def move_tables_to_memory(data, source):
"""Create a petl.MemorySource and copy data from the given tables into it. Can greatly decrease processing time for some operations."""
for s in source:
source_table = data.get(s)
a = petl.MemorySource()
source_table.tocsv(a)
b = petl.MemorySource(a.getvalue())
destination_table = petl.fromcsv(source=b)
data.set(s, destination_table)
def download(self, path=''):
logging.info('Start download from google drive')
logging.info(path)
report_filename = self.get_report_filename(self.report, self.from_date,
self.to_date)
if cache:
cache_key = path
cache_timeout = CONNECTOR_INFO.get('report_cache_timeout', 60 * 60)
z_report = cache.get(cache_key)
if z_report is not None:
return petl.io.fromjson(
petl.MemorySource(zlib.decompress(z_report)))
logging.info('Download Report from {}'.format(path))
storage = self.storage[0]
storage.init()
fname = '{}.json'.format(self.report)
with storage.open(path) as archive_file:
with zipfile.ZipFile(archive_file) as zip_file:
# logging.info(fname)
report = zip_file.read(fname)
z_report = zlib.compress(report)
cache.set(cache_key, z_report, timeout=cache_timeout)
return petl.io.fromjson(petl.MemorySource(report))
else:
# move to init
if not os.path.exists(self.report_folder):
os.makedirs(self.report_folder)
if not os.path.exists(report_filename):
logging.info('Download Report from {}'.format(path))
storage = self.storage[0]
storage.init()
fname = '{}.json'.format(self.report)
with storage.open(path) as archive_file:
with zipfile.ZipFile(archive_file) as zip_file:
# logging.info(fname)
report = zip_file.read(fname)
with open(report_filename, 'wb') as f:
f.write(report)
logging.info('Read from {}'.format(report_filename))
report = petl.io.fromjson(report_filename)
return report
return []
def _persist_data(self, data: etl.Table) -> None:
sink = etl.MemorySource()
data.tocsv(sink)
collection = Collection.objects.create()
collection.csv_file.save(f"{str(uuid.uuid4())}.csv",
ContentFile(sink.getvalue()))
def display(self, collection: Collection, limit: int) -> etl.Table:
if not collection.csv_file.name:
return etl.Table()
with collection.csv_file.open() as f:
source = etl.MemorySource(b"".join(islice(f, 1, limit + 1)))
table = etl.fromcsv(source)
return table
def count_values(self, collection: Collection, columns: List[str],
save_as: str) -> etl.Table:
if not collection.csv_file.name:
return etl.Table()
with collection.csv_file.open() as f:
source = etl.MemorySource(f.read())
table = etl.fromcsv(source)
return table.aggregate(columns, {save_as: len})
def fromcsvwithheader(source, **kwargs):
"""
Call `petl.fromcsv` and automatically parse metadata header if present.
