def latex(self):
"""Render latex template"""
gtx = self.gtx
rc = self.rc
for group in self.gtx["groups"]:
gtx["grants"] = list(sorted(
all_docs_from_collection(rc.client, "grants"), key=_id_key
))
gtx["proposals"] = list(sorted(
all_docs_from_collection(rc.client, "proposals"), key=_id_key
))
grp = group["_id"]
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))
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
)
summed_grants = pending_grants + current_grants
for grant in summed_grants:
grant.update(
award_start_date="{}/{}/{}".format(
grant.get("begin_date").month,
grant.get("begin_date").day,
grant.get("begin_date").year,
),
award_end_date="{}/{}/{}".format(
grant.get("end_date").month,
grant.get("end_date").day,
grant.get("end_date").year,
),
)
badids = [i["_id"] for i in current_grants if
not i.get('cpp_info').get('cppflag', "")]
iter = copy(current_grants)
for grant in iter:
if grant["_id"] in badids:
current_grants.remove(grant)
piname = HumanName(pi["name"])
outfile = "current-pending-{}-{}".format(grp, piname.last.lower())
self.render(
"current_pending.tex",
outfile + ".tex",
pi=pi,
pending=pending_grants,
current=current_grants,
pi_upper=pi["name"].upper(),
group=group,
)
self.pdf(outfile)
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")