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["projecta"], rc.filter)
else:
collection = self.gtx["projecta"]
if not rc.date:
now = datetime.date.today()
else:
now = date_parser.parse(rc.date).date()
# remove checklist prums from the report
collection = [
prum for prum in collection
if "checklist" not in prum.get('deliverable', {}).get('scope', [])
]
title = f"\nProgress report for {rc.lead}, generated {now.isoformat()}"
print(title)
projecta = [
valid_prum for valid_prum in collection
if valid_prum.get("lead") == rc.lead
]
finishedp, proposedp, startedp, otherp = [], [], [], []
for prum in projecta:
if prum.get('status') == "finished":
finishedp.append(prum)
elif prum.get('status') == "proposed":
proposedp.append(prum)
elif prum.get('status') == "started":
startedp.append(prum)
else:
otherp.append(prum)
print(
f"*************************[Orphan Projecta]*************************"
)
for prum in otherp:
print(f"{prum.get('_id')}, status: {prum.get('status')}")
print(
f"*************************[Finished Projecta]*************************"
)
for prum in finishedp:
print(f"{prum.get('_id')}, grant: {prum.get('grants')}")
print(f" description: {prum.get('description')}")
print(f" finished: {prum.get('end_date')}")
print(
f"*************************[Proposed Projecta]*************************"
)
self.print_projectum(proposedp)
print(
f"*************************[In Progress Projecta]*************************"
)
self.print_projectum(startedp)
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 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 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 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 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 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):
gtx = self.gtx
rc = self.rc
if rc.filter:
collection = key_value_pair_filter(self.gtx["people"], rc.filter)
else:
collection = self.gtx["people"]
bad_stati = ["finished", "cancelled", "paused", "back_burner"]
people = []
if rc.filter:
if not rc.verbose:
results = (collection_str(collection, rc.keys))
# "scopatz"
print(results, end="")
return
else:
for person in collection:
print("{}, {} | group_id: {}".format(
person.get('name'), person.get('position'),
person.get('_id')))
print(" orcid: {} | github_id: {}".format(
person.get('orcid_id'), person.get('github_id')))
pass
#code to print verbosely on filtering
if not rc.filter:
for person in gtx["people"]:
if rc.current:
if not person.get('active'):
continue
people.append(person)
elif rc.prior:
if person.get('active'):
continue
people.append(person)
else:
people.append(person)
for i in people:
if rc.verbose:
print("{}, {}".format(i.get('name'), i.get('position')))
print(" email: {} | group_id: {}".format(
i.get('email'), i.get('_id')))
print(" github_id: {} | orcid: {}".format(
i.get('github_id'), i.get('orcid_id')))
not_current_positions = [
emp for emp in i.get('employment') if not is_current(emp)
]
not_current_positions.sort(
key=lambda x: get_dates(x)["end_date"])
current_positions = [
emp for emp in i.get('employment') if is_current(emp)
]
current_positions.sort(
key=lambda x: get_dates(x)["begin_date"])
positions = not_current_positions + current_positions
for position in positions:
if is_current(position):
inst = fuzzy_retrieval(gtx["institutions"],
["aka", "name", "_id"],
position.get("organization"))
if inst:
instname = inst.get("name")
else:
print(
f"WARNING: {position.get('organization')} not in institutions collection"
)
print(" current organization: {}".format(instname))
print(" current position: {}".format(
position.get('full_position',
position.get('position').title())))
if not i.get('active'):
if position.get('group') == "bg":
print(" billinge group position: {}".format(
position.get('position')))
else:
print("{}".format(i.get('name')))
return
def sout(self):
rc = self.rc
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 test_key_value_pair_filter(input, expected):
assert (key_value_pair_filter(input[0], input[1]) == expected)
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 sout(self):
rc = self.rc
if rc.filter:
collection = key_value_pair_filter(self.gtx["projecta"], rc.filter)
else:
collection = self.gtx["projecta"]
projecta = []
for projectum in collection:
if (not rc.lead) and (not rc.stati):
projecta.append(projectum)
continue
if rc.lead and projectum.get('lead') != rc.lead:
continue
if rc.stati and projectum.get('status') not in rc.stati:
continue
projecta.append(projectum)
selected_projecta = []
for p in projecta:
if p.get('status') != "proposed":
continue
selected_projecta.append(p)
if selected_projecta:
print(
f"*************************[Proposed Projecta]*************************"
)
print_projectum(selected_projecta, rc)
selected_projecta = []
for p in projecta:
if p.get('status') != "started":
continue
selected_projecta.append(p)
if selected_projecta:
print(
f"*************************[Started Projecta]**************************"
)
print_projectum(selected_projecta, rc)
selected_projecta = []
for p in projecta:
if p.get('status') != "finished":
continue
selected_projecta.append(p)
if selected_projecta:
print(
f"*************************[Finished Projecta]*************************"
)
print_projectum(selected_projecta, rc)
selected_projecta = []
for p in projecta:
if p.get('status') not in ["back_burner", "paused", "cancelled"]:
continue
selected_projecta.append(p)
if selected_projecta:
print(
f"*************************[Others]************************************"
)
print_projectum(selected_projecta, rc)
