def sout(self):
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 = []
for person in collection:
if rc.current and not person.get('active'):
continue
people.append(person)
if rc.filter and not rc.verbose:
results = (collection_str(people, rc.keys))
print(results, end="")
return
for i in people:
if rc.verbose:
print("{}, {} | group_id: {}".format(i.get('name'), i.get('position'), i.get('_id')))
print(" orcid: {} | github_id: {}".format(i.get('orcid_id'), i.get('github_id')))
else:
print("{}".format(i.get('name')))
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:
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
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 sout(self):
rc = self.rc
if rc.filter:
collection = key_value_pair_filter(self.gtx["projecta"], rc.filter)
else:
collection = self.gtx["projecta"]
if (not rc.lead) and (not rc.person) and (not rc.ended) and (not rc.grant) and (not rc.verbose) and (not rc.grp_by_lead) and (not rc.filter) and (not rc.all):
return
if rc.date:
desired_date = date_parser.parse(rc.date).date()
else:
desired_date = dt.date.today()
if rc.range:
num_of_days = int(rc.range)
else:
num_of_days = 7
projecta = []
end_projecta = []
grouped_projecta = {}
if rc.lead and rc.person:
raise RuntimeError(f"please specify either lead or person, not both")
for projectum in collection:
if rc.all and projectum.get('status') != "finished":
projecta.append(projectum)
continue
if isinstance(projectum.get('group_members'), str):
projectum['group_members'] = [projectum.get('group_members')]
if rc.lead and projectum.get('lead') != rc.lead:
continue
if rc.person:
if isinstance(rc.person, str):
rc.person = [rc.person]
good_p = []
for i in rc.person:
if projectum.get('lead') == rc.person:
good_p.append(i)
if projectum.get('group_members') and i in projectum.get('group_members'):
good_p.append(i)
if len(good_p) == 0:
continue
if rc.grant and rc.grant not in projectum.get('grants'):
continue
if rc.ended and not projectum.get('end_date'):
continue
if rc.ended:
end_date = projectum.get('end_date')
if isinstance(end_date, str):
end_date = date_parser.parse(end_date).date()
low_range = desired_date - dt.timedelta(days=num_of_days)
high_range = desired_date + dt.timedelta(days=num_of_days)
if low_range <= end_date <= high_range:
end_projecta.append(projectum)
continue
projecta.append(projectum)
if rc.ended:
for p in end_projecta:
members, collaborators = None, None
if p.get("group_members"):
members = ', '.join(p.get("group_members"))
if p.get("collaborators"):
collaborators = ', '.join(p.get("collaborators"))
print("{} {}\n Lead: {} Members: {} Collaborators: {}".format(p.get("_id"),
p.get("description"),
p.get("lead"), members,
collaborators))
return
if rc.verbose:
for p in projecta:
grants = None
if p.get('grants'):
if isinstance(p.get('grants'), list):
grants = ' ,'.join(p.get('grants'))
else:
grants = p.get('grants')
print(p.get('_id'))
print(f" status: {p.get('status')}, begin_date: {p.get('begin_date')}, due_date: {p.get('due_date')}, end_date: {p.get('end_date')}, grant: {grants}")
print(f" description: {p.get('description')}")
print(" team:")
print(f" lead: {p.get('lead')}")
grp_members = None
if p.get('group_members'):
grp_members = ', '.join(p.get('group_members'))
collaborators = None
if p.get('collaborators'):
collaborators = ', '.join(p.get('collaborators'))
print(f" group_members: {grp_members}")
print(f" collaborators: {collaborators}")
return
if rc.grp_by_lead:
for p in projecta:
if p.get('lead') not in grouped_projecta:
grouped_projecta[p.get('lead')] = [p.get('_id')]
else:
grouped_projecta[p.get('lead')].append(p.get('_id'))
for key, values in grouped_projecta.items():
print(f"{key}:")
for v in values:
print(f" {v}")
return
projecta.sort(key=lambda prum: prum.get("_id"))
if rc.keys:
results = (collection_str(projecta, rc.keys))
print(results, end="")
return
for i in projecta:
print(i.get("_id"))
return
def sout(self):
rc = self.rc
# This if statement should be in all listers. Make sure to change self.gtx to get the database the lister needs
if rc.filter:
collection = key_value_pair_filter(self.gtx["projecta"], rc.filter)
else:
collection = self.gtx["projecta"]
if (not rc.lead) and (not rc.verbose) and (not rc.stati) and (
not rc.current) and (not rc.person) and (not rc.all):
return
# fixme there must be a better way, but for now use magic to
# to remove checklists
# print(collection)
collection = [
prum for prum in collection
if "checklist" not in prum.get('deliverable', {}).get('scope', [])
]
if rc.lead:
if rc.person:
raise RuntimeError(
f"please specify either lead or person, not both")
collection = [
prum for prum in collection if prum.get('lead') == rc.lead
]
if rc.person:
if isinstance(rc.person, str):
rc.person = [rc.person]
collection = [
prum for prum in collection
if prum.get('lead') in rc.person or bool(
set(prum.get('group_members', [])).intersection(
set(rc.person))) or bool(
set(prum.get('collaborators', [])).intersection(
set(rc.person)))
]
if not rc.all:
collection = [
prum for prum in collection
if prum.get('status') not in INACTIVE_STATI
]
all_milestones = []
if not rc.stati and not rc.all and not rc.finished:
rc.stati = PROJECTUM_ACTIVE_STATI
elif rc.finished:
rc.stati = PROJECTUM_FINISHED_STATI
elif rc.all:
rc.stati = PROJECTUM_STATI
for projectum in collection:
projectum["deliverable"].update({
"name": "deliverable",
"objective": "deliver"
})
milestones = [projectum["deliverable"]]
if projectum.get("kickoff"):
projectum["kickoff"].update({"type": "meeting"})
milestones = [projectum["kickoff"], projectum["deliverable"]]
milestones.extend(projectum["milestones"])
milestones = [
ms for ms in milestones if ms.get('status') in rc.stati
]
for ms in milestones:
due_date = get_due_date(ms)
ms.update({
'lead': projectum.get('lead'),
'group_members': projectum.get('group_members'),
'collaborators': projectum.get('collaborators'),
'id': projectum.get('_id'),
'due_date': due_date,
'log_url': projectum.get('log_url'),
'pi': projectum.get('pi_id')
})
milestones.sort(key=lambda x: x['due_date'], reverse=True)
all_milestones.extend(milestones)
if rc.keys:
results = (collection_str(all_milestones, rc.keys))
print(results, end="")
return
if not rc.by_prum:
all_milestones.sort(key=lambda x: x['due_date'], reverse=True)
prum = ""
for ms in all_milestones:
if rc.by_prum:
if prum != ms.get("id"):
print("-" * 50)
prum = ms.get("id")
if rc.verbose:
print(
f"{ms.get('due_date')}: lead: {ms.get('lead')}, {ms.get('id')}, status: {ms.get('status')}"
)
print(f" Type: {ms.get('type', '')}")
print(f" Title: {ms.get('name')}")
print(f" log url: {ms.get('log_url')}")
print(f" Purpose: {ms.get('objective')}")
audience = []
for i in ms.get('audience', []):
if isinstance(ms.get(i, i), str):
audience.append(ms.get(i, i))
else:
if ms.get(i):
audience.extend(ms.get(i))
out = ", ".join(audience)
print(f" Audience: {out}")
if ms.get("notes"):
print(f" Notes:")
for note in ms.get("notes"):
print(f" - {note}")
else:
print(
f"{ms.get('due_date')}: lead: {ms.get('lead')}, {ms.get('id')}, {ms.get('name')}, status: {ms.get('status')}"
)
return
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 test_collection_str(input, expected):
assert (collection_str(input[0], input[1]) == expected)
def sout(self):
rc = self.rc
if rc.filter:
collection = key_value_pair_filter(self.gtx["projecta"], rc.filter)
else:
collection = self.gtx["projecta"]
if (not rc.lead) and (not rc.person) and (not rc.ended) and (
not rc.grant) and (not rc.verbose) and (
not rc.grp_by_lead) and (not rc.filter) and (
not rc.current) and (not rc.all):
return
if rc.date:
now = date_parser.parse(rc.date).date()
else:
now = dt.date.today()
if not rc.range:
rc.range = 7
since_date = now - dt.timedelta(days=int(rc.range))
