request.page_token, 1)
while currentIndex < numObjects:
object_ = getByIndexMethod(currentIndex)
currentIndex += 1
nextPageToken = None
if currentIndex < numObjects:
nextPageToken = str(currentIndex)
yield object_.toProtocolElement(), nextPageToken
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train
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https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L74-L93
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend._protocolObjectGenerator
|
def _protocolObjectGenerator(self, request, numObjects, getByIndexMethod):
"""
Returns a generator over the results for the specified request, from
a set of protocol objects of the specified size. The objects are
returned by call to the specified method, which must take a single
integer as an argument. The returned generator yields a sequence of
(object, nextPageToken) pairs, which allows this iteration to be picked
up at any point.
"""
currentIndex = 0
if request.page_token:
currentIndex, = paging._parsePageToken(
request.page_token, 1)
while currentIndex < numObjects:
object_ = getByIndexMethod(currentIndex)
currentIndex += 1
nextPageToken = None
if currentIndex < numObjects:
nextPageToken = str(currentIndex)
yield object_, nextPageToken
|
python
|
def _protocolObjectGenerator(self, request, numObjects, getByIndexMethod):
"""
Returns a generator over the results for the specified request, from
a set of protocol objects of the specified size. The objects are
returned by call to the specified method, which must take a single
integer as an argument. The returned generator yields a sequence of
(object, nextPageToken) pairs, which allows this iteration to be picked
up at any point.
"""
currentIndex = 0
if request.page_token:
currentIndex, = paging._parsePageToken(
request.page_token, 1)
while currentIndex < numObjects:
object_ = getByIndexMethod(currentIndex)
currentIndex += 1
nextPageToken = None
if currentIndex < numObjects:
nextPageToken = str(currentIndex)
yield object_, nextPageToken
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train
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https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L95-L114
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend._protocolListGenerator
|
def _protocolListGenerator(self, request, objectList):
"""
Returns a generator over the objects in the specified list using
_protocolObjectGenerator to generate page tokens.
"""
return self._protocolObjectGenerator(
request, len(objectList), lambda index: objectList[index])
|
python
|
def _protocolListGenerator(self, request, objectList):
"""
Returns a generator over the objects in the specified list using
_protocolObjectGenerator to generate page tokens.
"""
return self._protocolObjectGenerator(
request, len(objectList), lambda index: objectList[index])
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train
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https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L116-L122
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend._objectListGenerator
|
def _objectListGenerator(self, request, objectList):
"""
Returns a generator over the objects in the specified list using
_topLevelObjectGenerator to generate page tokens.
"""
return self._topLevelObjectGenerator(
request, len(objectList), lambda index: objectList[index])
|
python
|
def _objectListGenerator(self, request, objectList):
"""
Returns a generator over the objects in the specified list using
_topLevelObjectGenerator to generate page tokens.
"""
return self._topLevelObjectGenerator(
request, len(objectList), lambda index: objectList[index])
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L124-L130
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.datasetsGenerator
|
def datasetsGenerator(self, request):
"""
Returns a generator over the (dataset, nextPageToken) pairs
defined by the specified request
"""
return self._topLevelObjectGenerator(
request, self.getDataRepository().getNumDatasets(),
self.getDataRepository().getDatasetByIndex)
|
python
|
def datasetsGenerator(self, request):
"""
Returns a generator over the (dataset, nextPageToken) pairs
defined by the specified request
"""
return self._topLevelObjectGenerator(
request, self.getDataRepository().getNumDatasets(),
self.getDataRepository().getDatasetByIndex)
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L132-L139
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.phenotypeAssociationSetsGenerator
|
def phenotypeAssociationSetsGenerator(self, request):
"""
Returns a generator over the (phenotypeAssociationSet, nextPageToken)
pairs defined by the specified request
"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
return self._topLevelObjectGenerator(
request, dataset.getNumPhenotypeAssociationSets(),
dataset.getPhenotypeAssociationSetByIndex)
|
python
|
def phenotypeAssociationSetsGenerator(self, request):
"""
Returns a generator over the (phenotypeAssociationSet, nextPageToken)
pairs defined by the specified request
"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
return self._topLevelObjectGenerator(
request, dataset.getNumPhenotypeAssociationSets(),
dataset.getPhenotypeAssociationSetByIndex)
|
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L168-L176
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.readGroupSetsGenerator
|
def readGroupSetsGenerator(self, request):
"""
Returns a generator over the (readGroupSet, nextPageToken) pairs
defined by the specified request.
"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
return self._readGroupSetsGenerator(
request, dataset.getNumReadGroupSets(),
dataset.getReadGroupSetByIndex)
|
python
|
def readGroupSetsGenerator(self, request):
"""
Returns a generator over the (readGroupSet, nextPageToken) pairs
defined by the specified request.
"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
return self._readGroupSetsGenerator(
request, dataset.getNumReadGroupSets(),
dataset.getReadGroupSetByIndex)
|
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train
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https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L178-L186
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend._readGroupSetsGenerator
|
def _readGroupSetsGenerator(self, request, numObjects, getByIndexMethod):
"""
Returns a generator over the results for the specified request, which
is over a set of objects of the specified size. The objects are
returned by call to the specified method, which must take a single
integer as an argument. The returned generator yields a sequence of
(object, nextPageToken) pairs, which allows this iteration to be picked
up at any point.
"""
currentIndex = 0
if request.page_token:
currentIndex, = paging._parsePageToken(
request.page_token, 1)
while currentIndex < numObjects:
obj = getByIndexMethod(currentIndex)
include = True
rgsp = obj.toProtocolElement()
if request.name and request.name != obj.getLocalId():
include = False
if request.biosample_id and include:
rgsp.ClearField("read_groups")
for readGroup in obj.getReadGroups():
if request.biosample_id == readGroup.getBiosampleId():
rgsp.read_groups.extend(
[readGroup.toProtocolElement()])
# If none of the biosamples match and the readgroupset
# contains reagroups, don't include in the response
if len(rgsp.read_groups) == 0 and \
len(obj.getReadGroups()) != 0:
include = False
currentIndex += 1
nextPageToken = None
if currentIndex < numObjects:
nextPageToken = str(currentIndex)
if include:
yield rgsp, nextPageToken
|
python
|
def _readGroupSetsGenerator(self, request, numObjects, getByIndexMethod):
"""
Returns a generator over the results for the specified request, which
is over a set of objects of the specified size. The objects are
returned by call to the specified method, which must take a single
integer as an argument. The returned generator yields a sequence of
(object, nextPageToken) pairs, which allows this iteration to be picked
up at any point.
"""
currentIndex = 0
if request.page_token:
currentIndex, = paging._parsePageToken(
request.page_token, 1)
while currentIndex < numObjects:
obj = getByIndexMethod(currentIndex)
include = True
rgsp = obj.toProtocolElement()
if request.name and request.name != obj.getLocalId():
include = False
if request.biosample_id and include:
rgsp.ClearField("read_groups")
for readGroup in obj.getReadGroups():
if request.biosample_id == readGroup.getBiosampleId():
rgsp.read_groups.extend(
[readGroup.toProtocolElement()])
# If none of the biosamples match and the readgroupset
# contains reagroups, don't include in the response
if len(rgsp.read_groups) == 0 and \
len(obj.getReadGroups()) != 0:
include = False
currentIndex += 1
nextPageToken = None
if currentIndex < numObjects:
nextPageToken = str(currentIndex)
if include:
yield rgsp, nextPageToken
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L188-L223
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.referenceSetsGenerator
|
def referenceSetsGenerator(self, request):
"""
Returns a generator over the (referenceSet, nextPageToken) pairs
defined by the specified request.
