def ndex(username, password):
"""Upload to NDEx."""
try:
from ndex2 import NiceCXBuilder
except ImportError:
click.secho('Need to `pip install ndex2` before uploading to NDEx', fg='red')
return
miriam_validator = MiriamValidator()
positive_mappings = load_mappings()
cx = NiceCXBuilder()
cx.set_name('Biomappings')
cx.add_network_attribute('description', 'Manually curated mappings (skos:exactMatch) between biological entities.')
cx.add_network_attribute('reference', 'https://github.com/biomappings/biomappings')
cx.add_network_attribute('rights', 'Waiver-No rights reserved (CC0)')
context = {'orcid': 'https://identifiers.org/orcid:'}
for mapping in positive_mappings:
for prefix in (mapping['source prefix'], mapping['target prefix']):
if miriam_validator.namespace_embedded(prefix):
prefix = prefix.upper()
context[prefix] = f'https://identifiers.org/{prefix}:'
cx.set_context(context)
cx.add_network_attribute('version', get_git_hash())
authors = sorted(set(
mapping['source']
for mapping in positive_mappings
if mapping['source'].startswith('orcid:')
))
cx.add_network_attribute('author', authors, type='list_of_string')
for mapping in tqdm(positive_mappings, desc='Loading NiceCXBuilder'):
source = cx.add_node(
represents=mapping['source name'],
name=miriam_validator.get_curie(mapping["source prefix"], mapping["source identifier"]),
)
target = cx.add_node(
represents=mapping['target name'],
name=miriam_validator.get_curie(mapping["target prefix"], mapping["target identifier"]),
)
edge = cx.add_edge(
source=source,
target=target,
interaction=mapping['relation'],
)
cx.add_edge_attribute(edge, 'type', mapping['type'])
cx.add_edge_attribute(edge, 'provenance', mapping['source'])
nice_cx = cx.get_nice_cx()
nice_cx.update_to(
uuid=BIOMAPPINGS_NDEX_UUID,
server=pystow.get_config('ndex', 'server', 'http://public.ndexbio.org'),
username=pystow.get_config('ndex', 'username', username),
password=pystow.get_config('ndex', 'password', password),
)
def get_sssom_df():
"""Get an SSSOM dataframe."""
import pandas as pd
rows = []
prefixes = set()
columns = [
"subject_id",
"predicate_id",
"object_id",
"subject_label",
"object_label",
"match_type",
"creator_id",
"confidence",
"mapping_tool",
]
for mapping in load_mappings():
prefixes.add(mapping["source prefix"])
prefixes.add(mapping["target prefix"])
rows.append(
(
validator.get_curie(mapping["source prefix"], mapping["source identifier"]),
f'{mapping["relation"]}',
validator.get_curie(mapping["target prefix"], mapping["target identifier"]),
mapping["source name"],
mapping["target name"],
"HumanCurated", # match type
mapping["source"], # curator CURIE
None, # no confidence necessary
None, # mapping tool: none necessary for manually curated
)
)
for mapping in load_predictions():
prefixes.add(mapping["source prefix"])
prefixes.add(mapping["target prefix"])
rows.append(
(
validator.get_curie(mapping["source prefix"], mapping["source identifier"]),
f'{mapping["relation"]}',
validator.get_curie(mapping["target prefix"], mapping["target identifier"]),
mapping["source name"],
mapping["target name"],
"LexicalEquivalenceMatch", # match type
None, # no curator CURIE
mapping["confidence"],
mapping["source"], # mapping tool: source script
)
)
df = pd.DataFrame(rows, columns=columns)
return prefixes, df
# -*- coding: utf-8 -*-
"""Validation tests for :mod:`biomappings`."""
import itertools as itt
from collections import Counter
from biomappings import load_false_mappings, load_mappings, load_predictions, load_unsure
from biomappings.resources import mapping_sort_key
from biomappings.utils import MiriamValidator, get_canonical_tuple
mappings = load_mappings()
predictions = load_predictions()
incorrect = load_false_mappings()
unsure = load_unsure()
miriam_validator = MiriamValidator()
def test_valid_mappings():
"""Test the validity of the prefixes and identifiers in the mappings."""
for mapping in itt.chain(mappings, incorrect, predictions):
miriam_validator.check_valid_prefix_id(
mapping["source prefix"],
mapping["source identifier"],
)
miriam_validator.check_valid_prefix_id(
mapping["target prefix"],
mapping["target identifier"],
)
def ndex(username, password):
"""Upload to NDEx."""
try:
from ndex2 import NiceCXBuilder
except ImportError:
click.secho("Need to `pip install ndex2` before uploading to NDEx",
fg="red")
return
miriam_validator = MiriamValidator()
positive_mappings = load_mappings()
cx = NiceCXBuilder()
cx.set_name("Biomappings")
cx.add_network_attribute(
"description",
"Manually curated mappings (skos:exactMatch) between biological entities."
)
cx.add_network_attribute("reference",
"https://github.com/biomappings/biomappings")
cx.add_network_attribute("rights", "Waiver-No rights reserved (CC0)")
context = {"orcid": "https://identifiers.org/orcid:"}
for mapping in positive_mappings:
for prefix in (mapping["source prefix"], mapping["target prefix"]):
if miriam_validator.namespace_embedded(prefix):
prefix = prefix.upper()
context[prefix] = f"https://identifiers.org/{prefix}:"
cx.set_context(context)
cx.add_network_attribute("version", get_git_hash())
authors = sorted(
set(mapping["source"] for mapping in positive_mappings
if mapping["source"].startswith("orcid:")))
cx.add_network_attribute("author", authors, type="list_of_string")
for mapping in tqdm(positive_mappings, desc="Loading NiceCXBuilder"):
source = cx.add_node(
represents=mapping["source name"],
name=miriam_validator.get_curie(mapping["source prefix"],
mapping["source identifier"]),
)
target = cx.add_node(
represents=mapping["target name"],
name=miriam_validator.get_curie(mapping["target prefix"],
mapping["target identifier"]),
)
edge = cx.add_edge(
source=source,
target=target,
interaction=mapping["relation"],
)
cx.add_edge_attribute(edge, "type", mapping["type"])
cx.add_edge_attribute(edge, "provenance", mapping["source"])
nice_cx = cx.get_nice_cx()
nice_cx.update_to(
uuid=BIOMAPPINGS_NDEX_UUID,
server=pystow.get_config("ndex",
"server",
default="http://public.ndexbio.org"),
username=pystow.get_config("ndex", "username", passthrough=username),
password=pystow.get_config("ndex", "password", passthrough=password),
)