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Source code for galaxy.visualization.data_providers.phyloviz

""" Data providers code for PhyloViz """
from typing import Any, Dict

from galaxy.visualization.data_providers.basic import BaseDataProvider
from galaxy.visualization.data_providers.phyloviz.newickparser import Newick_Parser
from galaxy.visualization.data_providers.phyloviz.nexusparser import Nexus_Parser
from galaxy.visualization.data_providers.phyloviz.phyloxmlparser import Phyloxml_Parser

[docs]class PhylovizDataProvider(BaseDataProvider): dataset_type = "phylo"
[docs] def __init__(self, original_dataset=None): super().__init__(original_dataset=original_dataset)
[docs] def get_data(self, tree_index=0): """ Returns trees. Trees are actually an array of JsonDicts. It's usually one tree, except in the case of Nexus """ file_ext = self.original_dataset.datatype.file_ext file_name = self.original_dataset.file_name parseMsg = None jsonDicts = [] rval: Dict[str, Any] = {'dataset_type': self.dataset_type} if file_ext in ["newick", "nhx"]: # parses newick files newickParser = Newick_Parser() jsonDicts, parseMsg = newickParser.parseFile(file_name) elif file_ext == "phyloxml": # parses phyloXML files phyloxmlParser = Phyloxml_Parser() jsonDicts, parseMsg = phyloxmlParser.parseFile(file_name) elif file_ext == "nex": # parses nexus files nexusParser = Nexus_Parser() jsonDicts, parseMsg = nexusParser.parseFile(file_name) jsonDicts = jsonDicts[int(tree_index)] rval["trees"] = parseMsg rval["data"] = jsonDicts rval["msg"] = parseMsg return rval