"""
results = []
for obj in self.getDataRepository().getReferenceSets():
include = True
if request.md5checksum:
if request.md5checksum != obj.getMd5Checksum():
include = False
if request.accession:
if request.accession not in obj.getSourceAccessions():
include = False
if request.assembly_id:
if request.assembly_id != obj.getAssemblyId():
include = False
if include:
results.append(obj)
return self._objectListGenerator(request, results)
|
python
|
def referenceSetsGenerator(self, request):
"""
Returns a generator over the (referenceSet, nextPageToken) pairs
defined by the specified request.
"""
results = []
for obj in self.getDataRepository().getReferenceSets():
include = True
if request.md5checksum:
if request.md5checksum != obj.getMd5Checksum():
include = False
if request.accession:
if request.accession not in obj.getSourceAccessions():
include = False
if request.assembly_id:
if request.assembly_id != obj.getAssemblyId():
include = False
if include:
results.append(obj)
return self._objectListGenerator(request, results)
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train
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https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L225-L244
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.referencesGenerator
|
def referencesGenerator(self, request):
"""
Returns a generator over the (reference, nextPageToken) pairs
defined by the specified request.
"""
referenceSet = self.getDataRepository().getReferenceSet(
request.reference_set_id)
results = []
for obj in referenceSet.getReferences():
include = True
if request.md5checksum:
if request.md5checksum != obj.getMd5Checksum():
include = False
if request.accession:
if request.accession not in obj.getSourceAccessions():
include = False
if include:
results.append(obj)
return self._objectListGenerator(request, results)
|
python
|
def referencesGenerator(self, request):
"""
Returns a generator over the (reference, nextPageToken) pairs
defined by the specified request.
"""
referenceSet = self.getDataRepository().getReferenceSet(
request.reference_set_id)
results = []
for obj in referenceSet.getReferences():
include = True
if request.md5checksum:
if request.md5checksum != obj.getMd5Checksum():
include = False
if request.accession:
if request.accession not in obj.getSourceAccessions():
include = False
if include:
results.append(obj)
return self._objectListGenerator(request, results)
|
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L246-L264
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.variantSetsGenerator
|
def variantSetsGenerator(self, request):
"""
Returns a generator over the (variantSet, nextPageToken) pairs defined
by the specified request.
"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
return self._topLevelObjectGenerator(
request, dataset.getNumVariantSets(),
dataset.getVariantSetByIndex)
|
python
|
def variantSetsGenerator(self, request):
"""
Returns a generator over the (variantSet, nextPageToken) pairs defined
by the specified request.
"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
return self._topLevelObjectGenerator(
request, dataset.getNumVariantSets(),
dataset.getVariantSetByIndex)
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train
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https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L266-L274
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.variantAnnotationSetsGenerator
|
def variantAnnotationSetsGenerator(self, request):
"""
Returns a generator over the (variantAnnotationSet, nextPageToken)
pairs defined by the specified request.
"""
compoundId = datamodel.VariantSetCompoundId.parse(
request.variant_set_id)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(request.variant_set_id)
return self._topLevelObjectGenerator(
request, variantSet.getNumVariantAnnotationSets(),
variantSet.getVariantAnnotationSetByIndex)
|
python
|
def variantAnnotationSetsGenerator(self, request):
"""
Returns a generator over the (variantAnnotationSet, nextPageToken)
pairs defined by the specified request.
"""
compoundId = datamodel.VariantSetCompoundId.parse(
request.variant_set_id)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(request.variant_set_id)
return self._topLevelObjectGenerator(
request, variantSet.getNumVariantAnnotationSets(),
variantSet.getVariantAnnotationSetByIndex)
|
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L276-L287
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.readsGenerator
|
def readsGenerator(self, request):
"""
Returns a generator over the (read, nextPageToken) pairs defined
by the specified request
"""
if not request.reference_id:
raise exceptions.UnmappedReadsNotSupported()
if len(request.read_group_ids) < 1:
raise exceptions.BadRequestException(
"At least one readGroupId must be specified")
elif len(request.read_group_ids) == 1:
return self._readsGeneratorSingle(request)
else:
return self._readsGeneratorMultiple(request)
|
python
|
def readsGenerator(self, request):
"""
Returns a generator over the (read, nextPageToken) pairs defined
by the specified request
"""
if not request.reference_id:
raise exceptions.UnmappedReadsNotSupported()
if len(request.read_group_ids) < 1:
raise exceptions.BadRequestException(
"At least one readGroupId must be specified")
elif len(request.read_group_ids) == 1:
return self._readsGeneratorSingle(request)
else:
return self._readsGeneratorMultiple(request)
|
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L289-L302
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.variantsGenerator
|
def variantsGenerator(self, request):
"""
Returns a generator over the (variant, nextPageToken) pairs defined
by the specified request.
"""
compoundId = datamodel.VariantSetCompoundId \
.parse(request.variant_set_id)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(compoundId.variant_set_id)
intervalIterator = paging.VariantsIntervalIterator(
request, variantSet)
return intervalIterator
|
python
|
def variantsGenerator(self, request):
"""
Returns a generator over the (variant, nextPageToken) pairs defined
by the specified request.
"""
compoundId = datamodel.VariantSetCompoundId \
.parse(request.variant_set_id)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(compoundId.variant_set_id)
intervalIterator = paging.VariantsIntervalIterator(
request, variantSet)
return intervalIterator
|
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L338-L349
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.variantAnnotationsGenerator
|
def variantAnnotationsGenerator(self, request):
"""
Returns a generator over the (variantAnnotaitons, nextPageToken) pairs
defined by the specified request.
"""
compoundId = datamodel.VariantAnnotationSetCompoundId.parse(
request.variant_annotation_set_id)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(compoundId.variant_set_id)
variantAnnotationSet = variantSet.getVariantAnnotationSet(
request.variant_annotation_set_id)
iterator = paging.VariantAnnotationsIntervalIterator(
request, variantAnnotationSet)
return iterator
|
python
|
def variantAnnotationsGenerator(self, request):
"""
Returns a generator over the (variantAnnotaitons, nextPageToken) pairs
defined by the specified request.
"""
compoundId = datamodel.VariantAnnotationSetCompoundId.parse(
request.variant_annotation_set_id)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(compoundId.variant_set_id)
variantAnnotationSet = variantSet.getVariantAnnotationSet(
request.variant_annotation_set_id)
iterator = paging.VariantAnnotationsIntervalIterator(
request, variantAnnotationSet)
return iterator
|
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train
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https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L351-L364
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.featuresGenerator
|
def featuresGenerator(self, request):
"""
Returns a generator over the (features, nextPageToken) pairs
defined by the (JSON string) request.
"""
compoundId = None
parentId = None
if request.feature_set_id != "":
compoundId = datamodel.FeatureSetCompoundId.parse(
request.feature_set_id)
if request.parent_id != "":
compoundParentId = datamodel.FeatureCompoundId.parse(
request.parent_id)
parentId = compoundParentId.featureId
# A client can optionally specify JUST the (compound) parentID,
# and the server needs to derive the dataset & featureSet
# from this (compound) parentID.
if compoundId is None:
compoundId = compoundParentId
else:
# check that the dataset and featureSet of the parent
# compound ID is the same as that of the featureSetId
mismatchCheck = (
compoundParentId.dataset_id != compoundId.dataset_id or
compoundParentId.feature_set_id !=
compoundId.feature_set_id)
if mismatchCheck:
raise exceptions.ParentIncompatibleWithFeatureSet()
if compoundId is None:
raise exceptions.FeatureSetNotSpecifiedException()
dataset = self.getDataRepository().getDataset(
compoundId.dataset_id)
featureSet = dataset.getFeatureSet(compoundId.feature_set_id)
iterator = paging.FeaturesIterator(
request, featureSet, parentId)
return iterator
|
python
|
def featuresGenerator(self, request):
"""
Returns a generator over the (features, nextPageToken) pairs
defined by the (JSON string) request.
