def latex(self):
"""Render latex template"""
rc = self.rc
for p in self.gtx['people']:
names = frozenset(p.get('aka', []) + [p['name']])
pubs = filter_publications(
all_docs_from_collection(rc.client, 'citations'),
names, reverse=True)
bibfile = make_bibtex_file(pubs, pid=p['_id'],
person_dir=self.bldir)
emp = p.get('employment', [])
emp.sort(key=ene_date_key, reverse=True)
edu = p.get('education', [])
edu.sort(key=ene_date_key, reverse=True)
projs = filter_projects(
all_docs_from_collection(rc.client, 'projects'), names)
grants = list(all_docs_from_collection(rc.client, 'grants'))
pi_grants, pi_amount, _ = filter_grants(grants, names, pi=True)
coi_grants, coi_amount, coi_sub_amount = filter_grants(grants,
names,
pi=False)
aghs = awards_grants_honors(p)
self.render('cv.tex', p['_id'] + '.tex', p=p,
title=p.get('name', ''), aghs=aghs,
pubs=pubs, names=names, bibfile=bibfile,
education=edu, employment=emp, projects=projs,
pi_grants=pi_grants, pi_amount=pi_amount,
coi_grants=coi_grants, coi_amount=coi_amount,
coi_sub_amount=coi_sub_amount,
)
def people(self):
"""Render people, former members, and each person"""
rc = self.rc
peeps_dir = os.path.join(self.bldir, "people")
former_peeps_dir = os.path.join(self.bldir, "former")
os.makedirs(peeps_dir, exist_ok=True)
os.makedirs(former_peeps_dir, exist_ok=True)
peeps = self.gtx["people"]
#peeps = all_docs_from_collection(rc.client), "people")
for p in peeps:
names = frozenset(p.get("aka", []) + [p["name"]])
pubs = filter_publications(
all_docs_from_collection(rc.client, "citations"),
names,
reverse=True,
bold=False,
)
bibfile = make_bibtex_file(pubs,
pid=p["_id"],
person_dir=peeps_dir)
ene = p.get("employment", []) + p.get("education", [])
ene.sort(key=ene_date_key, reverse=True)
for e in ene:
dereference_institution(
e, all_docs_from_collection(rc.client, "institutions"))
projs = filter_projects(
all_docs_from_collection(rc.client, "projects"), names)
for serve in p.get("service", []):
serve_dates = get_dates(serve)
date = serve_dates.get("date")
if not date:
date = serve_dates.get("end_date")
if not date:
date = serve_dates.get("begin_date")
serve["year"] = date.year
serve["month"] = date.month
sns = p.get("service", [])
sns.sort(key=ene_date_key, reverse=True)
p["service"] = sns
self.render(
"person.html",
os.path.join("people", p["_id"] + ".html"),
p=p,
title=p.get("name", ""),
pubs=pubs,
names=names,
bibfile=bibfile,
education_and_employment=ene,
projects=projs,
)
self.render("people.html",
os.path.join("people", "index.html"),
title="People")
self.render(
"former.html",
os.path.join("former", "index.html"),
title="Former Members",
)
def latex(self):
"""Render latex template"""
rc = self.rc
if rc.people:
people = [
fuzzy_retrieval(self.gtx["people"], ["aka", "_id", "name"],
rc.people[0])
]
else:
people = self.gtx["people"]
for p in people:
names = frozenset(p.get("aka", []) + [p["name"]])
pubs = filter_publications(
all_docs_from_collection(rc.client, "citations"),
names,
reverse=True,
)
bibfile = make_bibtex_file(pubs,
pid=p["_id"],
person_dir=self.bldir)
emp = p.get("employment", [])
emp = [em for em in emp if not em.get("not_in_cv", False)]
for e in emp:
e['position'] = e.get('position_full',
e.get('position').title())
emp.sort(key=ene_date_key, reverse=True)
edu = p.get("education", [])
edu.sort(key=ene_date_key, reverse=True)
projs = filter_projects(
all_docs_from_collection(rc.client, "projects"), names)
grants = list(all_docs_from_collection(rc.client, "grants"))
proposals = list(all_docs_from_collection(rc.client, "proposals"))
grants = merge_collections_superior(proposals, grants,
"proposal_id")
pi_grants, pi_amount, _ = filter_grants(grants, names, pi=True)
coi_grants, coi_amount, coi_sub_amount = filter_grants(grants,
names,
pi=False)
aghs = awards_grants_honors(p, "honors")
self.render(
"resume.tex",
p["_id"] + ".tex",
p=p,
title=p.get("name", ""),
aghs=aghs,
pubs=pubs,
names=names,
bibfile=bibfile,
education=edu,
employment=emp,
projects=projs,
pi_grants=pi_grants,
pi_amount=pi_amount,
coi_grants=coi_grants,
coi_amount=coi_amount,
coi_sub_amount=coi_sub_amount,
)
self.pdf(p["_id"])
def latex(self):
"""Render latex template"""
rc = self.rc
for p in self.gtx["people"]:
# so we don't modify the dbs when de-referencing
names = frozenset(p.get("aka", []) + [p["name"]])
pubs = filter_publications(
all_docs_from_collection(rc.client, "citations"),
names,
reverse=True,
)
bibfile = make_bibtex_file(
pubs, pid=p["_id"], person_dir=self.bldir
)
emp = p.get("employment", [])
for e in emp:
e['position'] = e.get('position_full', e.get('position').title())
emp.sort(key=ene_date_key, reverse=True)
edu = p.get("education", [])
edu.sort(key=ene_date_key, reverse=True)
teach = p.get("teaching", [])
for t in teach:
t['position'] = t.get('position').title()
projs = filter_projects(
all_docs_from_collection(rc.client, "projects"), names
)
grants = list(all_docs_from_collection(rc.client, "grants"))
pi_grants, pi_amount, _ = filter_grants(grants, names, pi=True)
coi_grants, coi_amount, coi_sub_amount = filter_grants(
grants, names, pi=False
)
aghs = awards_grants_honors(p)
# TODO: pull this out so we can use it everywhere
for ee in [emp, edu]:
for e in ee:
dereference_institution(e, self.gtx["institutions"])
self.render(
"cv.tex",
p["_id"] + ".tex",
p=p,
title=p.get("name", ""),
aghs=aghs,
pubs=pubs,
names=names,
bibfile=bibfile,
education=edu,
employment=emp,
projects=projs,
pi_grants=pi_grants,
pi_amount=pi_amount,
coi_grants=coi_grants,
coi_amount=coi_amount,
coi_sub_amount=coi_sub_amount,
)
self.pdf(p["_id"])
def get_person_pubs(coll, person):
"""Get the publications from one person."""
