def construct_global_ctx(self):
self.gtx = gtx = {}
rc = self.rc
gtx["len"] = len
gtx["sum"] = sum
gtx["zip"] = zip
gtx["True"] = True
gtx["False"] = False
gtx["None"] = None
gtx["sorted"] = sorted
gtx["groupby"] = groupby
gtx["range"] = range
gtx["gets"] = gets
gtx["id_key"] = lambda x: x["_id"]
gtx["date_key"] = date_key
gtx["doc_date_key"] = doc_date_key
gtx["level_val"] = level_val
gtx["category_val"] = category_val
gtx["rfc822now"] = rfc822now
gtx["date_to_rfc822"] = date_to_rfc822
gtx["month_and_year"] = month_and_year
gtx["latex_safe"] = latex_safe
gtx["all_docs_from_collection"] = all_docs_from_collection
gtx["grades"] = list(all_docs_from_collection(rc.client, "grades"))
gtx["courses"] = list(all_docs_from_collection(rc.client, "courses"))
gtx["assignments"] = list(all_docs_from_collection(rc.client, "assignments"))
def class_email(rc):
"""Sends an email to all students in the active classes."""
gradedir = os.path.join(rc.builddir, GradeReportBuilder.btype)
addresses = {x['_id']: x['email'] for x in \
list(all_docs_from_collection(rc.client, 'students'))}
messages = []
for course in all_docs_from_collection(rc.client, 'courses'):
if not course.get('active', True):
continue
course_id = course['_id']
subject = '[{0}] {1}'.format(course_id, rc.subject)
for student_id in course['students']:
message = make_message(rc, addresses[student_id],
subject=subject,
body=rc.body,
attachments=rc.attachments)
messages.append(message)
return messages
def filter_publications(self, authors, reverse=False):
rc = self.rc
pubs = []
for pub in all_docs_from_collection(rc.client, 'citations'):
if len(set(pub['author']) & authors) == 0:
continue
pubs.append(pub)
pubs.sort(key=doc_date_key, reverse=reverse)
return pubs
def construct_global_ctx(self):
self.gtx = gtx = {}
rc = self.rc
gtx['len'] = len
gtx['True'] = True
gtx['False'] = False
gtx['None'] = None
gtx['sorted'] = sorted
gtx['groupby'] = groupby
gtx['gets'] = gets
gtx['date_key'] = date_key
gtx['doc_date_key'] = doc_date_key
gtx['level_val'] = level_val
gtx['category_val'] = category_val
gtx['rfc822now'] = rfc822now
gtx['date_to_rfc822'] = date_to_rfc822
gtx['jobs'] = list(all_docs_from_collection(rc.client, 'jobs'))
gtx['people'] = list(all_docs_from_collection(rc.client, 'people'))
gtx['all_docs_from_collection'] = all_docs_from_collection
def filter_projects(self, authors, reverse=False):
rc = self.rc
projs = []
for proj in all_docs_from_collection(rc.client, 'projects'):
team_names = set(gets(proj['team'], 'name'))
if len(team_names & authors) == 0:
continue
proj = dict(proj)
proj['team'] = [x for x in proj['team'] if x['name'] in authors]
projs.append(proj)
projs.sort(key=id_key, reverse=reverse)
return projs
def blog(self):
rc = self.rc
blog_dir = os.path.join(self.bldir, 'blog')
os.makedirs(blog_dir, exist_ok=True)
posts = list(all_docs_from_collection(rc.client, 'blog'))
posts.sort(key=ene_date_key, reverse=True)
for post in posts:
self.render('blog_post.html', os.path.join('blog', post['_id'] + '.html'),
post=post, title=post['title'])
self.render('blog_index.html', os.path.join('blog', 'index.html'), title='Blog',
posts=posts)
self.render('rss.xml', os.path.join('blog', 'rss.xml'), items=posts)
def grade_email(rc):
"""Sends grade report emails to students."""
gradedir = os.path.join(rc.builddir, GradeReportBuilder.btype)
addresses = {x['_id']: x['email'] for x in \
list(all_docs_from_collection(rc.client, 'students'))}
messages = []
for course in all_docs_from_collection(rc.client, 'courses'):
if not course.get('active', True):
continue
course_id = course['_id']
for student_id in course['students']:
base = GradeReportBuilder.basename(student_id, course_id) + '.pdf'
fname = os.path.join(gradedir, base)
if not os.path.isfile(fname):
raise RuntimeError(fname + ' does not exist, please run '
'"regolith build grade" prior to emailing '
'grades.')
