def eod_position_pd_run(pricing_environment, valuation_date):
r = utils.get_redis_conn(redis_ip)
position_result = r.get(EOD_BASIC_POSITIONS)
position = pd.read_msgpack(position_result)
risk_result = r.get(EOD_BASIC_RISKS_ + pricing_environment.lower())
risk = pd.read_msgpack(risk_result)
cash_flow_result = r.get(EOD_BASIC_CASH_FLOW)
cash_flow = pd.read_msgpack(cash_flow_result)
listed_option_positions_result = r.get(EOD_BASIC_LISTED_OPTION_POSITION_ +
pricing_environment.lower())
listed_option_positions = pd.read_msgpack(listed_option_positions_result)
headers = utils.login(data_resource_ip, login_body)
rpt = []
if not position.empty:
rpt = eod_position_report_pd.eod_position_report(
position, risk, cash_flow, listed_option_positions,
pricing_environment, data_resource_ip, headers, valuation_date)
position_result = JSONEncoder().encode(rpt)
r.set(EOD_CUSTOM_POSITION_ + pricing_environment.lower(),
str(position_result))
def msgpack_assertMeta(filename, frames=None, redo=False):
'''Asserts that the .meta file for a given .msg file exists and returns the data in the .meta file once it exists'''
meta_out_file = filename.replace(".msg", ".meta")
print(meta_out_file)
meta_frames = None
if (os.path.exists(meta_out_file) and not redo):
#Need to check for latin encodings due to weird pandas default
try:
meta_frames = pd.read_msgpack(meta_out_file)
except UnicodeDecodeError as e:
meta_frames = pd.read_msgpack(meta_out_file, encoding='latin-1')
if (meta_frames == None):
if (frames == None):
print(
"Bulk reading .msg for metaData assertion. Be patient, reading in slices not supported."
)
print(filename)
#Need to check for latin encodings due to weird pandas default
try:
frames = pd.read_msgpack(filename)
except UnicodeDecodeError as e:
frames = pd.read_msgpack(filename, encoding='latin-1')
meta_frames = {"NumValues": frames["NumValues"]}
if (not os.path.exists(meta_out_file) or redo):
pd.to_msgpack(meta_out_file, meta_frames)
return meta_frames
def recommend_by_shop(self, start_date, end_date):
start_date = DateStrToDate(start_date)
end_date = DateStrToDate(end_date, hour=23, minute=59, seconds=59)
case_data = pd.read_msgpack(red.get('case_data'))
payment_logs = pd.read_msgpack(red.get('payment_logs'))
shop_reflect = json.loads(red.get('shop_data').decode())
result_list = []
data = case_data[case_data['apply_date'] <= end_date]
payment_limit = payment_logs[(payment_logs['date'] >= start_date)
& (payment_logs['date'] < end_date)]
data_excute = Data_Execute()
date_index = "%s/%s" % (start_date.strftime('%Y-%m-%d'),
end_date.strftime('%m-%d'))
for shop_id in shop_reflect:
shop_data = data_excute.recommend_by_shop(
table=data[data['shop_id'] == int(shop_id)],
payment_logs=payment_limit[payment_limit['shop_id'] == int(
shop_id)],
date_index=date_index,
data_name=shop_reflect[str(shop_id)],
start_date=start_date)
result_list.append(shop_data)
return result_list
def learn(basepath, features_file, labels_file):
# Load the data
print 'Loading data...'
features_data = pd.read_msgpack(load_data(basepath, features_file)['data'])
labels_data = pd.read_msgpack(load_data(basepath, labels_file)['data'])
df = pd.concat([features_data, labels_data], axis=1)
# Process features
samples, labels = preprocess.process_data(df)
# How many samples are we going to leave out for the test set?
nb_test = int(len(labels) * 0.2)
split = len(labels) - nb_test
# Prepare training and test sets
X_train = np.array(samples[:split])
y_train = labels[:split]
X_test = np.array(samples[split + 1:])
y_test = labels[split + 1:]
print len(X_train), 'train sequences'
print len(X_test), 'test sequences'
# How many classes?
num_classes = np.max(labels) + 1
print num_classes, 'classes'
# Train Model
train_and_save(X_train, X_test, y_train, y_test, num_classes, basepath)
def learn(basepath, features_file, labels_file):
# Load the data
print 'Loading data...'
features_data = pd.read_msgpack(load_data(basepath, features_file)['data'])
labels_data = pd.read_msgpack(load_data(basepath, labels_file)['data'])
df = pd.concat([features_data,labels_data], axis=1)
# Process features
samples, labels = preprocess.process_data(df)
# How many samples are we going to leave out for the test set?
nb_test = int(len(labels) * 0.2)
split = len(labels) - nb_test
# Prepare training and test sets
X_train = np.array(samples[:split])
y_train = labels[:split]
X_test = np.array(samples[split+1:])
y_test = labels[split+1:]
print len(X_train), 'train sequences'
print len(X_test), 'test sequences'
