def sout(self):
rc = self.rc
if rc.filter:
collection = key_value_pair_filter(self.gtx["grants"], rc.filter)
else:
collection = self.gtx["grants"]
grants = []
if rc.date:
desired_date = date_parser.parse(rc.date).date()
else:
desired_date = dt.date.today()
for grant in collection:
if rc.current and not is_current(grant, now=desired_date):
continue
if not rc.verbose:
if grant.get("alias") not in BLACKLIST:
grants.append(grant)
else:
grants.append(grant)
# Sort the grants by end date in reverse chronological order
grants.sort(key=lambda k: get_dates(k).get('end_date'), reverse=True)
if rc.keys:
results = (collection_str(grants, rc.keys))
print(results, end="")
return
for g in grants:
print("{}, awardnr: {}, acctn: {}, {} to {}".format(
g.get('alias', ''), g.get('awardnr', ''), g.get('account', ''),
get_dates(g).get('begin_date'),
get_dates(g).get('end_date')))
return
def sout(self):
rc = self.rc
list_search = []
collection = self.gtx["contacts"]
if rc.name:
list_search.extend(["name", rc.name])
if rc.inst:
list_search.extend(["institution", rc.inst])
if rc.notes:
list_search.extend(["notes", rc.notes])
if rc.filter:
list_search.extend(rc.filter)
filtered_contacts_id = (search_collection(collection, list_search)).strip(' \n')
filtered_contacts_id = list(filtered_contacts_id.split(' \n'))
if rc.date:
date_list = []
temp_dat = date_parser.parse(rc.date).date()
temp_dict = {"begin_date": (temp_dat - dateutil.relativedelta.relativedelta(
months=int(rc.range))).isoformat(),
"end_date": (temp_dat + dateutil.relativedelta.relativedelta(
months=int(rc.range))).isoformat()}
for contact in collection:
curr_d = get_dates(contact)['date']
if is_current(temp_dict, now=curr_d):
date_list.append(contact.get('_id'))
filtered_contacts_id = [value for value in filtered_contacts_id if value in date_list]
filtered_contacts = []
string_contacts = ''
for contact in collection:
if contact.get('_id') in filtered_contacts_id:
filtered_contacts.append(contact)
institution = contact.get('institution')
institution_name = fuzzy_retrieval(self.gtx['institutions'],
['name', '_id', 'aka'], institution)
if institution_name:
contact['institution'] = institution_name.get('name')
if rc.verbose:
contact_str = f"{contact.get('name')}\n"
for k in ['_id', 'email', 'institution', 'department', 'notes', 'aka']:
if contact.get(k):
if isinstance(contact.get(k), list):
lst_expanded = '\n -'.join(map(str, contact.get(k)))
contact_str += f" {k}:\n -{lst_expanded}\n"
else:
contact_str += f" {k}: {contact.get(k)}\n"
string_contacts += contact_str
else:
string_contacts += f"{contact.get('name')} | {contact.get('_id')} |" \
f" institution: {contact.get('institution')} |" \
f" email: {contact.get('email', 'missing')}\n"
print(string_contacts.strip('\n'))
return
def sout(self):
rc = self.rc
grants = []
if rc.date:
desired_date = date_parser.parse(rc.date).date()
else:
desired_date = dt.date.today()
for grant in self.gtx["grants"]:
if rc.current and not is_current(grant, now=desired_date):
continue
grants.append(grant)
# Sort the grants by end date in reverse chronological order
grants.sort(key=lambda k: get_dates(k).get('end_date'), reverse=True)
for g in grants:
print("{}, awardnr: {}, acctn: {}, {} to {}".format(
g.get('alias', ''), g.get('awardnr', ''), g.get('account', ''),
get_dates(g).get('begin_date'),
get_dates(g).get('end_date')))
return
def sout(self):
rc = self.rc
if rc.filter:
collection = key_value_pair_filter(self.gtx["grants"], rc.filter)
else:
