def __init__(self, parser, writer=None):
self.parser = parser
self.writer = writer
self.graf = graf.Graph()
self.tier_hierarchies = []
self.meta_information = None
self.primary_data = None
def write(self, outputfile, ag):
"""Writes an AnnotationGraph object as GrAF files.
Parameters
----------
outputfile : str
The filename of the output file. The filename should be the header
file for GrAF with the extension ".hdr".
ag : poioapi.annotationgraph.AnnotationGraph
An AnnotationGraph object. The AG object containes the data that
will be use for output.
"""
(basedirname, _) = os.path.splitext(outputfile)
self._get_parents(ag.tier_hierarchies)
standoffrenderer = graf.StandoffHeaderRenderer(
"{0}.hdr".format(basedirname))
for tier_name in self._flatten_hierarchy_elements(ag.tier_hierarchies):
annotation_space = tier_name.split(GRAFSEPARATOR)[0]
out_graf = graf.Graph()
renderer = graf.GrafRenderer("{0}-{1}.xml".format(
basedirname, annotation_space))
out_graf.nodes = [
n for n in ag.graf.nodes if n.id.startswith(tier_name)
]
out_graf.edges = [
e for e in ag.graf.edges if e.to_node.id.startswith(tier_name)
]
out_graf.regions = [
r for r in ag.graf.regions if r.id.startswith(tier_name)
]
out_graf.annotation_spaces.add(
graf.AnnotationSpace(annotation_space))
out_graf.header.add_dependency(self._parent[tier_name])
out_graf = self._add_root_nodes(ag.graf, annotation_space,
out_graf)
renderer.render(out_graf)
basename = os.path.basename(basedirname)
self.standoffheader.datadesc.add_annotation(
"{0}-{1}.xml".format(basename, annotation_space),
annotation_space)
self._add_primary_data(ag.primary_data, basedirname)
standoffrenderer.render(self.standoffheader)
self._generate_metafile(basedirname, ag.meta_information)
def write(self,
outputfile,
graf_graph,
tier_hierarchies,
primary_data=None,
meta_information=None):
"""Writes the converter object as GrAF files.
Parameters
----------
outputfile : str
The filename of the output file. The filename should be the header
file for GrAF with the extension ".hdr".
graf_graph : GrAF
tier_hierarchies : array_like
primary_data : object
This object will contain the information to the dataDesc primaryData.
meta_information : ElementTree
Element tree contains extra information about a specific object.
"""
(basedirname, _) = os.path.splitext(outputfile)
self._get_parents(tier_hierarchies)
standoffrenderer = graf.StandoffHeaderRenderer(
"{0}.hdr".format(basedirname))
for tier_name in self._flatten_hierarchy_elements(tier_hierarchies):
annotation_space = tier_name.split(GRAFSEPARATOR)[0]
out_graf = graf.Graph()
renderer = graf.GrafRenderer("{0}-{1}.xml".format(
basedirname, annotation_space))
out_graf.nodes = [
n for n in graf_graph.nodes if n.id.startswith(tier_name)
]
out_graf.edges = [
e for e in graf_graph.edges
if e.to_node.id.startswith(tier_name)
]
out_graf.regions = [
r for r in graf_graph.regions if r.id.startswith(tier_name)
]
out_graf.annotation_spaces.add(
graf.AnnotationSpace(annotation_space))
out_graf.header.add_dependency(self._parent[tier_name])
out_graf = self._add_root_nodes(graf_graph, annotation_space,
out_graf)
renderer.render(out_graf)
basename = os.path.basename(basedirname)
self.standoffheader.datadesc.add_annotation(
"{0}-{1}.xml".format(basename, annotation_space),
annotation_space)
self._add_primary_data(primary_data, basedirname)
standoffrenderer.render(self.standoffheader)
self._generate_metafile(basedirname, meta_information)