def load_table(file_path, metadata_ext='.pklmetadata'):
"""
Loads a pickled DataFrame from a file along with its metadata.
This function loads a DataFrame from a file stored in pickle format.
Further, this function looks for a metadata file with the same file name
but with an extension given by the user (defaults to '.pklmetadata'. If the
metadata file is present, the function will update the metadata for that
DataFrame in the catalog.
Args:
file_path (string): The file path to load the file from.
metadata_ext (string): The metadata file extension (defaults to
'.pklmetadata') that should be used to generate metadata file name.
Returns:
If the loading is successful, the function will return a pandas
DataFrame read from the file. The catalog will be updated with the
metadata read from the metadata file (if the file was present).
Raises:
AssertionError: If `file_path` is not of type string.
AssertionError: If `metadata_ext` is not of type string.
Examples:
>>> A = em.load_table('./A.pkl')
>>> A = em.load_table('./A.pkl', metadata_ext='.pklmeta')
See Also:
:meth:`~py_entitymatching.save_table`
Note:
This function is different from read_csv_metadata in two aspects.
First, this function currently does not support reading in candidate
set tables, where there are more metadata such as ltable,
rtable than just 'key', and conceptually the user is expected to
provide ltable and rtable information while calling this function. (
this support will be added shortly). Second, this function loads the
table stored in a pickle format.
"""
# Validate input parameters
validate_object_type(file_path, six.string_types)
validate_object_type(metadata_ext, six.string_types)
# Load the object from the file path. Note that we use a generic load
# object to load in the DataFrame too.
data_frame = load_object(file_path)
# Load metadata from file path
# # Check if the meta data file is present
if ps._is_metadata_file_present(file_path, extension=metadata_ext):
# Construct the metadata file name, and read it from the disk.
# # Get the file name used to load the DataFrame
file_name, _ = os.path.splitext(file_path)
# # Construct the metadata file name
metadata_filename = file_name + metadata_ext
# # Load the metadata from the disk
metadata_dict = load_object(metadata_filename)
# Update the catalog with the properties read from the disk
for property_name, property_value in six.iteritems(metadata_dict):
if property_name == 'key':
# If the property_name is key call set_key as the function
# will check for the integrity of key before setting it in
# the catalog
cm.set_key(data_frame, property_value)
else:
cm.set_property(data_frame, property_name, property_value)
else:
# If the metadata file is not present then issue a warning
logger.warning('There is no metadata file')
# Return the DataFrame
return data_frame
def test_set_property_invalid_df(self):
# cm.del_catalog()
cm.set_property(None, 'key', 'ID')
def test_set_property_valid_df_invalid_prop(self):
# cm.del_catalog()
A = pd.read_csv(path_a)
cm.set_property(A, None, 'ID')
def test_set_property_valid_df_name_value(self):
# cm.del_catalog()
df = pd.read_csv(path_a)
cm.set_property(df, 'key', 'ID')
self.assertEqual(cm.get_property(df, 'key'), 'ID')
def load_table(file_path, metadata_ext='.pklmetadata'):
"""
Loads a pickled DataFrame from a file along with its metadata.
This function loads a DataFrame from a file stored in pickle format.
Further, this function looks for a metadata file with the same file name
but with an extension given by the user (defaults to '.pklmetadata'. If the
metadata file is present, the function will update the metadata for that
DataFrame in the catalog.
Args:
file_path (string): The file path to load the file from.
metadata_ext (string): The metadata file extension (defaults to
'.pklmetadata') that should be used to generate metadata file name.
Returns:
If the loading is successful, the function will return a pandas
DataFrame read from the file. The catalog will be updated with the
metadata read from the metadata file (if the file was present).
Raises:
AssertionError: If `file_path` is not of type string.
AssertionError: If `metadata_ext` is not of type string.
Examples:
>>> A = em.load_table('./A.pkl')
>>> A = em.load_table('./A.pkl', metadata_ext='.pklmeta')
See Also:
:meth:`~py_entitymatching.save_table`
Note:
This function is different from read_csv_metadata in two aspects.
First, this function currently does not support reading in candidate
set tables, where there are more metadata such as ltable,
rtable than just 'key', and conceptually the user is expected to
provide ltable and rtable information while calling this function. (
this support will be added shortly). Second, this function loads the
table stored in a pickle format.