message = make_message(rc, addresses[student_id],
subject="Current grades for " + course_id,
body='Please see the attached PDF and '
'please report any errors.',
attachments=[fname])
messages.append(message)
return messages
def filter_publications(self, authors, reverse=False):
rc = self.rc
pubs = []
for pub in all_docs_from_collection(rc.client, 'citations'):
if len(set(pub['author']) & authors) == 0:
continue
bold_self = []
for a in pub['author']:
if a in authors:
bold_self.append('\\textbf{' + a + '}')
else:
bold_self.append(a)
pub['author'] = bold_self
pubs.append(pub)
pubs.sort(key=doc_date_key, reverse=reverse)
return pubs
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}"
rc.database = rc.databases[0]["name"]
gtx[rc.coll] = sorted(all_docs_from_collection(rc.client, rc.coll),
key=_id_key)
gtx["all_docs_from_collection"] = all_docs_from_collection
gtx["float"] = float
gtx["str"] = str
gtx["zip"] = zip
def filter_publications(self, authors, reverse=False):
rc = self.rc
pubs = []
for pub in all_docs_from_collection(rc.client, "citations"):
if len(set(pub["author"]) & authors) == 0:
continue
bold_self = []
for a in pub["author"]:
if a in authors:
bold_self.append("\\textbf{" + a + "}")
else:
bold_self.append(a)
pub["author"] = bold_self
pubs.append(pub)
pubs.sort(key=doc_date_key, reverse=reverse)
return pubs
def blog(self):
"""Render the blog and rss"""
rc = self.rc
blog_dir = os.path.join(self.bldir, 'blog')
os.makedirs(blog_dir, exist_ok=True)
posts = list(all_docs_from_collection(rc.client, 'blog'))
posts.sort(key=ene_date_key, reverse=True)
for post in posts:
self.render('blog_post.html',
os.path.join('blog', post['_id'] + '.html'),
post=post,
title=post['title'])
self.render('blog_index.html',
os.path.join('blog', 'index.html'),
title='Blog',
posts=posts)
self.render('rss.xml', os.path.join('blog', 'rss.xml'), items=posts)
def format_last_first_instutition_names(rc, ppl_names, excluded_inst_name=None):
"""Get the last name, first name and institution name."""
ppl = []
for ppl_tup in ppl_names:
inst = fuzzy_retrieval(
all_docs_from_collection(rc.client, "institutions"),
['aka', 'name', '_id'], ppl_tup[1],
case_sensitive=False)
if inst:
inst_name = inst.get("name", "")
else:
inst_name = ppl_tup[1]
# remove all people who are in the institution of the person
if inst_name != excluded_inst_name:
name = HumanName(ppl_tup[0])
yield name.last, " ".join([name.first, name.middle]), ppl_tup[1], " ", ppl_tup[2]
return ppl
def filter_publications(self, authors, reverse=False):
rc = self.rc
pubs = []
for pub in all_docs_from_collection(rc.client, 'citations'):
if len(set(pub['author']) & authors) == 0:
continue
pub = deepcopy(pub)
bold_self = []
for a in pub['author']:
if a in authors:
bold_self.append('\\textbf{' + a + '}')
else:
bold_self.append(a)
pub['author'] = bold_self
pubs.append(pub)
pubs.sort(key=doc_date_key, reverse=reverse)
return pubs
def query_ppl(self, target, **filters):
"""Query the data base for the target's collaborators' information."""
rc = self.rc
gtx = self.gtx
person = fuzzy_retrieval(all_docs_from_collection(rc.client, "people"),
['aka', 'name', '_id'],
target,
case_sensitive=False)
if not person:
raise RuntimeError("Person {} not found in people.".format(
target).encode('utf-8'))
pubs = get_person_pubs(gtx["citations"], person)
if 'since_date' in filters:
since_date = filters.get('since_date')
pubs = filter_since_date(pubs, since_date)
try:
if rc.verbose:
for pub in pubs:
print(f"{pub.get('title')}, ({pub.get('year')})")
except AttributeError:
pass
my_collabs = get_coauthors_from_pubs(pubs, person)
people, institutions = query_people_and_institutions(rc, my_collabs)
ppl_names = set(zip(people, institutions))
collab_3tups = set(format_last_first_instutition_names(rc, ppl_names))
advisors_3tups = set(get_advisors_name_inst(person, rc))
advisees_3tups = set(get_advisees_name_inst(gtx["people"], person, rc))
ppl_3tups = sorted(list(collab_3tups | advisors_3tups
| advisees_3tups))
person_3tups = make_person_3tups(person, rc)
coeditors_info = find_coeditors(person, rc)
ppl_tab1 = format_to_nsf(person_3tups, '')
ppl_tab3 = format_to_nsf(advisors_3tups, 'G:') + format_to_nsf(
advisees_3tups, 'T:')
ppl_tab4 = format_to_nsf(collab_3tups, 'A:')
ppl_tab5 = format_to_nsf(coeditors_info, 'E:')
results = {
'person_info': person,
'ppl_tab1': ppl_tab1,
'ppl_tab3': ppl_tab3,
'ppl_tab4': ppl_tab4,
'ppl_tab5': ppl_tab5,
'ppl_3tups': ppl_3tups
}
return results
def construct_global_ctx(self):
"""Constructs the global context"""
super().construct_global_ctx()
gtx = self.gtx
rc = self.rc
if "groups" in self.needed_colls:
rc.pi_id = get_pi_id(rc)
rc.coll = f"{TARGET_COLL}"
colls = [
sorted(all_docs_from_collection(rc.client, collname), key=_id_key)
for collname in self.needed_colls
]
for db, coll in zip(self.needed_colls, colls):
gtx[db] = coll
gtx["all_docs_from_collection"] = all_docs_from_collection
gtx["float"] = float
gtx["str"] = str
gtx["zip"] = zip
def get_inst_name(person, rc):
"""Get the name of instituion of the person's lastest employment."""