collection = self.gtx["grants"]
grants = []
if rc.date:
desired_date = date_parser.parse(rc.date).date()
else:
desired_date = dt.date.today()
for grant in collection:
# fixme maybe change this logic and change the name of "year" in proposal to "submitted_year" or sthg
if grant.get(
'year'
): # year is used for prop submission but breaks get_dates
del grant['year']
if rc.current and not is_current(grant, now=desired_date):
continue
if not rc.verbose:
if grant.get("alias") not in BLACKLIST:
grants.append(grant)
else:
grants.append(grant)
# Sort the grants by end date in reverse chronological order
grants.sort(key=lambda k: get_dates(k).get('end_date'), reverse=True)
if rc.keys:
results = (collection_str(grants, rc.keys))
print(results, end="")
return
for g in grants:
print("{}, awardnr: {}, acctn: {}, {} to {}".format(
g.get('alias', ''), g.get('awardnr', ''), g.get('account', ''),
get_dates(g).get('begin_date'),
get_dates(g).get('end_date')))
return
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 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 sout(self):
rc = self.rc
outdated, depleted, underspent, overspent = [], [], [], []
all_appts = collect_appts(self.gtx['people'])
if rc.no_gui:
matplotlib.use('agg')
for person in self.gtx['people']:
appts = collect_appts([person])
if not appts:
continue
this_begin = min(get_dates(appt)['begin_date'] for appt in appts)
this_end = max(get_dates(appt)['end_date'] for appt in appts)
is_fully_appointed(person, this_begin, this_end)
for appt in appts:
if appt.get("grant") in BLACKLIST:
print(appt.get("grant"))
continue
grant = rc.client.find_one(rc.database, "grants",
{"_id": appt.get("grant")})
if not grant:
raise RuntimeError(
" grant: {}, person: {}, appointment: {}, grant not found in grants database"
.format(appt.get("grant"), person.get("_id"),
appt.get("_id")))
prop = rc.client.find_one(rc.database, "proposals",
{"_id": grant.get("proposal_id")})
if prop.get('year'):
del prop['year']
grant_begin = get_dates(grant)['begin_date'] if grant.get('begin_date') or grant.get('begin_year') \
else get_dates(prop)['begin_date']
grant_end = get_dates(grant)['end_date'] if grant.get('end_date') or grant.get('end_year') \
else get_dates(prop)['end_date']
grant.update({
'begin_date': grant_begin,
'end_date': grant_end
})
appt_begin, appt_end = get_dates(
appt)['begin_date'], get_dates(appt)['end_date']
this_burn = grant_burn(grant,
all_appts,
grant_begin,
grant_end,
begin_date=appt_begin,
end_date=appt_end)
timespan = appt_end - appt_begin
outdated_period, depleted_period = False, False
for x in range(timespan.days + 1):
day = appt_begin + relativedelta(days=x)
if not outdated_period:
if not is_current(grant, now=day):
outdated.append(
" person: {}, appointment: {}, grant: {},\n"
" from {} until {}".format(
person.get('_id'), appt.get('_id'),
grant.get('_id'), str(day),
str(
min(appt_end,
get_dates(grant)['begin_date']))))
outdated_period = True
if not depleted_period and not outdated_period:
day_burn = 0
if appt.get('type') == 'gra':
day_burn = this_burn[x].get('student_days')
elif appt.get('type') == 'pd':
day_burn = this_burn[x].get('postdoc_days')
elif appt.get('type') == 'ss':
day_burn = this_burn[x].get('ss_days')
if day_burn < 0:
depleted.append(
" person: {}, appointment: {}, grant: {},\n"
" from {} until {}".format(
person.get('_id'), appt.get('_id'),
grant.get('_id'), str(day), str(appt_end)))
depleted_period = True
datearray, cum_student, cum_pd, cum_ss = [], None, None, None