"""
# Validate input parameters
validate_object_type(file_path, six.string_types, error_prefix='Input file path')
validate_object_type(metadata_ext, six.string_types)
# Load the object from the file path. Note that we use a generic load
# object to load in the DataFrame too.
data_frame = load_object(file_path)
# Load metadata from file path
# # Check if the meta data file is present
if ps._is_metadata_file_present(file_path, extension=metadata_ext):
# Construct the metadata file name, and read it from the disk.
# # Get the file name used to load the DataFrame
file_name, _ = os.path.splitext(file_path)
# # Construct the metadata file name
metadata_filename = file_name + metadata_ext
# # Load the metadata from the disk
metadata_dict = load_object(metadata_filename)
# Update the catalog with the properties read from the disk
for property_name, property_value in six.iteritems(metadata_dict):
if property_name == 'key':
# If the property_name is key call set_key as the function
# will check for the integrity of key before setting it in
# the catalog
cm.set_key(data_frame, property_value)
else:
cm.set_property(data_frame, property_name, property_value)
else:
# If the metadata file is not present then issue a warning
logger.warning('There is no metadata file')
# Return the DataFrame
return data_frame
def read_csv_metadata(file_path, **kwargs):
"""
Reads a CSV (comma-separated values) file into a pandas DataFrame
and update the catalog with the metadata. The CSV files typically contain
data for the input tables or a candidate set.
Specifically, this function first reads the CSV file from the given file
path into a pandas DataFrame, by using pandas' in-built 'read_csv'
method. Then, it updates the catalog with the metadata. There are three
ways to update the metadata: (1) using a metadata file, (2) using the
key-value parameters supplied in the function, and (3) using both
metadata file and key-value parameters.
To update the metadata in the catalog using the metadata file,
the function will look for a file in the same directory with same file name
but with a specific extension. This extension can be optionally given by
the user (defaults to '.metadata'). If the metadata file is present,
the function will read and update the catalog appropriately. If the
metadata file is not present, the function will issue a warning that the
metadata file is not present.
The metadata information can also be given as parameters to the function
(see description of arguments for more details). If given, the function
will update the catalog with the given information.
Further, the metadata can partly reside in the metdata file and partly as
supplied parameters. The function will take a union of the two and
update the catalog appropriately.
If the same metadata is given in both the metadata file
and the function, then the metadata in the function takes precedence over
the metadata given in the file.
Args:
file_path(string): The CSV file path
kwargs(dictionary): A Python dictionary containing key-value arguments.
There are a few key-value pairs that are specific to
read_csv_metadata and all the other key-value pairs are passed
to pandas read_csv method
Returns:
A pandas DataFrame read from the input CSV file.
Raises:
AssertionError: If `file_path` is not of type string.
AssertionError: If a file does not exist in the
given `file_path`.
Examples:
*Example 1:* Read from CSV file and set metadata
>>> A = em.read_csv_metadata('path_to_csv_file', key='id')
>>> em.get_key(A)
# 'id'
*Example 2:* Read from CSV file (with metadata file in the same directory
Let the metadata file contain the following contents:
#key = id
>>> A = em.read_csv_metadata('path_to_csv_file')
>>> em.get_key(A)
# 'id'
See Also:
:meth:`~py_entitymatching.to_csv_metadata`
"""
# Validate the input parameters.
# # File path is expected to be of type string.
if not isinstance(file_path, six.string_types):
logger.error('Input file path is not of type string')
raise AssertionError('Input file path is not of type string')
# # Check if the given path is valid.
if not os.path.exists(file_path):
logger.error('File does not exist at path %s' % file_path)
raise AssertionError('File does not exist at path %s' % file_path)
# Check if the user has specified the metadata file's extension.
extension = kwargs.pop('metadata_extn', None)
# If the extension is not specified then set the extension to .metadata'.
if extension is None:
extension = '.metadata'
# Format the extension to include a '.' in front if the user has not
# given one.
if not extension.startswith('.'):
extension = '.' + extension
# If the file is present, then update metadata from file.
if _is_metadata_file_present(file_path, extension=extension):
file_name, _ = os.path.splitext(file_path)
file_name = ''.join([file_name, extension])
metadata, _ = _get_metadata_from_file(file_name)
# Else issue a warning that the metadata file is not present
else:
logger.warning('Metadata file is not present in the given path; '
'proceeding to read the csv file.')
