mirror of
https://gitlab.ub.uni-bielefeld.de/sfb1288inf/nopaque.git
synced 2024-11-14 16:55:42 +00:00
Add compression to static corpus data, use chunked computation, hide read corpus ids in corpus analysis
This commit is contained in:
Patrick Jentsch
parent
413b6111df
commit
a9973e9c8e
@ -19,6 +19,9 @@ def reset():
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for corpus in [x for x in Corpus.query.all() if x.status in status]:
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print(f'Resetting corpus {corpus}')
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shutil.rmtree(os.path.join(corpus.path, 'cwb'), ignore_errors=True)
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os.mkdir(os.path.join(corpus.path, 'cwb'))
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os.mkdir(os.path.join(corpus.path, 'cwb', 'data'))
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os.mkdir(os.path.join(corpus.path, 'cwb', 'registry'))
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corpus.status = CorpusStatus.UNPREPARED
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corpus.num_analysis_sessions = 0
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db.session.commit()
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@ -7,6 +7,7 @@ from threading import Lock
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from app import db, hashids, socketio
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from app.decorators import socketio_login_required
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from app.models import Corpus, CorpusStatus
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import math
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'''
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@ -83,7 +84,7 @@ def connect(auth):
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socketio.sleep(3)
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retry_counter -= 1
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db.session.refresh(corpus)
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cqi_client = CQiClient(f'cqpserver_{corpus_id}')
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cqi_client = CQiClient(f'cqpserver_{corpus_id}', timeout=math.inf)
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session['cqi_over_sio'] = {
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'corpus_id': corpus_id,
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'cqi_client': cqi_client,
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@ -1,12 +1,18 @@
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from collections import Counter
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from cqi import CQiClient
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from cqi.models.corpora import Corpus
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from cqi.status import StatusOk
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from cqi.models.corpora import Corpus as CQiCorpus
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from cqi.models.attributes import (
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PositionalAttribute as CQiPositionalAttribute,
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StructuralAttribute as CQiStructuralAttribute
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)
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from cqi.status import StatusOk as CQiStatusOk
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from flask import session
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from typing import Dict, List
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import gzip
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import json
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import math
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import os
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import shutil
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from app import db
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from app.models import Corpus
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from .utils import lookups_by_cpos, partial_export_subcorpus, export_subcorpus
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@ -22,43 +28,28 @@ CQI_EXTENSION_FUNCTION_NAMES: List[str] = [
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]
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def ext_corpus_update_db(corpus: str):
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def ext_corpus_update_db(corpus: str) -> CQiStatusOk:
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db_corpus = Corpus.query.get(session['cqi_over_sio']['corpus_id'])
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cqi_client: CQiClient = session['cqi_over_sio']['cqi_client']
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cqi_corpus = cqi_client.corpora.get(corpus)
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cqi_corpus: CQiCorpus = cqi_client.corpora.get(corpus)
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db_corpus.num_tokens = cqi_corpus.size
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db.session.commit()
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return StatusOk()
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return CQiStatusOk()
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def ext_corpus_static_data(corpus: str) -> Dict:
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db_corpus = Corpus.query.get(session['cqi_over_sio']['corpus_id'])
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static_corpus_data_file = os.path.join(db_corpus.path, 'cwb', 'static.json')
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static_corpus_data_file = os.path.join(db_corpus.path, 'cwb', 'static.json.gz')
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if os.path.exists(static_corpus_data_file):
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with open(static_corpus_data_file, 'r') as f:
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return json.load(f)
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with open(static_corpus_data_file, 'rb') as f:
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return f.read()
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cqi_client: CQiClient = session['cqi_over_sio']['cqi_client']
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cqi_corpus = cqi_client.corpora.get(corpus)
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##########################################################################
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# A faster way to get cpos boundaries for smaller s_attrs #
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##########################################################################
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# cqi_corpus.query('Last', '<s> []* </s>;')
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# cqi_subcorpus = cqi_corpus.subcorpora.get('Last')
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# print(cqi_subcorpus.size)
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# first_match = 0
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# last_match = cqi_subcorpus.attrs['size'] - 1
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# match_boundaries = zip(
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# list(range(first_match, last_match + 1)),
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# cqi_subcorpus.dump(cqi_subcorpus.attrs['fields']['match'], first_match, last_match),
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# cqi_subcorpus.dump(cqi_subcorpus.attrs['fields']['matchend'], first_match, last_match)
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# )
