def construct_global_ctx(self):
"""Constructs the global context"""
super().construct_global_ctx()
gtx = self.gtx
rc = self.rc
if "groups" in self.needed_dbs:
rc.pi_id = get_pi_id(rc)
rc.coll = f"{TARGET_COLL}"
try:
if not rc.database:
rc.database = rc.databases[0]["name"]
except:
pass
colls = [
sorted(all_docs_from_collection(rc.client, collname), key=_id_key)
for collname in self.needed_dbs
]
for db, coll in zip(self.needed_dbs, colls):
gtx[db] = coll
gtx["grants"] = merge_collections(gtx["proposals"], gtx["grants"],
"proposal_id")
gtx["all_docs_from_collection"] = all_docs_from_collection
gtx["float"] = float
gtx["str"] = str
gtx["zip"] = zip
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"))
proposals = list(all_docs_from_collection(rc.client, "proposals"))
grants = merge_collections(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)
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"""
for group in self.gtx["groups"]:
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(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)
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)
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.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 test_merge_collections(input, expected):
a = input[0]
b = input[1]
target_id = "linked_to"
assert merge_collections(a, b, target_id) == expected
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
#fixme this won't work if end_month is january
if rc.to_date:
end_year = rc.to_date.split("-")[0]
end_month = rc.to_date.split("-")[0]
else:
end_year = begin_year + 1
end_month = begin_month - 1
post_end_year = end_year + 1
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(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
)
# print("current: {}".format(current_grants))
pending_grants = [
g
for g in self.gtx["proposals"]
if g["status"] == "pending"
]
# print("pending: {}".format(pending_grants))
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
#########################
# "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")