if not rc.no_plot:
grants_begin, grants_end = None, None
for grant in self.gtx['grants']:
if grant.get('_id') in BLACKLIST or grant.get(
'alias') in BLACKLIST:
continue
prop = rc.client.find_one(rc.database, "proposals",
{"_id": grant.get("proposal_id")})
if prop.get('year'):
del prop['year']
grant_begin = get_dates(grant)['begin_date'] if grant.get('begin_date') or grant.get('begin_year') \
else get_dates(prop)['begin_date']
grant_end = get_dates(grant)['end_date'] if grant.get('end_date') or grant.get('end_year') \
else get_dates(prop)['end_date']
if not grants_begin or grant_begin < grants_begin:
grants_begin = grant_begin
if not grants_end or grant_end > grants_end:
grants_end = grant_end
grants_timespan = grants_end - grants_begin
for x in range(grants_timespan.days + 1):
datearray.append(grants_begin + relativedelta(days=x))
cum_student, cum_pd, cum_ss = [0.0] * len(datearray), [
0.0
] * len(datearray), [0.0] * len(datearray)
for grant in self.gtx["grants"]:
if grant.get('_id') in BLACKLIST or grant.get(
'alias') in BLACKLIST:
continue
prop = rc.client.find_one(rc.database, "proposals",
{"_id": grant.get("proposal_id")})
if prop.get('year'):
del prop['year']
grant_begin = get_dates(grant)['begin_date'] if grant.get('begin_date') or grant.get('begin_year') \
else get_dates(prop)['begin_date']
grant_end = get_dates(grant)['end_date'] if grant.get('end_date') or grant.get('end_year') \
else get_dates(prop)['end_date']
grant.update({'begin_date': grant_begin, 'end_date': grant_end})
grant_amounts = grant_burn(grant, all_appts, grant_begin,
grant_end)
end_amount = grant_amounts[-1].get('student_days') + grant_amounts[-1].get('postdoc_days') + \
grant_amounts[-1].get('ss_days')
if end_amount > 30.5:
underspent.append(
" {}: grant: {}, underspend amount: {} months".format(
str(grant_end), grant.get('_id'),
round(end_amount / 30.5, 2)))
elif end_amount < -30.5:
overspent.append(
" {}: grant: {}, overspend amount: {} months".format(
str(grant_end), grant.get('_id'),
round(end_amount / 30.5, 2)))
if not rc.no_plot:
grant_dates = []
grant_duration = (grant_end - grant_begin).days + 1
this_student, this_pd, this_ss = [0.0] * grant_duration, [
0.0
] * grant_duration, [0.0] * grant_duration
counter = 0
for x in range(len(datearray)):
if is_current(grant, now=datearray[x]):
grant_dates.append(datearray[x])
this_student[counter] = grant_amounts[counter].get(
'student_days')
cum_student[x] += grant_amounts[counter].get(
'student_days')
this_pd[counter] = grant_amounts[counter].get(
'postdoc_days')
cum_pd[x] += grant_amounts[counter].get('postdoc_days')
this_ss[counter] = grant_amounts[counter].get(
'ss_days')
cum_ss[x] += grant_amounts[counter].get('ss_days')
counter += 1
plotter(grant_dates,
student=this_student,
pd=this_pd,
ss=this_ss,
title=f"{grant.get('_id')}")
if outdated:
print("appointments on outdated grants:")
for appt in outdated:
print(appt)
if depleted:
print("appointments on depleted grants:")
for appt in depleted:
print(appt)
if underspent:
print("underspent grants:")
for grant in underspent:
print(grant)
if overspent:
print("overspent grants:")
for grant in overspent:
print(grant)
if not rc.no_plot:
print(
plotter(datearray,
student=cum_student,
pd=cum_pd,
ss=cum_ss,
title="Cumulative burn"))
return
def latex(self):
"""Render latex template"""
rc = self.rc
# Convert Date Strings to Datetime Objects
if not rc.from_date:
raise ValueError(
"ERROR: need begin for the report period."