if 'employment' in person:
org = get_recent_org(person)
person_inst_abbr = org
elif 'institution' in person:
person_inst_abbr = person.get('institution')
else:
person_inst_abbr = ''
person_inst = fuzzy_retrieval(all_docs_from_collection(
rc.client, "institutions"), ["name", "aka", "_id"],
person_inst_abbr, case_sensitive=False)
if person_inst is not None:
person_inst_name = person_inst.get("name")
else:
person_inst_name = person_inst_abbr
print(f"WARNING: {person_inst_abbr} is not found in institutions.")
return person_inst_name
def construct_global_ctx(self):
self.gtx = gtx = {}
rc = self.rc
gtx['len'] = len
gtx['True'] = True
gtx['False'] = False
gtx['None'] = None
gtx['sorted'] = sorted
gtx['groupby'] = groupby
gtx['gets'] = gets
gtx['date_key'] = date_key
gtx['doc_date_key'] = doc_date_key
gtx['level_val'] = level_val
gtx['category_val'] = category_val
gtx['rfc822now'] = rfc822now
gtx['date_to_rfc822'] = date_to_rfc822
gtx['month_and_year'] = month_and_year
gtx['latex_safe'] = latex_safe
gtx['people'] = sorted(all_docs_from_collection(rc.client, 'people'),
key=position_key, reverse=True)
gtx['all_docs_from_collection'] = all_docs_from_collection
def blog(self):
"""Render the blog and rss"""
rc = self.rc
blog_dir = os.path.join(self.bldir, "blog")
os.makedirs(blog_dir, exist_ok=True)
posts = list(all_docs_from_collection(rc.client, "blog"))
posts.sort(key=ene_date_key, reverse=True)
for post in posts:
self.render(
"blog_post.html",
os.path.join("blog", post["_id"] + ".html"),
post=post,
title=post["title"],
)
self.render(
"blog_index.html",
os.path.join("blog", "index.html"),
title="Blog",
posts=posts,
)
self.render("rss.xml", os.path.join("blog", "rss.xml"), items=posts)
def construct_global_ctx(self):
self.gtx = gtx = {}
rc = self.rc
gtx['len'] = len
gtx['True'] = True
gtx['False'] = False
gtx['None'] = None
gtx['sorted'] = sorted
gtx['groupby'] = groupby
gtx['gets'] = gets
gtx['date_key'] = date_key
gtx['doc_date_key'] = doc_date_key
gtx['level_val'] = level_val
gtx['category_val'] = category_val
gtx['rfc822now'] = rfc822now
gtx['date_to_rfc822'] = date_to_rfc822
gtx['month_and_year'] = month_and_year
gtx['latex_safe'] = latex_safe
gtx['people'] = sorted(all_docs_from_collection(rc.client, 'people'),
key=position_key,
reverse=True)
gtx['all_docs_from_collection'] = all_docs_from_collection
def construct_global_ctx(self):
"""Constructs the global context"""
super().construct_global_ctx()
gtx = self.gtx
rc = self.rc
rc.pi_id = get_pi_id(rc)
rc.coll = f"{TARGET_COLL}"
if not rc.payee:
if rc.default_user_id:
rc.payee = rc.default_user_id
else:
raise RuntimeError(" No default_user_id set. Please specify this "
f"either in the ~/.conf/regolith/user.json or in"
f" regolithrc.json")
if not rc.database:
rc.database = rc.databases[0]["name"]
gtx[rc.coll] = sorted(
all_docs_from_collection(rc.client, rc.coll), key=_id_key
)
gtx["all_docs_from_collection"] = all_docs_from_collection
gtx["float"] = float
gtx["str"] = str
gtx["zip"] = zip
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 BaseException:
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["all_docs_from_collection"] = all_docs_from_collection
gtx["float"] = float
gtx["str"] = str
gtx["zip"] = zip
def get_advisees_name_inst(coll, advisor, rc):
"""Get advisor's advisees. Yield (last name, first name, institutions)"""
advisor_names = advisor.get('aka', []) + [advisor.get('name'), advisor.get('_id')]
for person in coll:
edus = person.get("education", [])
for edu in edus:
if 'advisor' in edu and edu['advisor'] in advisor_names:
# if edu['status'] == 'postdoc'
person_name = HumanName(person.get("name"))
inst_name = edu.get("institution")
inst = fuzzy_retrieval(
all_docs_from_collection(rc.client, "institutions"),
['aka', 'name', '_id'], inst_name,
case_sensitive=False)
first_name = " ".join([person_name.first, person_name.middle])
if inst is None:
print("WARNING: {} not in institutions".format(
inst_name))
yield person_name.last, first_name, inst_name
else:
yield person_name.last, first_name, inst.get('name', "")
break
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
if not rc.assigned_to:
try:
rc.assigned_to = rc.default_user_id
except AttributeError:
print(
"Please set default_user_id in '~/.config/regolith/user.json', or you need to enter your group id "
"in the command line")
return
try:
person = document_by_value(
all_docs_from_collection(rc.client, "todos"), "_id",
rc.assigned_to)
gather_todos = person.get("todos", [])
except:
print("The id you entered can't be found in todos.yml.")