my_names = frozenset(person.get("aka", []) + [person["name"]])
pubs = filter_publications(
coll,
my_names,
reverse=True,
bold=False
)
return pubs
def latex(self):
"""Render latex template"""
rc = self.rc
for p in self.gtx["people"]:
names = frozenset(p.get("aka", []) + [p["name"]])
pubs = filter_publications(
all_docs_from_collection(rc.client, "citations"),
names,
reverse=True,
)
bibfile = make_bibtex_file(pubs,
pid=p["_id"],
person_dir=self.bldir)
emp = p.get("employment", [])
for e in emp:
e['position'] = e.get('position_full',
e.get('position').title())
emp.sort(key=ene_date_key, reverse=True)
edu = p.get("education", [])
edu.sort(key=ene_date_key, reverse=True)
projs = filter_projects(
all_docs_from_collection(rc.client, "projects"), names)
grants = list(all_docs_from_collection(rc.client, "grants"))
pi_grants, pi_amount, _ = filter_grants(grants, names, pi=True)
coi_grants, coi_amount, coi_sub_amount = filter_grants(grants,
names,
pi=False)
aghs = awards_grants_honors(p)
self.render(
"resume.tex",
p["_id"] + ".tex",
p=p,
title=p.get("name", ""),
aghs=aghs,
pubs=pubs,
names=names,
bibfile=bibfile,
education=edu,
employment=emp,
projects=projs,
pi_grants=pi_grants,
pi_amount=pi_amount,
coi_grants=coi_grants,
coi_amount=coi_amount,
coi_sub_amount=coi_sub_amount,
)
self.pdf(p["_id"])
def people(self):
"""Render people, former members, and each person"""
rc = self.rc
peeps_dir = os.path.join(self.bldir, 'people')
former_peeps_dir = os.path.join(self.bldir, 'former')
os.makedirs(peeps_dir, exist_ok=True)
os.makedirs(former_peeps_dir, exist_ok=True)
for p in self.gtx['people']:
names = frozenset(p.get('aka', []) + [p['name']])
pubs = filter_publications(all_docs_from_collection(
rc.client, 'citations'),
names,
reverse=True,
bold=False)
bibfile = make_bibtex_file(pubs,
pid=p['_id'],
person_dir=peeps_dir)
ene = p.get('employment', []) + p.get('education', [])
ene.sort(key=ene_date_key, reverse=True)
projs = filter_projects(
all_docs_from_collection(rc.client, 'projects'), names)
self.render('person.html',
os.path.join('people', p['_id'] + '.html'),
p=p,
title=p.get('name', ''),
pubs=pubs,
names=names,
bibfile=bibfile,
education_and_employment=ene,
projects=projs)
self.render('people.html',
os.path.join('people', 'index.html'),
title='People')
self.render('former.html',
os.path.join('former', 'index.html'),
title='Former Members')
def latex(self):
fd = gr = False
filestub, qualifiers = "", ""
if self.rc.from_date:
from_date = date_parser.parse(self.rc.from_date).date()
filestub = filestub + "_from{}".format(from_date)
qualifiers = qualifiers + "in the period from {}".format(from_date)
if self.rc.to_date:
to_date = date_parser.parse(self.rc.to_date).date()
filestub = filestub + "_to{}".format(to_date)
qualifiers = qualifiers + " to {}".format(to_date)
else:
to_date = None
else:
from_date, to_date = None, None
if self.rc.grants:
gr = True
grants = self.rc.grants
if isinstance(grants, str):
grants = [grants]
if len(grants) > 2:
text_grants = ", and ".join(
[",".join(grants[:-1]), grants[-1]])
elif len(grants) == 2:
text_grants = "and ".join([grants[0], grants[1]])
elif len(grants) == 1:
text_grants = grants[0]
cat_grants, all_grants = "", ""
for g in grants:
cat_grants = cat_grants + "_" + g
filestub = filestub + "".format(cat_grants)
qualifiers = qualifiers + " from grants {}".format(text_grants)
for p in self.gtx["people"]:
if self.rc.people[0] != 'all':
if p.get("_id") != self.rc.people[0]:
continue
outfile = p["_id"] + filestub
p['qualifiers'] = qualifiers
names = frozenset(p.get("aka", []) + [p["name"]])
citations = list(self.gtx["citations"])
grants = self.rc.grants
pubs_nobold = filter_publications(citations,
names,
reverse=True,
bold=False,
ackno=False,
since=from_date,
before=to_date,
grants=grants)
pubs_ackno = filter_publications(citations,
names,
reverse=True,
bold=False,
ackno=True,
since=from_date,
before=to_date,
grants=grants)
pubs = filter_publications(citations,
names,
reverse=True,
ackno=False,
bold=True,
since=from_date,
before=to_date,
grants=grants)
bibfile = self.make_bibtex_file(pubs,
pid=p["_id"],
person_dir=self.bldir)
bibfile_nobold = self.make_bibtex_file(pubs_nobold,
pid=f"{p['_id']}_nobold",
person_dir=self.bldir)
bibfile_ackno = self.make_bibtex_file(pubs_ackno,
pid=f"{p['_id']}_ackno",
person_dir=self.bldir)
if not p.get('email'):
p['email'] = ""
emp = p.get("employment", [{'organization': ""}])
emp.sort(key=ene_date_key, reverse=True)
self.render(
"publist.tex",
outfile + ".tex",
p=p,
title=p.get("name", ""),
pubs=pubs,
names=names,
bibfile=bibfile,
employment=emp,
)
self.render(
"publist_nobold.tex",
outfile + "_nobold.tex",
p=p,
title=p.get("name", ""),
pubs=pubs_nobold,
names=names,
bibfile=bibfile_nobold,
employment=emp,
)
self.render(
"publist_ackno.tex",
outfile + "_ackno.tex",
p=p,
title=p.get("name", ""),
pubs=pubs_ackno,
names=names,
bibfile=bibfile_ackno,
employment=emp,
)
self.pdf(p["_id"])