# How many classes?
num_classes = np.max(labels)+1
print num_classes, 'classes'
# Train Model
train_and_save(X_train, X_test, y_train, y_test, num_classes, basepath)
def concat_data():
df_ohlc = pd.read_msgpack(f'{DATASET_PATH}/twse_ohlc.msgpack').rename(
columns={
'日期': 'date',
'開盤指數': 'open',
'最高指數': 'high',
'最低指數': 'low',
'收盤指數': 'close'
}).reset_index(drop=True)
df_ob = pd.read_msgpack(f'{DATASET_PATH}/twse_orderbook.msgpack')
df_ob_open = df_ob[df_ob['時間'].map(
lambda x: x.time() == dt.time(9, 0, 0))].copy()
df_ob_close = df_ob[df_ob['時間'].map(
lambda x: x.time() == dt.time(13, 30, 0))].copy()
df_ob_open['date'] = df_ob_open['時間'].map(
lambda x: x.date()) #.strftime('%Y%m%d')
df_ob_open = df_ob_open.rename(columns={
'累積委託買進筆數': 'order_buy',
'累積委託賣出筆數': 'order_sell'
})[['date', 'order_buy', 'order_sell']]
df_ob_close['date'] = df_ob_close['時間'].map(lambda x: x.date())
df_ob_close = df_ob_close.rename(columns={'累積成交金額': 'volume'})[[
'date', 'volume'
]]
df_twse = df_ohlc.set_index('date').join(
df_ob_open.set_index('date')).join(
df_ob_close.set_index('date')).dropna()
print('data concat done.')
return df_twse
def load(self, fn):
self.xs_not_decomposed = pd.read_msgpack(fn + '.X.msg')
self.xs_not_decomposed = self.xs_not_decomposed.to_dict()
self.ys_not_decomposed = pd.read_msgpack(fn + '.Y.msg')
self.idx = self.ys_not_decomposed.index.max()
self.ys_not_decomposed = self.ys_not_decomposed.to_dict()
self.start()
def main():
with TLOG('read data'):
df = pd.read_msgpack('data/z6_ts_events.msgpack')
df_discount = pd.read_msgpack('data/z6_ts_discount.msgpack')
ids = np.load('data/z6_ts_user_id_merchant_id.npy')
feature = UserMerchantFeature(df, df_discount=df_discount, keys=ids)
df = feature.process()
df.to_msgpack('data/z6_ts_feature_user_merchant.msgpack')
def Files_Read_Qo_Q190(link, listEvents=False, umbral=0.5, MinDays=15):
#Read observed
try:
Qo = pd.read_msgpack('/Users/nicolas/LambdaExp/BaseData/USGS/' + link +
'.msg')
except:
#Read information from the links
LinksData = pd.read_msgpack('LinkData.msg')
USGS_id = LinksData.index[LinksData['Link'] == int(link)].values[0]
#Read from the web.
print('Warning: reading from the web...')
Qo = db.WEB_Get_USGS(USGS_id, '2008-01-01', '2018-12-30')
Qo.to_msgpack('/Users/nicolas/LambdaExp/BaseData/USGS/' + link +
'.msg')
print('Message: Streamflow saved as a msgpack as link:' + link)
Qo = Qo.resample('H').mean()
#Read simulated
Qs = pd.read_msgpack('/Users/nicolas/LambdaExp/BaseData/HLM190/' + link +
'.msg')
Qs = Qs.resample('H').mean()
#Find events
shared = Qo.index.intersection(Qs.index)
Qs = Qs[shared]
Qo = Qo[shared]
pos1, pos2 = ser.Runoff_FindEvents(Qo, Qs, umbral=umbral)
#Estimates the max anual Streeamflow
QmaxA = np.median(Qo.resample('A').max())
Qbase = Qo.resample('A').apply(
lambda x: np.percentile(x[np.isfinite(x)], 50)).mean()
#Selects only the good events
pos1V2 = []
pos2V2 = []
for i, j in zip(pos1, pos2):
M = Qo[i:j].max()
if M > QmaxA * umbral:
#Check amount of nans.
NaNPercent = Qo[i:j][np.isnan(Qo[i:j])].size / Qo[i:j].size
if NaNPercent < 0.2:
#Check the time between peak and strt of the event
while Qo[i] < Qbase * 2.5:
i = i + pd.Timedelta('5h')
Td = j - i
if Td.days < MinDays:
pos1V2.append(i)
pos2V2.append(j)
#List the events
if listEvents:
c = 0
for p1, p2 in zip(pos1V2, pos2V2):
qp = '%.2f ' % np.nanmax(Qo[p1:p2])
print(c, qp, p1)
c += 1
#Updates the class Evento
Evento.Qobs = Qo
Evento.Qsim = Qs
Evento.pos1 = pos1V2
Evento.pos2 = pos2V2
def load(self, only_get=None):
train_data = pandas.read_msgpack('cache/dataset/train.msg')
merge_data = pandas.read_msgpack('cache/dataset/merge.msg')
valid_data = pandas.read_msgpack('cache/dataset/valid.msg')
if only_get is not None:
return train_data.head(only_get), merge_data.head(
only_get), valid_data.head(only_get)
else:
return train_data, merge_data, valid_data
def _load(self, as_df):
with gzip.open('rf_cache/dataset/train.msg.gz', 'r') as f:
if as_df:
td = pandas.read_msgpack(f)
else:
td = pandas.read_msgpack(f).values
f = np.load('rf_cache/folds.npz')['data']
return td, f
def read_events(self):
split = self.split.name
with TLOG('read events'):
df_events = pd.read_msgpack(f'data/z6_ts_{split}_events.msgpack')
df_discount = pd.read_msgpack(
f'data/z6_ts_{split}_discount.msgpack')
df = with_discount(df_events, df_discount)
with TLOG('build index events'):
events = IndexedEvents(df, key_column=self.key_column)
return events
def main():
with TLOG('read data'):