projecta, end_projecta, error_projecta = [], [], []
grouped_projecta = {}
if rc.grant:
collection = [
prum for prum in collection if rc.grant in prum.get('grants')
]
if rc.lead:
if rc.person:
raise RuntimeError(
f"please specify either lead or person, not both")
collection = [
prum for prum in collection if prum.get('lead') == rc.lead
]
if rc.person:
if isinstance(rc.person, str):
rc.person = [rc.person]
collection = [
prum for prum in collection
if prum.get('lead') in rc.person or bool(
set(prum.get('group_members', [])).intersection(
set(rc.person)))
]
if rc.current:
collection = [
prum for prum in collection
if prum.get('status') in ACTIVE_STATI
]
if not rc.all:
collection = [
prum for prum in collection
if prum.get('status') not in INACTIVE_STATI
]
for projectum in collection:
if rc.ended:
if projectum.get('status') not in ACTIVE_STATI:
if projectum.get('status') in INACTIVE_STATI:
continue
elif projectum.get('status') not in FINISHED_STATI \
or not isinstance(projectum.get('end_date'),
dt.date):
error_projecta.append(projectum)
else:
end_date = projectum.get('end_date')
if isinstance(end_date, str):
end_date = date_parser.parse(end_date).date()
if since_date <= end_date <= now:
end_projecta.append(projectum)
if end_projecta != []:
projecta = end_projecta
continue
projecta.append(projectum)
if rc.verbose:
for p in projecta:
grants = None
if p.get('grants'):
if isinstance(p.get('grants'), list):
grants = ' ,'.join(p.get('grants'))
else:
grants = p.get('grants')
print(p.get('_id'))
print(
f" status: {p.get('status')}, begin_date: {p.get('begin_date')}, due_date: {p.get('due_date')}, end_date: {p.get('end_date')}, grant: {grants}"
)
print(f" description: {p.get('description')}")
print(" team:")
print(f" lead: {p.get('lead')}")
grp_members = None
if p.get('group_members'):
grp_members = ', '.join(p.get('group_members'))
collaborators = None
if p.get('collaborators'):
collaborators = ', '.join(p.get('collaborators'))
print(f" group_members: {grp_members}")
print(f" collaborators: {collaborators}")
return
if rc.grp_by_lead:
for p in projecta:
if p.get('lead') not in grouped_projecta:
grouped_projecta[p.get('lead')] = [p.get('_id')]
else:
grouped_projecta[p.get('lead')].append(p.get('_id'))
for key, values in grouped_projecta.items():
print(f"{key}:")
for v in values:
print(f" {v}")
return
projecta.sort(key=lambda prum: prum.get("_id"))
if rc.keys:
results = (collection_str(projecta, rc.keys))
print(results, end="")
return
if end_projecta != []:
if now == dt.date.today() and rc.range == 7:
print("\nProjecta finished this past week! o(*^v^*)o")
else:
print(
f"\nProjecta finished within the {rc.range} days leading up to {now}"
)
elif end_projecta == [] and rc.ended:
if now == dt.date.today() and rc.range == 7:
print("\nNo projecta finished this week")
else:
print(
f"\nNo projecta finished within the {rc.range} days leading up to {now}"
)
for i in projecta:
print(i.get("_id"))
if error_projecta:
print(
"\nWARNING: These projecta have an issue with the end date and/or status, "
"please run f_prum to set status to finished and add an end date"
)
for i in error_projecta:
print(i.get("_id"))
def sout(self):
rc = self.rc
# This if statement should be in all listers. Make sure to change self.gtx to get the database the lister needs
if rc.filter:
collection = key_value_pair_filter(self.gtx["projecta"], rc.filter)
else:
collection = self.gtx["projecta"]
all_milestones = []
if not rc.stati:
rc.stati = ['started']
for projectum in collection:
if rc.lead and projectum.get('lead') != rc.lead:
continue
projectum["deliverable"].update({
"name": "deliverable",
"objective": "deliver"
})
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 rc.stati or \
'all' in rc.stati:
if ms.get('status') not in \
["finished", "cancelled"]:
due_date = get_due_date(ms)
ms.update({
'lead':
projectum.get('lead'),
'group_members':
projectum.get('group_members'),