return
if not rc.date:
today = dt.date.today()
else:
today = date_parser.parse(rc.date).date()
if rc.stati == ["started"]:
rc.stati = PROJECTUM_ACTIVE_STATI
running_index = 0
for projectum in self.gtx["projecta"]:
if projectum.get('lead') != rc.assigned_to:
continue
if "checklist" in projectum.get('deliverable').get('scope'):
continue
projectum["deliverable"].update({"name": "deliverable"})
gather_miles = [projectum["deliverable"]]
if projectum.get("kickoff"):
projectum['kickoff'].update({"type": "meeting"})
gather_miles = [projectum["kickoff"], projectum["deliverable"]]
gather_miles.extend(projectum["milestones"])
for ms in gather_miles:
if projectum["status"] in PROJECTUM_ACTIVE_STATI:
if ms.get('status') in PROJECTUM_ACTIVE_STATI:
due_date = get_due_date(ms)
ms.update({
'status': "started",
'id': projectum.get('_id'),
'due_date': due_date,
'assigned_by': projectum.get('pi_id'),
'importance': 2,
'duration': 3600,
'running_index': 9900 + running_index
})
running_index += 1
ms.update({
'description':
f'milestone: {ms.get("name")} ({ms.get("id")})'
})
gather_todos.append(ms)
if rc.filter:
gather_todos = key_value_pair_filter(gather_todos, rc.filter)
if rc.short:
for todo in gather_todos[::-1]:
if todo.get('duration') is None or float(
todo.get('duration')) > float(rc.short):
gather_todos.remove(todo)
if rc.tags:
for todo in gather_todos[::-1]:
takeme = False
for tag in rc.tags:
if tag in todo.get('tags', []):
takeme = True
if not takeme:
gather_todos.remove(todo)
if rc.assigned_by:
if rc.assigned_by == "default_id":
rc.assigned_by = rc.default_user_id
for todo in gather_todos[::-1]:
if todo.get('assigned_by') != rc.assigned_by:
gather_todos.remove(todo)
len_of_started_tasks = 0
milestones = 0
for todo in gather_todos:
if 'milestone: ' in todo['description']:
milestones += 1
elif todo["status"] == 'started':
len_of_started_tasks += 1
len_of_tasks = len(gather_todos) #- milestones
for todo in gather_todos:
_format_todos(todo, today)
gather_todos[:len_of_tasks] = sorted(
gather_todos[:len_of_tasks],
key=lambda k: (k['status'], k['importance'], k['order'], -k.get(
'duration', 10000)))
gather_todos[len_of_started_tasks:len_of_tasks] = sorted(
gather_todos[len_of_started_tasks:len_of_tasks],
key=lambda k: (-k["sort_finished"]))
gather_todos[len_of_tasks:] = sorted(
gather_todos[len_of_tasks:],
key=lambda k: (k['status'], k['order'], -k.get('duration', 10000)))
print(
"If the indices are far from being in numerical order, please renumber them by running regolith helper u_todo -r"
)
print(
"(index) action (days to due date|importance|expected duration (mins)|tags|assigned by)"
)
print("-" * 80)
if len(gather_todos) != 0:
print_task(gather_todos, stati=rc.stati)
if rc.outstandingreview:
prop = self.gtx['proposalReviews']
man = self.gtx['refereeReports']
outstanding_todo = []
for manuscript in man:
if manuscript.get("reviewer") != rc.assigned_to:
continue
if manuscript.get("status") in STATI:
out = f"Manuscript by {manuscript.get('first_author_last_name')} in {manuscript.get('journal')} " \
f"is due on {manuscript.get('due_date')}"
outstanding_todo.append((out, manuscript.get('due_date'),
manuscript.get("status")))
for proposal in prop:
if proposal.get("reviewer") != rc.assigned_to:
continue
if proposal.get("status") in STATI:
if isinstance(proposal.get('names'), str):
name = HumanName(proposal.get('names'))
else:
name = HumanName(proposal.get('names')[0])
out = f"Proposal by {name.last} for {proposal.get('agency')} ({proposal.get('requester')})" \
f"is due on {proposal.get('due_date')}"
outstanding_todo.append((out, proposal.get('due_date'),
proposal.get("status")))
if len(outstanding_todo) != 0:
print("-" * 30)
print("Outstanding Reviews:")
print("-" * 30)
outstanding_todo = sorted(outstanding_todo,
key=lambda k: str(k[1]))
for stati in STATI:
if stati in [output[2] for output in outstanding_todo]:
print(f'{stati}:')
else:
continue
for output in outstanding_todo:
if output[2] == stati:
print(output[0])
return
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 construct_global_ctx(self):
"""Constructs the global context"""
super().construct_global_ctx()
gtx = self.gtx
rc = self.rc
gtx["people"] = sorted(
all_docs_from_collection(rc.client, "people"),
key=position_key,
reverse=True,
)
gtx["institutions"] = sorted(all_docs_from_collection(
rc.client, "institutions"),
key=_id_key)
gtx["contacts"] = sorted(all_docs_from_collection(
rc.client, "institutions"),
key=_id_key)
gtx["groups"] = sorted(all_docs_from_collection(rc.client, "groups"),
key=_id_key)
gtx["grants"] = sorted(all_docs_from_collection(rc.client, "grants"),
key=_id_key)
gtx["proposals"] = sorted(all_docs_from_collection(
rc.client, "proposals"),
key=_id_key)
gtx["projects"] = sorted(all_docs_from_collection(
rc.client, "projects"),
key=_id_key)
gtx["presentations"] = sorted(all_docs_from_collection(
rc.client, "presentations"),
key=_id_key)