df = pd.read_msgpack('data/z6_ts_events.msgpack')
df_discount = pd.read_msgpack('data/z6_ts_discount.msgpack')
coupon_ids = np.load('data/z6_ts_coupon_id.npy')
coupon_feature = CouponFeature(df,
df_discount=df_discount,
keys=coupon_ids)
df = coupon_feature.process()
df.to_msgpack('data/z6_ts_feature_coupon.msgpack')
def read_input_to_pandas(self, columnList=[], indexCol="Sample"):
if self.isGzipped:
with gzip.open(self.filePath) as path:
df = pd.read_msgpack(path)
else:
df = pd.read_msgpack(self.filePath)
df = df.reset_index()
if len(columnList) > 0:
df = df[columnList]
return df
def get_human_22_fake_genome():
from mbf_genomics.testing import MockGenome
import gzip
genes = pd.read_msgpack(
gzip.GzipFile(get_sample_data(Path("mbf_align/hs_22_genes.msgpack.gz")))
).reset_index()
tr = pd.read_msgpack(
gzip.GzipFile(get_sample_data(Path("mbf_align/hs_22_transcripts.msgpack.gz")))
).reset_index()
return MockGenome(df_genes=genes, df_transcripts=tr, chr_lengths={"22": 50_818_468})
def get_translational_efficiency(project_id):
from main import get_db
rdb = get_db()
rp = rdb.get("{}_rpkm_rp".format(project_id))
rna = rdb.get("{}_rpkm_rna".format(project_id))
list_of_samples = []
if rp is None or rna is None:
return render_template("translational_efficiency.html", samples=list_of_samples,
error="No data for project: {}".format(project_id))
rp_df = pd.read_msgpack(rp)
rna_df = pd.read_msgpack(rna)
samples = list(rp_df.columns)
samples.remove('gene_name')
list_of_samples = samples
if request.method == "GET":
return render_template("translational_efficiency.html", samples=list_of_samples)
selected_samples = request.form.getlist('selected_samples')
if not selected_samples:
return render_template("translational_efficiency.html", samples=list_of_samples, error="No samples selected")
apply_filter = request.form.get('apply_filter') == "True"
min_y = request.form.get('min_y', -100)
max_y = request.form.get('max_y', 100)
min_y = int(min_y)
max_y = int(max_y)
plot_series = []
for sample in selected_samples:
gene_names = rp_df['gene_name'].tolist()
rp = rp_df[sample].astype(float).tolist()
rna = rna_df[sample].astype(float).tolist()
df = pd.DataFrame(columns=['gene_name', 'x', 'y'])
df['gene_name'] = gene_names
df['rpkm_rna'] = rna
df['rpkm_rp'] = rp
df['log2(rp)'] = np.log2(df['rpkm_rp'])
df['log2(rna)'] = np.log2(df['rpkm_rna'])
df['x'] = df['log2(rna)']
df['y'] = df['log2(rna)'] / df['log2(rp)']
if apply_filter:
df = df.loc[df['y'] >= min_y]
df = df.loc[df['y'] <= max_y]
df = df.replace([np.inf, -np.inf], np.nan)
df = df.dropna()
series = {
'name': sample,
'data': df.to_dict('records')
}
plot_series.append(series)
return render_template("translational_efficiency.html", samples=list_of_samples, selected_samples=selected_samples,
apply_filter=apply_filter, min_y=min_y, max_y=max_y, plot_series=plot_series)
def FeedToRedis(r=r, source_dir="intermediate-results/", mode="batch"):
if not mode in ["batch", "recent"]:
print "[Error] the mode is not correct!"
exit()
result_filename = "mirror-news-ann-distance-20.result"
msg_filename = "news-id-tfidf50-topic-category.msg"
if mode == "recent":
result_filename = "recent-" + result_filename
msg_filename = "recent-" + msg_filename
if os.path.exists(source_dir + result_filename) == True:
f = open(source_dir + result_filename, 'r')
else:
print(
"[Warning] Cannot find the latest list of related news. Use the fallback list now. Please run daily_batch.sh to get the latest related news"
)
f = open('fallback/fallback.result', 'r')
if os.path.exists(source_dir + msg_filename) == True:
df = pd.read_msgpack(source_dir + msg_filename)
else:
print(
"[Warning] Cannot find the latest metadata of related news. Use the fallback metadata now. Please run daily_batch.sh to get the latest metadata"
)
df = pd.read_msgpack('fallback/fallback.msg')
print("Loading the KNN list...")
news_dict = dict()
for line in f:
news_id, knn_raw = line.replace("\n", "").split("\t")
knn_list = json.loads(knn_raw)
r_news = []
for (r_id, _) in knn_list:
r_dict = get_facets(df, r_id)
r_news.append(r_dict)
n_dict = get_facets(df, news_id)
n_dict['knn_list'] = knn_list
n_dict['related_news'] = r_news
news_dict["related-news-v2-" + news_id] = json.dumps(n_dict)
"""
if you find error msg: MISCONF Redis is configured to save RDB snapshots,
try this on redis-cli: config set stop-writes-on-bgsave-error no
"""
print "Total: " + str(len(news_dict))
print "Feed all to Redis..."
r.mset(news_dict)
print "Done!"