"""
# preliminary open for inspection
rawtable = petl.fromcsv(source, header=None, **kwargs)
metadata, header, data = parse_metadata_header(rawtable)
# transfer data to a in-memory data buffer
databuffer = petl.MemorySource()
petl.tocsv(data, databuffer, write_header=True, encoding='utf-8')
databuffer.s = databuffer.getvalue()
# re-open with right headers and add metadata
table = petl.fromcsv(databuffer, header=header)
table.metadata = metadata
return table
def read_raw(self, file):
# return etl.fromcsv(file.name)
in_memory_file = StringIO()
csv_writer = csv.writer(in_memory_file)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
wb = openpyxl.load_workbook(file.name)
sh = wb.worksheets[0]
for r in sh.rows:
csv_writer.writerow([cell.value for cell in r])
in_memory_file.seek(0)
rawlines = in_memory_file.read().encode()
raw = etl.MemorySource(rawlines)
rdr = etl.fromcsv(raw)
return rdr
def etl_data_from_teragon(url, data, tranpose, indexed):
"""handles making request to the teragon service and transform the response
Arguments:
url {str} -- Teragon API endpoint
data {dict} -- request payload (always sent as data via POST)
tranpose {bool} -- transpose the resulting table (default: False)
Returns:
{dict} -- Teragon API response transformed into a nested dictionary, ready to be transmitted as JSON
"""
# get the data
start_time = timeit.default_timer()
response = requests.post(url, data=data)
elapsed = timeit.default_timer() - start_time
print("response received in {0} seconds".format(elapsed))
# post-process and return the response
start_time = timeit.default_timer()
table = etl.MemorySource(response.text.encode())
result = transform_teragon_csv(table, tranpose, indexed)
elapsed = timeit.default_timer() - start_time
print("data processed received in {0} seconds".format(elapsed))
return result
def _convert_to_html(table):
table_output = petl.MemorySource()
table.tohtml(table_output)
return table_output.getvalue().decode('utf-8')
def to_csv(data: Table) -> bytes:
output = etl.MemorySource()
etl.tocsv(data, output)
return output.getvalue()
def time_report(request):
"""
The main view for the Time Report. Using the Auth Token retrieves the necessary data
and displays to the user as a table. Data can be downloaded to a CSV file.
"""
data = None
if request.method == 'POST':
form = TimeReportForm(request.POST)
if form.is_valid():
form_data = form.cleaned_data
client = HubstaffApiClient(form_data["app_token"], form_data["auth_token"])
try:
users_t = (petl.fromdicts(client.list_users())
.cut("id", "name").rename("name", "user"))
projects_t = (petl.fromdicts(client.list_projects())
.cut("id", "name").rename("name", "project"))
main_t = petl.fromdicts(client.list_activities_for_date(form_data["for_date"]))
except HTTPError as e:
form.add_error(None, "The Hubstaff responded with an error: {} {}".format(
e.response.status_code, e.response.reason)
)
if main_t.nrows() > 0:
# Now some PETL processing, remove unnecessary fields, join with 'users' and
# 'projects' tables, aggregate on time spend and pivot, apply formatting to time
data = (main_t
.cut("user_id", "project_id", "tracked")
.join(users_t, lkey="user_id", rkey="id")
.join(projects_t, lkey="project_id", rkey="id")
.aggregate(("user", "project"), sum, "tracked")
.convert("value",
convert_seconds_to_iso if form_data["format"] == "csv" else
convert_seconds_to_human
)
.pivot("project", "user", "value", lambda a: a[0])
)
if request.POST.get("action") == "Download":
filename = "activities_report_{}.{}".format(
form_data["for_date"].strftime("%Y%m%d"), form_data["format"]
)
resp = HttpResponse(content_type='text/{}'.format(
form_data["format"] if form_data["format"] != "txt" else "plain"
))
resp['Content-Disposition'] = 'attachment; filename="{}"'.format(filename)
if form_data["format"] == "html":
buf = petl.MemorySource()
resp.write("<!DOCTYPE html><html><body>")
resp.write("<style type='text/css'>table,th,td {border: solid}</style>")
data.tohtml(buf, encoding="utf-8")
resp.write(buf.getvalue().decode())
resp.write("</body></html>")
elif form_data["format"] == "csv":
buf = petl.MemorySource()
data.tocsv(buf, encoding="utf-8")
resp.write(buf.getvalue().decode())
elif form_data["format"] == "txt":
resp.write(data.lookall())
return resp
else:
buf = petl.MemorySource()
data.tohtml(buf, encoding="utf-8")
data = buf.getvalue().decode()
else:
form = TimeReportForm(request.GET)
if not form.data.get("app_token") or not form.data.get("auth_token") or not form.data.get(
"name") or not form.data.get("id") or not form.data.get("for_date"):
return HttpResponseRedirect(urls.reverse('index'))
context = {"form": form, "table": data, "submitted": request.method == 'POST'}
return render(request, 'time_report.html', context)
"pixels": pixels
}
# print(payload)
url = 'http://web.3riverswetweather.org/trp:API.pixel'
# request data from Teragon API
start_time = timeit.default_timer()
response = requests.get(url, data=payload)
elapsed = timeit.default_timer() - start_time
print("response received in {0} seconds".format(elapsed))
# read and transform Teragon response
start_time = timeit.default_timer()
# convert text of response to bytes and read through memory
source = etl.MemorySource(response.text.encode())
# read from memory as if it were a csv file on disk
# table1 = etl.fromcsv(source)
# transform table into dict, ready for conversion to structured JSON
table1_json = transform_teragon_csv(source)
# print(json.dumps(table1_json, indent=2))
print("processing table took {0} seconds".format(
timeit.default_timer() - start_time))