"""
compoundId = None
parentId = None
if request.feature_set_id != "":
compoundId = datamodel.FeatureSetCompoundId.parse(
request.feature_set_id)
if request.parent_id != "":
compoundParentId = datamodel.FeatureCompoundId.parse(
request.parent_id)
parentId = compoundParentId.featureId
# A client can optionally specify JUST the (compound) parentID,
# and the server needs to derive the dataset & featureSet
# from this (compound) parentID.
if compoundId is None:
compoundId = compoundParentId
else:
# check that the dataset and featureSet of the parent
# compound ID is the same as that of the featureSetId
mismatchCheck = (
compoundParentId.dataset_id != compoundId.dataset_id or
compoundParentId.feature_set_id !=
compoundId.feature_set_id)
if mismatchCheck:
raise exceptions.ParentIncompatibleWithFeatureSet()
if compoundId is None:
raise exceptions.FeatureSetNotSpecifiedException()
dataset = self.getDataRepository().getDataset(
compoundId.dataset_id)
featureSet = dataset.getFeatureSet(compoundId.feature_set_id)
iterator = paging.FeaturesIterator(
request, featureSet, parentId)
return iterator
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L366-L403
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.continuousGenerator
|
def continuousGenerator(self, request):
"""
Returns a generator over the (continuous, nextPageToken) pairs
defined by the (JSON string) request.
"""
compoundId = None
if request.continuous_set_id != "":
compoundId = datamodel.ContinuousSetCompoundId.parse(
request.continuous_set_id)
if compoundId is None:
raise exceptions.ContinuousSetNotSpecifiedException()
dataset = self.getDataRepository().getDataset(
compoundId.dataset_id)
continuousSet = dataset.getContinuousSet(request.continuous_set_id)
iterator = paging.ContinuousIterator(request, continuousSet)
return iterator
|
python
|
def continuousGenerator(self, request):
"""
Returns a generator over the (continuous, nextPageToken) pairs
defined by the (JSON string) request.
"""
compoundId = None
if request.continuous_set_id != "":
compoundId = datamodel.ContinuousSetCompoundId.parse(
request.continuous_set_id)
if compoundId is None:
raise exceptions.ContinuousSetNotSpecifiedException()
dataset = self.getDataRepository().getDataset(
compoundId.dataset_id)
continuousSet = dataset.getContinuousSet(request.continuous_set_id)
iterator = paging.ContinuousIterator(request, continuousSet)
return iterator
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https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L405-L421
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.phenotypesGenerator
|
def phenotypesGenerator(self, request):
"""
Returns a generator over the (phenotypes, nextPageToken) pairs
defined by the (JSON string) request
"""
# TODO make paging work using SPARQL?
compoundId = datamodel.PhenotypeAssociationSetCompoundId.parse(
request.phenotype_association_set_id)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
phenotypeAssociationSet = dataset.getPhenotypeAssociationSet(
compoundId.phenotypeAssociationSetId)
associations = phenotypeAssociationSet.getAssociations(request)
phenotypes = [association.phenotype for association in associations]
return self._protocolListGenerator(
request, phenotypes)
|
python
|
def phenotypesGenerator(self, request):
"""
Returns a generator over the (phenotypes, nextPageToken) pairs
defined by the (JSON string) request
"""
# TODO make paging work using SPARQL?
compoundId = datamodel.PhenotypeAssociationSetCompoundId.parse(
request.phenotype_association_set_id)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
phenotypeAssociationSet = dataset.getPhenotypeAssociationSet(
compoundId.phenotypeAssociationSetId)
associations = phenotypeAssociationSet.getAssociations(request)
phenotypes = [association.phenotype for association in associations]
return self._protocolListGenerator(
request, phenotypes)
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train
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https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L423-L437
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.genotypesPhenotypesGenerator
|
def genotypesPhenotypesGenerator(self, request):
"""
Returns a generator over the (phenotypes, nextPageToken) pairs
defined by the (JSON string) request
"""
# TODO make paging work using SPARQL?
compoundId = datamodel.PhenotypeAssociationSetCompoundId.parse(
request.phenotype_association_set_id)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
phenotypeAssociationSet = dataset.getPhenotypeAssociationSet(
compoundId.phenotypeAssociationSetId)
featureSets = dataset.getFeatureSets()
annotationList = phenotypeAssociationSet.getAssociations(
request, featureSets)
return self._protocolListGenerator(request, annotationList)
|
python
|
def genotypesPhenotypesGenerator(self, request):
"""
Returns a generator over the (phenotypes, nextPageToken) pairs
defined by the (JSON string) request
"""
# TODO make paging work using SPARQL?
compoundId = datamodel.PhenotypeAssociationSetCompoundId.parse(
request.phenotype_association_set_id)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
phenotypeAssociationSet = dataset.getPhenotypeAssociationSet(
compoundId.phenotypeAssociationSetId)
featureSets = dataset.getFeatureSets()
annotationList = phenotypeAssociationSet.getAssociations(
request, featureSets)
return self._protocolListGenerator(request, annotationList)
|
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L439-L453
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.callSetsGenerator
|
def callSetsGenerator(self, request):
"""
Returns a generator over the (callSet, nextPageToken) pairs defined
by the specified request.
"""
compoundId = datamodel.VariantSetCompoundId.parse(
request.variant_set_id)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(compoundId.variant_set_id)
results = []
for obj in variantSet.getCallSets():
include = True
if request.name:
if request.name != obj.getLocalId():
include = False
if request.biosample_id:
if request.biosample_id != obj.getBiosampleId():
include = False
if include:
results.append(obj)
return self._objectListGenerator(request, results)
|
python
|
def callSetsGenerator(self, request):
"""
Returns a generator over the (callSet, nextPageToken) pairs defined
by the specified request.
"""
compoundId = datamodel.VariantSetCompoundId.parse(
request.variant_set_id)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(compoundId.variant_set_id)
results = []
for obj in variantSet.getCallSets():
include = True
if request.name:
if request.name != obj.getLocalId():
include = False
if request.biosample_id:
if request.biosample_id != obj.getBiosampleId():
include = False
if include:
results.append(obj)
return self._objectListGenerator(request, results)
|
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L455-L475
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.featureSetsGenerator
|
def featureSetsGenerator(self, request):
"""
Returns a generator over the (featureSet, nextPageToken) pairs
defined by the specified request.
"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
return self._topLevelObjectGenerator(
request, dataset.getNumFeatureSets(),
dataset.getFeatureSetByIndex)
|
python
|
def featureSetsGenerator(self, request):
"""
Returns a generator over the (featureSet, nextPageToken) pairs
defined by the specified request.
"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
return self._topLevelObjectGenerator(
request, dataset.getNumFeatureSets(),
dataset.getFeatureSetByIndex)
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L477-L485
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.continuousSetsGenerator
|
def continuousSetsGenerator(self, request):
"""
Returns a generator over the (continuousSet, nextPageToken) pairs
defined by the specified request.