def histogram(wild_card='*thrown', key='energy', bins=10):
paths = glob(wild_card)
df = pd.read_msgpack(paths[0])
df.dropna(inplace=True)
counts, bins = np.histogram(df[key], bins=bins)
total_bincounts = np.zeros(len(bins) - 1)
for path in paths:
df = pd.read_msgpack(path)
df.dropna(inplace=True)
bincounts = np.histogram(df[key], bins=bins)[0]
total_bincounts += bincounts
return total_bincounts, bins
def load(file_name, mode=None):
if mode == 'HD5':
df = pd.read_hdf(file_name, 'dataframe')
elif mode == 'msgpack':
pd.read_msgpack(file_name)
elif mode == 'parquet':
df = pd.read_parquet(file_name,
engine='pyarrow',
use_pandas_metadata=True)
elif mode == 'pickle.gzip':
df = pd.read_pickle(file_name, compression='gzip')
elif mode == 'feather':
read_feather(file_name)
def msgpack_revert(self, val, cls=dict, checker=None, **kw):
if cls == pandas_df_type.__name__ or cls == pandas_df_type:
import pandas
if isinstance(val, requests.Response):
return pandas.read_msgpack(val.content, **keep(kw, []))
else:
return pandas.read_msgpack(io.BytesIO(val), **keep(kw, []))
if isinstance(val, requests.Response):
val = val.content
import msgpack
val = msgpack.loads(val, **keep(kw, []))
val = self.schema_revert(val, cls, checker=checker)
return val
def Statistic_index(self, statistic_date, statistic_date_end, compare_date,
compare_date_end, shop_get):
statistic_date = DateStrToDate(statistic_date)
statistic_end_date = DateStrToDate(statistic_date_end,
hour=23,
minute=59,
seconds=59)
compare_date = DateStrToDate(compare_date)
compare_end_date = DateStrToDate(compare_date_end,
hour=23,
minute=59,
seconds=59)
if int(shop_get) == 0 or not shop_get:
shop_ids = [i for i in range(2, 24)]
else:
shop_ids = [int(shop_get)]
case_data = pd.read_msgpack(red.get('case_data'))
payment_logs = pd.read_msgpack(red.get('payment_logs'))
data_execute = Data_Execute()
statistic_data = case_data[
(case_data['apply_date'] >= statistic_date)
& (case_data['apply_date'] < statistic_end_date) &
(case_data['shop_id'].isin(shop_ids))]
statistic_compare = case_data[
(case_data['apply_date'] >= compare_date)
& (case_data['apply_date'] < compare_end_date) &
(case_data['shop_id'].isin(shop_ids))]
payment_data = payment_logs[(payment_logs['date'] >= statistic_date) &
(payment_logs['date'] < statistic_end_date)
& (payment_logs['shop_id'].isin(shop_ids))]
payment_compare = payment_logs[
(payment_logs['date'] >= compare_date)
& (payment_logs['date'] < compare_end_date) &
(payment_logs['shop_id'].isin(shop_ids))]
statistic = data_execute.index_stactic(
statistic_data,
1,
statistic_date.strftime('%Y-%m-%d'),
index=True,
payment_logs=payment_data)
compare = data_execute.index_stactic(statistic_compare,
2,
compare_date.strftime('%Y-%m-%d'),
index=True,
payment_logs=payment_compare)
result_list = [statistic, compare]
return result_list
def main(cls, split):
df_raw_offline = pd.read_msgpack(f'data/z1_raw_offline.msgpack')
df_raw_test = pd.read_msgpack(f'data/z1_raw_test.msgpack')
user_id_index = np.unique(
np.concatenate([
df_raw_offline['user_id'].unique(),
df_raw_test['user_id'].unique()
]))
events = cls(user_id_index)
LOG.info('events feed_offline')
events.feed_offline(df_raw_offline)
df_online_coupon = pd.read_msgpack(
f'data/z1_raw_online_coupon.msgpack')
LOG.info('events feed_online_coupon')
events.feed_online_coupon(df_online_coupon)
df_online_click = pd.read_msgpack(f'data/z1_raw_online_click.msgpack')
LOG.info('events feed_online_click')
events.feed_online_click(df_online_click)
LOG.info('events feed_test')
events.feed_test(df_raw_test)
LOG.info('events to_frame')
df = events.to_frame(split)
df.to_msgpack(f'data/z6_ts_{split.name}_events.msgpack')
LOG.info('build_discount_table')
df_discount = cls.build_discount_table(df)
df_discount.to_msgpack(f'data/z6_ts_{split.name}_discount.msgpack')
df_offline_events = df[df['event_type'].isin([
'offline_receive_coupon',
'offline_buy_with_coupon',
'offline_buy_without_coupon',
])]
LOG.info('build_index_of user_id')
user_id_index = cls.build_index_of(df_offline_events, 'user_id')
np.save(f'data/z6_ts_{split.name}_user_id.npy', user_id_index)
for key in ['merchant_id', 'coupon_id']:
LOG.info('build_index_of {}', key)
arr = cls.build_index_of(df_offline_events, key)
np.save('data/z6_ts_{}_{}.npy'.format(split.name, key), arr)
LOG.info('build_index_of user_id_merchant_id')
arr = cls.build_index_of(df_offline_events, ['user_id', 'merchant_id'])
np.save(f'data/z6_ts_{split.name}_user_id_merchant_id.npy', arr)
LOG.info('build_index_of user_id_coupon_id')
arr = cls.build_index_of(df_offline_events, ['user_id', 'coupon_id'])
np.save(f'data/z6_ts_{split.name}_user_id_coupon_id.npy', arr)
def histogram2d(wild_card='*thrown', x='energy', y='number_photons', bins=10):
paths = glob(wild_card)
df = pd.read_msgpack(paths[0])
df.dropna(inplace=True)
h = np.histogram2d(x=df[x], y=df[y], bins=bins)
total_counts = h[0]
bins = h[1]
total_counts = 0
for path in paths:
df = pd.read_msgpack(path)
df.dropna(inplace=True)
bincounts = np.histogram2d(x=df[x], y=df[y], bins=bins)[0]
total_counts += bincounts
return total_counts, bins
def _getStore(f, storeType):
'''Helper Function - Gets the HDFStore or frames for the file and storeType'''
frames = None
if (storeType == "hdf5"):
store = pd.HDFStore(f)
elif (storeType == "msgpack"):
print(
"Bulk reading .msg. Be patient, reading in slices not supported.")
