def test_load(get_data_file, test_output_dir):
file_name = get_data_file(
"meteorites.csv",
"https://data.nasa.gov/api/views/gh4g-9sfh/rows.csv?accessType=DOWNLOAD",
)
# For reproducibility
np.random.seed(7331)
df = pd.read_csv(file_name)
# Note: Pandas does not support dates before 1880, so we ignore these for this analysis
df["year"] = pd.to_datetime(df["year"], errors="coerce")
# Example: Constant variable
df["source"] = "NASA"
# Example: Boolean variable
df["boolean"] = np.random.choice([True, False], df.shape[0])
# Example: Mixed with base types
df["mixed"] = np.random.choice([1, "A"], df.shape[0])
# Example: Highly correlated variables
df["reclat_city"] = df["reclat"] + np.random.normal(scale=5, size=(len(df)))
# Example: Duplicate observations
duplicates_to_add = pd.DataFrame(df.iloc[0:10].copy())
df = pd.concat([df, duplicates_to_add], ignore_index=True)
profile1 = ProfileReport(
df,
title="NASA Meteorites",
samples={"head": 5, "tail": 5},
duplicates={"head": 10},
minimal=True,
progress_bar=False,
)
test_output_path = test_output_dir / "NASA-Meteorites.pp"
json1 = profile1.to_json()
profile1.dump(test_output_path)
_ = profile1.to_html()
assert test_output_path.exists(), "Output file does not exist"
profile2 = ProfileReport(df, progress_bar=False).load(test_output_path)
# json1 are compute before dumps, so _description_set should be the same
assert isinstance(profile2._description_set, dict)
# profile1 is lazy, html1 are compute after dumps, so report should be None
assert profile2._report is None
json2 = profile2.to_json()
# both profile should generate same output
assert json1 == json2
def find(self, topic_id: TopicId, start_time: datetime, end_time: datetime) -> Optional[TopicProfile]:
schema = get_topic_schema(topic_id, self.principalService)
if is_raw_topic(schema.get_topic()):
raise DqcException(f'Raw topic[name={schema.get_topic().name}] is not supported for profiling.')
storage = ask_topic_storage(schema, self.principalService)
service = ask_topic_data_service(schema, storage, self.principalService)
criteria = [
EntityCriteriaExpression(
left=ColumnNameLiteral(columnName=TopicDataColumnNames.TENANT_ID.value),
right=self.principalService.get_tenant_id()),
EntityCriteriaExpression(
left=ColumnNameLiteral(columnName=TopicDataColumnNames.UPDATE_TIME.value),
operator=EntityCriteriaOperator.GREATER_THAN_OR_EQUALS,
right=start_time),
EntityCriteriaExpression(
left=ColumnNameLiteral(columnName=TopicDataColumnNames.UPDATE_TIME.value),
operator=EntityCriteriaOperator.LESS_THAN_OR_EQUALS,
right=end_time)
]
data = service.find(criteria)
columns = [
TopicDataColumnNames.ID.value,
*ArrayHelper(schema.get_topic().factors).map(lambda x: x.name).to_list(),
TopicDataColumnNames.TENANT_ID.value,
TopicDataColumnNames.INSERT_TIME.value,
TopicDataColumnNames.UPDATE_TIME.value
]
def row_to_list(row: Dict[str, Any]) -> List[Any]:
return ArrayHelper(columns).map(lambda x: row.get(x)).to_list()
data_frame = build_data_frame(ArrayHelper(data).map(row_to_list).to_list(), columns)
data_frame = convert_data_frame_type_by_topic(data_frame, schema.get_topic())
data_frame.drop([
TopicDataColumnNames.TENANT_ID,
TopicDataColumnNames.UPDATE_TIME,
TopicDataColumnNames.INSERT_TIME,
TopicDataColumnNames.AGGREGATE_ASSIST,
TopicDataColumnNames.ID,
TopicDataColumnNames.VERSION
], axis=1, inplace=True, errors='ignore')
if data_frame.empty or len(data_frame.index) == 1:
return None
else:
logger.info(f'memory_usage {data_frame.memory_usage(deep=True).sum()} bytes')
profile = ProfileReport(data_frame, title=f'{schema.get_topic().name} data profile report', minimal=True)
json_data = profile.to_json()
json_constants_map = {
'-Infinity': float('-Infinity'),
'Infinity': float('Infinity'),
'NaN': None,
}
return loads(json_data, parse_constant=lambda x: json_constants_map[x])
def pandas_profile(df: pd.DataFrame, result_html: str = 'report.html'):
"""
This method will be responsible to extract a pandas profiling report from the dataset.