# Transpose (can take a really long time with PETL!)
# start_time = timeit.default_timer()
# table2 = etl.transpose(t2_rows)
# print("{0} rows after transpose eval".format(etl.nrows(table2)))
# print("transposing took {0} seconds".format(
# timeit.default_timer() - start_time))
# # print(etl.lookall(table2, style='minimal'))
def download(self, path=''):
logging.info('Start download from google drive')
logging.info(path)
report_filename = self.get_report_filename(self.report, self.from_date,
self.to_date)
time_range = {'since': self.from_date, 'until': self.to_date}
if cache:
cache_key = path
cache_timeout = CONNECTOR_INFO.get('report_cache_timeout', 60 * 60)
z_report = cache.get(cache_key)
if z_report is not None:
return petl.io.fromjson(
petl.MemorySource(zlib.decompress(z_report)))
###############################
logging.info('Download Report from {}'.format(path))
request = fbAdAccount.get_insights(
# pending=True,
async=True,
fields=fb_ads_insight_fields,
params={
'time_increment': 1,
# 'limit': 1,
'level': fbAdsInsights.Level.ad,
# 'breakdowns': report.,
'time_range': time_range
})
# storage = self.storage[0]
# storage.init()
#
# fname = '{}.json'.format(self.report)
#
# with storage.open(path) as archive_file:
# with zipfile.ZipFile(archive_file) as zip_file:
# # logging.info(fname)
# report = zip_file.read(fname)
# z_report = zlib.compress(report)
# cache.set(cache_key, z_report, timeout=cache_timeout)
#
# return petl.io.fromjson(petl.MemorySource(report))
# else:
# # move to init
# if not os.path.exists(self.report_folder):
# os.makedirs(self.report_folder)
#
# if not os.path.exists(report_filename):
# logging.info('Download Report from {}'.format(path))
# storage = self.storage[0]
# storage.init()
#
# fname = '{}.json'.format(self.report)
#
# with storage.open(path) as archive_file:
# with zipfile.ZipFile(archive_file) as zip_file:
# # logging.info(fname)
# report = zip_file.read(fname)
#
# with open(report_filename, 'wb') as f:
# f.write(report)
#
# logging.info(
# 'Read from {}'.format(report_filename))
# report = petl.io.fromjson(report_filename)
# return report
return []
for p in pop_colors:
h = '#%02x%02x%02x' % tuple(int(255 * c) for c in pop_colors[p])
# chromatin
_data_chromatin = b"""CHX chro X 20009764 24393108
CH2R chro 2R 58984778 61545105
CH2L chro 2L 1 2431617
PEU2L chro 2L 2487770 5042389
IH2L chro 2L 5078962 5788875
IH3R chro 3R 38988757 41860198
CH3R chro 3R 52161877 53200684
CH3L chro 3L 1 1815119
PEU3L chro 3L 1896830 4235209
IH3L chro 3L 4264713 5031692
"""
tbl_chromatin = (etl.fromtext(etl.MemorySource(_data_chromatin)).split(
'lines', '\s+', ['name', 'type', 'chrom', 'start', 'stop']).convert(
('start', 'stop'), int).cutout('type'))
# genome regions
region_X_speciation = 'X-speciation', 'X', 15000000, 24000000
region_X_free = 'X-free', 'X', 1, 14000000
region_3L_free = '3L-free', '3L', 15000000, 41000000
region_3R_free = '3R-free', '3R', 1, 37000000
# noinspection PyGlobalUndefined
def init(release_dir, load_geneset=False):
"""Initialise data resources.