"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
return self._topLevelObjectGenerator(
request, dataset.getNumContinuousSets(),
dataset.getContinuousSetByIndex)
|
python
|
def continuousSetsGenerator(self, request):
"""
Returns a generator over the (continuousSet, nextPageToken) pairs
defined by the specified request.
"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
return self._topLevelObjectGenerator(
request, dataset.getNumContinuousSets(),
dataset.getContinuousSetByIndex)
|
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L487-L495
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.rnaQuantificationSetsGenerator
|
def rnaQuantificationSetsGenerator(self, request):
"""
Returns a generator over the (rnaQuantificationSet, nextPageToken)
pairs defined by the specified request.
"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
return self._topLevelObjectGenerator(
request, dataset.getNumRnaQuantificationSets(),
dataset.getRnaQuantificationSetByIndex)
|
python
|
def rnaQuantificationSetsGenerator(self, request):
"""
Returns a generator over the (rnaQuantificationSet, nextPageToken)
pairs defined by the specified request.
"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
return self._topLevelObjectGenerator(
request, dataset.getNumRnaQuantificationSets(),
dataset.getRnaQuantificationSetByIndex)
|
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L497-L505
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.rnaQuantificationsGenerator
|
def rnaQuantificationsGenerator(self, request):
"""
Returns a generator over the (rnaQuantification, nextPageToken) pairs
defined by the specified request.
"""
if len(request.rna_quantification_set_id) < 1:
raise exceptions.BadRequestException(
"Rna Quantification Set Id must be specified")
else:
compoundId = datamodel.RnaQuantificationSetCompoundId.parse(
request.rna_quantification_set_id)
dataset = self.getDataRepository().getDataset(
compoundId.dataset_id)
rnaQuantSet = dataset.getRnaQuantificationSet(
compoundId.rna_quantification_set_id)
results = []
for obj in rnaQuantSet.getRnaQuantifications():
include = True
if request.biosample_id:
if request.biosample_id != obj.getBiosampleId():
include = False
if include:
results.append(obj)
return self._objectListGenerator(request, results)
|
python
|
def rnaQuantificationsGenerator(self, request):
"""
Returns a generator over the (rnaQuantification, nextPageToken) pairs
defined by the specified request.
"""
if len(request.rna_quantification_set_id) < 1:
raise exceptions.BadRequestException(
"Rna Quantification Set Id must be specified")
else:
compoundId = datamodel.RnaQuantificationSetCompoundId.parse(
request.rna_quantification_set_id)
dataset = self.getDataRepository().getDataset(
compoundId.dataset_id)
rnaQuantSet = dataset.getRnaQuantificationSet(
compoundId.rna_quantification_set_id)
results = []
for obj in rnaQuantSet.getRnaQuantifications():
include = True
if request.biosample_id:
if request.biosample_id != obj.getBiosampleId():
include = False
if include:
results.append(obj)
return self._objectListGenerator(request, results)
|
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L507-L530
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.expressionLevelsGenerator
|
def expressionLevelsGenerator(self, request):
"""
Returns a generator over the (expressionLevel, nextPageToken) pairs
defined by the specified request.
Currently only supports searching over a specified rnaQuantification
"""
rnaQuantificationId = request.rna_quantification_id
compoundId = datamodel.RnaQuantificationCompoundId.parse(
request.rna_quantification_id)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
rnaQuantSet = dataset.getRnaQuantificationSet(
compoundId.rna_quantification_set_id)
rnaQuant = rnaQuantSet.getRnaQuantification(rnaQuantificationId)
rnaQuantificationId = rnaQuant.getLocalId()
iterator = paging.ExpressionLevelsIterator(
request, rnaQuant)
return iterator
|
python
|
def expressionLevelsGenerator(self, request):
"""
Returns a generator over the (expressionLevel, nextPageToken) pairs
defined by the specified request.
Currently only supports searching over a specified rnaQuantification
"""
rnaQuantificationId = request.rna_quantification_id
compoundId = datamodel.RnaQuantificationCompoundId.parse(
request.rna_quantification_id)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
rnaQuantSet = dataset.getRnaQuantificationSet(
compoundId.rna_quantification_set_id)
rnaQuant = rnaQuantSet.getRnaQuantification(rnaQuantificationId)
rnaQuantificationId = rnaQuant.getLocalId()
iterator = paging.ExpressionLevelsIterator(
request, rnaQuant)
return iterator
|
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Returns a generator over the (expressionLevel, nextPageToken) pairs
defined by the specified request.
Currently only supports searching over a specified rnaQuantification
|
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"."
] |
train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L532-L549
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runGetRequest
|
def runGetRequest(self, obj):
"""
Runs a get request by converting the specified datamodel
object into its protocol representation.
"""
protocolElement = obj.toProtocolElement()
jsonString = protocol.toJson(protocolElement)
return jsonString
|
python
|
def runGetRequest(self, obj):
"""
Runs a get request by converting the specified datamodel
object into its protocol representation.
"""
protocolElement = obj.toProtocolElement()
jsonString = protocol.toJson(protocolElement)
return jsonString
|
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L568-L575
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runSearchRequest
|
def runSearchRequest(
self, requestStr, requestClass, responseClass, objectGenerator):
"""
Runs the specified request. The request is a string containing
a JSON representation of an instance of the specified requestClass.
We return a string representation of an instance of the specified
responseClass in JSON format. Objects are filled into the page list
using the specified object generator, which must return
(object, nextPageToken) pairs, and be able to resume iteration from
any point using the nextPageToken attribute of the request object.
"""
self.startProfile()
try:
request = protocol.fromJson(requestStr, requestClass)
except protocol.json_format.ParseError:
raise exceptions.InvalidJsonException(requestStr)
# TODO How do we detect when the page size is not set?
if not request.page_size:
request.page_size = self._defaultPageSize
if request.page_size < 0:
raise exceptions.BadPageSizeException(request.page_size)
responseBuilder = response_builder.SearchResponseBuilder(
responseClass, request.page_size, self._maxResponseLength)
nextPageToken = None
for obj, nextPageToken in objectGenerator(request):
responseBuilder.addValue(obj)
if responseBuilder.isFull():
break
responseBuilder.setNextPageToken(nextPageToken)
responseString = responseBuilder.getSerializedResponse()
self.endProfile()
return responseString
|
python
|
def runSearchRequest(
self, requestStr, requestClass, responseClass, objectGenerator):
"""
Runs the specified request. The request is a string containing
a JSON representation of an instance of the specified requestClass.
We return a string representation of an instance of the specified
responseClass in JSON format. Objects are filled into the page list
using the specified object generator, which must return
(object, nextPageToken) pairs, and be able to resume iteration from
any point using the nextPageToken attribute of the request object.
"""
self.startProfile()
try:
request = protocol.fromJson(requestStr, requestClass)
except protocol.json_format.ParseError:
raise exceptions.InvalidJsonException(requestStr)
# TODO How do we detect when the page size is not set?
if not request.page_size:
request.page_size = self._defaultPageSize
if request.page_size < 0:
raise exceptions.BadPageSizeException(request.page_size)
responseBuilder = response_builder.SearchResponseBuilder(
responseClass, request.page_size, self._maxResponseLength)
nextPageToken = None
for obj, nextPageToken in objectGenerator(request):
responseBuilder.addValue(obj)
if responseBuilder.isFull():
break
responseBuilder.setNextPageToken(nextPageToken)
responseString = responseBuilder.getSerializedResponse()
self.endProfile()
return responseString
|
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L577-L608
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runListReferenceBases
|
def runListReferenceBases(self, requestJson):
"""
Runs a listReferenceBases request for the specified ID and
request arguments.