Do not change this method, but run it and look through the html report it generated.
Always be sure to investigate the profile of your dataset (max, min, missing values, number of 0, etc).
"""
from pandas_profiling import ProfileReport
profile = ProfileReport(df, title="Pandas Profiling Report")
if result_html is not None:
profile.to_file(result_html)
return profile.to_json()
def test_json(data):
report = ProfileReport(data)
report_json = report.to_json()
data = json.loads(report_json)
assert set(data.keys()) == {
"table",
"variables",
"correlations",
"missing",
"messages",
"package",
}
def topic_profile(topic, from_, to_, data_source):
topic_name = topic.name
df = query_topic_data_by_datetime(topic.name, from_, to_, topic,
data_source)
if df.empty or len(df.index) == 1:
return None
else:
log.info("memory_usage {0} bytes".format(
df.memory_usage(deep=True).sum()))
profile = ProfileReport(
df,
title="{0} data profile report".format(topic_name),
minimal=True)
json = profile.to_json()
return json
def test_json(data):
report = ProfileReport(data)
report_json = report.to_json()
data = json.loads(report_json)
assert set(data.keys()) == {
"analysis",
"correlations",
"duplicates",
"alerts",
"missing",
"package",
"sample",
"scatter",
"table",
"variables",
}
def write_csv(dirs, file_format, database_name):
ds_set = []
ds_header = ["ds_id", "ds_name"]
att_cat_set = []
att_cat_header = ["ds_id", "att_name"]
att_num_set = []
att_num_header = ["ds_id", "att_name"]
ds_data = None
ds_names = []
set_ds = []
set_at_num = []
set_at_cat = []
final_ds_set = []
final_nom_set = []
final_num_set = []
final_ds_set_header = []
final_nom_set_header = []
final_num_set_header = []
output_step = output_path + database_name + "/"
input_step = input_path + database_name + "/"
df = None
att_list = []
csv = []
d = 0
#read file
for f in dirs[0][2]:
sufix = f.split(".")[-1]
dataset = f.split("." + sufix)[0]
ds_names.append(dataset)
f = input_step + f
if file_format == "csv":
df = pd.read_csv(f, error_bad_lines=False)
if file_format == "excel":
df = pd.read_excel(f)
if file_format == "json":
df = pd.read_json(f, orient='records')
df = df.to_csv(sep="~", index=False)
df = pd.read_csv(io.StringIO(df), error_bad_lines=False, sep="~")
if len(df) > 10000:
df = df.sample(10000)
#get profile inf
profile = ProfileReport(df, minimal=True)
json_data = profile.to_json()
mf_json = json.loads(json_data)
ds_mf = mf_json["table"]
ds_mf["name"] = ds_names[d]
print(ds_names[d])
ds_mf["nominal"] = {}
ds_mf["numeric"] = {}
set_ds.append(ds_mf)
variables = mf_json["variables"]
for key in variables.keys():
at_mf = variables[key]
at_mf["ds_id"] = d
if at_mf["type"] == "Variable.TYPE_NUM":
try:
del at_mf["histogram_data"]
del at_mf["scatter_data"]
del at_mf["histogram_bins"]
except:
print("Something hapenned..meh")
ds_mf["numeric"][key] = at_mf
else:
ds_mf["nominal"][key] = at_mf
att_numeric = ds_mf.pop("numeric")
att_cat = ds_mf.pop("nominal")
# data = concat_values(ds_mf)
data = ds_mf
try:
del data["CAT"]
del data["BOOL"]
del data["NUM"]
del data["DATE"]
del data["URL"]
del data["COMPLEX"]
del data["PATH"]
del data["FILE"]
del data["IMAGE"]
del data["UNSUPPORTED"]
except:
print("...")