gtx["proprevs"] = sorted(all_docs_from_collection(
rc.client, "proposalReviews"),
key=_id_key)
gtx["manrevs"] = sorted(all_docs_from_collection(
rc.client, "refereeReports"),
key=_id_key)
gtx["recletts"] = sorted(all_docs_from_collection(
rc.client, "recletts"),
key=_id_key)
gtx["patents"] = sorted(all_docs_from_collection(rc.client, "patents"),
key=_id_key)
gtx["all_docs_from_collection"] = all_docs_from_collection
gtx["float"] = float
gtx["str"] = str
gtx["zip"] = zip
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"]
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
)
emps = p.get("employment", [])
emps = [em for em in emps
if not em.get("not_in_cv", False)]
for e in emps:
e['position'] = e.get('position_full', e.get('position').title())
ene = emps + 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 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 sout(self):
rc = self.rc
if not rc.assigned_to:
try:
rc.assigned_to = rc.default_user_id
except AttributeError:
print(
"Please set default_user_id in '~/.config/regolith/user.json', or you need to enter your group id "
"in the command line")
return
try:
person = document_by_value(
all_docs_from_collection(rc.client, "people"), "_id",
rc.assigned_to)
gather_todos = person.get("todos", [])
except:
print("The id you entered can't be found in people.yml.")
return
if not rc.certain_date:
today = dt.date.today()
else:
today = date_parser.parse(rc.certain_date).date()
if rc.stati == ["started"]:
rc.stati = ACTIVE_STATI
for projectum in self.gtx["projecta"]:
if projectum.get('lead') != rc.assigned_to:
continue
projectum["deliverable"].update({"name": "deliverable"})
gather_miles = [projectum["kickoff"], projectum["deliverable"]]
gather_miles.extend(projectum["milestones"])
for ms in gather_miles:
if projectum["status"] not in ["finished", "cancelled"]:
if ms.get('status') not in \
["finished", "cancelled"]:
due_date = get_due_date(ms)
ms.update({
'id': projectum.get('_id'),
'due_date': due_date,
'assigned_by': projectum.get('pi_id')
})
ms.update({
'description':
f'milestone: {ms.get("name")} ({ms.get("id")})'
})
gather_todos.append(ms)
if rc.filter:
gather_todos = key_value_pair_filter(gather_todos, rc.filter)
if rc.short:
for todo in gather_todos[::-1]:
if todo.get('duration') is None or float(
todo.get('duration')) > float(rc.short):
gather_todos.remove(todo)
if rc.assigned_by:
if rc.assigned_by == "default_id":
rc.assigned_by = rc.default_user_id
for todo in gather_todos[::-1]:
if todo.get('assigned_by') != rc.assigned_by:
gather_todos.remove(todo)
elif rc.assigned_to == rc.assigned_by:
gather_todos.remove(todo)
len_of_started_tasks = 0
milestones = 0
for todo in gather_todos:
if 'milestone: ' in todo['description']:
milestones += 1
elif todo["status"] == 'started':
len_of_started_tasks += 1
len_of_tasks = len(gather_todos) - milestones
for todo in gather_todos:
if not todo.get('importance'):
todo['importance'] = 1
if type(todo["due_date"]) == str:
todo["due_date"] = date_parser.parse(todo["due_date"]).date()
if type(todo.get("end_date")) == str:
todo["end_date"] = date_parser.parse(todo["end_date"]).date()
todo["days_to_due"] = (todo.get('due_date') - today).days
todo["sort_finished"] = (
todo.get("end_date", dt.date(1900, 1, 1)) -
dt.date(1900, 1, 1)).days
try:
todo["order"] = todo['importance'] + 1 / (
1 + math.exp(abs(todo["days_to_due"] - 0.5))) - (
todo["days_to_due"] < -7) * 10
except OverflowError:
todo["order"] = float('inf')
gather_todos[:len_of_tasks] = sorted(
gather_todos[:len_of_tasks],
key=lambda k: (k['status'], k['order'], -k.get('duration', 10000)),
reverse=True)
gather_todos[len_of_started_tasks:len_of_tasks] = sorted(
gather_todos[len_of_started_tasks:len_of_tasks],
key=lambda k: (-k["sort_finished"]))
gather_todos[len_of_tasks:] = sorted(
gather_todos[len_of_tasks:],
key=lambda k: (k['status'], k['order'], -k.get('duration', 10000)),
reverse=True)
print(
"If the indices are far from being in numerical order, please reorder them by running regolith helper u_todo -r"
)
print(
"(index) action (days to due date|importance|expected duration (mins)|assigned by)"
)
print("-" * 81)
if len_of_tasks != 0:
print("tasks from people collection:")
print("-" * 30)
print_task(gather_todos[:len_of_tasks], stati=rc.stati)
if milestones != 0:
print("-" * 42)
print("tasks from projecta and other collections:")
print("-" * 42)
print_task(gather_todos[len_of_tasks:],
stati=rc.stati,
index=False)
print("-" * 81)
return
def sout(self):
rc = self.rc
if not rc.assigned_to:
try:
rc.assigned_to = rc.default_user_id
except AttributeError:
print(
"Please set default_user_id in '~/.config/regolith/user.json', or you need to enter your group id "
"in the command line")
return
try:
person = document_by_value(
all_docs_from_collection(rc.client, "people"), "_id",
rc.assigned_to)
gather_todos = person.get("todos", [])
except:
print("The id you entered can't be found in people.yml.")