Parameters
def dof9_import_dates(
data, input_file, teacher_absences_destination,
period_replacements_destination,
emergency_teacher_availables_destination,
emergency_teacher_yard_duty_available_destination,
yard_duty_replacements_destination, room_replacements_destination,
room_edits_destination, lesson_cancellations_destination,
yard_duty_cancellations_destination, load_adjustments_destination,
room_availables_destination, attendence_changes_destination):
"""Import the dates and definitions for the replacements that need to happen."""
namespaces = {'x': 'http://www.timetabling.com.au/DOV9'}
all_teacher_absences = petl.wrap([[]])
all_period_replacements = petl.wrap([[]])
all_emergency_teacher_availables = petl.wrap([[]])
all_emergency_teacher_yard_duty_available = petl.wrap([[]])
all_yard_duty_replacements = petl.wrap([[]])
all_room_replacements = petl.wrap([[]])
all_room_edits = petl.wrap([[]])
all_lesson_cancellations = petl.wrap([[]])
all_yard_duty_cancellations = petl.wrap([[]])
all_load_adjustments = petl.wrap([[]])
all_room_availables = petl.wrap([[]])
all_attendence_changes = petl.wrap([[]])
tree = lxml.etree.parse(open(input_file)) # Read Everything
date_subtrees = tree.xpath(
'/x:DailyOrganiserData/x:Dates/x:Date',
namespaces={'x': 'http://www.timetabling.com.au/DOV9'})
for date_subtree in date_subtrees:
cf_date = date_subtree.findtext('x:Date', namespaces=namespaces)
cf_datestring = date_subtree.findtext('x:DateString',
namespaces=namespaces)
cf_day = date_subtree.findtext('x:Day', namespaces=namespaces)
add_common_fields = lambda i, cf_date=cf_date, cf_datestring=cf_datestring, cf_day=cf_day: i.addfield(
'Date', cf_date).addfield('DateString', cf_datestring).addfield(
'Day', cf_day) # noqa
subtree_data = petl.MemorySource(lxml.etree.tostring(date_subtree))
if teacher_absences_destination is not None:
teacher_absences = petl.fromxml(
subtree_data,
'{http://www.timetabling.com.au/DOV9}TeacherAbsences/{http://www.timetabling.com.au/DOV9}TeacherAbsence',
{
'TeacherAbsenceID':
'{http://www.timetabling.com.au/DOV9}TeacherAbsenceID',
'TeacherCode':
'{http://www.timetabling.com.au/DOV9}TeacherCode',
'SessionNo':
'{http://www.timetabling.com.au/DOV9}SessionNo',
'Precedes':
'{http://www.timetabling.com.au/DOV9}Precedes',
'IsYardDuty':
'{http://www.timetabling.com.au/DOV9}IsYardDuty',
'PeriodCode':
'{http://www.timetabling.com.au/DOV9}PeriodCode',
'TeacherAbsenceReasonID':
'{http://www.timetabling.com.au/DOV9}TeacherAbsenceID',
'Counted':
'{http://www.timetabling.com.au/DOV9}Counted',
'Load':
'{http://www.timetabling.com.au/DOV9}Load',
'ArchiveTimetableReference':
'{http://www.timetabling.com.au/DOV9}ArchiveTimetableReference',
'ArchiveErrorType':
'{http://www.timetabling.com.au/DOV9}ArchiveErrorType'
})
teacher_absences = add_common_fields(teacher_absences)
all_teacher_absences = all_teacher_absences.cat(teacher_absences)
if period_replacements_destination is not None:
period_replacements = petl.fromxml(
subtree_data,
'{http://www.timetabling.com.au/DOV9}PeriodReplacements/{http://www.timetabling.com.au/DOV9}PeriodReplacement',
{
'PeriodReplacementID':