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# for x in match_boundaries:
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# print(x)
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cqi_p_attrs = {
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cqi_corpus: CQiCorpus = cqi_client.corpora.get(corpus)
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cqi_p_attrs: Dict[str, CQiPositionalAttribute] = {
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p_attr.name: p_attr
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for p_attr in cqi_corpus.positional_attributes.list()
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}
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cqi_s_attrs = {
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cqi_s_attrs: Dict[str, CQiStructuralAttribute] = {
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s_attr.name: s_attr
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for s_attr in cqi_corpus.structural_attributes.list()
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}
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@ -75,73 +66,121 @@ def ext_corpus_static_data(corpus: str) -> Dict:
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'values': {'p_attrs': {}, 's_attrs': {}}
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}
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for p_attr in cqi_p_attrs.values():
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static_corpus_data['corpus']['freqs'][p_attr.name] = dict(
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zip(
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range(0, p_attr.lexicon_size),
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p_attr.freqs_by_ids(list(range(0, p_attr.lexicon_size)))
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static_corpus_data['corpus']['freqs'][p_attr.name] = {}
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chunk_size = 5000
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p_attr_id_list = list(range(p_attr.lexicon_size))
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chunks = [p_attr_id_list[i:i+chunk_size] for i in range(0, len(p_attr_id_list), chunk_size)]
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del p_attr_id_list
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for chunk in chunks:
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print(f'corpus.freqs.{p_attr.name}: {chunk[0]} - {chunk[-1]}')
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static_corpus_data['corpus']['freqs'][p_attr.name].update(
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dict(zip(chunk, p_attr.freqs_by_ids(chunk)))
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)
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)
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static_corpus_data['p_attrs'][p_attr.name] = dict(
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zip(
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range(0, cqi_corpus.size),
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p_attr.ids_by_cpos(list(range(0, cqi_corpus.size)))
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del chunks
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static_corpus_data['p_attrs'][p_attr.name] = {}
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cpos_list = list(range(cqi_corpus.size))
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chunks = [cpos_list[i:i+chunk_size] for i in range(0, len(cpos_list), chunk_size)]
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del cpos_list
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for chunk in chunks:
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print(f'p_attrs.{p_attr.name}: {chunk[0]} - {chunk[-1]}')
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static_corpus_data['p_attrs'][p_attr.name].update(
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dict(zip(chunk, p_attr.ids_by_cpos(chunk)))
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)
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)
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static_corpus_data['values']['p_attrs'][p_attr.name] = dict(
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zip(
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range(0, p_attr.lexicon_size),
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p_attr.values_by_ids(list(range(0, p_attr.lexicon_size)))
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del chunks
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static_corpus_data['values']['p_attrs'][p_attr.name] = {}
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p_attr_id_list = list(range(p_attr.lexicon_size))
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chunks = [p_attr_id_list[i:i+chunk_size] for i in range(0, len(p_attr_id_list), chunk_size)]
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del p_attr_id_list
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for chunk in chunks:
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print(f'values.p_attrs.{p_attr.name}: {chunk[0]} - {chunk[-1]}')
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static_corpus_data['values']['p_attrs'][p_attr.name].update(
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dict(zip(chunk, p_attr.values_by_ids(chunk)))
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)
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)
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del chunks
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for s_attr in cqi_s_attrs.values():
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if s_attr.has_values:
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continue
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static_corpus_data['corpus']['counts'][s_attr.name] = s_attr.size
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static_corpus_data['s_attrs'][s_attr.name] = {'lexicon': {}, 'values': None}
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static_corpus_data['values']['s_attrs'][s_attr.name] = {}
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if s_attr.name in ['s', 'ent']:
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cqi_corpus.query('Last', f'<{s_attr.name}> []* </{s_attr.name}>;')
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cqi_subcorpus = cqi_corpus.subcorpora.get('Last')
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first_match = 0
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last_match = cqi_subcorpus.size - 1
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match_boundaries = zip(
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range(first_match, last_match + 1),
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cqi_subcorpus.dump(cqi_subcorpus.fields['match'], first_match, last_match),
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cqi_subcorpus.dump(cqi_subcorpus.fields['matchend'], first_match, last_match)
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)
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for id, lbound, rbound in match_boundaries:
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static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id] = {}
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static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['bounds'] = [lbound, rbound]
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static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['counts'] = {}
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static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['counts']['token'] = rbound - lbound + 1
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cqi_subcorpus.drop()