self.render(
"publist_pandoc_friendly.tex",
outfile + "_pandoc.tex",
p=p,
title=p.get("name", ""),
pubs=pubs_nobold,
names=names,
bibfile=bibfile_nobold,
employment=emp,
)
def latex(self):
"""Render latex template"""
rc = self.rc
if not rc.people:
raise RuntimeError("ERROR: please rerun specifying --people name")
if not rc.from_date:
raise RuntimeError("ERROR: please rerun specifying --from")
build_target = get_id_from_name(
all_docs_from_collection(rc.client, "people"), rc.people[0])
begin_year = int(rc.from_date.split("-")[0])
begin_period = date_parser.parse(rc.from_date).date()
pre_begin_period = begin_period - relativedelta(years=1)
if rc.to_date:
to_date = date_parser.parse(rc.to_date).date()
end_period = to_date
post_end_period = to_date + relativedelta(years=1)
else:
end_period = begin_period + relativedelta(years=1) - relativedelta(
days=1)
post_end_period = begin_period + relativedelta(
years=2) - relativedelta(days=1)
me = [p for p in self.gtx["people"] if p["_id"] == build_target][0]
me["begin_period"] = dt.date.strftime(begin_period, "%m/%d/%Y")
me["begin_period"] = dt.date.strftime(begin_period, "%m/%d/%Y")
me["pre_begin_period"] = dt.date.strftime(pre_begin_period, "%m/%d/%Y")
me["end_period"] = dt.date.strftime(end_period, "%m/%d/%Y")
me["post_end_period"] = dt.date.strftime(post_end_period, "%m/%d/%Y")
projs = filter_projects(self.gtx["projects"],
set([build_target]),
group="bg")
#########
# highlights
#########
for proj in projs:
if proj.get('highlights'):
proj["current_highlights"] = False
for highlight in proj.get('highlights'):
highlight_date = dt.date(
highlight.get("year"),
month_to_int(highlight.get("month", 1)), 1)
if highlight_date > begin_period and highlight_date < end_period:
highlight["is_current"] = True
proj["current_highlights"] = True
#########
# current and pending
#########
pi = fuzzy_retrieval(self.gtx["people"], ["aka", "name", "_id"],
build_target)
# pi['initials'] = "SJLB"
grants = merge_collections_superior(self.gtx["proposals"],
self.gtx["grants"], "proposal_id")
for g in grants:
for person in g["team"]:
rperson = fuzzy_retrieval(self.gtx["people"], ["aka", "name"],
person["name"])
if rperson:
person["name"] = rperson["name"]
if g.get('budget'):
amounts = [i.get('amount') for i in g.get('budget')]
g['subaward_amount'] = sum(amounts)
current_grants = [dict(g) for g in grants if is_current(g)]
current_grants, _, _ = filter_grants(current_grants, {pi["name"]},
pi=False,
multi_pi=True)
pending_grants = [
g for g in self.gtx["proposals"] if g["status"] == "pending"
]
for g in pending_grants:
for person in g["team"]:
rperson = fuzzy_retrieval(self.gtx["people"], ["aka", "name"],
person["name"])
if rperson:
person["name"] = rperson["name"]
pending_grants, _, _ = filter_grants(pending_grants, {pi["name"]},
pi=False,
multi_pi=True)
grants = pending_grants + current_grants
for grant in grants:
grant.update(
award_start_date="{2}/{1}/{0}".format(
grant["begin_day"],
month_to_int(grant["begin_month"]),
grant["begin_year"],
),
award_end_date="{2}/{1}/{0}".format(
grant["end_day"],
month_to_int(grant["end_month"]),
grant["end_year"],
),
)
badids = [
i["_id"] for i in current_grants
if not i['cpp_info'].get('cppflag', "")
]
iter = copy(current_grants)
for grant in iter:
if grant["_id"] in badids:
current_grants.remove(grant)
#########
# end current and pending
#########
#########
# advising
#########
undergrads = filter_employment_for_advisees(self.gtx["people"],
begin_period, "undergrad")
masters = filter_employment_for_advisees(self.gtx["people"],
begin_period, "ms")
currents = filter_employment_for_advisees(self.gtx["people"],
begin_period, "phd")
graduateds = filter_employment_for_advisees(
self.gtx["people"], begin_period.replace(year=begin_year - 5),
"phd")
postdocs = filter_employment_for_advisees(self.gtx["people"],
begin_period, "postdoc")
visitors = filter_employment_for_advisees(self.gtx["people"],
begin_period,
"visitor-unsupported")
iter = deepcopy(graduateds)
for g in iter:
if g.get("active"):
graduateds.remove(g)
iter = deepcopy(currents)
for g in iter:
if not g.get("active"):
currents.remove(g)
######################
# service
#####################
mego = deepcopy(me)
dept_service = filter_service([mego], begin_period, "department")
mego = deepcopy(me)
school_service = filter_service([mego], begin_period, "school")
mego = deepcopy(me)
uni_service = filter_service([mego], begin_period, "university")
uni_service.extend(school_service)
mego = deepcopy(me)
prof_service = filter_service([mego], begin_period, "profession")
mego = deepcopy(me)
outreach = filter_service([mego], begin_period, "outreach")
mego = deepcopy(me)
lab = filter_facilities([mego], begin_period, "research")
mego = deepcopy(me)
shared = filter_facilities([mego], begin_period, "shared")
mego = deepcopy(me)
fac_other = filter_facilities([mego], begin_period, "other")
mego = deepcopy(me)
fac_teaching = filter_facilities([mego], begin_period, "teaching")