"""
# In the case when an empty post request is made to the endpoint
# we instantiate an empty ListReferenceBasesRequest.
if not requestJson:
request = protocol.ListReferenceBasesRequest()
else:
try:
request = protocol.fromJson(
requestJson,
protocol.ListReferenceBasesRequest)
except protocol.json_format.ParseError:
raise exceptions.InvalidJsonException(requestJson)
compoundId = datamodel.ReferenceCompoundId.parse(request.reference_id)
referenceSet = self.getDataRepository().getReferenceSet(
compoundId.reference_set_id)
reference = referenceSet.getReference(request.reference_id)
start = request.start
end = request.end
if end == 0: # assume meant "get all"
end = reference.getLength()
if request.page_token:
pageTokenStr = request.page_token
start = paging._parsePageToken(pageTokenStr, 1)[0]
chunkSize = self._maxResponseLength
nextPageToken = None
if start + chunkSize < end:
end = start + chunkSize
nextPageToken = str(start + chunkSize)
sequence = reference.getBases(start, end)
# build response
response = protocol.ListReferenceBasesResponse()
response.offset = start
response.sequence = sequence
if nextPageToken:
response.next_page_token = nextPageToken
return protocol.toJson(response)
|
python
|
def runListReferenceBases(self, requestJson):
"""
Runs a listReferenceBases request for the specified ID and
request arguments.
"""
# In the case when an empty post request is made to the endpoint
# we instantiate an empty ListReferenceBasesRequest.
if not requestJson:
request = protocol.ListReferenceBasesRequest()
else:
try:
request = protocol.fromJson(
requestJson,
protocol.ListReferenceBasesRequest)
except protocol.json_format.ParseError:
raise exceptions.InvalidJsonException(requestJson)
compoundId = datamodel.ReferenceCompoundId.parse(request.reference_id)
referenceSet = self.getDataRepository().getReferenceSet(
compoundId.reference_set_id)
reference = referenceSet.getReference(request.reference_id)
start = request.start
end = request.end
if end == 0: # assume meant "get all"
end = reference.getLength()
if request.page_token:
pageTokenStr = request.page_token
start = paging._parsePageToken(pageTokenStr, 1)[0]
chunkSize = self._maxResponseLength
nextPageToken = None
if start + chunkSize < end:
end = start + chunkSize
nextPageToken = str(start + chunkSize)
sequence = reference.getBases(start, end)
# build response
response = protocol.ListReferenceBasesResponse()
response.offset = start
response.sequence = sequence
if nextPageToken:
response.next_page_token = nextPageToken
return protocol.toJson(response)
|
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L610-L651
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runGetCallSet
|
def runGetCallSet(self, id_):
"""
Returns a callset with the given id
"""
compoundId = datamodel.CallSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(compoundId.variant_set_id)
callSet = variantSet.getCallSet(id_)
return self.runGetRequest(callSet)
|
python
|
def runGetCallSet(self, id_):
"""
Returns a callset with the given id
"""
compoundId = datamodel.CallSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(compoundId.variant_set_id)
callSet = variantSet.getCallSet(id_)
return self.runGetRequest(callSet)
|
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[
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] |
train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L655-L663
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runGetInfo
|
def runGetInfo(self, request):
"""
Returns information about the service including protocol version.
"""
return protocol.toJson(protocol.GetInfoResponse(
protocol_version=protocol.version))
|
python
|
def runGetInfo(self, request):
"""
Returns information about the service including protocol version.
"""
return protocol.toJson(protocol.GetInfoResponse(
protocol_version=protocol.version))
|
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[
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L665-L670
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runAddAnnouncement
|
def runAddAnnouncement(self, flaskrequest):
"""
Takes a flask request from the frontend and attempts to parse
into an AnnouncePeerRequest. If successful, it will log the
announcement to the `announcement` table with some other metadata
gathered from the request.
"""
announcement = {}
# We want to parse the request ourselves to collect a little more
# data about it.
try:
requestData = protocol.fromJson(
flaskrequest.get_data(), protocol.AnnouncePeerRequest)
announcement['hostname'] = flaskrequest.host_url
announcement['remote_addr'] = flaskrequest.remote_addr
announcement['user_agent'] = flaskrequest.headers.get('User-Agent')
except AttributeError:
# Sometimes in testing we will send protocol requests instead
# of flask requests and so the hostname and user agent won't
# be present.
try:
requestData = protocol.fromJson(
flaskrequest, protocol.AnnouncePeerRequest)
except Exception as e:
raise exceptions.InvalidJsonException(e)
except Exception as e:
raise exceptions.InvalidJsonException(e)
# Validate the url before accepting the announcement
peer = datamodel.peers.Peer(requestData.peer.url)
peer.setAttributesJson(protocol.toJson(
requestData.peer.attributes))
announcement['url'] = peer.getUrl()
announcement['attributes'] = peer.getAttributes()
try:
self.getDataRepository().insertAnnouncement(announcement)
except:
raise exceptions.BadRequestException(announcement['url'])
return protocol.toJson(
protocol.AnnouncePeerResponse(success=True))
|
python
|
def runAddAnnouncement(self, flaskrequest):
"""
Takes a flask request from the frontend and attempts to parse
into an AnnouncePeerRequest. If successful, it will log the
announcement to the `announcement` table with some other metadata
gathered from the request.
"""
announcement = {}
# We want to parse the request ourselves to collect a little more
# data about it.
try:
requestData = protocol.fromJson(
flaskrequest.get_data(), protocol.AnnouncePeerRequest)
announcement['hostname'] = flaskrequest.host_url
announcement['remote_addr'] = flaskrequest.remote_addr
announcement['user_agent'] = flaskrequest.headers.get('User-Agent')
except AttributeError:
# Sometimes in testing we will send protocol requests instead
# of flask requests and so the hostname and user agent won't
# be present.
try:
requestData = protocol.fromJson(
flaskrequest, protocol.AnnouncePeerRequest)
except Exception as e:
raise exceptions.InvalidJsonException(e)
except Exception as e:
raise exceptions.InvalidJsonException(e)
# Validate the url before accepting the announcement
peer = datamodel.peers.Peer(requestData.peer.url)
peer.setAttributesJson(protocol.toJson(
requestData.peer.attributes))
announcement['url'] = peer.getUrl()
announcement['attributes'] = peer.getAttributes()
try:
self.getDataRepository().insertAnnouncement(announcement)
except:
raise exceptions.BadRequestException(announcement['url'])
return protocol.toJson(
protocol.AnnouncePeerResponse(success=True))
|
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] |
train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L672-L711
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runListPeers
|
def runListPeers(self, request):
"""
Takes a ListPeersRequest and returns a ListPeersResponse using
a page_token and page_size if provided.
"""
return self.runSearchRequest(
request,
protocol.ListPeersRequest,
protocol.ListPeersResponse,
self.peersGenerator)
|
python
|
def runListPeers(self, request):
"""
Takes a ListPeersRequest and returns a ListPeersResponse using
a page_token and page_size if provided.