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##########################################################################
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# A faster way to get cpos boundaries for smaller s_attrs #
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##########################################################################
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# if s_attr.name in ['s', 'ent']:
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# cqi_corpus.query('Last', f'<{s_attr.name}> []* </{s_attr.name}>;')
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# cqi_subcorpus = cqi_corpus.subcorpora.get('Last')
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# first_match = 0
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# last_match = cqi_subcorpus.size - 1
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# match_boundaries = zip(
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# range(first_match, last_match + 1),
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# cqi_subcorpus.dump(cqi_subcorpus.fields['match'], first_match, last_match),
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# cqi_subcorpus.dump(cqi_subcorpus.fields['matchend'], first_match, last_match)
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# )
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# for id, lbound, rbound in match_boundaries:
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# static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id] = {}
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# static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['bounds'] = [lbound, rbound]
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# static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['counts'] = {}
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# static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['counts']['token'] = rbound - lbound + 1
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# cqi_subcorpus.drop()
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for id in range(0, s_attr.size):
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if s_attr.name not in ['s', 'ent']:
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static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id] = {}
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lbound, rbound = s_attr.cpos_by_id(id)
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static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['bounds'] = [lbound, rbound]
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static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['counts'] = {}
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static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['counts']['token'] = rbound - lbound + 1
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if s_attr.name not in ['text', 's']:
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continue
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cpos_range = range(lbound, rbound + 1)
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static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['counts']['ent'] = len({x for x in cqi_s_attrs['ent'].ids_by_cpos(list(cpos_range)) if x != -1})
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print(f's_attrs.{s_attr.name}.lexicon.{id}')
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static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id] = {
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'bounds': None,
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'counts': None,
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'freqs': None
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}
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if s_attr.name != 'text':
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continue
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static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['counts']['s'] = len({x for x in cqi_s_attrs['s'].ids_by_cpos(list(cpos_range)) if x != -1})
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lbound, rbound = s_attr.cpos_by_id(id)
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print(f's_attrs.{s_attr.name}.lexicon.{id}.bounds')
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static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['bounds'] = [lbound, rbound]
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print(f's_attrs.{s_attr.name}.lexicon.{id}.counts')
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static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['counts'] = {}
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static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['counts']['token'] = rbound - lbound + 1
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cpos_list = list(range(lbound, rbound + 1))
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chunks = [cpos_list[i:i+chunk_size] for i in range(0, len(cpos_list), chunk_size)]
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del cpos_list
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ent_ids = set()
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for chunk in chunks:
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print(f'Gather ent_ids from cpos: {chunk[0]} - {chunk[-1]}')
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ent_ids.update({x for x in cqi_s_attrs['ent'].ids_by_cpos(chunk) if x != -1})
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static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['counts']['ent'] = len(ent_ids)
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del ent_ids
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s_ids = set()
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for chunk in chunks:
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print(f'Gather s_ids from cpos: {chunk[0]} - {chunk[-1]}')
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s_ids.update({x for x in cqi_s_attrs['s'].ids_by_cpos(chunk) if x != -1})
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static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['counts']['s'] = len(s_ids)
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del s_ids
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print(f's_attrs.{s_attr.name}.lexicon.{id}.freqs')
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static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['freqs'] = {}
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for p_attr in cqi_p_attrs.values():
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static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['freqs'][p_attr.name] = dict(Counter(p_attr.ids_by_cpos(list(cpos_range))))
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p_attr_ids = []
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for chunk in chunks:
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print(f'Gather p_attr_ids from cpos: {chunk[0]} - {chunk[-1]}')
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p_attr_ids.extend(p_attr.ids_by_cpos(chunk))
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static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['freqs'][p_attr.name] = dict(Counter(p_attr_ids))
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del p_attr_ids
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del chunks
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sub_s_attrs = cqi_corpus.structural_attributes.list(filters={'part_of': s_attr})
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s_attr_value_names = [
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s_attr_value_names: List[str] = [
