from collections import defaultdict
from itertools import combinations
import numpy as np
from gismap.sources.bibtex import pub_to_bibtex
[docs]
def initials(name):
"""
Parameters
----------
name: :class:`str`
Person's name.
Returns
-------
:class:`str`
Person's initials (2 letters only).
"""
first_letters = [w[0] for w in name.split()]
return first_letters[0].upper() + first_letters[-1].upper()
def _publication_metadata(pub):
md = getattr(pub, "metadata", None)
if md is not None:
return md
sources = getattr(pub, "sources", None)
if sources:
return getattr(sources[0], "metadata", None) or {}
return {}
def _resolve_author_url(author):
url = getattr(author, "url", None)
if hasattr(author, "metadata"):
meta_url = getattr(author.metadata, "url", None)
if meta_url:
url = meta_url
elif getattr(author, "sources", None) and hasattr(author.sources[0], "url"):
url = author.sources[0].url
return url
def _author_to_dict(author):
"""Compact dict ``{name, url?}`` for an author of any flavor."""
d = {"name": getattr(author, "name", "Unknown Author")}
url = _resolve_author_url(author)
if url:
d["url"] = url
return d
def _pub_to_dict(pub):
"""Per-publication payload shipped once to JS.
Empty fields are dropped to keep the JSON small.
"""
d = {
"title": pub.title,
"year": pub.year,
"venue": getattr(pub, "venue", "") or "",
"authors": [_author_to_dict(a) for a in getattr(pub, "authors", []) or []],
"bib": pub_to_bibtex(pub),
}
url = getattr(pub, "url", None)
if url:
d["url"] = url
abstract = _publication_metadata(pub).get("abstract") or ""
if abstract:
d["abstract"] = abstract
return d
[docs]
def to_node(s, pub_keys):
"""
Parameters
----------
s: :class:`~gismap.lab.lab_author.LabAuthor`
Author.
pub_keys: :class:`list`
Publication keys associated with this author, year-desc order.
Returns
-------
:class:`dict`
Display-ready data for the node. Modal HTML is rendered on click by
the JS layer using ``pub_keys`` and the shared publications dict.
"""
res = {
"id": s.key,
"name": s.name,
"hover": f"Click for details on {s.name}.",
"group": s.metadata.group,
"pub_keys": pub_keys,
}
url = _resolve_author_url(s)
if url:
res["url"] = url
if s.metadata.img:
res.update({"image": s.metadata.img, "shape": "circularImage"})
else:
res["label"] = initials(s.name)
if s.metadata.position:
x, y = s.metadata.position
res.update({"x": x, "y": y, "fixed": True})
return res
[docs]
def to_edge(k, pub_keys, searchers):
"""
Parameters
----------
k: :class:`tuple`
Keys of the two authors.
pub_keys: :class:`list`
Joint publication keys, year-desc order.
searchers: :class:`dict`
Authors keyed by author key.
Returns
-------
:class:`dict`
Display-ready data for the collaboration edge.
"""
strength = 1 + np.log2(len(pub_keys))
res = {
"from": k[0],
"to": k[1],
"hover": f"Show joint publications from {searchers[k[0]].name} and {searchers[k[1]].name}",
"width": int(strength),
"length": int(200 / strength),
"pub_keys": pub_keys,
}
g1, g2 = searchers[k[0]].metadata.group, searchers[k[1]].metadata.group
if g1 and g2 and g1 != g2:
res["color"] = "rgba(0,0,0,0)"
return res
[docs]
def lab_to_graph(lab):
"""
Parameters
----------
lab: :class:`~gismap.lab.labmap.LabMap`
A lab populated with authors and publications.
Returns
-------
:class:`tuple`
``(nodes, edges, publications)`` where ``nodes`` and ``edges`` carry
only display data plus ``pub_keys`` references, and ``publications``
is a dict keyed by publication key with the full per-pub payload
(title, authors, venue, year, url, abstract, bib). Modal HTML is
built JS-side from this shared dict, so each publication is shipped
only once even when it touches many authors and pairs.
Examples
--------
>>> from gismap.lab import ListMap as Map
>>> lab = Map(author_list=['Tixeuil Sébastien', 'Mathieu Fabien'], name='mini', dbs="hal")
>>> lab.update_authors()
>>> lab.update_publis()
>>> len(lab.authors)
2
>>> 320 < len(lab.publications) < 430
True
>>> nodes, edges, pubs = lab_to_graph(lab)
>>> nodes[0]['group']
'mini'
>>> edges[0]['hover']
'Show joint publications from Mathieu Fabien and Tixeuil Sébastien'
>>> sample = next(iter(pubs.values()))
>>> {'title', 'authors', 'bib'} <= set(sample)
True
>>> html = lab.html(groups={"mini": {"color": "#777"}})
"""
node_pubs = defaultdict(list)
edges_dict = defaultdict(list)
for p in lab.publications.values():
# Strange things can happen with multiple sources. This should take care of it.
lauths = {a.key: a for source in p.sources for a in source.authors if a.__class__.__name__ == "LabAuthor"}
lauths = sorted([a for a in lauths.values()], key=lambda a: str(a.key))
for a in lauths:
node_pubs[a.key].append(p)
for a1, a2 in combinations(lauths, 2):
edges_dict[a1.key, a2.key].append(p)
for k, v in node_pubs.items():
node_pubs[k] = [p.key for p in sorted(v, key=lambda p: -p.year)]
for k, v in edges_dict.items():
edges_dict[k] = [p.key for p in sorted(v, key=lambda p: -p.year)]
nodes = [to_node(s, node_pubs.get(s.key, [])) for s in lab.authors.values()]
edges = [to_edge(k, v, lab.authors) for k, v in edges_dict.items()]
publications = {pk: _pub_to_dict(p) for pk, p in lab.publications.items()}
return nodes, edges, publications