data_final = {}
id_name = data["name"].split("__")
if len(id_name) > 1:
data_final["ds_id"] = id_name[0]
data_final["dataset name"] = id_name[1]
else:
data_final["ds_id"] = id_name[0]
data_final["dataset name"] = id_name[0]
ds_row = []
final_ds_row = []
ds_row.append(d)
ds_row.append(data["name"])
if len(ds_header) <= 2:
for key in data.keys():
ds_header.append(key)
for key in data.keys():
ds_row.append(data[key])
ds_set.append(ds_row)
##meta-features according alserafi
data_final["number of instances"] = data["n"]
data_final["number of attributes"] = data["n_var"]
data_final["dimensionality"] = float(data["n_var"]) / float(data["n"])
num_cat = 0
num_num = 0
for key_types in data["types"].keys():
if key_types == "NUM":
num_num += data["types"][key_types]
else:
print(data["types"][key_types])
num_cat += data["types"][key_types]
data_final["number of nominal"] = num_cat
data_final["number of numeric"] = num_num
data_final["percentage of nominal"] = num_cat / float(data["n_var"])
data_final["percentage of numeric"] = num_num / float(data["n_var"])
#missing
data_final["missing attribute count"] = data["n_vars_with_missing"]
data_final["missing attribute percentage"] = float(
data["n_vars_with_missing"]) / float(data["n_var"])
num_missing_values = []
ptg_missing_values = []
numeric_final = {}
#numeric
means = []
for key in att_numeric.keys():
att_num_row = []
att_num_row.append(att_numeric[key].pop("ds_id"))
att_num_row.append(key)
# att_numeric[key] = concat_values(att_numeric[key])
if len(att_num_header) <= 2:
for k in att_numeric[key].keys():
att_num_header.append(k)
for k in att_numeric[key].keys():
att_num_row.append(att_numeric[key][k])
att_num_set.append(att_num_row)
####
final_num_row = []
means.append(att_numeric[key]["mean"])
num_missing_values.append(att_numeric[key]["n_missing"])
ptg_missing_values.append(att_numeric[key]["p_missing"])
numeric_final["dataset id"] = data_final["ds_id"]
numeric_final["attribute name"] = att_num_row[1]
numeric_final["number distinct values"] = att_numeric[key][
"distinct_count_without_nan"]
numeric_final["percentage distinct values"] = float(
att_numeric[key]["distinct_count_without_nan"]) / float(
att_numeric[key]["n"])
numeric_final["percentage missing values"] = att_numeric[key][
"p_missing"]
numeric_final["mean"] = att_numeric[key]["mean"]
numeric_final["standard deviation"] = att_numeric[key]["std"]
numeric_final["minimum value"] = att_numeric[key]["min"]
numeric_final["maximum value"] = att_numeric[key]["max"]
numeric_final["range"] = att_numeric[key]["range"]
numeric_final["coefficient of variance"] = att_numeric[key]["cv"]
if len(final_num_set_header) == 0:
for final_key in numeric_final.keys():
final_num_set_header.append(final_key)
for final_key in numeric_final.keys():
final_num_row.append(numeric_final[final_key])
final_num_set.append(final_num_row)
if len(means) == 0:
means = [0]
means = np.array(means)
data_final["average of means"] = np.average(means)
data_final["standard deviation of means"] = np.std(means)
data_final["minimum number of means"] = np.amin(means)
data_final["maximum number of means"] = np.amax(means)
#nominal
nominal_final = {}
num_distinct = []
for key in att_cat.keys():
if key == "<page title>":
continue
att_cat_row = []
num_distinct.append(len(att_cat[key]["value_counts"].keys()))
att_cat_row.append(att_cat[key].pop("ds_id"))
att_cat_row.append(key)
vcounts = []
pvcounts = []