sys.stdout.flush()
#Need to check for latin encodings due to weird pandas default
try:
frames = pd.read_msgpack(f)
except UnicodeDecodeError as e:
frames = pd.read_msgpack(f, encoding='latin-1')
return store, frames
def read_dataset():
with TLOG('read dataframes'):
df_test_full = pd.read_msgpack(
f'data/z6_ts_{SPLIT.name}_merged_test.msgpack')
df_train_full = pd.read_msgpack(
f'data/z6_ts_{SPLIT.name}_merged_train.msgpack')
# columns
features = list(
df_test_full.columns.difference([
'user_id',
'merchant_id',
'coupon_id',
'discount_name',
'date',
'label',
]))
features = GOOD_FEATURES
# features = list(
# set(itertools.chain(*FEATULE_LEVELS.values()))
# - set(BAD_FEATURES)
# )
print(pretty(features))
test_submit_cols = ['user_id', 'coupon_id', 'date']
if TEST_HAS_LABEL:
test_submit_cols += ['label']
train_submit_cols = ['user_id', 'coupon_id', 'date', 'label']
# test submit
df_test = df_test_full[features]
df_submit = format_date(df_test_full.loc[df_test.index, test_submit_cols])
LOG.info('df_test {}', df_test.shape)
LOG.info('df_submit {}', df_submit.shape)
# split train validate
mask = np.random.rand(len(df_train_full)) < 0.05
df_validate = df_train_full.loc[mask, features + ['label']]
df_validate_submit = format_date(df_train_full.loc[mask,
train_submit_cols])
df_train = df_train_full.loc[~mask, features + ['label']]
df_train_submit = format_date(df_train_full.loc[~mask, train_submit_cols])
LOG.info('df_train {}', df_train.shape)
LOG.info('df_train_submit {}', df_train_submit.shape)
LOG.info('df_validate {}', df_validate.shape)
LOG.info('df_validate_submit {}', df_validate_submit.shape)
df_train_x, df_train_y = split_feature_label(df_train)
df_validate_x, df_validate_y = split_feature_label(df_validate)
ret = df_train_x, df_train_y, df_validate_x, df_validate_y, df_test, df_submit, df_validate_submit, df_train_submit
return [x.copy() for x in ret]
def read_all(self, freq, **kwargs):
"""
Read the entire timeseries record for all matching timeseries instances.
Optionally exclude timeseries from the final DataFrame by specifying IDs in the exclude argument.
:param identifier: Identifier of the timeseries.
:type identifier: string
:param freq: Timeseries data frequency.
:type freq: string
:param excludes: IDs of timeseries to exclude from final DataFrame.
:type excludes: array[string]
:param kwargs: Attributes to match against timeseries instances (e.g. source, measurand).
:type kwargs: kwargs
:returns: pandas.DataFrame -- Timeseries data.
"""
url = self.__attach_kwargs_to_url(
self.server + '/read_all/{0}.{1}'.format(freq, self.format),
kwargs
)
if self.format == 'msgpack':
return pd.read_msgpack(urlopen(url))
elif self.format == 'json':
return pd.read_json(urlopen(url))
else:
raise NotImplementedError('Unsupported format: {0}'.format(self.format))
def _load_chunks(self):
for chunk in pandas.read_msgpack(self.buf, iterator=True):
for col in self.schema.cols:
if isinstance(col, big_dt):
# converting big_dt column
chunk[col.name] = chunk[col.name].map(datetime.datetime.fromtimestamp, na_action='ignore')
yield chunk
def testrun(gname):
method = 'tepitope' #'iedbmhc1'#'netmhciipan'
path = 'test'
gfile = os.path.join(genomespath, '%s.gb' % gname)
df = sequtils.genbank2Dataframe(gfile, cds=True)
#names = list(df.locus_tag[:1])
names = ['VP24']
alleles1 = [
"HLA-A*02:02", "HLA-A*11:01", "HLA-A*32:07", "HLA-B*15:17",
"HLA-B*51:01", "HLA-C*04:01", "HLA-E*01:03"
]
alleles2 = [
"HLA-DRB1*0101", "HLA-DRB1*0305", "HLA-DRB1*0812", "HLA-DRB1*1196",
"HLA-DRB1*1346", "HLA-DRB1*1455", "HLA-DRB1*1457", "HLA-DRB1*1612",
"HLA-DRB4*0107", "HLA-DRB5*0203"
]
P = base.getPredictor(method)
P.iedbmethod = 'IEDB_recommended' #'netmhcpan'
P.predictProteins(df,
length=11,
alleles=alleles2,
names=names,
save=True,
path=path)
f = os.path.join('test', names[0] + '.mpk')
df = pd.read_msgpack(f)
P.data = df
#b = P.get_binders(data=df)
#print b[:20]
base.getScoreDistributions(method, path)
return
def read_python2_hdf5_dataframe(h5_filepath, key):
h5_filepath = os.path.realpath(h5_filepath)
msgpack_filepath = h5_filepath + '.' + key.replace('/', '_') + '.msgpack'
filepath_time = os.path.getmtime(h5_filepath)
if not os.path.exists(
msgpack_filepath) or filepath_time > os.path.getmtime(
msgpack_filepath):
logging.info(
'msgpack file {} doesnt exists, creating'.format(msgpack_filepath))
convert_python2_hdf5_to_msgpack(h5_filepath, key, msgpack_filepath)
else:
logging.info('msgpack file {} exists'.format(msgpack_filepath))
data = pd.read_msgpack(msgpack_filepath)
# Fix columns names and string columns that are bytes
data.columns = data.columns.astype(str)
for col in data:
try:
newcol = data[col].str.decode('utf-8')
except AttributeError:
continue
if not newcol.isnull().any():
data[col] = newcol
return data
def getScoreDistributions(method, path):
"""Get global score distributions and save quantile values for each allele
Assumes all the files in path represent related proteins"""
files = glob.glob(os.path.join(path, '*.mpk'))
results = []
P = getPredictor(method)
key = P.scorekey
#if method == 'iedbmhc1':
# P.data = pd.read_msgpack(files[0])
# key = P.getScoreKey()
print key
for f in files[:200]:
df = pd.read_msgpack(f)
#df = df.dropna()
x = df.pivot_table(index='peptide', columns='allele', values=key)
#print x[:5]
results.append(x)
result = pd.concat(results)
percs = np.arange(0.01,1,0.01)
bins = result.quantile(percs)
#reverse is best values are lower
if P.operator == '<':
bins.index = pd.Series(bins.index).apply(lambda x: 1-x)