'{http://www.timetabling.com.au/DOV9}PeriodReplacementID',
'RollClassCode':
'{http://www.timetabling.com.au/DOV9}RollClassCode',
'ClassCode':
'{http://www.timetabling.com.au/DOV9}ClassCode',
'ClassGroupRowID':
'{http://www.timetabling.com.au/DOV9}ClassGroupRowID',
'PeriodCode':
'{http://www.timetabling.com.au/DOV9}PeriodCode',
'PeriodNo':
'{http://www.timetabling.com.au/DOV9}PeriodNo',
'ReplacementTeacherCode':
'{http://www.timetabling.com.au/DOV9}ReplacementTeacherCode',
'Load':
'{http://www.timetabling.com.au/DOV9}Load',
'Count':
'{http://www.timetabling.com.au/DOV9}Count',
'InLieu':
'{http://www.timetabling.com.au/DOV9}InLieu',
'Notes':
'{http://www.timetabling.com.au/DOV9}Notes',
'Index':
'{http://www.timetabling.com.au/DOV9}Index',
'NotRequired':
'{http://www.timetabling.com.au/DOV9}NotRequired',
'DuplicateReplacementID':
'{http://www.timetabling.com.au/DOV9}DuplicateReplacementID',
'ReferenceTeacherCode':
'{http://www.timetabling.com.au/DOV9}ReferenceTeacherCode',
'IsComposites':
'{http://www.timetabling.com.au/DOV9}IsComposites',
'ArchiveTimetableReference':
'{http://www.timetabling.com.au/DOV9}ArchiveTimetableReference',
'ArchiveErrorType':
'{http://www.timetabling.com.au/DOV9}ArchiveErrorType'
})
period_replacements = add_common_fields(period_replacements)
all_period_replacements = all_period_replacements.cat(
period_replacements)
if yard_duty_replacements_destination is not None:
yard_duty_replacements = petl.fromxml(
subtree_data,
'{http://www.timetabling.com.au/DOV9}YardDutyReplacements/{http://www.timetabling.com.au/DOV9}YardDutyReplacement',
{
'YardDutyReplacementID':
'{http://www.timetabling.com.au/DOV9}YardDutyReplacementID',
'YardDutyCode':
'{http://www.timetabling.com.au/DOV9}YardDutyCode',
'PeriodCode':
'{http://www.timetabling.com.au/DOV9}PeriodCode',
'PeriodNo':
'{http://www.timetabling.com.au/DOV9}PeriodNo',
'Precedes':
'{http://www.timetabling.com.au/DOV9}Precedes',
'SessionNo':
'{http://www.timetabling.com.au/DOV9}SessionNo',
'ReplacementTeacherCode':
'{http://www.timetabling.com.au/DOV9}ReplacementTeacherCode',
'Load':
'{http://www.timetabling.com.au/DOV9}Load',
'Count':
'{http://www.timetabling.com.au/DOV9}Count',
'InLieu':
'{http://www.timetabling.com.au/DOV9}InLieu',
'Notes':
'{http://www.timetabling.com.au/DOV9}Notes',
'Index':
'{http://www.timetabling.com.au/DOV9}Index',
'NotRequired':
'{http://www.timetabling.com.au/DOV9}NotRequired',
'ActivityCode':
'{http://www.timetabling.com.au/DOV9}ActivityCode',
'ReferenceTeacherCode':
'{http://www.timetabling.com.au/DOV9}ReferenceTeacherCode',
'DuplicateReplacementID':
'{http://www.timetabling.com.au/DOV9}DuplicateReplacementID',
'ArchiveTimetableReference':
'{http://www.timetabling.com.au/DOV9}ArchiveTimetableReference',
'ArchiveErrorType':
'{http://www.timetabling.com.au/DOV9}ArchiveErrorType'
})
yard_duty_replacements = add_common_fields(yard_duty_replacements)
all_yard_duty_replacements = all_yard_duty_replacements.cat(
yard_duty_replacements)
if room_edits_destination is not None:
room_edits = petl.fromxml(
subtree_data,
