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"""Utility functions for Annif""" |
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import glob |
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import logging |
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import os |
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import os.path |
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import tempfile |
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from shutil import rmtree |
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import numpy as np |
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from annif import logger |
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from annif.suggestion import VectorSuggestionResult |
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class DuplicateFilter(logging.Filter): |
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"""Filter out log messages that have already been displayed.""" |
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def __init__(self): |
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super().__init__() |
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self.logged = set() |
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def filter(self, record): |
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current_log = hash((record.module, record.levelno, record.msg, record.args)) |
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if current_log not in self.logged: |
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self.logged.add(current_log) |
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return True |
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return False |
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def atomic_save(obj, dirname, filename, method=None): |
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"""Save the given object (which must have a .save() method, unless the |
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method parameter is given) into the given directory with the given |
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filename, using a temporary file and renaming the temporary file to the |
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final name. The .save() mehod or the function provided in the method argument |
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will be called with the path to the temporary file.""" |
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prefix, suffix = os.path.splitext(filename) |
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tempfd, tempfilename = tempfile.mkstemp(prefix=prefix, suffix=suffix, dir=dirname) |
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os.close(tempfd) |
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logger.debug("saving %s to temporary file %s", str(obj)[:90], tempfilename) |
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if method is not None: |
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method(obj, tempfilename) |
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else: |
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obj.save(tempfilename) |
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for fn in glob.glob(tempfilename + "*"): |
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newname = fn.replace(tempfilename, os.path.join(dirname, filename)) |
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logger.debug("renaming temporary file %s to %s", fn, newname) |
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os.rename(fn, newname) |
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def atomic_save_folder(obj, dirname, method=None): |
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"""Save the given object (which must have a .save() method, unless the |
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method parameter is given) into the given directory, |
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using a temporary directory and renaming the temporary directory to the |
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final name. The .save() method or the function provided in the method argument |
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will be called with the path to the temporary directory.""" |
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tldir = os.path.dirname(dirname.rstrip("/")) |
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os.makedirs(dirname, exist_ok=tldir) |
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tempdir = tempfile.TemporaryDirectory(dir=tldir) |
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temp_dir_name = tempdir.name |
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target_pth = dirname |
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logger.debug("saving %s to temporary file %s", str(obj)[:90], temp_dir_name) |
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if method is not None: |
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method(obj, temp_dir_name) |
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else: |
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obj.save(temp_dir_name) |
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for fn in glob.glob(temp_dir_name + "*"): |
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newname = fn.replace(temp_dir_name, target_pth) |
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logger.debug("renaming temporary file %s to %s", fn, newname) |
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if os.path.isdir(newname): |
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rmtree(newname) |
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os.replace(fn, newname) |
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def cleanup_uri(uri): |
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"""remove angle brackets from a URI, if any""" |
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if uri.startswith("<") and uri.endswith(">"): |
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return uri[1:-1] |
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return uri |
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def merge_hits(weighted_hits_batches, size): |
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"""Merge hit sets from multiple sources. Input is a sequence of |
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WeightedSuggestionsBatch objects. The size parameter determines the length of the |
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subject vector. Returns a list of SuggestionResult objects.""" |
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weights = [batch.weight for batch in weighted_hits_batches] |
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score_vectors = np.array( |
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[ |
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[whits.as_vector(size) for whits in batch.hit_sets] |
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for batch in weighted_hits_batches |
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] |
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) |
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results = np.average(score_vectors, axis=0, weights=weights) |
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return [VectorSuggestionResult(res) for res in results] |
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def parse_sources(sourcedef): |
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"""parse a source definition such as 'src1:1.0,src2' into a sequence of |
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tuples (src_id, weight)""" |
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sources = [] |
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totalweight = 0.0 |
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for srcdef in sourcedef.strip().split(","): |
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srcval = srcdef.strip().split(":") |
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src_id = srcval[0] |
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if len(srcval) > 1: |
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weight = float(srcval[1]) |
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else: |
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weight = 1.0 |
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sources.append((src_id, weight)) |
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totalweight += weight |
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return [(srcid, weight / totalweight) for srcid, weight in sources] |
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def parse_args(param_string): |
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"""Parse a string of comma separated arguments such as '42,43,key=abc' into |
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a list of positional args [42, 43] and a dict of keyword args {key: abc}""" |
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if not param_string: |
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return [], {} |
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posargs = [] |
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kwargs = {} |
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param_strings = param_string.split(",") |
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for p_string in param_strings: |
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parts = p_string.split("=") |
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if len(parts) == 1: |
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posargs.append(p_string) |
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elif len(parts) == 2: |
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kwargs[parts[0]] = parts[1] |
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return posargs, kwargs |
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def apply_param_parse_config(configs, params): |
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"""Applies a parsing configuration to a parameter dict.""" |
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return { |
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param: configs[param](val) |
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for param, val in params.items() |
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if param in configs and val is not None |
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} |
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def boolean(val): |
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"""Convert the given value to a boolean True/False value, if it isn't already. |
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True values are '1', 'yes', 'true', and 'on' (case insensitive), everything |
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else is False.""" |
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return str(val).lower() in ("1", "yes", "true", "on") |
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def identity(x): |
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"""Identity function: return the given argument unchanged""" |
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return x |
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def metric_code(metric): |
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"""Convert a human-readable metric name into an alphanumeric string""" |
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return metric.translate(metric.maketrans(" ", "_", "()")) |
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NatLibFi /
Annif