"Please rerun specifying --from and --to in YYYY-MM-DD format."
)
else:
rp_start_date = date_parser.parse(rc.from_date).date()
if not rc.to_date:
rp_end_date = date.today()
else:
rp_end_date = date_parser.parse(rc.to_date).date()
report_dates = {'begin_date': rp_start_date, 'end_date': rp_end_date}
# NSF Grant _id
if not rc.grants:
raise RuntimeError(
"Error: no grant specified. Please rerun specifying a grant")
if isinstance(rc.grants, str):
rc.grants = [rc.grants]
if len(rc.grants) > 1:
raise RuntimeError(
"Error: more than one grant specified. Please rerun with"
"only a single grant.")
grant_id = rc.grants[0]
# Get prum associated to grant and active during reporting period
# institutions_coll = [inst for inst in self.gtx["institutions"]]
institutions_coll = self.gtx["institutions"]
grant_prums = [
prum for prum in self.gtx['projecta']
if grant_id in prum.get('grants', [])
and "checklist" not in prum.get("deliverable").get("scope")
]
# for prum in self.gtx['projecta']:
# if grant_name in prum['grants']:
# begin_date = get_dates(prum).get('begin_date')
# due_date = get_due_date(prum['deliverable'])
# # if projectum was finished during reporting period or is still current
# # some projectum don't have an "end date", but all projecta have a deliverable
# # due_date
# if (rp_start_date <= due_date <= rp_end_date and prum['status'] is "finished") or is_current(prum):
# grant_prums.append(prum)
# Get people associated with grant
grant_prums_finished_this_period = [
prum for prum in grant_prums
if is_current(report_dates,
get_dates(prum).get('end_date'))
]
grant_prum_leads = list(set([prum['lead'] for prum in grant_prums]))
grant_prum_collaborators = list(
set([
collab for prum in grant_prums
for collab in prum.get('collaborators', [])
]))
grant_prum_group_members = list(
set([
grp_mbr for prum in grant_prums
for grp_mbr in prum.get('group_members', [])
]))
grant_people = grant_prum_leads
# Accomplishments
major_activities = []
significant_results = []
for prum in grant_prums:
if prum['status'] == "finished":
continue
else:
major_activities.append(prum)
for prum in grant_prums_finished_this_period:
significant_results.append(prum)
# Opportunities for Training and Professional Development
training_and_professional_development = []
# presentations
for id in grant_people:
training_and_professional_development.extend(
filter_presentations(self.gtx["people"],
self.gtx["presentations"],
institutions_coll,
id,
types=["all"],
since=rp_start_date,
before=rp_end_date,
statuses=["accepted"]))