outfile = os.path.join(path,'quantiles.csv')
print outfile
bins.to_csv(outfile,float_format='%.3f')
df= pd.read_csv(outfile,index_col=0)
print df.ix[0.96]
return
def load_pandas(file_name='review.json', use_cache=True):
cache_path = os.path.join(CACHE_PATH, f'load_pandas.msgpack')
if use_cache and os.path.exists(cache_path):
print(f'Loading from {cache_path}')
ratings, user_counts, active_users = pd.read_msgpack(cache_path)
print(f'Loaded from {cache_path}')
else:
line_count = len(
open(os.path.join(EXCEL_PATH, file_name),
encoding='utf8').readlines())
user_ids, business_ids, stars, dates, text = [], [], [], [], []
with open(os.path.join(EXCEL_PATH, file_name), encoding='utf8') as f:
for line in tqdm(f, total=line_count):
blob = json.loads(line)
user_ids += [blob["user_id"]]
business_ids += [blob["business_id"]]
stars += [blob["stars"]]
dates += [blob["date"]]
text += [blob["text"]]
ratings = pd.DataFrame({
"user_id": user_ids,
"business_id": business_ids,
"rating": stars,
"text": text,
"date": dates
})
user_counts = ratings["user_id"].value_counts()
active_users = user_counts.loc[user_counts >= 5].index.tolist()
pd.to_msgpack(cache_path, (ratings, user_counts, active_users))
print(f'Dumping to {cache_path}')
return ratings, user_counts, active_users
def read_df_from_redis(self, redisConn, key):
try:
return pd.read_msgpack(redisConn.get(key))
except:
if DEBUG:
traceback.print_exc()
return -1
def test_mse(neighborhood_size=5, filtertype="collaborative filtering"):
"""Tests the mse of predictions based on a given number of neighborhood sizes
neighborhood_size -- the sizes of neighborhoods between the number and 1 (so 5 tests for neighborhood of length 1, 2, 3, 4, 5)
filtertype -- the type of similarity you want to test the mse of
"""
# init variables
all_df = helpers.json_to_df()
df = helpers.split_data(all_df)
ut = helpers.create_utility_matrix(df[0])
if filtertype == "collaborative filtering":
print("Creating needed variables...")
sim = helpers.similarity_matrix_cosine(ut)
elif filtertype == "content based":
print("Creating needed variables...")
cats = helpers.json_to_df_categories()
fancy_cats = helpers.extract_genres(cats)
ut_cats = helpers.pivot_genres(fancy_cats)
sim = helpers.create_similarity_matrix_categories(ut_cats)
elif filtertype == "spacy":
print("Creating needed variables...")
sim = pd.read_msgpack("spacy_similarity.msgpack")
else:
print("Please enter a valid filtertype")
return
print("Starting calculations...")
mses = {}
# test the mse based on the length of the neighborhood
for i in range(1, neighborhood_size + 1):
predictions = helpers.predict_ratings(sim, ut, df[1], i).dropna()
amount = len(predictions)
mses[i] = helpers.mse(predictions)
return mses, amount
def loadProject(self, filename=None, asksave=False):
"""Open project file"""
w=True
if asksave == True:
w = self.closeProject()
if w == None:
return
if filename == None:
filename = filedialog.askopenfilename(defaultextension='.dexpl"',
initialdir=os.getcwd(),
filetypes=[("project","*.dexpl"),
("All files","*.*")],
parent=self.main)
if not filename:
return
if os.path.isfile(filename):
#pb = self.progressDialog()
#t = threading.Thread()
#t.__init__(target=pd.read_msgpack, args=(filename))
#t.start()
data = pd.read_msgpack(filename)
self.newProject(data)
self.filename = filename
self.main.title('%s - DataExplore' %filename)
self.projopen = True
return
def read_output(path,layer_dims):
""" Input: layer_dims, length 3 list of dimensions of the output of bottleneck layer
Returns ndarray of shape (num_batches, layer_dims) """
data = pd.read_msgpack(path)
batch_size = data.index.size
dims = [batch_size] + layer_dims
return data.as_matrix().reshape(dims)
def _load(self):
df = pandas.read_msgpack(self.buf)
for col in self.schema.cols:
if isinstance(col, big_dt):
# converting big_dt column
df[col.name] = df[col.name].map(datetime.datetime.fromtimestamp, na_action='ignore')
return df
def testLoad(self):
"""Test re-loading predictions"""
infile = os.path.join(self.testdir, 'ZEBOVgp1.mpk')
pred = pd.read_msgpack(infile)
P = base.getPredictor('iedbmhc1')
P.data = pred
return
def data():
# Set CSS properties for th elements in dataframe
try:
rdb.get("data")
data = pd.read_msgpack(rdb.get("data"))
return render_template('index.html', data=data.to_html(index=False, justify='center', classes="table table-striped"))
except Exception as e:
return render_template('index.html', data="<p>no data found</p><br/>Exception: " + str(e) + "<p></br></br>run /timereport-fetch in slack first</p></br>")
def load(self, filename, filetype=None):
"""Load file, if no filetype given assume it's msgpack format"""
if filetype == '.pickle':
self.df = pd.read_pickle(filename)
else:
self.df = pd.read_msgpack(filename)
return
def load_msgpack(self, filename):
"""Load a msgpack file"""
size = round((os.path.getsize(filename)/1.0485e6),2)
print (size)
df = pd.read_msgpack(filename)
name = os.path.splitext(os.path.basename(filename))[0]
self.load_dataframe(df, name)
return
def get_val(self, key):
## mined에서 사용하게 될 모든 데이터는 TICKERS 데이터가 아니면 pandas df이다
## TICKERS 데이터는 리스트 형식이다
if 'TICKERS' in key:
data = self.redis_client.lrange(key, 0, -1)
data = list(map(lambda x: x.decode('utf-8'), data))
else:
data = pd.read_msgpack(self.redis_client.get(key)) # 레디스에서 df 형식의 데이터를 가지고 오는 방법
### 참고: 레디스에 df를 저장하는 방법은: redis.set(key, df.to_msgpack(compress='zlib'))와 같은 형식이다
return data
def msg_io(self, name, func, **kwargs):
"""Read data from msgpack. If not available, calculate and store."""