mego = deepcopy(me)
fac_wishlist = filter_facilities([mego],
begin_period,
"research_wish",
verbose=False)
mego = deepcopy(me)
tch_wishlist = filter_facilities([mego], begin_period, "teaching_wish")
mego = deepcopy(me)
curric_dev = filter_activities([mego], begin_period, "teaching")
mego = deepcopy(me)
other_activities = filter_activities([mego], begin_period, "other")
##########################
# Presentation list
##########################
keypres = filter_presentations(self.gtx["people"],
self.gtx["presentations"],
self.gtx["institutions"],
build_target,
types=["award", "plenary", "keynote"],
since=begin_period,
before=end_period,
statuses=["accepted"])
invpres = filter_presentations(self.gtx["people"],
self.gtx["presentations"],
self.gtx["institutions"],
build_target,
types=["invited"],
since=begin_period,
before=end_period,
statuses=["accepted"])
sempres = filter_presentations(self.gtx["people"],
self.gtx["presentations"],
self.gtx["institutions"],
build_target,
types=["colloquium", "seminar"],
since=begin_period,
before=end_period,
statuses=["accepted"])
declpres = filter_presentations(self.gtx["people"],
self.gtx["presentations"],
self.gtx["institutions"],
build_target,
types=["all"],
since=begin_period,
before=end_period,
statuses=["declined"])
#########################
# Awards
#########################
ahs = awards(me, since=begin_period)
########################
# Publications
########################
names = frozenset(me.get("aka", []) + [me["name"]])
pubs = filter_publications(all_docs_from_collection(
rc.client, "citations"),
names,
reverse=True,
bold=False,
since=begin_period)
bibfile = make_bibtex_file(pubs, pid=me["_id"], person_dir=self.bldir)
articles = [prc for prc in pubs if prc.get("entrytype") in "article"]
nonarticletypes = [
"book", "inbook", "proceedings", "inproceedings", "incollection",
"unpublished", "phdthesis", "misc"
]
nonarticles = [
prc for prc in pubs if prc.get("entrytype") in nonarticletypes
]
peer_rev_conf_pubs = [prc for prc in pubs if prc.get("peer_rev_conf")]
pubiter = deepcopy(pubs)
for prc in pubiter:
if prc.get("peer_rev_conf"):
peer_rev_conf_pubs = prc
pubs.pop(prc)
##############
# TODO: add Current Projects to Research summary section
##############
#############
# IP
#############
patents = filter_patents(self.gtx["patents"],
self.gtx["people"],
build_target,
since=begin_period)
licenses = filter_licenses(self.gtx["patents"],
self.gtx["people"],
build_target,
since=begin_period)
#############
# hindex
#############
hindex = sorted(me["hindex"], key=doc_date_key).pop()
#########################
# render
#########################
self.render(
"columbia_annual_report.tex",
"billinge-ann-report.tex",
pi=pi,
p=me,
projects=projs,
pending=pending_grants,
current=current_grants,
undergrads=undergrads,
masters=masters,
currentphds=currents,
graduatedphds=graduateds,
postdocs=postdocs,
visitors=visitors,
dept_service=dept_service,
uni_service=uni_service,
prof_service=prof_service,
outreach=outreach,
lab=lab,
shared=shared,
facilities_other=fac_other,
fac_teaching=fac_teaching,
fac_wishlist=fac_wishlist,
tch_wishlist=tch_wishlist,
curric_dev=curric_dev,
other_activities=other_activities,
keypres=keypres,
invpres=invpres,
sempres=sempres,
declpres=declpres,
sentencecase=sentencecase,
monthstyle=month_fullnames,
ahs=ahs,
pubs=articles,
nonarticles=nonarticles,
peer_rev_conf_pubs=peer_rev_conf_pubs,
bibfile=bibfile,
patents=patents,
licenses=licenses,
hindex=hindex,
)
self.pdf("billinge-ann-report")
def test_author_publications():
citations = [{'author': ['CJ', 'SJLB']}, {'editor': 'SJLB'}]
filter_publications(citations, {'SJLB'})
def latex(self):
"""Render latex template"""
rc = self.rc
for p in self.gtx["people"]:
# so we don't modify the dbs when de-referencing
names = frozenset(p.get("aka", []) + [p["name"]] + [p["_id"]])
begin_period = date(1650, 1, 1)
pubs = filter_publications(
all_docs_from_collection(rc.client, "citations"),
names,
reverse=True,
)
bibfile = make_bibtex_file(pubs,
pid=p["_id"],
person_dir=self.bldir)
emp = p.get("employment", [])
for e in emp:
e['position'] = e.get('position_full',
e.get('position').title())
emp.sort(key=ene_date_key, reverse=True)
edu = p.get("education", [])
edu.sort(key=ene_date_key, reverse=True)
teach = p.get("teaching", [])
for t in teach:
t['position'] = t.get('position').title()
projs = filter_projects(
all_docs_from_collection(rc.client, "projects"), names)
just_grants = list(all_docs_from_collection(rc.client, "grants"))
just_proposals = list(
all_docs_from_collection(rc.client, "proposals"))
grants = merge_collections_superior(just_proposals, just_grants,
"proposal_id")
presentations = filter_presentations(self.gtx["people"],
self.gtx["presentations"],
self.gtx["institutions"],
p.get("_id"),
statuses=["accepted"])
for grant in grants:
for member in grant.get("team"):
dereference_institution(member, self.gtx["institutions"])