"""
return self.runSearchRequest(
request,
protocol.ListPeersRequest,
protocol.ListPeersResponse,
self.peersGenerator)
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L713-L722
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runGetVariant
|
def runGetVariant(self, id_):
"""
Returns a variant with the given id
"""
compoundId = datamodel.VariantCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(compoundId.variant_set_id)
gaVariant = variantSet.getVariant(compoundId)
# TODO variant is a special case here, as it's returning a
# protocol element rather than a datamodel object. We should
# fix this for consistency.
jsonString = protocol.toJson(gaVariant)
return jsonString
|
python
|
def runGetVariant(self, id_):
"""
Returns a variant with the given id
"""
compoundId = datamodel.VariantCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(compoundId.variant_set_id)
gaVariant = variantSet.getVariant(compoundId)
# TODO variant is a special case here, as it's returning a
# protocol element rather than a datamodel object. We should
# fix this for consistency.
jsonString = protocol.toJson(gaVariant)
return jsonString
|
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L724-L736
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runGetBiosample
|
def runGetBiosample(self, id_):
"""
Runs a getBiosample request for the specified ID.
"""
compoundId = datamodel.BiosampleCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
biosample = dataset.getBiosample(id_)
return self.runGetRequest(biosample)
|
python
|
def runGetBiosample(self, id_):
"""
Runs a getBiosample request for the specified ID.
"""
compoundId = datamodel.BiosampleCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
biosample = dataset.getBiosample(id_)
return self.runGetRequest(biosample)
|
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[
"Runs",
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L738-L745
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runGetIndividual
|
def runGetIndividual(self, id_):
"""
Runs a getIndividual request for the specified ID.
"""
compoundId = datamodel.BiosampleCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
individual = dataset.getIndividual(id_)
return self.runGetRequest(individual)
|
python
|
def runGetIndividual(self, id_):
"""
Runs a getIndividual request for the specified ID.
"""
compoundId = datamodel.BiosampleCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
individual = dataset.getIndividual(id_)
return self.runGetRequest(individual)
|
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] |
train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L747-L754
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runGetFeature
|
def runGetFeature(self, id_):
"""
Returns JSON string of the feature object corresponding to
the feature compoundID passed in.
"""
compoundId = datamodel.FeatureCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
featureSet = dataset.getFeatureSet(compoundId.feature_set_id)
gaFeature = featureSet.getFeature(compoundId)
jsonString = protocol.toJson(gaFeature)
return jsonString
|
python
|
def runGetFeature(self, id_):
"""
Returns JSON string of the feature object corresponding to
the feature compoundID passed in.
"""
compoundId = datamodel.FeatureCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
featureSet = dataset.getFeatureSet(compoundId.feature_set_id)
gaFeature = featureSet.getFeature(compoundId)
jsonString = protocol.toJson(gaFeature)
return jsonString
|
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L756-L766
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runGetReadGroupSet
|
def runGetReadGroupSet(self, id_):
"""
Returns a readGroupSet with the given id_
"""
compoundId = datamodel.ReadGroupSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
readGroupSet = dataset.getReadGroupSet(id_)
return self.runGetRequest(readGroupSet)
|
python
|
def runGetReadGroupSet(self, id_):
"""
Returns a readGroupSet with the given id_
"""
compoundId = datamodel.ReadGroupSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
readGroupSet = dataset.getReadGroupSet(id_)
return self.runGetRequest(readGroupSet)
|
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[
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L768-L775
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runGetReadGroup
|
def runGetReadGroup(self, id_):
"""
Returns a read group with the given id_
"""
compoundId = datamodel.ReadGroupCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
readGroupSet = dataset.getReadGroupSet(compoundId.read_group_set_id)
readGroup = readGroupSet.getReadGroup(id_)
return self.runGetRequest(readGroup)
|
python
|
def runGetReadGroup(self, id_):
"""
Returns a read group with the given id_
"""
compoundId = datamodel.ReadGroupCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
readGroupSet = dataset.getReadGroupSet(compoundId.read_group_set_id)
readGroup = readGroupSet.getReadGroup(id_)
return self.runGetRequest(readGroup)
|
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L777-L785
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runGetReference
|
def runGetReference(self, id_):
"""
Runs a getReference request for the specified ID.
"""
compoundId = datamodel.ReferenceCompoundId.parse(id_)
referenceSet = self.getDataRepository().getReferenceSet(
compoundId.reference_set_id)
reference = referenceSet.getReference(id_)
return self.runGetRequest(reference)
|
python
|
def runGetReference(self, id_):
"""
Runs a getReference request for the specified ID.
"""
compoundId = datamodel.ReferenceCompoundId.parse(id_)
referenceSet = self.getDataRepository().getReferenceSet(
compoundId.reference_set_id)
reference = referenceSet.getReference(id_)
return self.runGetRequest(reference)
|
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[
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L787-L795
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runGetReferenceSet
|
def runGetReferenceSet(self, id_):
"""
Runs a getReferenceSet request for the specified ID.
"""
referenceSet = self.getDataRepository().getReferenceSet(id_)
return self.runGetRequest(referenceSet)
|
python
|
def runGetReferenceSet(self, id_):
"""
Runs a getReferenceSet request for the specified ID.
"""
referenceSet = self.getDataRepository().getReferenceSet(id_)
return self.runGetRequest(referenceSet)
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L797-L802
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runGetVariantSet
|
def runGetVariantSet(self, id_):
"""
Runs a getVariantSet request for the specified ID.
"""
compoundId = datamodel.VariantSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(id_)
return self.runGetRequest(variantSet)
|
python
|
def runGetVariantSet(self, id_):
"""
Runs a getVariantSet request for the specified ID.
"""
compoundId = datamodel.VariantSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(id_)
return self.runGetRequest(variantSet)
|
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L804-L811
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runGetFeatureSet
|
def runGetFeatureSet(self, id_):
"""
Runs a getFeatureSet request for the specified ID.
"""
compoundId = datamodel.FeatureSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
featureSet = dataset.getFeatureSet(id_)
return self.runGetRequest(featureSet)
|
python
|
def runGetFeatureSet(self, id_):
"""
Runs a getFeatureSet request for the specified ID.
"""
compoundId = datamodel.FeatureSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
featureSet = dataset.getFeatureSet(id_)
return self.runGetRequest(featureSet)
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L813-L820
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runGetContinuousSet
|
def runGetContinuousSet(self, id_):
"""
Runs a getContinuousSet request for the specified ID.
"""
compoundId = datamodel.ContinuousSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
continuousSet = dataset.getContinuousSet(id_)
return self.runGetRequest(continuousSet)
|
python
|
def runGetContinuousSet(self, id_):
"""
Runs a getContinuousSet request for the specified ID.
"""
compoundId = datamodel.ContinuousSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
continuousSet = dataset.getContinuousSet(id_)
return self.runGetRequest(continuousSet)
|
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|
[
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L822-L829
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runGetDataset
|
def runGetDataset(self, id_):
"""
Runs a getDataset request for the specified ID.
"""
dataset = self.getDataRepository().getDataset(id_)
return self.runGetRequest(dataset)
|
python
|
def runGetDataset(self, id_):
"""
Runs a getDataset request for the specified ID.
"""
dataset = self.getDataRepository().getDataset(id_)
return self.runGetRequest(dataset)
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L831-L836
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runGetVariantAnnotationSet
|
def runGetVariantAnnotationSet(self, id_):
"""
Runs a getVariantSet request for the specified ID.
"""
compoundId = datamodel.VariantAnnotationSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(compoundId.variant_set_id)
variantAnnotationSet = variantSet.getVariantAnnotationSet(id_)
return self.runGetRequest(variantAnnotationSet)
|
python
|
def runGetVariantAnnotationSet(self, id_):
"""
Runs a getVariantSet request for the specified ID.