# thesis defendings
# how do i access people.yml in rg-db-public vs the people.yml file in rg-db-group?
# defended_theses = []
# for id in grant_people:
# for prsn in self.gtx['people']:
# if prsn["_id"] != id:
# continue
# else:
# person = prsn
# for education in person['education']:
# edu_dates = get_dates(education)
# if 'phd' in education['degree'].lower() and 'columbia' in education['institution'].lower() and \
# rp_start_date.year <= edu_dates.get('end_date', edu_dates['date']).year <= rp_end_date.year:
# defended_theses.append(id)
# Products
# need rg-db-public's citation.yml
# publications = filter_publications(self.gtx["citations"],
## set(grant_people),
# since=rp_start_date,
# before=rp_end_date)
publications = [
publ for publ in self.gtx["citations"]
if grant_id in publ.get("grant", "")
]
for publ in publications:
doi = publ.get('doi')
if doi and doi != 'tbd':
publ = get_formatted_crossref_reference(doi)
names = [
HumanName(author).full_name for author in publ.get("author")
]
publ['author'] = names
# Participants/Organizations
participants = []
for person in self.gtx["people"]:
months_on_grant, months_left = self.months_on(
grant_id, person, rp_start_date, rp_end_date)
if months_on_grant > 0:
participants.append({
"name":
person.get("name"),
"email":
person.get("email"),
"position":
person.get('position'),
"months_on_grant":
int(round(months_on_grant, 0))
})
collaborators = {}
missing_contacts = []
for id in grant_prum_collaborators:
for contact in self.gtx["contacts"]:
if contact["_id"] == id:
name = contact.get("name")
aka = contact.get("aka")
institution_id = contact.get("institution")
institution = fuzzy_retrieval(institutions_coll,
["name", "aka", "_id"],
institution_id)
if institution:
inst_name = institution.get("name")
else:
print(
f"WARNING: institution {institution_id} not found "
f"in institutions collection")
inst_name = institution_id
collaborators[id] = {
"aka": aka,
"name": name,
"institution": inst_name
}
missing_contacts = [
id for id in grant_prum_collaborators if not collaborators.get(id)
]
missing_contacts = list(set(missing_contacts))
for person_id in missing_contacts:
print(
f"WARNING contact {person_id} not found in contacts collection"
)
# Impacts
begin_date_str = rp_start_date.isoformat()
end_date_str = rp_end_date.isoformat()
self.render(
"grantreport.txt",
f"{grant_id}_report_{begin_date_str}_{end_date_str}.txt",
begin_date=begin_date_str,
end_date=end_date_str,
majorActivities=major_activities,
significantResults=significant_results,
trainingAndProfessionalDevelopment=
training_and_professional_development,
# defendedTheses=defended_theses,
products=publications,
grantPeople=grant_people,
participants=participants,
collaborators=collaborators,
hline=
"------------------------------------------------------------------------------"
)
def test_is_current(thing, expected, now=TEST_DATE):
assert is_current(thing, now=now) == expected
def sout(self):
gtx = self.gtx
rc = self.rc
if rc.filter:
collection = key_value_pair_filter(self.gtx["people"], rc.filter)
else:
collection = self.gtx["people"]
bad_stati = ["finished", "cancelled", "paused", "back_burner"]
people = []
group = fuzzy_retrieval(gtx['groups'], ["_id", "aka", "name"],
rc.groupname)
group_id = group.get("_id")
if rc.filter:
if not rc.verbose:
results = (collection_str(collection, rc.keys))
print(results, end="")
return
else:
for person in collection:
print("{}, {} | group_id: {}".format(
person.get('name'), person.get('position'),
person.get('_id')))
print(" orcid: {} | github_id: {}".format(
person.get('orcid_id'), person.get('github_id')))
pass
#code to print verbosely on filtering
if not rc.filter:
for person in gtx["people"]:
if rc.current:
if not person.get('active'):
continue
people.append(person)
elif rc.prior:
if person.get('active'):
continue
people.append(person)
else:
people.append(person)
cleaned_people = []
for person in people:
not_current_positions = [
emp for emp in person.get('employment') if not is_current(emp)
]
not_current_positions.sort(key=lambda x: get_dates(x)["end_date"])
current_positions = [
emp for emp in person.get('employment') if is_current(emp)
]
current_positions.sort(key=lambda x: get_dates(x)["begin_date"])
positions = not_current_positions + current_positions
position_keys = [
position_key(position) for position in positions
if position.get("group", "") == group_id
]
if position_keys:
person["position_key"] = max(position_keys)[0]
cleaned_people.append(person)
else:
print(
f"Person {person['name']} has no positions in group {group_id}"
)
cleaned_people.sort(key=lambda k: k['position_key'], reverse=True)
position_names = {
1: "Undergrads",
2.5: "Masters Students",
2: "Visiting Students",
3: "Graduate Students",
4: "Post Docs",
5: "Visitors",
8: "Assistant Scientists",
9: "Associate Scientists",
10: "Scientists",
11: "PI"
}
accounting = 12
for person in cleaned_people:
if person.get('position_key') < accounting:
accounting = person.get('position_key')
print(
f" -- {position_names.get(accounting,position_names.get(5))} --"
)
if rc.verbose:
print("{}, {}".format(person.get('name'),
person.get('position')))
print(" email: {} | group_id: {}".format(
person.get('email'), person.get('_id')))
print(" github_id: {} | orcid: {}".format(
person.get('github_id'), person.get('orcid_id')))
for position in positions:
if is_current(position):
inst = fuzzy_retrieval(gtx["institutions"],
["aka", "name", "_id"],
position.get("organization"))
if inst:
instname = inst.get("name")
else:
print(
f"WARNING: {position.get('organization')} not in institutions collection"
)
print(" current organization: {}".format(instname))
print(" current position: {}".format(
position.get('full_position',
position.get('position').title())))
if not person.get('active'):
if position.get('group') == "bg":
print(" billinge group position: {}".format(
position.get('position')))
else:
print("{}".format(person.get('name')))
return
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")
def sout(self):
gtx = self.gtx
rc = self.rc
if rc.filter:
collection = key_value_pair_filter(self.gtx["people"], rc.filter)
else:
collection = self.gtx["people"]
bad_stati = ["finished", "cancelled", "paused", "back_burner"]
people = []
if rc.filter:
if not rc.verbose:
results = (collection_str(collection, rc.keys))
# "scopatz"
print(results, end="")
return
else:
for person in collection:
print("{}, {} | group_id: {}".format(
person.get('name'), person.get('position'),
person.get('_id')))
print(" orcid: {} | github_id: {}".format(
person.get('orcid_id'), person.get('github_id')))
pass
#code to print verbosely on filtering
if not rc.filter:
for person in gtx["people"]:
if rc.current:
if not person.get('active'):
continue
people.append(person)
elif rc.prior:
if person.get('active'):
continue
people.append(person)
else:
people.append(person)
for i in people:
if rc.verbose:
print("{}, {}".format(i.get('name'), i.get('position')))
print(" email: {} | group_id: {}".format(
i.get('email'), i.get('_id')))
print(" github_id: {} | orcid: {}".format(
i.get('github_id'), i.get('orcid_id')))
not_current_positions = [
emp for emp in i.get('employment') if not is_current(emp)
]
not_current_positions.sort(
key=lambda x: get_dates(x)["end_date"])
current_positions = [
emp for emp in i.get('employment') if is_current(emp)
]
current_positions.sort(
key=lambda x: get_dates(x)["begin_date"])
positions = not_current_positions + current_positions
for position in positions:
if is_current(position):
inst = fuzzy_retrieval(gtx["institutions"],
["aka", "name", "_id"],
position.get("organization"))
if inst:
instname = inst.get("name")
else:
print(
f"WARNING: {position.get('organization')} not in institutions collection"
)
print(" current organization: {}".format(instname))
print(" current position: {}".format(