pi_grants, pi_amount, _ = filter_grants(grants, names, pi=True)
coi_grants, coi_amount, coi_sub_amount = filter_grants(grants,
names,
pi=False)
aghs = awards_grants_honors(p, "honors")
service = awards_grants_honors(p, "service", funding=False)
# TODO: pull this out so we can use it everywhere
for ee in [emp, edu]:
for e in ee:
dereference_institution(e, self.gtx["institutions"])
undergrads = filter_employment_for_advisees(
self.gtx["people"], begin_period, "undergrad")
masters = filter_employment_for_advisees(self.gtx["people"],
begin_period, "ms")
currents = filter_employment_for_advisees(self.gtx["people"],
begin_period, "phd")
graduateds = filter_employment_for_advisees(
self.gtx["people"], begin_period, "phd")
postdocs = filter_employment_for_advisees(self.gtx["people"],
begin_period, "postdoc")
visitors = filter_employment_for_advisees(self.gtx["people"],
begin_period,
"visitor-unsupported")
iter = deepcopy(graduateds)
for g in iter:
if g.get("active"):
graduateds.remove(g)
iter = deepcopy(currents)
for g in iter:
if not g.get("active"):
currents.remove(g)
self.render(
"cv.tex",
p["_id"] + ".tex",
p=p,
title=p.get("name", ""),
aghs=aghs,
service=service,
undergrads=undergrads,
masters=masters,
currentphds=currents,
graduatedphds=graduateds,
postdocs=postdocs,
visitors=visitors,
pubs=pubs,
names=names,
bibfile=bibfile,
education=edu,
employment=emp,
presentations=presentations,
sentencecase=sentencecase,
monthstyle=month_fullnames,
projects=projs,
pi_grants=pi_grants,
pi_amount=pi_amount,
coi_grants=coi_grants,
coi_amount=coi_amount,
coi_sub_amount=coi_sub_amount,
)
self.pdf(p["_id"])
def test_author_publications():
citations = [{"author": ["CJ", "SJLB"]}, {"editor": "SJLB"}]
filter_publications(citations, {"SJLB"})
def latex(self):
"""Render latex template"""
rc = self.rc
group = fuzzy_retrieval(self.gtx['groups'], ["_id", "aka", "name"],
rc.groupname)
if not rc.people:
raise RuntimeError("ERROR: please rerun specifying --people name")
if not rc.from_date:
raise RuntimeError("ERROR: please rerun specifying --from")
build_target = get_id_from_name(
all_docs_from_collection(rc.client, "people"), rc.people[0])
begin_year = int(rc.from_date.split("-")[0])
begin_period = date_parser.parse(rc.from_date).date()
pre_begin_period = begin_period - relativedelta(years=1)
if rc.to_date:
to_date = date_parser.parse(rc.to_date).date()
end_period = to_date
post_end_period = to_date + relativedelta(years=1)
else:
end_period = begin_period + relativedelta(years=1) - relativedelta(
days=1)
post_end_period = begin_period + relativedelta(
years=2) - relativedelta(days=1)
me = [p for p in self.gtx["people"] if p["_id"] == build_target][0]
me["begin_period"] = dt.date.strftime(begin_period, "%m/%d/%Y")
me["begin_period"] = dt.date.strftime(begin_period, "%m/%d/%Y")
me["pre_begin_period"] = dt.date.strftime(pre_begin_period, "%m/%d/%Y")
me["end_period"] = dt.date.strftime(end_period, "%m/%d/%Y")
me["post_end_period"] = dt.date.strftime(post_end_period, "%m/%d/%Y")
projs = filter_projects(self.gtx["projects"],
set([build_target]),
group=group["_id"])
########
# Recommendation Letters count
########
recletts = self.gtx['recletts']
num_recletts = len([
reclett["_id"] for reclett in recletts
if get_dates(reclett).get("end_date") >= begin_period
])
########
# Proposal review count
########
proprevs = self.gtx['proprevs']
num_proprevs = len([
proprev["_id"] for proprev in proprevs
if get_dates(proprev).get("end_date") >= begin_period
and proprev.get('status') == 'submitted'
])
########
# Manuscript review count
########
manrevs = self.gtx['manrevs']
num_manrevs = len([
manrev["_id"] for manrev in manrevs
if manrev.get("status") == "submitted"
and get_dates(manrev, date_field_prefix="submitted").get(
"submitted_date", dt.date(1971, 1, 1)) is not None
and get_dates(manrev, date_field_prefix="submitted").get(
"submitted_date", dt.date(1971, 1, 1)) >= begin_period
])
#########
# highlights
#########
for proj in projs:
if proj.get('highlights'):
proj["current_highlights"] = False
for highlight in proj.get('highlights'):
highlight_date = get_dates(highlight)
if highlight_date.get("end_date") >= begin_period:
highlight["is_current"] = True
proj["current_highlights"] = True
#########
# current and pending
#########
pi = fuzzy_retrieval(self.gtx["people"], ["aka", "name"],
group["pi_name"])
pinames = pi["name"].split()
piinitialslist = [i[0] for i in pinames]
pi['initials'] = "".join(piinitialslist).upper()
grants = merge_collections_all(self.gtx["proposals"],
self.gtx["grants"], "proposal_id")
for g in grants:
g['end_date'] = get_dates(g).get('end_date')
g['begin_date'] = get_dates(g).get('begin_date',
dt.date(1900, 1, 2))
g['award_start_date'] = "{}/{}/{}".format(
g.get("begin_date").month,
g.get("begin_date").day,
g.get("begin_date").year,
)
g['award_end_date'] = "{}/{}/{}".format(
g.get("end_date").month,
g.get("end_date").day,
g.get("end_date").year)