"""
compoundId = datamodel.VariantAnnotationSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(compoundId.variant_set_id)
variantAnnotationSet = variantSet.getVariantAnnotationSet(id_)
return self.runGetRequest(variantAnnotationSet)
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L838-L846
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runGetRnaQuantification
|
def runGetRnaQuantification(self, id_):
"""
Runs a getRnaQuantification request for the specified ID.
"""
compoundId = datamodel.RnaQuantificationCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
rnaQuantificationSet = dataset.getRnaQuantificationSet(
compoundId.rna_quantification_set_id)
rnaQuantification = rnaQuantificationSet.getRnaQuantification(id_)
return self.runGetRequest(rnaQuantification)
|
python
|
def runGetRnaQuantification(self, id_):
"""
Runs a getRnaQuantification request for the specified ID.
"""
compoundId = datamodel.RnaQuantificationCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
rnaQuantificationSet = dataset.getRnaQuantificationSet(
compoundId.rna_quantification_set_id)
rnaQuantification = rnaQuantificationSet.getRnaQuantification(id_)
return self.runGetRequest(rnaQuantification)
|
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L848-L857
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runGetRnaQuantificationSet
|
def runGetRnaQuantificationSet(self, id_):
"""
Runs a getRnaQuantificationSet request for the specified ID.
"""
compoundId = datamodel.RnaQuantificationSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
rnaQuantificationSet = dataset.getRnaQuantificationSet(id_)
return self.runGetRequest(rnaQuantificationSet)
|
python
|
def runGetRnaQuantificationSet(self, id_):
"""
Runs a getRnaQuantificationSet request for the specified ID.
"""
compoundId = datamodel.RnaQuantificationSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
rnaQuantificationSet = dataset.getRnaQuantificationSet(id_)
return self.runGetRequest(rnaQuantificationSet)
|
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L859-L866
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runGetExpressionLevel
|
def runGetExpressionLevel(self, id_):
"""
Runs a getExpressionLevel request for the specified ID.
"""
compoundId = datamodel.ExpressionLevelCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
rnaQuantificationSet = dataset.getRnaQuantificationSet(
compoundId.rna_quantification_set_id)
rnaQuantification = rnaQuantificationSet.getRnaQuantification(
compoundId.rna_quantification_id)
expressionLevel = rnaQuantification.getExpressionLevel(compoundId)
return self.runGetRequest(expressionLevel)
|
python
|
def runGetExpressionLevel(self, id_):
"""
Runs a getExpressionLevel request for the specified ID.
"""
compoundId = datamodel.ExpressionLevelCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
rnaQuantificationSet = dataset.getRnaQuantificationSet(
compoundId.rna_quantification_set_id)
rnaQuantification = rnaQuantificationSet.getRnaQuantification(
compoundId.rna_quantification_id)
expressionLevel = rnaQuantification.getExpressionLevel(compoundId)
return self.runGetRequest(expressionLevel)
|
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|
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L868-L879
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runSearchReadGroupSets
|
def runSearchReadGroupSets(self, request):
"""
Runs the specified SearchReadGroupSetsRequest.
"""
return self.runSearchRequest(
request, protocol.SearchReadGroupSetsRequest,
protocol.SearchReadGroupSetsResponse,
self.readGroupSetsGenerator)
|
python
|
def runSearchReadGroupSets(self, request):
"""
Runs the specified SearchReadGroupSetsRequest.
"""
return self.runSearchRequest(
request, protocol.SearchReadGroupSetsRequest,
protocol.SearchReadGroupSetsResponse,
self.readGroupSetsGenerator)
|
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Runs the specified SearchReadGroupSetsRequest.
|
[
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] |
train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L883-L890
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runSearchIndividuals
|
def runSearchIndividuals(self, request):
"""
Runs the specified search SearchIndividualsRequest.
"""
return self.runSearchRequest(
request, protocol.SearchIndividualsRequest,
protocol.SearchIndividualsResponse,
self.individualsGenerator)
|
python
|
def runSearchIndividuals(self, request):
"""
Runs the specified search SearchIndividualsRequest.
"""
return self.runSearchRequest(
request, protocol.SearchIndividualsRequest,
protocol.SearchIndividualsResponse,
self.individualsGenerator)
|
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] |
Runs the specified search SearchIndividualsRequest.
|
[
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] |
train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L892-L899
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runSearchBiosamples
|
def runSearchBiosamples(self, request):
"""
Runs the specified SearchBiosamplesRequest.
"""
return self.runSearchRequest(
request, protocol.SearchBiosamplesRequest,
protocol.SearchBiosamplesResponse,
self.biosamplesGenerator)
|
python
|
def runSearchBiosamples(self, request):
"""
Runs the specified SearchBiosamplesRequest.
"""
return self.runSearchRequest(
request, protocol.SearchBiosamplesRequest,
protocol.SearchBiosamplesResponse,
self.biosamplesGenerator)
|
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] |
Runs the specified SearchBiosamplesRequest.
|
[
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] |
train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L901-L908
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runSearchReads
|
def runSearchReads(self, request):
"""
Runs the specified SearchReadsRequest.
"""
return self.runSearchRequest(
request, protocol.SearchReadsRequest,
protocol.SearchReadsResponse,
self.readsGenerator)
|
python
|
def runSearchReads(self, request):
"""
Runs the specified SearchReadsRequest.
"""
return self.runSearchRequest(
request, protocol.SearchReadsRequest,
protocol.SearchReadsResponse,
self.readsGenerator)
|
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Runs the specified SearchReadsRequest.
|
[
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] |
train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L910-L917
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runSearchReferenceSets
|
def runSearchReferenceSets(self, request):
"""
Runs the specified SearchReferenceSetsRequest.
"""
return self.runSearchRequest(
request, protocol.SearchReferenceSetsRequest,
protocol.SearchReferenceSetsResponse,
self.referenceSetsGenerator)
|
python
|
def runSearchReferenceSets(self, request):
"""
Runs the specified SearchReferenceSetsRequest.
"""
return self.runSearchRequest(
request, protocol.SearchReferenceSetsRequest,
protocol.SearchReferenceSetsResponse,
self.referenceSetsGenerator)
|
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Runs the specified SearchReferenceSetsRequest.
|
[
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] |
train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L919-L926
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runSearchReferences
|
def runSearchReferences(self, request):
"""
Runs the specified SearchReferenceRequest.
"""
return self.runSearchRequest(
request, protocol.SearchReferencesRequest,
protocol.SearchReferencesResponse,
self.referencesGenerator)
|
python
|
def runSearchReferences(self, request):
"""
Runs the specified SearchReferenceRequest.
"""
return self.runSearchRequest(
request, protocol.SearchReferencesRequest,
protocol.SearchReferencesResponse,
self.referencesGenerator)
|
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Runs the specified SearchReferenceRequest.
|
[
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L928-L935
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runSearchVariantSets
|
def runSearchVariantSets(self, request):
"""
Runs the specified SearchVariantSetsRequest.
"""
return self.runSearchRequest(
request, protocol.SearchVariantSetsRequest,
protocol.SearchVariantSetsResponse,
self.variantSetsGenerator)
|
python
|
def runSearchVariantSets(self, request):
"""
Runs the specified SearchVariantSetsRequest.
"""
return self.runSearchRequest(
request, protocol.SearchVariantSetsRequest,
protocol.SearchVariantSetsResponse,
self.variantSetsGenerator)
|
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Runs the specified SearchVariantSetsRequest.
|
[
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train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L937-L944
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runSearchVariantAnnotationSets
|
def runSearchVariantAnnotationSets(self, request):
"""
Runs the specified SearchVariantAnnotationSetsRequest.