metadata = {}
# Update the metadata with the key-value pairs given in the command. The
# function _update_metadata_for_read_cmd takes care of updating the
# metadata with only the key-value pairs specific to read_csv_metadata
# method
metadata, kwargs = _update_metadata_for_read_cmd(metadata, **kwargs)
# Validate the metadata.
_check_metadata_for_read_cmd(metadata)
# Read the csv file using pandas read_csv method.
data_frame = pd.read_csv(file_path, **kwargs)
# Get the value for 'key' property and update the catalog.
key = metadata.pop('key', None)
if key is not None:
cm.set_key(data_frame, key)
fk_ltable = metadata.pop('fk_ltable', None)
if fk_ltable is not None:
cm.set_fk_ltable(data_frame, fk_ltable)
fk_rtable = metadata.pop('fk_rtable', None)
if fk_ltable is not None:
cm.set_fk_rtable(data_frame, fk_rtable)
# Update the catalog with other properties.
for property_name, property_value in six.iteritems(metadata):
cm.set_property(data_frame, property_name, property_value)
if not cm.is_dfinfo_present(data_frame):
cm.init_properties(data_frame)
# Return the DataFrame
return data_frame
def sample_table(table, sample_size, replace=False, verbose=False):
"""
Samples a candidate set of tuple pairs (for labeling purposes).
This function samples a DataFrame, typically used for labeling
purposes. This function expects the input DataFrame containing the
metadata of a candidate set (such as key, fk_ltable, fk_rtable, ltable,
rtable). Specifically, this function creates a copy of the input
DataFrame, samples the data using uniform random sampling (uses 'random'
function from numpy to sample) and returns the sampled DataFrame.
Further, also copies the properties from the input DataFrame to the output
DataFrame.
Args:
table (DataFrame): The input DataFrame to be sampled.
Specifically,
a DataFrame containing the metadata of a candidate set (such as
key, fk_ltable, fk_rtable, ltable, rtable) in the catalog.
sample_size (int): The number of samples to be picked from the input
DataFrame.
replace (boolean): A flag to indicate whether sampling should be
done with replacement or not (defaults to False).
verbose (boolean): A flag to indicate whether more detailed information
about the execution steps should be printed out (defaults to False).
Returns:
A new DataFrame with 'sample_size' number of rows.
Further,
this function sets the output DataFrame's properties same as input
DataFrame.
Raises:
AssertionError: If `table` is not of type pandas DataFrame.
AssertionError: If the size of `table` is 0.
AssertionError: If the `sample_size` is greater than the input
DataFrame size.
Examples:
>>> import py_entitymatching as em
>>> S = em.sample_table(C, sample_size=450) # C is the candidate set to be sampled from.
Note:
As mentioned in the above description, the output DataFrame is
updated (in the catalog) with the properties from the input
DataFrame. A subtle point to note here is, when the replace flag is
set to True, then the output DataFrame can contain duplicate keys.
In that case, this function will not set the key and it is up to
the user to fix it after the function returns.
"""
# Validate input parameters.
# # The input DataFrame is expected to be of type pandas DataFrame.
validate_object_type(table, pd.DataFrame)
# # There should at least not-zero rows to sample from
if len(table) == 0:
logger.error('Size of the input table is 0')
raise AssertionError('Size of the input table is 0')
# # The sample size should be less than or equal to the number of rows in
# the input DataFrame
if len(table) < sample_size:
logger.error('Sample size is larger than the input table size')
raise AssertionError('Sample size is larger than the input table size')
# Now, validate the metadata for the input DataFrame as we have to copy
# these properties to the output DataFrame
# # First, display what metadata is required for this function
ch.log_info(
logger, 'Required metadata: cand.set key, fk ltable, '
'fk rtable, ltable, rtable, ltable key, rtable key', verbose)
# # Second, get the metadata
key, fk_ltable, fk_rtable, ltable, rtable, l_key, r_key = \
cm.get_metadata_for_candset(table, logger, verbose)
# # Third, validate the metadata
cm._validate_metadata_for_candset(table, key, fk_ltable, fk_rtable, ltable,
rtable, l_key, r_key, logger, verbose)
# Get the sample set for the output table
sample_indices = np.random.choice(len(table), sample_size, replace=replace)
# Sort the indices ordered by index value
sample_indices = sorted(sample_indices)
sampled_table = table.iloc[list(sample_indices)]
# Copy the properties
cm.init_properties(sampled_table)
# # If the replace is set to True, then we should check for the validity
# of key before setting it
if replace:
properties = cm.get_all_properties(table)
for property_name, property_value in six.iteritems(properties):
if property_name == 'key':
# Check for the validity of key before setting it
cm.set_key(sampled_table, property_value)
else:
# Copy the other properties as is
cm.set_property(sampled_table, property_name, property_value)
else:
cm.copy_properties(table, sampled_table)
# Return the sampled table
return sampled_table
def sample_table(table, sample_size, replace=False, verbose=False):
"""
Samples a candidate set of tuple pairs (for labeling purposes).