for person in g.get("team", []):
rperson = fuzzy_retrieval(self.gtx["people"], ["aka", "name"],
person["name"])
if rperson:
person["name"] = rperson["name"]
if g.get('budget'):
amounts = [i.get('amount') for i in g.get('budget')]
g['subaward_amount'] = sum(amounts)
current_grants = [dict(g) for g in grants if is_current(g)]
current_grants, _, _ = filter_grants(current_grants, {pi["name"]},
pi=False,
multi_pi=True)
current_grants = [
g for g in current_grants if g.get("status") != "declined"
]
for g in current_grants:
if g.get('budget'):
amounts = [i.get('amount') for i in g.get('budget')]
g['subaward_amount'] = sum(amounts)
pending_grants = [
g for g in self.gtx["proposals"] if is_pending(g["status"])
]
for g in pending_grants:
for person in g["team"]:
rperson = fuzzy_retrieval(self.gtx["people"], ["aka", "name"],
person["name"])
if rperson:
person["name"] = rperson["name"]
pending_grants, _, _ = filter_grants(pending_grants, {pi["name"]},
pi=False,
multi_pi=True)
badids = [
i["_id"] for i in current_grants
if not i.get('cpp_info').get('cppflag', "")
]
declined_proposals = [
g for g in self.gtx["proposals"] if is_declined(g["status"])
]
for g in declined_proposals:
for person in g["team"]:
rperson = fuzzy_retrieval(self.gtx["people"], ["aka", "name"],
person["name"])
if rperson:
person["name"] = rperson["name"]
declined_proposals, _, _ = filter_grants(declined_proposals,
{pi["name"]},
pi=False,
multi_pi=True)
declined_proposals = [
proposal for proposal in declined_proposals
if get_dates(proposal).get('begin_date') >= begin_period
and get_dates(proposal, date_field_prefix="submitted").get(
'submitted_date', end_period) <= end_period
]
iter = copy(current_grants)
for grant in iter:
if grant["_id"] in badids:
current_grants.remove(grant)
#########
# end current and pending
#########
#########
# advising
#########
undergrads = filter_employment_for_advisees(self.gtx["people"],
begin_period, "undergrad",
rc.people[0])
masters = filter_employment_for_advisees(self.gtx["people"],
begin_period, "ms",
rc.people[0])
currents = filter_employment_for_advisees(self.gtx["people"],
begin_period, "phd",
rc.people[0])
graduateds = filter_employment_for_advisees(
self.gtx["people"], begin_period.replace(year=begin_year - 5),
"phd", rc.people[0])
postdocs = filter_employment_for_advisees(self.gtx["people"],
begin_period, "postdoc",
rc.people[0])
visitors = filter_employment_for_advisees(self.gtx["people"],
begin_period,
"visitor-unsupported",
rc.people[0])
iter = deepcopy(graduateds)
for g in iter:
if g.get("active"):
graduateds.remove(g)
iter = deepcopy(currents)
for g in iter:
if not g.get("active"):
currents.remove(g)
######################
# service
#####################
mego = deepcopy(me)
dept_service = filter_service(mego, begin_period, "department")
mego = deepcopy(me)
school_service = filter_service(mego, begin_period, "school")
mego = deepcopy(me)
uni_service = filter_service(mego, begin_period, "university")
uni_service.extend(school_service)
if num_recletts > 0:
uni_service.append({
"name":
f"Wrote recommendation letters for {num_recletts} "
f"people this period"
})
mego = deepcopy(me)
prof_service = filter_service(mego, begin_period, "profession")
if num_proprevs > 0:
prof_service.append({
"name":
f"Reviewed {num_proprevs} funding proposals for "
f"national agencies this period"
})
if num_manrevs > 0:
prof_service.append({
"name":
f"Reviewed {num_manrevs} manuscripts for "
f"peer reviewed journals this period"
})
mego = deepcopy(me)
phd_defenses = filter_committees(mego, begin_period, "phddefense")
phd_proposals = filter_committees(mego, begin_period, "phdproposal")
phd_orals = filter_committees(mego, begin_period, "phdoral")
mego = deepcopy(me)
outreach = filter_service(mego, begin_period, "outreach")
mego = deepcopy(me)
lab = filter_facilities([mego], begin_period, "research")
mego = deepcopy(me)
shared = filter_facilities([mego], begin_period, "shared")
mego = deepcopy(me)
fac_other = filter_facilities([mego], begin_period, "other")
mego = deepcopy(me)
fac_teaching = filter_facilities([mego], begin_period, "teaching")
mego = deepcopy(me)
fac_wishlist = filter_facilities([mego],
begin_period,
"research_wish",
verbose=False)
mego = deepcopy(me)
tch_wishlist = filter_facilities([mego], begin_period, "teaching_wish")
mego = deepcopy(me)
curric_dev = filter_activities([mego], begin_period, "teaching")
mego = deepcopy(me)
other_activities = filter_activities([mego], begin_period, "other")
##########################
# Presentation list
##########################
keypres = filter_presentations(self.gtx["people"],
self.gtx["presentations"],
self.gtx["institutions"],
build_target,
types=["award", "plenary", "keynote"],
since=begin_period,
before=end_period,
statuses=["accepted"])
invpres = filter_presentations(self.gtx["people"],
self.gtx["presentations"],
self.gtx["institutions"],
build_target,
types=["invited"],
since=begin_period,
before=end_period,