'collaborators':
projectum.get('collaborators'),
'id':
projectum.get('_id'),
'due_date':
due_date,
'log_url':
projectum.get('log_url'),
'pi':
projectum.get('pi_id')
})
all_milestones.append(ms)
all_milestones.sort(key=lambda x: x['due_date'], reverse=True)
if rc.keys:
results = (collection_str(all_milestones, rc.keys))
print(results, end="")
return
for ms in all_milestones:
if rc.verbose:
print(
f"{ms.get('due_date')}: lead: {ms.get('lead')}, {ms.get('id')}, status: {ms.get('status')}"
)
print(f" Type: {ms.get('type', '')}")
print(f" Title: {ms.get('name')}")
print(f" log url: {ms.get('log_url')}")
print(f" Purpose: {ms.get('objective')}")
audience = []
for i in ms.get('audience'):
if isinstance(ms.get(i, i), str):
audience.append(ms.get(i, i))
else:
if ms.get(i):
audience.extend(ms.get(i))
out = ", ".join(audience)
print(f" Audience: {out}")
else:
print(
f"{ms.get('due_date')}: lead: {ms.get('lead')}, {ms.get('id')}, {ms.get('name')}, status: {ms.get('status')}"
)
return
def sout(self):
rc = self.rc
# This if statement should be in all listers. Make sure to change self.gtx to get the database the lister needs
if rc.filter:
collection = key_value_pair_filter(self.gtx["projecta"], rc.filter)
else:
collection = self.gtx["projecta"]
if (not rc.lead) and (not rc.verbose) and (not rc.stati) and (
not rc.current) and (not rc.person) and (not rc.all):
return
if rc.lead:
if rc.person:
raise RuntimeError(
f"please specify either lead or person, not both")
collection = [
prum for prum in collection if prum.get('lead') == rc.lead
]
if rc.person:
if isinstance(rc.person, str):
rc.person = [rc.person]
collection = [
prum for prum in collection
if prum.get('lead') in rc.person or bool(
set(prum.get('group_members', [])).intersection(
set(rc.person)))
]
# if rc.current:
# collection = [prum for prum in collection if
# prum.get('status') in ACTIVE_STATI]
# if rc.finished:
# collection = [prum for prum in collection if
# prum.get('status') in FINISHED_STATI]
if not rc.all:
collection = [
prum for prum in collection
if prum.get('status') not in INACTIVE_STATI
]
all_milestones = []
if not rc.stati:
rc.stati = ['started']
for projectum in collection:
projectum["deliverable"].update({
"name": "deliverable",
"objective": "deliver"
})
projectum["kickoff"].update({"type": "meeting"})
milestones = [projectum["kickoff"], projectum["deliverable"]]
milestones.extend(projectum["milestones"])
if rc.current:
milestones = [
ms for ms in milestones if ms.get('status') in ACTIVE_STATI
]
if rc.finished:
milestones = [
ms for ms in milestones
if ms.get('status') in FINISHED_STATI
]
if not rc.all:
milestones = [
ms for ms in milestones
if ms.get('status') not in INACTIVE_STATI
]
for ms in milestones:
due_date = get_due_date(ms)
ms.update({
'lead': projectum.get('lead'),
'group_members': projectum.get('group_members'),
'collaborators': projectum.get('collaborators'),
'id': projectum.get('_id'),
'due_date': due_date,
'log_url': projectum.get('log_url'),
'pi': projectum.get('pi_id')
})
all_milestones.append(ms)
all_milestones.sort(key=lambda x: x['due_date'], reverse=True)
if rc.keys:
results = (collection_str(all_milestones, rc.keys))
print(results, end="")
return
for ms in all_milestones:
if rc.verbose:
print(
f"{ms.get('due_date')}: lead: {ms.get('lead')}, {ms.get('id')}, status: {ms.get('status')}"
)
print(f" Type: {ms.get('type', '')}")
print(f" Title: {ms.get('name')}")
print(f" log url: {ms.get('log_url')}")
print(f" Purpose: {ms.get('objective')}")
audience = []
for i in ms.get('audience'):
if isinstance(ms.get(i, i), str):
audience.append(ms.get(i, i))
else:
if ms.get(i):
audience.extend(ms.get(i))
out = ", ".join(audience)
print(f" Audience: {out}")
else:
print(
f"{ms.get('due_date')}: lead: {ms.get('lead')}, {ms.get('id')}, {ms.get('name')}, status: {ms.get('status')}"
)
return
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