This function samples a DataFrame, typically used for labeling
purposes. This function expects the input DataFrame containing the
metadata of a candidate set (such as key, fk_ltable, fk_rtable, ltable,
rtable). Specifically, this function creates a copy of the input
DataFrame, samples the data using uniform random sampling (uses 'random'
function from numpy to sample) and returns the sampled DataFrame.
Further, also copies the properties from the input DataFrame to the output
DataFrame.
Args:
table (DataFrame): The input DataFrame to be sampled.
Specifically,
a DataFrame containing the metadata of a candidate set (such as
key, fk_ltable, fk_rtable, ltable, rtable) in the catalog.
sample_size (int): The number of samples to be picked from the input
DataFrame.
replace (boolean): A flag to indicate whether sampling should be
done with replacement or not (defaults to False).
verbose (boolean): A flag to indicate whether more detailed information
about the execution steps should be printed out (defaults to False).
Returns:
A new DataFrame with 'sample_size' number of rows.
Further,
this function sets the output DataFrame's properties same as input
DataFrame.
Raises:
AssertionError: If `table` is not of type pandas DataFrame.
AssertionError: If the size of `table` is 0.
AssertionError: If the `sample_size` is greater than the input
DataFrame size.
Examples:
>>> import py_entitymatching as em
>>> S = em.sample_table(C, sample_size=450) # C is the candidate set to be sampled from.
Note:
As mentioned in the above description, the output DataFrame is
updated (in the catalog) with the properties from the input
DataFrame. A subtle point to note here is, when the replace flag is
set to True, then the output DataFrame can contain duplicate keys.
In that case, this function will not set the key and it is up to
the user to fix it after the function returns.
"""
# Validate input parameters.
# # The input DataFrame is expected to be of type pandas DataFrame.
validate_object_type(table, pd.DataFrame)
# # There should at least not-zero rows to sample from
if len(table) == 0:
logger.error('Size of the input table is 0')
raise AssertionError('Size of the input table is 0')
# # The sample size should be less than or equal to the number of rows in
# the input DataFrame
if len(table) < sample_size:
logger.error('Sample size is larger than the input table size')
raise AssertionError('Sample size is larger than the input table size')
# Now, validate the metadata for the input DataFrame as we have to copy
# these properties to the output DataFrame
# # First, display what metadata is required for this function
ch.log_info(logger, 'Required metadata: cand.set key, fk ltable, '
'fk rtable, ltable, rtable, ltable key, rtable key',
verbose)
# # Second, get the metadata
key, fk_ltable, fk_rtable, ltable, rtable, l_key, r_key = \
cm.get_metadata_for_candset(table, logger, verbose)
# # Third, validate the metadata
cm._validate_metadata_for_candset(table, key, fk_ltable, fk_rtable,
ltable, rtable, l_key, r_key,
logger, verbose)
# Get the sample set for the output table
sample_indices = pd.np.random.choice(len(table), sample_size,
replace=replace)
# Sort the indices ordered by index value
sample_indices = sorted(sample_indices)
sampled_table = table.iloc[list(sample_indices)]
# Copy the properties
cm.init_properties(sampled_table)
# # If the replace is set to True, then we should check for the validity
# of key before setting it
if replace:
properties = cm.get_all_properties(table)
for property_name, property_value in six.iteritems(properties):
if property_name == 'key':
# Check for the validity of key before setting it
cm.set_key(sampled_table, property_value)
else:
# Copy the other properties as is
cm.set_property(sampled_table, property_name, property_value)
else:
cm.copy_properties(table, sampled_table)
# Return the sampled table
return sampled_table