cd = self.cache_dir()
msgpath = os.path.join(cd, name + MSGTLD)
if os.path.isfile(msgpath):
data = pd.read_msgpack(msgpath)
else:
ensure_dir(cd)
data = func(**kwargs)
data.to_msgpack(msgpath)
return data
def loadmsgpack(self, filename):
"""Load a msgpack file"""
df = pd.read_msgpack(filename)
name = os.path.splitext(os.path.basename(filename))[0]
if hasattr(self,'sheets'):
self.addSheet(sheetname=name, df=df)
else:
data = {name:df}
self.newProject(data)
return
def read_msgpack(path_or_buf,
encoding='utf-8',
iterator=False):
warnings.warn("Defaulting to Pandas implementation",
PendingDeprecationWarning)
port_frame = pd.read_msgpack(path_or_buf, encoding, iterator)
ray_frame = from_pandas(port_frame, get_npartitions())
return ray_frame
def loadmsgpack(self, filename):
"""Load a msgpack file"""
size = round((os.path.getsize(filename)/1.0485e6),2)
print (size)
df = pd.read_msgpack(filename)
name = os.path.splitext(os.path.basename(filename))[0]
if hasattr(self,'sheets'):
self.addSheet(sheetname=name, df=df)
else:
data = {name:{'table':df}}
self.newProject(data)
return
def __get_list(self, list_name, kwargs):
url = self.__attach_kwargs_to_url(
self.server + '/list/{0}.{1}'.format(list_name, self.format),
kwargs
)
if self.format == 'msgpack':
return pd.read_msgpack(urlopen(url)).values.tolist()
elif self.format == 'json':
return pd.read_json(urlopen(url)).values.tolist()
else:
raise NotImplementedError('Unsupported format: {0}'.format(self.format))
def pull_df(self, md5):
"""Wrapper for the Workbench get_dataframe method
Args:
md5: pull the dataframe identified by this md5
Returns:
The uncompressed/unserialized dataframe
"""
try:
_packed_df = self.workbench.get_dataframe(md5)
_df = pd.read_msgpack(lz4.loads(_packed_df))
return _df
except zerorpc.exceptions.RemoteError as e:
return repr_to_str_decorator.r_to_s(self._data_not_found)(e)
def initialize_mission_control(memory):
# Get subscription sockets
subscription_sender, subscription_receiver = subscription_sockets()
# Initialize subscriptions
initialize_subscriptions(subscription_sender)
# Initialize Feed Handler
while True:
message = subscription_receiver.recv()
ticker = message.split('_', 1)[0]
message = pd.read_msgpack(message.split('_', 1)[1])
print message
def getPredictions(path,tag,method='tepitope',q=0.96):
"""Get predictions from file system"""
q=round(q,2)
#preds = OrderedDict()
cutoffs = {}
filename = os.path.join(path, tag+'.mpk')
if not os.path.exists(filename):
return
df = pd.read_msgpack(filename)
pred = base.getPredictor(name=method, data=df)
cutoffs = pred.allelecutoffs = getCutoffs(path, method, q)
pred = pred
return pred
def openProject(self, filename=None):
"""Open project file"""
if filename == None:
filename = filedialog.askopenfilename(defaultextension='.dexpl"',
initialdir=os.getcwd(),
filetypes=[("project","*.dexpl"),
("All files","*.*")],
parent=self.main)
if not filename:
return
if os.path.isfile(filename):
data = pd.read_msgpack(filename)
self.newProject(data)
self.filename = filename
return
def read(site_loc, sheet=0, verbose=True):
"Read saved excel sheet into dataframe"
fn = join("data", site_loc, "all_{}.msg".format(sheet))
exfile = glob(join("data", site_loc, "*.xlsx"))[0]
xl_workbook = xlrd.open_workbook(exfile)
sheet_names = xl_workbook.sheet_names()
del xl_workbook
df = pd.read_msgpack(fn)
if verbose:
print("{} => {}".format(sheet_names, sheet_names[sheet]))
with open(join("data", site_loc, "description.txt")) as f:
print(f.read())
print("Nulls: {} / {}".format(df["2"].isnull().sum(), len(df)))
return df
def param_table(e=None, query_str=QSTR, debug=False, rho_limits=None,
use_cache=True):
cached_table = files['params_cache']
if path.isfile(cached_table) and use_cache:
return pd.read_msgpack(cached_table)
if e is None:
if debug:
e = test_events()
else:
e = pip2015events()
if rho_limits is None:
rho_limits = rholimits
data = e.summary(col='paper', split_date=pd.datetime(2014,7,1))
del(e)
gc.collect()
data = sf.apply_rho_intervals(data, rho_limits)
if len(query_str)<1:
return data
return data.query(query_str)