position.get('full_position',
position.get('position').title())))
if not i.get('active'):
if position.get('group') == "bg":
print(" billinge group position: {}".format(
position.get('position')))
else:
print("{}".format(i.get('name')))
return
def sout(self):
rc = self.rc
outdated, depleted, underspent, overspent = [], [], [], []
all_appts = collect_appts(self.gtx['people'])
if rc.projection_from_date:
projection_from_date = date_parser.parse(
rc.projection_from_date).date()
else:
projection_from_date = date.today()
grants_with_appts = []
cum_months_to_cover = 0
for person in self.gtx['people']:
person_dates = group_member_employment_start_end(person, "bg")
last_emp, months_to_cover = 0, 0
if person_dates:
last_emp = max(
[emp.get('end_date', 0) for emp in person_dates])
if last_emp:
months_to_cover = round(
(last_emp - projection_from_date).days / 30.5, 2)
if months_to_cover > 0:
print(
f"{person['_id']} needs to be covered for {months_to_cover} months"
)
cum_months_to_cover += months_to_cover
appts = collect_appts([person])
if not appts:
continue
this_begin = min(get_dates(appt)['begin_date'] for appt in appts)
this_end = max(get_dates(appt)['end_date'] for appt in appts)
is_fully_appointed(person, this_begin, this_end)
for appt in appts:
grants_with_appts.append(appt.get("grant"))
if appt.get("grant") in BLACKLIST:
if rc.verbose:
print(
f"skipping {appt.get('grant')} since it is in the blacklist"
)
continue
if appt.get("grant") not in grants_with_appts:
if rc.verbose:
print(
f"skipping {appt.get('grant')} since it has no appointments assigned to it"
)
continue
grant = rc.client.find_one(rc.database, "grants",
{"alias": appt.get("grant")})
if not grant:
raise RuntimeError(
" grant: {}, person: {}, appointment: {}, grant not found in grants database"
.format(appt.get("grant"), person.get("_id"),
appt.get("_id")))
prop = rc.client.find_one(rc.database, "proposals",
{"_id": grant.get("proposal_id")})
if prop.get('year'):
del prop['year']
grant_begin = get_dates(grant)['begin_date'] if grant.get('begin_date') or grant.get('begin_year') \
else get_dates(prop)['begin_date']
grant_end = get_dates(grant)['end_date'] if grant.get('end_date') or grant.get('end_year') \
else get_dates(prop)['end_date']
grant.update({
'begin_date': grant_begin,
'end_date': grant_end
})
appt_begin, appt_end = get_dates(
appt)['begin_date'], get_dates(appt)['end_date']
this_burn = grant_burn(grant,
all_appts,
begin_date=appt_begin,
end_date=appt_end)
timespan = appt_end - appt_begin
outdated_period, depleted_period = False, False
for x in range(timespan.days + 1):
day = appt_begin + relativedelta(days=x)
if not outdated_period:
if not is_current(grant, now=day):
outdated.append(
" person: {}, appointment: {}, grant: {},\n"
" from {} until {}".format(
person.get('_id'), appt.get('_id'),
grant.get('_id'), str(day),
str(
min(appt_end,
get_dates(grant)['begin_date']))))
outdated_period = True
if not depleted_period and not outdated_period:
day_burn = 0
if appt.get('type') == 'gra':
day_burn = this_burn[x].get('student_days')
elif appt.get('type') == 'pd':
day_burn = this_burn[x].get('postdoc_days')
elif appt.get('type') == 'ss':
day_burn = this_burn[x].get('ss_days')
if day_burn < -5:
depleted.append(
" person: {}, appointment: {}, grant: {},\n"
" from {} until {}".format(
person.get('_id'), appt.get('_id'),
grant.get('alias'), str(day),
str(appt_end)))
depleted_period = True
grants_with_appts = list(set(grants_with_appts))
datearray, cum_student, cum_pd, cum_ss = [], None, None, None
if not rc.no_plot:
grants_begin, grants_end = None, None
for grant in self.gtx['grants']:
if grant.get('_id') in BLACKLIST or grant.get(
'alias') in BLACKLIST:
continue
if grant.get('alias') not in grants_with_appts:
continue
prop = rc.client.find_one(rc.database, "proposals",
{"_id": grant.get("proposal_id")})
if prop.get('year'):
del prop['year']