string_values = ""
for vkey in att_cat[key]["value_counts"].keys():
vcounts.append(float(att_cat[key]["value_counts"][vkey]))
pvcounts.append(
float(att_cat[key]["value_counts"][vkey]) /
float(att_cat[key]["n"]))
if string_values != "":
string_values = string_values + "|"
text = att_cat[key]["value_counts"][vkey]
text = ''.join(char for char in text if ord(char) < 128)
text = text.replace("~", "").replace("\n", " ")
text2 = vkey
text2 = ''.join(char for char in text2 if ord(char) < 128)
text2 = text2.replace("~", "").replace("\n", " ")
string_values = string_values + str(text2) + " " + str(text)
if len(vcounts) == 0:
vcounts = [0]
if len(pvcounts) == 0:
pvcounts = [0]
vcounts = np.array(vcounts)
pvcounts = np.array(pvcounts)
# att_cat[key] = concat_values(att_cat[key])
if len(att_cat_header) <= 2:
for k in att_cat[key].keys():
att_cat_header.append(k)
for k in att_cat[key].keys():
att_cat_row.append(att_cat[key][k])
att_cat_set.append(att_cat_row)
#####
final_nom_row = []
num_missing_values.append(att_cat[key]["n_missing"])
ptg_missing_values.append(att_cat[key]["p_missing"])
nominal_final["dataset id"] = data_final["ds_id"]
nominal_final["attribute name"] = att_cat_row[1]
#############################33
# if ds_names[d] == "www.best-deal-items.com":
# print("################THE KEY##############: "+key)
# print(att_cat[key])
#############################33333333
nominal_final["number distinct values"] = att_cat[key][
"distinct_count_without_nan"]
nominal_final["percentage distinct values"] = float(
att_cat[key]["distinct_count_without_nan"]) / float(
att_cat[key]["n"])
nominal_final["percentage missing values"] = att_cat[key][
"p_missing"]
nominal_final["mean number of string values"] = np.average(vcounts)
nominal_final[
"standard deviation number of string values"] = np.std(vcounts)
nominal_final["minimum number of string values"] = np.amin(vcounts)
nominal_final["maximum number of string values"] = np.amax(vcounts)
nominal_final["median percentage of string values"] = np.median(
pvcounts)
nominal_final[
"standard deviation percentage of string values"] = np.std(
pvcounts)
nominal_final["minimum percentage of string values"] = np.amin(
pvcounts)
nominal_final["maximum percentage of string values"] = np.amax(
pvcounts)
nominal_final["string values"] = string_values
if len(final_nom_set_header) == 0:
for final_key in nominal_final.keys():
final_nom_set_header.append(final_key)
for final_key in nominal_final.keys():
final_nom_row.append(nominal_final[final_key])
final_nom_set.append(final_nom_row)
data_final["average number of distintc values"] = None
data_final["standard deviation of distintc values"] = None
data_final["minimum number of distintc values"] = None
data_final["maximum number of distintc values"] = None
if len(att_cat.keys()) > 0:
num_distinct = np.array(num_distinct)
data_final["average number of distintc values"] = np.average(
num_distinct)
data_final["standard deviation of distintc values"] = np.std(
num_distinct)
data_final["minimum number of distintc values"] = np.amin(
num_distinct)
data_final["maximum number of distintc values"] = np.amax(
num_distinct)
##missing
num_missing_values = np.array(num_missing_values)
ptg_missing_values = np.array(ptg_missing_values)
data_final["average number of missing values"] = np.average(
num_missing_values)
data_final["standard deviation of missing values"] = np.std(
num_missing_values)
