mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-08-31 01:02:04 +08:00
mvdbeek
63 lines
2.2 KiB
Python
63 lines
2.2 KiB
Python
"""This script loads a Galaxy datatypes registry against Galaxy's datatypes_conf.xml.sample file
|
|
and uses it to generate a tabular file with four columns
|
|
|
|
- Galaxy datatype as short extension (e.g. bam)
|
|
- EDAM format (e.g. format_XXXX)
|
|
- EDAM label.
|
|
- EDAM definition.
|
|
|
|
This file is printed to standard out. This script is designed to be
|
|
run from the Galaxy root.
|
|
|
|
% python script/edam_mapping.py > edam_mapping.tsv
|
|
"""
|
|
|
|
import os
|
|
import sys
|
|
from xml import etree
|
|
|
|
from galaxy.util import requests
|
|
|
|
sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib")))
|
|
|
|
import galaxy.datatypes.registry
|
|
import galaxy.model
|
|
|
|
SCRIPTS_DIR = os.path.dirname(__file__)
|
|
PROJECT_DIR = os.path.abspath(os.path.join(SCRIPTS_DIR, os.pardir))
|
|
CONFIG_FILE = os.path.join(PROJECT_DIR, "config", "datatypes_conf.xml.sample")
|
|
|
|
datatypes_registry = galaxy.datatypes.registry.Registry()
|
|
datatypes_registry.load_datatypes(root_dir=PROJECT_DIR, config=CONFIG_FILE)
|
|
|
|
EDAM_OWL_URL = (
|
|
"http://data.bioontology.org/ontologies/EDAM/submissions/25/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb"
|
|
)
|
|
|
|
|
|
if not os.path.exists("/tmp/edam.owl"):
|
|
open("/tmp/edam.owl", "w").write(requests.get(EDAM_OWL_URL).text)
|
|
|
|
|
|
owl_xml_tree = etree.ElementTree.parse("/tmp/edam.owl")
|
|
format_info = {}
|
|
for child in owl_xml_tree.getroot().findall("{http://www.w3.org/2002/07/owl#}Class"):
|
|
about = child.attrib.get("{http://www.w3.org/1999/02/22-rdf-syntax-ns#}about")
|
|
if not about:
|
|
continue
|
|
if not about.startswith("http://edamontology.org/format_"):
|
|
continue
|
|
the_format = about[len("http://edamontology.org/") :]
|
|
label = child.find("{http://www.w3.org/2000/01/rdf-schema#}label").text
|
|
definition = ""
|
|
def_el = child.find("{http://www.geneontology.org/formats/oboInOwl#}hasDefinition")
|
|
if def_el is not None:
|
|
definition = def_el.text
|
|
format_info[the_format] = {"label": label, "definition": definition}
|
|
|
|
for ext, edam_format in sorted(datatypes_registry.edam_formats.items()):
|
|
edam_info = format_info[edam_format]
|
|
edam_label = edam_info["label"]
|
|
edam_definition = edam_info["definition"]
|
|
print(f"{ext}\t{edam_format}\t{edam_label}\t{edam_definition}")
|