grant_begin = get_dates(grant)['begin_date'] if grant.get('begin_date') or grant.get('begin_year') \
else get_dates(prop)['begin_date']
grant_end = get_dates(grant)['end_date'] if grant.get('end_date') or grant.get('end_year') \
else get_dates(prop)['end_date']
if not grants_begin or grant_begin < grants_begin:
grants_begin = grant_begin
if not grants_end or grant_end > grants_end:
grants_end = grant_end
grants_timespan = grants_end - grants_begin
for x in range(grants_timespan.days + 1):
datearray.append(grants_begin + relativedelta(days=x))
cum_student, cum_pd, cum_ss = [0.0] * len(datearray), [
0.0
] * len(datearray), [0.0] * len(datearray)
plots = []
cum_underspend = 0
for grant in self.gtx["grants"]:
if grant.get('_id') in BLACKLIST or grant.get(
'alias') in BLACKLIST:
continue
if grant.get('alias') not in grants_with_appts:
continue
prop = rc.client.find_one(rc.database, "proposals",
{"_id": grant.get("proposal_id")})
if prop.get('year'):
del prop['year']
grant_begin = get_dates(grant)['begin_date'] if grant.get('begin_date') or grant.get('begin_year') \
else get_dates(prop)['begin_date']
grant_end = get_dates(grant)['end_date'] if grant.get('end_date') or grant.get('end_year') \
else get_dates(prop)['end_date']
budget_begin = min(
get_dates(period)['begin_date']
for period in grant.get('budget'))
budget_end = max(
get_dates(period)['end_date']
for period in grant.get('budget'))
if grant_begin < budget_begin:
raise RuntimeError(
f"grant does not have a complete budget. grant begin: {grant_begin} "
f"budget begin: {budget_begin}")
elif grant_end > budget_end:
raise RuntimeError(
f"grant {grant.get('alias')} does not have a complete budget. grant end: {grant_end} "
f"budget end: {budget_end}")
days_to_go = (grant_end - projection_from_date).days
grant.update({'begin_date': grant_begin, 'end_date': grant_end})
grant_amounts = grant_burn(grant, all_appts)
end_amount = grant_amounts[-1].get('student_days') + grant_amounts[-1].get('postdoc_days') + \
grant_amounts[-1].get('ss_days')
if end_amount > 15.25:
underspent.append(
" end: {}, grant: {}, underspend amount: {} months,\n required ss+gra burn: {}"
.format(str(grant_end), grant.get('alias'),
round(end_amount / 30.5, 2),
round(end_amount / days_to_go, 2)))
cum_underspend += end_amount
elif end_amount < -30.5:
overspent.append(
" end: {}, grant: {}, overspend amount: {} months".
format(str(grant_end), grant.get('alias'),
round(end_amount / 30.5, 2)))
if not rc.no_plot:
grant_dates = []
grant_duration = (grant_end - grant_begin).days + 1
this_student, this_pd, this_ss = [0.0] * grant_duration, [
0.0
] * grant_duration, [0.0] * grant_duration
counter = 0
for x in range(len(datearray)):
if is_current(grant, now=datearray[x]):
grant_dates.append(datearray[x])
this_student[counter] = grant_amounts[counter].get(
'student_days')
cum_student[x] += grant_amounts[counter].get(
'student_days')
this_pd[counter] = grant_amounts[counter].get(
'postdoc_days')
cum_pd[x] += grant_amounts[counter].get('postdoc_days')
this_ss[counter] = grant_amounts[counter].get(
'ss_days')
cum_ss[x] += grant_amounts[counter].get('ss_days')
counter += 1
plots.append(
plotter(grant_dates,
student=this_student,
pd=this_pd,
ss=this_ss,
title=f"{grant.get('alias')}")[0])
if outdated:
print("appointments on outdated grants:")
for appt in outdated:
print(appt)
if depleted:
print("appointments on depleted grants:")
for appt in depleted:
print(appt)
if underspent:
print("underspent grants:")
for grant in underspent:
print(grant)
print(
f"cumulative underspend = {round(cum_underspend/30.5, 2)} months, cumulative months to support = {round(cum_months_to_cover, 2)}"
)
if overspent:
print("overspent grants:")
for grant in overspent:
print(grant)
if not rc.no_plot:
for plot in plots:
if not rc.no_gui:
plt.show()
cum_plot, cum_ax, outp = plotter(datearray,
student=cum_student,
pd=cum_pd,
ss=cum_ss,
title="Cumulative burn")
if not rc.no_gui:
plt.show()
print(outp)
return