return
if not rc.certain_date:
today = dt.date.today()
else:
today = date_parser.parse(rc.certain_date).date()
for projectum in self.gtx["projecta"]:
if projectum.get('lead') != rc.assigned_to:
continue
projectum["deliverable"].update({"name": "deliverable"})
gather_miles = [projectum["kickoff"], projectum["deliverable"]]
gather_miles.extend(projectum["milestones"])
for ms in gather_miles:
if projectum["status"] not in ["finished", "cancelled"]:
if ms.get('status') not in \
["finished", "cancelled"]:
due_date = get_due_date(ms)
ms.update({
'id': projectum.get('_id'),
'due_date': due_date,
})
ms.update({
'description':
f'milestone: {ms.get("name")} ({ms.get("id")})'
})
gather_todos.append(ms)
for todo in gather_todos:
if not todo.get('importance'):
todo['importance'] = 1
if type(todo["due_date"]) == str:
todo["due_date"] = date_parser.parse(todo["due_date"]).date()
todo["days_to_due"] = (todo.get('due_date') - today).days
todo["order"] = todo['importance'] + 1 / (
1 + math.exp(abs(todo["days_to_due"])))
gather_todos = sorted(gather_todos, key=lambda k: (-k['order']))
if rc.short_tasks:
for todo in gather_todos[::-1]:
if todo.get('duration') is None or float(
todo.get('duration')) > float(rc.short_tasks):
gather_todos.remove(t)
num = 1
print("-" * 50)
print(
" action (days to due date|importance|expected duration(mins))")
for todo in gather_todos:
if todo.get('status') not in ["finished", "cancelled"]:
print(
f"{num:>2}. {todo.get('description')}({todo.get('days_to_due')}|{todo.get('importance')}|{str(todo.get('duration'))})"
)
if todo.get('notes'):
for note in todo.get('notes'):
print(f" - {note}")
num += 1
if rc.all:
for todo in person.get("todos", []):
if todo.get('status') in ["finished", "cancelled"]:
print(
f"{num:>2}. ({todo.get('status')}) {todo.get('description')}"
)
if todo.get('notes'):
for note in todo.get('notes'):
print(f" - {note}")
num += 1
print("-" * 50)
return
def query_ppl(self, target):
"""Query the data base for the target's collaborators' information."""
rc = self.rc
gtx = self.gtx
person = fuzzy_retrieval(all_docs_from_collection(rc.client, "people"),
['aka', 'name', '_id'],
target,
case_sensitive=False)
if not person:
raise RuntimeError("Person {} not found in people.".format(
target).encode('utf-8'))
pubs = get_person_pubs(gtx["citations"], person)
pubs = filter_since_date(pubs, rc)
try:
if rc.verbose:
for pub in pubs:
print(f"{pub.get('title')}, ({pub.get('year')})")
except AttributeError:
pass
my_collabs = get_coauthors_from_pubs(rc, pubs, person)
# output = [f"{my_collab.get('name').last}, "
# f"{my_collab.get('name').first}, "
# f"{my_collab.get('institution')}, "
# f"{my_collab.get('interaction_date')}, "
# f"{my_collab.get('type')}\n" for my_collab in my_collabs]
# print(*output)
advisors = get_advisors_name_inst(person, rc)
# print("advisors:")
# output = [f"{my_collab.get('name').last}, "
# f"{my_collab.get('name').first}, "
# f"{my_collab.get('institution')}, "
# f"{my_collab.get('interaction_date')}, "
# f"{my_collab.get('advisor_type')}, "
# f"{my_collab.get('type')}\n" for my_collab in advisors]
# print(*output)
advisees = get_advisees_name_inst(
all_docs_from_collection(rc.client, "people"), person, rc)
# print("advisees:")
# output = [f"{my_collab.get('name').last}, "
# f"{my_collab.get('name').first}, "
# f"{my_collab.get('institution')}, "
# f"{my_collab.get('interaction_date')}, "
# f"{my_collab.get('advisor_type')}, "
# f"{my_collab.get('type')}\n" for my_collab in advisees]
# print(*output)
collabs = []
adviseors = advisors + advisees
for collab in my_collabs:
col_bool = True
for advis in adviseors:
if collab.get("name").last == advis.get("name").last \
and collab.get("name").first == advis.get("name").first:
col_bool = False
if collab.get("interaction_date") > advis.get(
"interaction_date"):
advis.update({
"interaction_date":
collab.get("interaction_date")
})
if col_bool == True:
collabs.append(collab)
collabs.extend(advisees)
collabs.extend(advisors)
collabs.sort(key=lambda d: d['name'].last)
if rc.verbose:
output = [
f"{my_collab.get('name').last}, "
f"{my_collab.get('name').first}, "
f"{my_collab.get('institution')}, "
f"{my_collab.get('interaction_date')}, "
f"{my_collab.get('advis_type', '')}, "
f"{my_collab.get('type')}\n" for my_collab in collabs
]
print(*output)
person["name"] = HumanName(person.get("name"))
results = {
'person_info': person,
# 'ppl_tab1': ppl_tab1,
# 'ppl_tab3': ppl_tab3,
# 'ppl_tab4': ppl_tab4,
# 'ppl_tab5': ppl_tab5,
'collabs': collabs
}
return results
def db_updater(self):
rc = self.rc
if not rc.assigned_to:
try:
rc.assigned_to = rc.default_user_id
except AttributeError:
print(
"Please set default_user_id in '~/.config/regolith/user.json', or you need to enter your group id "
"in the command line")
return
filterid = {'_id': rc.assigned_to}
if rc.reorder:
index = 1
for i in range(0, len(rc.databases)):
db_name = rc.databases[i]["name"]
person_idx = rc.client.find_one(db_name, rc.coll, filterid)
if isinstance(person_idx, dict):
todolist_idx = person_idx.get("todos", [])
else:
continue
if len(todolist_idx) == 0:
continue
else:
for todo in todolist_idx:
todo["running_index"] = index
index += 1
person = document_by_value(
all_docs_from_collection(rc.client, "people"), "_id",
rc.assigned_to)
if not person:
raise TypeError(
f"Id {rc.assigned_to} can't be found in people collection")
todolist = person.get("todos", [])
if len(todolist) == 0:
print(f"{rc.assigned_to} doesn't have todos in people collection.")
return
if not rc.certain_date:
today = dt.date.today()
else:
today = date_parser.parse(rc.certain_date).date()
if not rc.index:
started_todo = 0
for todo in todolist:
if todo["status"] == 'started':
started_todo += 1
if not todo.get('importance'):
todo['importance'] = 1
if type(todo["due_date"]) == str:
todo["due_date"] = date_parser.parse(
todo["due_date"]).date()
if type(todo.get("end_date")) == str:
todo["end_date"] = date_parser.parse(
todo["end_date"]).date()
todo["days_to_due"] = (todo.get('due_date') - today).days
todo["sort_finished"] = (
todo.get("end_date", dt.date(1900, 1, 1)) -
dt.date(1900, 1, 1)).days
todo["order"] = todo['importance'] + 1 / (
1 + math.exp(abs(todo["days_to_due"] - 0.5))) - (
todo["days_to_due"] < -7) * 10
todolist = sorted(
todolist,
key=lambda k:
(k['status'], k['order'], -k.get('duration', 10000)),
reverse=True)
todolist[started_todo:] = sorted(todolist[started_todo:],
key=lambda k:
(-k["sort_finished"]))
index_match = {}
if rc.reorder:
new_index_started = 1
new_index_finished = -1
for todo in todolist[:started_todo]:
index_match[todo["running_index"]] = new_index_started
new_index_started += 1
for todo in todolist[started_todo:]:
index_match[todo["running_index"]] = new_index_finished
new_index_finished += -1
for i in range(0, len(rc.databases)):
db_name = rc.databases[i]["name"]
person_idx = rc.client.find_one(db_name, rc.coll, filterid)
if isinstance(person_idx, dict):
todolist_idx = person_idx.get("todos", [])
else:
continue
if len(todolist_idx) != 0:
for todo in todolist_idx:
index = index_match[todo["running_index"]]
todo["running_index"] = index
rc.client.update_one(db_name,
rc.coll, {'_id': rc.assigned_to},
{"todos": todolist_idx},
upsert=True)
print(
f"Indices in {db_name} for {rc.assigned_to} have been updated."