def param_table(e=None, cond=cond, debug=False, rho_limits=None,
use_cache=True, split_date=pd.datetime(2014,7,1), **kws):
cached_table = files['params_cache']
if path.isfile(cached_table) and use_cache:
return pd.read_msgpack(cached_table)
if e is None:
if debug:
e = test_events(**kws)
else:
e = events(**kws)
if rho_limits is None:
rho_limits = RHO_LIMITS
data = e.summary(col='paper', split_date=split_date)
del(e)
gc.collect()
data = apply_rho_intervals(data, rho_limits)
if cond is None:
return data
return data.where(cond)
def read_frame(fname, ftype=None, return_ftype=False):
if ftype is None:
with magic.Magic() as m:
ftype = m.id_filename(fname)
if ftype[:4] == 'data':
ftype = 'msgpack'
elif ftype.find('ASCII') != -1 or ftype.find('Image') != -1:
ftype = 'csv'
elif ftype[:4] == '8086':
ftype = 'pickle'
else:
ftype = None
if ftype == 'msgpack':
df = pd.read_msgpack(fname)
elif ftype == 'csv':
df = pd.read_csv(fname, header=0, parse_dates=[0], index_col=0)
elif ftype == 'pickle':
df = pd.read_pickle(fname)
if ftype is not None:
return (df, ftype) if return_ftype else df
raise Exception('File type not recognized for {}'.format(fname))
def testrun(gname):
method = 'tepitope'#'iedbmhc1'#'netmhciipan'
path='test'
gfile = os.path.join(genomespath,'%s.gb' %gname)
df = sequtils.genbank2Dataframe(gfile, cds=True)
#names = list(df.locus_tag[:1])
names=['VP24']
alleles1 = ["HLA-A*02:02", "HLA-A*11:01", "HLA-A*32:07", "HLA-B*15:17", "HLA-B*51:01",
"HLA-C*04:01", "HLA-E*01:03"]
alleles2 = ["HLA-DRB1*0101", "HLA-DRB1*0305", "HLA-DRB1*0812", "HLA-DRB1*1196", "HLA-DRB1*1346",
"HLA-DRB1*1455", "HLA-DRB1*1457", "HLA-DRB1*1612", "HLA-DRB4*0107", "HLA-DRB5*0203"]
P = base.getPredictor(method)
P.iedbmethod='IEDB_recommended' #'netmhcpan'
P.predictProteins(df,length=11,alleles=alleles2,names=names,
save=True,path=path)
f = os.path.join('test', names[0]+'.mpk')
df = pd.read_msgpack(f)
P.data=df
#b = P.getBinders(data=df)
#print b[:20]
base.getScoreDistributions(method, path)
return
def getPredictions(label,genome,tag,q=0.96):
"""Get predictions from file system"""
q=round(q,2)
path = os.path.join(datapath, label)
print path
genomename = os.path.splitext(genome)[0]
preds = OrderedDict()
cutoffs = {}
bcell = None
for m in methods:
rpath = os.path.join(path, '%s/%s' %(genomename,m))
filename = os.path.join(rpath, tag+'.mpk')
if not os.path.exists(filename):
continue
df = pd.read_msgpack(filename)
pred = base.getPredictor(name=m, data=df)
if m == 'bcell':
bcell = pred
continue
cutoffs[m] = pred.allelecutoffs = analysis.getCutoffs(rpath, m, q)
preds[m] = pred
return preds, bcell, cutoffs
def getAllBinders(path, method='tepitope', n=3, cutoff=0.95, promiscuous=True):
"""Get all promiscuous binders from a set of proteins in path"""
print 'getting binders..'
binders = []
m=method
if m=='bcell': return #not applicable
l=9
P = base.getPredictor(m)
files = glob.glob(os.path.join(path, '*.mpk'))
#get allele specific cutoffs
P.allelecutoffs = getCutoffs(path, method, cutoff, overwrite=True)
for f in files:
df = pd.read_msgpack(f)
if promiscuous== True:
b = P.getPromiscuousBinders(data=df,n=n)
else:
b = P.getBinders(data=df)
#print b[:5]
binders.append(b)
result = pd.concat(binders)
result['start'] = result.pos
result['end'] = result.pos+result.peptide.str.len()
return result
def read(self, identifier, freq, **kwargs):
"""
Read the entire timeseries record for the requested timeseries instance.
:param identifier: Identifier of the timeseries.
:type identifier: string
:param freq: Timeseries data frequency.
:type freq: string
:param kwargs: Attributes to match against timeseries instances (e.g. source, measurand).
:type kwargs: kwargs
:returns: pandas.DataFrame -- Timeseries data.
"""
url = self.__attach_kwargs_to_url(
self.server + '/{0}/{1}.{2}'.format(identifier, freq, self.format),
kwargs
)
if self.format == 'msgpack':
return pd.read_msgpack(urlopen(url))
elif self.format == 'json':
return pd.read_json(urlopen(url))
else:
raise NotImplementedError('Unsupported format: {0}'.format(self.format))
def time_packers_read_pack(self):
pd.read_msgpack(self.f)