'{http://www.timetabling.com.au/DOV9}RoomEdits/{http://www.timetabling.com.au/DOV9}RoomEdit',
{
'ClassCode':
'{http://www.timetabling.com.au/DOV9}ClassCode',
'ClassGroupRowID':
'{http://www.timetabling.com.au/DOV9}ClassGroupRowID',
'RollClassCode':
'{http://www.timetabling.com.au/DOV9}RollClassCode',
'PeriodCode':
'{http://www.timetabling.com.au/DOV9}PeriodCode',
'ReplacementRoomCode':
'{http://www.timetabling.com.au/DOV9}ReplacementRoomCode',
'ArchiveTimetableReference':
'{http://www.timetabling.com.au/DOV9}ArchiveTimetableReference',
'ArchiveErrorType':
'{http://www.timetabling.com.au/DOV9}ArchiveErrorType'
})
room_edits = add_common_fields(room_edits)
all_room_edits = all_room_edits.cat(room_edits)
if teacher_absences_destination is not None:
data.set(teacher_absences_destination, all_teacher_absences)
if period_replacements_destination is not None:
data.set(period_replacements_destination, all_period_replacements)
if yard_duty_replacements_destination is not None:
data.set(yard_duty_replacements_destination,
all_yard_duty_replacements)
if room_edits_destination is not None:
data.set(room_edits_destination, all_room_edits)
def download(self, urls=[]):
# timeout setting for requests
# timeout = urllib3.Timeout(connect=2.0, read=7.0)
# http = urllib3.PoolManager(timeout=timeout)
http = urllib3.PoolManager()
report_data = []
for url in urls:
# print(url)
report_filename = self.get_report_filename(
hashlib.md5(url).hexdigest())
if cache:
# print('use cache')
cache_key = url
cache_timeout = CONNECTOR_INFO.get('report_cache_timeout',
60 * 60)
z_report = cache.get(cache_key)
if z_report is not None:
new_report_data = petl.io.fromcsv(
petl.MemorySource(zlib.decompress(z_report)))
# print(len(new_report_data))
if not report_data:
# print('NEw cat')
report_data = new_report_data
else:
report_data = petl.cat(report_data, new_report_data)
continue
logging.info('Download Report from {}'.format(url))
r = http.request('GET',
url,
retries=urllib3.Retry(
redirect=2,
backoff_factor=2,
))
if r.status == 200:
report = r.data
r.release_conn()
z_report = zlib.compress(report)
cache.set(cache_key, z_report, timeout=cache_timeout)
# return petl.io.fromcsv(petl.MemorySource(report))
new_report_data = petl.io.fromcsv(
petl.MemorySource(report))
# print(len(new_report_data))
if not report_data:
report_data = new_report_data
else:
report_data = petl.cat(report_data, new_report_data)
elif r.status == 403:
raise Exception(r.data)
else:
logging.info(r.data)
logging.info(r.status)
logging.info(r.headers)
else:
# move to init
# print('Not cache')
if not os.path.exists(self.report_folder):
os.makedirs(self.report_folder)
if not os.path.exists(report_filename):
logging.info('Download Report from {}'.format(url))
r = http.request('GET',
url,
retries=urllib3.Retry(
redirect=2,
backoff_factor=2,
))
if r.status == 200:
with open(report_filename, 'wb') as f:
f.write(r.data)
r.release_conn()
logging.info('Read from {}'.format(report_filename))
new_report_data = petl.io.fromcsv(report_filename)
if not report_data:
report_data = new_report_data
else:
report_data = petl.cat(report_data,
new_report_data)
return report_data