statuses=["accepted"])
sempres = filter_presentations(self.gtx["people"],
self.gtx["presentations"],
self.gtx["institutions"],
build_target,
types=["colloquium", "seminar"],
since=begin_period,
before=end_period,
statuses=["accepted"])
declpres = filter_presentations(self.gtx["people"],
self.gtx["presentations"],
self.gtx["institutions"],
build_target,
types=["all"],
since=begin_period,
before=end_period,
statuses=["declined"])
#########################
# Awards
#########################
ahs = awards(me, since=begin_period)
########################
# Publications
########################
names = frozenset(me.get("aka", []) + [me["name"]])
pubs = filter_publications(all_docs_from_collection(
rc.client, "citations"),
names,
reverse=True,
bold=False,
since=begin_period)
#remove unpublished papers
# unpubs = [pub for pub in pubs if len(pub.get("doi") == 0)]
pubed = [pub for pub in pubs if len(pub.get("doi")) > 0]
non_arts = [pub for pub in pubs if pub.get("entrytype") != "article"]
pubs = pubed + non_arts
bibfile = make_bibtex_file(pubs, pid=me["_id"], person_dir=self.bldir)
articles = [
prc for prc in pubs if prc.get("entrytype") == "article"
and not prc.get("peer_rev_conf")
]
NONARTICLETYPES = [
"book", "inbook", "proceedings", "inproceedings", "incollection",
"unpublished", "phdthesis", "misc"
]
nonarticles = [
prc for prc in pubs if prc.get("entrytype") in NONARTICLETYPES
]
peer_rev_conf_pubs = [prc for prc in pubs if prc.get("peer_rev_conf")]
##############
# TODO: add Current Projects to Research summary section
##############
#############
# IP
#############
patents = filter_patents(self.gtx["patents"],
self.gtx["people"],
build_target,
since=begin_period)
licenses = filter_licenses(self.gtx["patents"],
self.gtx["people"],
build_target,
since=begin_period)
#############
# hindex
#############
if not me.get("miscellaneous"):
me["miscellaneous"] = {"metrics_for_success": []}
if me.get("hindex"):
hindex = sorted(me["hindex"], key=doc_date_key).pop()
#########################
# render
#########################
self.render(
"columbia_annual_report.tex",
f"{pi['_id']}-ann-report.tex",
pi=pi,
p=me,
projects=projs,
pending=pending_grants,
current=current_grants,
declined=declined_proposals,
undergrads=undergrads,
masters=masters,
currentphds=currents,
graduatedphds=graduateds,
postdocs=postdocs,
visitors=visitors,
phd_defenses=phd_defenses,
phd_proposals=phd_proposals,
phd_orals=phd_orals,
dept_service=dept_service,
uni_service=uni_service,
prof_service=prof_service,
outreach=outreach,
lab=lab,
shared=shared,
facilities_other=fac_other,
fac_teaching=fac_teaching,
fac_wishlist=fac_wishlist,
tch_wishlist=tch_wishlist,
curric_dev=curric_dev,
other_activities=other_activities,
keypres=keypres,
invpres=invpres,
sempres=sempres,
declpres=declpres,
sentencecase=sentencecase,
monthstyle=month_fullnames,
ahs=ahs,
pubs=articles,
nonarticles=nonarticles,
peer_rev_conf_pubs=peer_rev_conf_pubs,
bibfile=bibfile,
patents=patents,
licenses=licenses,
hindex=hindex,
)
self.pdf("billinge-ann-report")
def latex(self):
"""Render latex template"""
rc = self.rc
if not rc.people:
raise RuntimeError("ERROR: please rerun specifying --people name")
if not rc.from_date:
raise RuntimeError("ERROR: please rerun specifying --from")
build_target = get_id_from_name(
all_docs_from_collection(rc.client, "people"), rc.people[0])
begin_year = int(rc.from_date.split("-")[0])
begin_month = int(rc.from_date.split("-")[1])
pre_begin_year = begin_year - 1
end_year = begin_year + 1
end_month = begin_month - 1
post_end_year = begin_year + 2
begin_period = dt.date(begin_year, begin_month, 1)
pre_begin_period = dt.date(pre_begin_year, begin_month, 1)
end_period = dt.date(end_year, end_month, 28)
post_end_period = dt.date(post_end_year, end_month, 28)
me = [p for p in self.gtx["people"] if p["_id"] == build_target][0]
me["begin_period"] = dt.date.strftime(begin_period, "%m/%d/%Y")
me["begin_period"] = dt.date.strftime(begin_period, "%m/%d/%Y")
me["pre_begin_period"] = dt.date.strftime(pre_begin_period, "%m/%d/%Y")
me["end_period"] = dt.date.strftime(end_period, "%m/%d/%Y")
me["post_end_period"] = dt.date.strftime(post_end_period, "%m/%d/%Y")
projs = filter_projects(
self.gtx["projects"], set([build_target]),
group="bg"
)
#########
# highlights
#########
for proj in projs:
if proj.get('highlights'):
proj["current_highlights"] = False
for highlight in proj.get('highlights'):
highlight_date = dt.date(highlight.get("year"),
month_to_int(highlight.get("month", 1)),
1)
if highlight_date > begin_period and highlight_date < end_period:
highlight["is_current"] = True
proj["current_highlights"] = True
#########
# current and pending
#########
#########
# end current and pending
#########
#########
# advising
#########
undergrads = filter_employment_for_advisees(self.gtx["people"],
begin_period,
"undergrad")
masters = filter_employment_for_advisees(self.gtx["people"],
begin_period,
"ms")
