class Biopepa_Model_Parser(): def __init__(self): self.loc_results = {} self.loc_tree = {} self.tree = None def parse(self, path): data = self.open_model(path) locations = self.get_locations(data) self.parse_location(locations) def open_model(self, model): with open(model, 'r') as f: data = f.read() return data def get_locations(self, data): locations = [] location_lines = re.findall("location (.*?)\n", data) for location in location_lines: locations.append("location " + location) return locations def parse_location(self, locations): for location in locations: try: loc_type = re.findall("type = (.*?);", location)[0].strip() loc_size = "Remove this" loc_name = re.findall("location (.*?) ", location)[0].strip() loc_parent = re.findall( "in (.*?):", location)[0].strip() if len( re.findall("in (.*?):", location)) > 0 else "root" if loc_name != "mechanisms": self.loc_results[loc_name] = Location( loc_name, loc_size, loc_parent, loc_type) except: print "malformed location line: " + location def __str__(self): output = "" for location in self.loc_results: output += self.loc_results[location].__str__() return output def build_graph(self): if self.loc_results != {}: self.tree = LocationTree(self.loc_results) return self.tree.build_tree() return {}
class Biopepa_Model_Parser(): def __init__(self): self.loc_results = {} self.loc_tree = {} self.tree = None def parse(self, path): data = self.open_model(path) locations = self.get_locations(data) self.parse_location(locations) def open_model(self, model): with open(model, 'r') as f: data = f.read() return data def get_locations(self, data): locations = [] location_lines = re.findall("location (.*?)\n", data) for location in location_lines: locations.append("location " + location) return locations def parse_location(self, locations): for location in locations: try: loc_type = re.findall("type = (.*?);", location)[0].strip() loc_size = "Remove this" loc_name = re.findall("location (.*?) ", location)[0].strip() loc_parent = re.findall("in (.*?):", location)[0].strip() if len(re.findall("in (.*?):", location)) > 0 else "root" if loc_name != "mechanisms": self.loc_results[loc_name] = Location(loc_name, loc_size, loc_parent, loc_type) except: print "malformed location line: " + location def __str__(self): output = "" for location in self.loc_results: output += self.loc_results[location].__str__() return output def build_graph(self): if self.loc_results != {}: self.tree = LocationTree(self.loc_results) return self.tree.build_tree() return {}
def build_graph(self): if self.loc_results != {}: self.tree = LocationTree(self.loc_results) return self.tree.build_tree() return {}
def build_graph(self): if self.loc_results != {}: self.tree = LocationTree(self.loc_results) return self.tree.build_tree() return {}