def latex(self):
"""Render latex template"""
for rlist in self.gtx["reading_lists"]:
listid = rlist["_id"]
outfile_bib = listid
n = 1
for paper in rlist['papers']:
doi = paper.get('doi')
url = paper.get('url')
if doi and doi != 'tbd':
ref, ref_date = get_formatted_crossref_reference(doi)
paper.update({
'reference': ref,
'ref_date': ref_date,
'n': n,
'label': 'DOI'
})
n += 1
elif url:
paper['doi'] = url
paper.update({'n': n, 'label': 'URL'})
n += 1
else:
paper.update({'n': n})
n += 1
self.render(
"rlistbibfile.txt",
outfile_bib + ".txt",
rlist=rlist,
)
def meetings(self):
"""Render projects"""
rc = self.rc
mtgsi = all_docs_from_collection(rc.client, "meetings")
pp_mtgs, f_mtgs = [], []
for mtg in mtgsi:
if not mtg.get('lead'):
print("{} missing a meeting lead".format(mtg["_id"]))
if not mtg.get('scribe'):
print("{} missing a meeting scribe".format(mtg["_id"]))
lead = fuzzy_retrieval(
all_docs_from_collection(rc.client, "people"),
["_id", "name", "aka"], mtg.get("lead"))
if not lead:
print("{} lead {} not found in people".format(
mtg["_id"], mtg.get("lead")))
mtg["lead"] = lead["name"]
scribe = fuzzy_retrieval(
all_docs_from_collection(rc.client, "people"),
["_id", "name", "aka"], mtg.get("scribe"))
if not scribe:
print("{} scribe {} not found in people".format(
mtg["_id"], mtg.get("scribe")))
mtg["scribe"] = scribe["name"]
if mtg.get("journal_club"):
prsn = fuzzy_retrieval(
all_docs_from_collection(rc.client,
"people"), ["_id", "name", "aka"],
mtg["journal_club"].get("presenter"))
if not prsn:
print("{} Jclub presenter {} not found in people".format(
mtg["_id"], mtg["journal_club"].get("presenter")))
mtg["journal_club"]["presenter"] = prsn["name"]
if mtg["journal_club"].get("doi", "tbd").casefold() != 'tbd':
ref, _ = get_formatted_crossref_reference(
mtg["journal_club"].get("doi"))
mtg["journal_club"]["doi"] = ref
if mtg.get("presentation"):
prsn = fuzzy_retrieval(
all_docs_from_collection(rc.client,
"people"), ["_id", "name", "aka"],
mtg["presentation"].get("presenter"))
if mtg["presentation"].get("presenter") == "hold":
prsn = {}
prsn["name"] = "Hold"
if not prsn:
print("{} presenter {} not found in people".format(
mtg["_id"], mtg["presentation"].get("presenter")))
mtg["presentation"]["presenter"] = prsn["name"]
mtg["presentation"]["link"] = mtg["presentation"].get(
"link", "tbd")
mtg['date'] = dt.date(mtg.get("year"), mtg.get("month"),
mtg.get("day"))
mtg['datestr'] = mtg['date'].strftime('%m/%d/%Y')
today = dt.date.today()
if mtg['date'] >= today:
f_mtgs.append(mtg)
else:
pp_mtgs.append(mtg)
pp_mtgs = sorted(pp_mtgs, key=lambda x: x.get('date'), reverse=True)
f_mtgs = sorted(f_mtgs, key=lambda x: x.get('date'))
self.render("grpmeetings.html",
"grpmeetings.html",
title="Group Meetings",
ppmeetings=pp_mtgs,
fmeetings=f_mtgs)
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=
"------------------------------------------------------------------------------"
)