currents = filter_employment_for_advisees(self.gtx["people"],
begin_period,
"phd")
graduateds = filter_employment_for_advisees(self.gtx["people"],
begin_period.replace(
year=begin_year - 5),
"phd")
postdocs = filter_employment_for_advisees(self.gtx["people"],
begin_period,
"postdoc")
visitors = filter_employment_for_advisees(self.gtx["people"],
begin_period,
"visitor-unsupported")
iter = deepcopy(graduateds)
for g in iter:
if g.get("active"):
graduateds.remove(g)
iter = deepcopy(currents)
for g in iter:
if not g.get("active"):
currents.remove(g)
######################
# service
#####################
mego = deepcopy(me)
dept_service = filter_service([mego],
begin_period, "department")
mego = deepcopy(me)
school_service = filter_service([mego],
begin_period, "school")
mego = deepcopy(me)
uni_service = filter_service([mego],
begin_period, "university")
uni_service.extend(school_service)
mego = deepcopy(me)
prof_service = filter_service([mego],
begin_period, "profession")
mego = deepcopy(me)
outreach = filter_service([mego],
begin_period, "outreach")
mego = deepcopy(me)
lab = filter_facilities([mego],
begin_period, "research")
mego = deepcopy(me)
shared = filter_facilities([mego],
begin_period, "shared")
mego = deepcopy(me)
fac_other = filter_facilities([mego],
begin_period, "other")
mego = deepcopy(me)
fac_teaching = filter_facilities([mego],
begin_period, "teaching")
mego = deepcopy(me)
fac_wishlist = filter_facilities([mego],
begin_period, "research_wish",
verbose=False)
mego = deepcopy(me)
tch_wishlist = filter_facilities([mego],
begin_period, "teaching_wish")
mego = deepcopy(me)
curric_dev = filter_activities([mego],
begin_period, "teaching")
mego = deepcopy(me)
other_activities = filter_activities([mego],
begin_period, "other")
##########################
# Presentation list
##########################
keypres = filter_presentations(self.gtx["people"],
self.gtx["presentations"],
self.gtx["institutions"],
build_target,
types=["award", "plenary", "keynote"],
since=begin_period, before=end_period,
statuses=["accepted"])
invpres = filter_presentations(self.gtx["people"],
self.gtx["presentations"],
self.gtx["institutions"],
build_target,
types=["invited"],
since=begin_period, before=end_period,
statuses=["accepted"])
sempres = filter_presentations(self.gtx["people"],
self.gtx["presentations"],
self.gtx["institutions"],
build_target,
types=["colloquium", "seminar"],
since=begin_period, before=end_period,
statuses=["accepted"])
declpres = filter_presentations(self.gtx["people"],
self.gtx["presentations"],
self.gtx["institutions"],
build_target,
types=["all"],
since=begin_period, before=end_period,
statuses=["declined"])
#########################
# Awards
#########################
ahs = awards(me, since=begin_period)
########################
# Publications
########################
names = frozenset(me.get("aka", []) + [me["name"]])
pubs = filter_publications(
all_docs_from_collection(rc.client, "citations"),
names,
reverse=True,
bold=False,
since=begin_period
)
bibfile = make_bibtex_file(
pubs, pid=me["_id"], person_dir=self.bldir
)
articles = [prc for prc in pubs if
prc.get("entrytype") in "article"]
nonarticletypes = ["book", "inbook", "proceedings", "inproceedings",
"incollection", "unpublished", "phdthesis", "misc"]
nonarticles = [prc for prc in pubs if
prc.get("entrytype") in nonarticletypes]
peer_rev_conf_pubs = [prc for prc in pubs if prc.get("peer_rev_conf")]
pubiter = deepcopy(pubs)
for prc in pubiter:
if prc.get("peer_rev_conf"):
peer_rev_conf_pubs = prc
pubs.pop(prc)
##############
# TODO: add Current Projects to Research summary section
##############
#############
# IP
#############
patents = filter_patents(self.gtx["patents"], self.gtx["people"],
build_target, since=begin_period)
licenses = filter_licenses(self.gtx["patents"], self.gtx["people"],
build_target, since=begin_period)
#############
# hindex
#############
hindex = sorted(me["hindex"], key=doc_date_key).pop()
#########################
# render
#########################
# "C:/Users/simon/scratch/billinge-ann-report.tex",
self.render(
"columbia_annual_report.tex",
"billinge-ann-report.tex",
pi=pi,
p=me,
projects=projs,
pending=pending_grants,
current=current_grants,
undergrads=undergrads,
masters=masters,
currentphds=currents,
graduatedphds=graduateds,
postdocs=postdocs,
visitors=visitors,
dept_service=dept_service,
uni_service=uni_service,
prof_service=prof_service,
outreach=outreach,
lab=lab,
shared=shared,
facilities_other=fac_other,
fac_teaching=fac_teaching,
fac_wishlist=fac_wishlist,
tch_wishlist=tch_wishlist,
curric_dev=curric_dev,
other_activities=other_activities,
keypres=keypres,
invpres=invpres,
sempres=sempres,
declpres=declpres,
sentencecase=sentencecase,
monthstyle=month_fullnames,
ahs=ahs,
pubs=articles,
nonarticles=nonarticles,
peer_rev_conf_pubs=peer_rev_conf_pubs,
bibfile=bibfile,
patents=patents,
licenses=licenses,
hindex=hindex,
)
self.pdf("billinge-ann-report")