data_final["minimum number of missing values"] = np.amin(
num_missing_values)
data_final["maximum number of missing values"] = np.amax(
num_missing_values)
data_final["average number of percentage missing values"] = np.average(
ptg_missing_values)
data_final["standard deviation of percentage missing values"] = np.std(
ptg_missing_values)
data_final["minimum number of percentage missing values"] = np.amin(
ptg_missing_values)
data_final["maximum number of percentage missing values"] = np.amax(
ptg_missing_values)
if len(final_ds_set_header) == 0:
for final_key in data_final.keys():
final_ds_set_header.append(final_key)
for final_key in data_final.keys():
final_ds_row.append(data_final[final_key])
final_ds_set.append(final_ds_row)
d += 1
# output_path = input_path+"/mf_output/"
# output_path = "../input/monitor_mf_output/"
if not os.path.exists(output_step):
Path(output_step).mkdir(parents=True, exist_ok=True)
df = pd.DataFrame(final_ds_set, columns=final_ds_set_header)
df.to_csv(output_step + "ds.csv", index=False, sep="~")
df = pd.DataFrame(final_nom_set, columns=final_nom_set_header)
df.to_csv(output_step + "attr_nom.csv", index=False, sep="~")
df = pd.DataFrame(final_num_set, columns=final_num_set_header)
df.to_csv(output_step + "attr_num.csv", index=False, sep="~")
def get_EDA(file_path):
try:
df = pd.read_csv(file_path)
profile = ProfileReport(df, minimal=True)
# profile.to_file(output_file="your_report.json")
profile = json.loads(profile.to_json())
features = set([])
ignore_features = set([
"value_counts", "value_counts_with_nan",
"value_counts_without_nan", "histogram_data", "scatter_data"
])
table_features = set(["memory_size", "n_cells_missing"])
# print(f'Profile: {profile.keys()}')
report = defaultdict(str)
overview = defaultdict(str)
report["rows"] = []
report["columns"] = [{
"label": "Column",
"field": "Column",
"sort": 'asc',
"width": 150
}]
#overview of table
for feature, val in profile['table'].items():
if feature in table_features:
overview[feature] = list(val.values())[0]
elif feature == "types":
overview[feature] = defaultdict(str)
for k, v in profile['table']['types'].items():
overview[feature][k] = list(v.values())[0]
else:
overview[feature] = val
#info about variables
for variable in profile['variables'].keys():
# print("variable", variable)
row = {"Column": variable}
for feature, val in profile['variables'][variable].items():
if feature not in ignore_features:
if feature not in features: features.add(feature)
if isinstance(val, dict):
# print(f'{feature:>30}')
row[feature] = list(val.values())[0]
elif 'date_warning' == feature and val == True:
row["type"] = "datetime"
else:
row[feature] = val
report["rows"].append(row)
for feature in features:
report["columns"].append({
"label": feature,
"field": feature,
# "sort": 'asc',
# "width": 200
})
sample = json.loads(df.sample(20).to_json(orient='index'))
sample_report = {"rows": [], "columns": []}
key = ""
for k, v in sample.items():
sample_report['rows'].append(v)
key = k
for k in sorted(sample[key].keys()):
sample_report['columns'].append({
"label": k,
"field": k,
"width": 200
# "sort": 'asc',
})
# with open('sample_json.json','w') as f:
# json.dump(sample_report,f)
return {
"report": json.dumps(report),
"overview": overview,
"sample": sample_report
}
except Exception as e:
tb = sys.exc_info()[-1]
print(
f'Error: {str(e)} in line {tb.tb_lineno} in function: {traceback.extract_tb(tb, 1)[0][2]}'
)