)
return
if rc.assigned_by:
if rc.assigned_by == "default_id":
rc.assigned_by = rc.default_user_id
for todo in todolist[::-1]:
if todo.get('assigned_by') != rc.assigned_by:
print(todo.get('assigned_by'))
todolist.remove(todo)
elif rc.assigned_to == rc.assigned_by:
todolist.remove(todo)
if rc.filter:
todolist = key_value_pair_filter(todolist, rc.filter)
if rc.stati == ["started"]:
rc.stati = ACTIVE_STATI
print(
"If the indices are far from being in numerical order, please reorder them by running regolith helper u_todo -r"
)
print("Please choose from one of the following to update:")
print(
"(index) action (days to due date|importance|expected duration (mins)|assigned by)"
)
print("-" * 81)
print_task(todolist, stati=rc.stati)
print("-" * 81)
else:
match_todo = [
i for i in todolist if i.get("running_index") == rc.index
]
if len(match_todo) == 0:
raise RuntimeError("Please enter a valid index.")
else:
todo = match_todo[0]
if rc.description:
todo["description"] = rc.description
if rc.due_date:
try:
relative_day = int(rc.due_date)
due_date = today + relativedelta(days=relative_day)
except ValueError:
due_date = date_parser.parse(rc.due_date).date()
todo["due_date"] = due_date
if rc.estimated_duration:
todo["duration"] = rc.estimated_duration
if rc.importance or rc.importance == 0:
if rc.importance in ALLOWED_IMPORTANCE:
todo["importance"] = rc.importance
else:
raise ValueError(
f"Importance should be chosen from{ALLOWED_IMPORTANCE}."
)
if rc.status:
if rc.status in ALLOWED_STATI:
todo["status"] = rc.status
else:
raise ValueError(
f"Status should be chosen from {ALLOWED_STATI}.")
if rc.notes:
try:
todo["notes"].extend(rc.notes)
except KeyError:
todo["notes"] = []
todo["notes"].extend(rc.notes)
if rc.begin_date:
todo["begin_date"] = date_parser.parse(
rc.begin_date).date()
if rc.end_date:
todo["end_date"] = date_parser.parse(rc.end_date).date()
for i in range(0, len(rc.databases)):
db_name = rc.databases[i]["name"]
person_update = rc.client.find_one(db_name, rc.coll,
filterid)
todolist_update = person_update.get("todos", [])
if len(todolist_update) != 0:
for i, todo_u in enumerate(todolist_update):
if rc.index == todo_u.get("running_index"):
todolist_update[i] = todo
rc.client.update_one(
db_name,
rc.coll, {'_id': rc.assigned_to},
{"todos": todolist_update},
upsert=True)
print(
f"The task \"({todo_u['running_index']}) {todo_u['description'].strip()}\" in {db_name} for {rc.assigned_to} has been updated."
)
return
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
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 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")
def db_updater(self):
rc = self.rc
if rc.index:
if rc.index >= 9900:
print("WARNING: indices >= 9900 are used for milestones which "
"should be finished using u_milestone and not f_todo")
return
if not rc.assigned_to:
try:
rc.assigned_to = rc.default_user_id
except AttributeError:
print(
"Please set default_user_id in '~/.config/regolith/user.json', or you need to enter your group id "
"in the command line")
return
person = document_by_value(
all_docs_from_collection(rc.client, "todos"), "_id",
rc.assigned_to)
filterid = {'_id': rc.assigned_to}
if not person:
raise TypeError(
f"Id {rc.assigned_to} can't be found in todos collection")
todolist = person.get("todos", [])
if len(todolist) == 0:
print(f"{rc.assigned_to} doesn't have todos in todos collection.")
return
now = dt.date.today()
if not rc.index:
if not rc.date:
today = now
else:
today = date_parser.parse(rc.date).date()
if rc.filter:
todolist = key_value_pair_filter(todolist, rc.filter)
for todo in todolist:
if type(todo["due_date"]) == str:
todo["due_date"] = date_parser.parse(
todo["due_date"]).date()
todo["days_to_due"] = (todo.get('due_date') - today).days
todo["order"] = 1 / (1 +
math.exp(abs(todo["days_to_due"] - 0.5)))
todolist = sorted(todolist,
key=lambda k: (k['status'], k['importance'], k[
'order'], -k.get('duration', 10000)))
print(
"If the indices are far from being in numerical order, please renumber them by running regolith helper u_todo -r"
)
print("Please choose from one of the following to update:")
print(
"(index) action (days to due date|importance|expected duration (mins)|tags|assigned by)"
)
print("-" * 80)
print_task(todolist, stati=['started'])
else:
match_todo = [
i for i in todolist if i.get("running_index") == rc.index
]
if len(match_todo) == 0:
raise RuntimeError("Please enter a valid index.")
else:
todo = match_todo[0]
todo["status"] = "finished"
if not rc.end_date:
end_date = now
else:
end_date = date_parser.parse(rc.end_date).date()
todo["end_date"] = end_date
for i in range(0, len(rc.databases)):
db_name = rc.databases[i]["name"]
person_update = rc.client.find_one(db_name, rc.coll,
filterid)
if person_update:
todolist_update = person_update.get("todos", [])
else:
continue
if len(todolist_update) != 0:
for i, todo_u in enumerate(todolist_update):
if rc.index == todo_u.get("running_index"):
todolist_update[i] = todo
rc.client.update_one(
db_name,
rc.coll, {'_id': rc.assigned_to},
{"todos": todolist_update},
upsert=True)
print(
f"The task \"({todo_u['running_index']}) {todo_u['description'].strip()}\" in {db_name} for {rc.assigned_to} has been marked as finished."
)
return
return
def projects(self):
rc = self.rc
projs = all_docs_from_collection(rc.client, 'projects')
self.render('projects.html', 'projects.html', title='Projects', projects=projs)