"""
return self.runSearchRequest(
request, protocol.SearchVariantAnnotationSetsRequest,
protocol.SearchVariantAnnotationSetsResponse,
self.variantAnnotationSetsGenerator)
|
python
|
def runSearchVariantAnnotationSets(self, request):
"""
Runs the specified SearchVariantAnnotationSetsRequest.
"""
return self.runSearchRequest(
request, protocol.SearchVariantAnnotationSetsRequest,
protocol.SearchVariantAnnotationSetsResponse,
self.variantAnnotationSetsGenerator)
|
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] |
Runs the specified SearchVariantAnnotationSetsRequest.
|
[
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"."
] |
train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L946-L953
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runSearchVariants
|
def runSearchVariants(self, request):
"""
Runs the specified SearchVariantRequest.
"""
return self.runSearchRequest(
request, protocol.SearchVariantsRequest,
protocol.SearchVariantsResponse,
self.variantsGenerator)
|
python
|
def runSearchVariants(self, request):
"""
Runs the specified SearchVariantRequest.
"""
return self.runSearchRequest(
request, protocol.SearchVariantsRequest,
protocol.SearchVariantsResponse,
self.variantsGenerator)
|
[
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] |
Runs the specified SearchVariantRequest.
|
[
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"."
] |
train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L955-L962
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runSearchVariantAnnotations
|
def runSearchVariantAnnotations(self, request):
"""
Runs the specified SearchVariantAnnotationsRequest.
"""
return self.runSearchRequest(
request, protocol.SearchVariantAnnotationsRequest,
protocol.SearchVariantAnnotationsResponse,
self.variantAnnotationsGenerator)
|
python
|
def runSearchVariantAnnotations(self, request):
"""
Runs the specified SearchVariantAnnotationsRequest.
"""
return self.runSearchRequest(
request, protocol.SearchVariantAnnotationsRequest,
protocol.SearchVariantAnnotationsResponse,
self.variantAnnotationsGenerator)
|
[
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",",
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",",
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"variantAnnotationsGenerator",
")"
] |
Runs the specified SearchVariantAnnotationsRequest.
|
[
"Runs",
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"."
] |
train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L964-L971
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runSearchCallSets
|
def runSearchCallSets(self, request):
"""
Runs the specified SearchCallSetsRequest.
"""
return self.runSearchRequest(
request, protocol.SearchCallSetsRequest,
protocol.SearchCallSetsResponse,
self.callSetsGenerator)
|
python
|
def runSearchCallSets(self, request):
"""
Runs the specified SearchCallSetsRequest.
"""
return self.runSearchRequest(
request, protocol.SearchCallSetsRequest,
protocol.SearchCallSetsResponse,
self.callSetsGenerator)
|
[
"def",
"runSearchCallSets",
"(",
"self",
",",
"request",
")",
":",
"return",
"self",
".",
"runSearchRequest",
"(",
"request",
",",
"protocol",
".",
"SearchCallSetsRequest",
",",
"protocol",
".",
"SearchCallSetsResponse",
",",
"self",
".",
"callSetsGenerator",
")"
] |
Runs the specified SearchCallSetsRequest.
|
[
"Runs",
"the",
"specified",
"SearchCallSetsRequest",
"."
] |
train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L973-L980
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runSearchDatasets
|
def runSearchDatasets(self, request):
"""
Runs the specified SearchDatasetsRequest.
"""
return self.runSearchRequest(
request, protocol.SearchDatasetsRequest,
protocol.SearchDatasetsResponse,
self.datasetsGenerator)
|
python
|
def runSearchDatasets(self, request):
"""
Runs the specified SearchDatasetsRequest.
"""
return self.runSearchRequest(
request, protocol.SearchDatasetsRequest,
protocol.SearchDatasetsResponse,
self.datasetsGenerator)
|
[
"def",
"runSearchDatasets",
"(",
"self",
",",
"request",
")",
":",
"return",
"self",
".",
"runSearchRequest",
"(",
"request",
",",
"protocol",
".",
"SearchDatasetsRequest",
",",
"protocol",
".",
"SearchDatasetsResponse",
",",
"self",
".",
"datasetsGenerator",
")"
] |
Runs the specified SearchDatasetsRequest.
|
[
"Runs",
"the",
"specified",
"SearchDatasetsRequest",
"."
] |
train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L982-L989
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runSearchFeatureSets
|
def runSearchFeatureSets(self, request):
"""
Returns a SearchFeatureSetsResponse for the specified
SearchFeatureSetsRequest object.
"""
return self.runSearchRequest(
request, protocol.SearchFeatureSetsRequest,
protocol.SearchFeatureSetsResponse,
self.featureSetsGenerator)
|
python
|
def runSearchFeatureSets(self, request):
"""
Returns a SearchFeatureSetsResponse for the specified
SearchFeatureSetsRequest object.
"""
return self.runSearchRequest(
request, protocol.SearchFeatureSetsRequest,
protocol.SearchFeatureSetsResponse,
self.featureSetsGenerator)
|
[
"def",
"runSearchFeatureSets",
"(",
"self",
",",
"request",
")",
":",
"return",
"self",
".",
"runSearchRequest",
"(",
"request",
",",
"protocol",
".",
"SearchFeatureSetsRequest",
",",
"protocol",
".",
"SearchFeatureSetsResponse",
",",
"self",
".",
"featureSetsGenerator",
")"
] |
Returns a SearchFeatureSetsResponse for the specified
SearchFeatureSetsRequest object.
|
[
"Returns",
"a",
"SearchFeatureSetsResponse",
"for",
"the",
"specified",
"SearchFeatureSetsRequest",
"object",
"."
] |
train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L991-L999
|
ga4gh/ga4gh-server
|
ga4gh/server/backend.py
|
Backend.runSearchFeatures
|
def runSearchFeatures(self, request):
"""
Returns a SearchFeaturesResponse for the specified
SearchFeaturesRequest object.
:param request: JSON string representing searchFeaturesRequest
:return: JSON string representing searchFeatureResponse
"""
return self.runSearchRequest(
request, protocol.SearchFeaturesRequest,
protocol.SearchFeaturesResponse,
self.featuresGenerator)
|
python
|
def runSearchFeatures(self, request):
"""
Returns a SearchFeaturesResponse for the specified
SearchFeaturesRequest object.
:param request: JSON string representing searchFeaturesRequest
:return: JSON string representing searchFeatureResponse
"""
return self.runSearchRequest(
request, protocol.SearchFeaturesRequest,
protocol.SearchFeaturesResponse,
self.featuresGenerator)
|
[
"def",
"runSearchFeatures",
"(",
"self",
",",
"request",
")",
":",
"return",
"self",
".",
"runSearchRequest",
"(",
"request",
",",
"protocol",
".",
"SearchFeaturesRequest",
",",
"protocol",
".",
"SearchFeaturesResponse",
",",
"self",
".",
"featuresGenerator",
")"
] |
Returns a SearchFeaturesResponse for the specified
SearchFeaturesRequest object.
:param request: JSON string representing searchFeaturesRequest
:return: JSON string representing searchFeatureResponse
|
[
"Returns",
"a",
"SearchFeaturesResponse",
"for",
"the",
"specified",
"SearchFeaturesRequest",
"object",
"."
] |
train
|
https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/backend.py#L1001-L1012
|
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