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sub_s_attr.name[(len(s_attr.name) + 1):]
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for sub_s_attr in sub_s_attrs
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]
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sub_s_attr_values = [
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sub_s_attr.values_by_ids(list(range(0, s_attr.size)))
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for sub_s_attr in sub_s_attrs
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]
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s_attr_id_list = list(range(s_attr.size))
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chunks = [s_attr_id_list[i:i+chunk_size] for i in range(0, len(s_attr_id_list), chunk_size)]
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del s_attr_id_list
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sub_s_attr_values = []
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for sub_s_attr in sub_s_attrs:
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tmp = []
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for chunk in chunks:
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tmp.extend(sub_s_attr.values_by_ids(chunk))
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sub_s_attr_values.append(tmp)
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del tmp
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del chunks
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print(f's_attrs.{s_attr.name}.values')
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static_corpus_data['s_attrs'][s_attr.name]['values'] = s_attr_value_names
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print(f'values.s_attrs.{s_attr.name}')
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static_corpus_data['values']['s_attrs'][s_attr.name] = {
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s_attr_id: {
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s_attr_value_name: sub_s_attr_values[s_attr_value_name_idx][s_attr_id_idx]
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@ -150,9 +189,12 @@ def ext_corpus_static_data(corpus: str) -> Dict:
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)
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} for s_attr_id_idx, s_attr_id in enumerate(range(0, s_attr.size))
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}
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with open(static_corpus_data_file, 'w') as f:
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del sub_s_attr_values
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with gzip.open(static_corpus_data_file, 'wt') as f:
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json.dump(static_corpus_data, f)
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return static_corpus_data
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del static_corpus_data
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with open(static_corpus_data_file, 'rb') as f:
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return f.read()
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def ext_corpus_paginate_corpus(
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@ -28,19 +28,19 @@ def _create_build_corpus_service(corpus):
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''' ## Command ## '''
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command = ['bash', '-c']
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command.append(
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f'mkdir /corpora/data/nopaque_{corpus.id}'
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f'mkdir /corpora/data/nopaque-{corpus.hashid.lower()}'
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' && '
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'cwb-encode'
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' -c utf8'
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f' -d /corpora/data/nopaque_{corpus.id}'
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f' -d /corpora/data/nopaque-{corpus.hashid.lower()}'
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' -f /root/files/corpus.vrt'
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f' -R /usr/local/share/cwb/registry/nopaque_{corpus.id}'
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f' -R /usr/local/share/cwb/registry/nopaque-{corpus.hashid.lower()}'
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' -P pos -P lemma -P simple_pos'
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' -S ent:0+type -S s:0'
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' -S text:0+address+author+booktitle+chapter+editor+institution+journal+pages+publisher+publishing_year+school+title'
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' -xsB -9'
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' && '
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f'cwb-make -V NOPAQUE_{corpus.id}'
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f'cwb-make -V NOPAQUE-{corpus.hashid.upper()}'
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)
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''' ## Constraints ## '''
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constraints = ['node.role==worker']
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@ -149,11 +149,15 @@ def _create_cqpserver_container(corpus):
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''' ### Corpus data volume ### '''
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data_volume_source = os.path.join(corpus.path, 'cwb', 'data')
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data_volume_target = '/corpora/data'
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# data_volume_source = os.path.join(corpus.path, 'cwb', 'data', f'nopaque_{corpus.id}')
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# data_volume_target = f'/corpora/data/nopaque_{corpus.hashid.lower()}'
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data_volume = f'{data_volume_source}:{data_volume_target}:rw'
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volumes.append(data_volume)
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''' ### Corpus registry volume ### '''
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registry_volume_source = os.path.join(corpus.path, 'cwb', 'registry')
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registry_volume_target = '/usr/local/share/cwb/registry'
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# registry_volume_source = os.path.join(corpus.path, 'cwb', 'registry', f'nopaque_{corpus.id}')
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# registry_volume_target = f'/usr/local/share/cwb/registry/nopaque_{corpus.hashid.lower()}'
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registry_volume = f'{registry_volume_source}:{registry_volume_target}:rw'
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volumes.append(registry_volume)
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# Check if a cqpserver container already exists. If this is the case,
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@ -1607,9 +1607,14 @@ class Corpus(HashidMixin, db.Model):
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return corpus
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def build(self):
|
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build_dir = os.path.join(self.path, 'cwb')
|
||||
shutil.rmtree(build_dir, ignore_errors=True)
|
||||
os.mkdir(build_dir)
|
||||
os.mkdir(os.path.join(build_dir, 'data'))
|
||||
os.mkdir(os.path.join(build_dir, 'registry'))
|
||||
corpus_element = ET.fromstring('<corpus>\n</corpus>')
|
||||
for corpus_file in self.files:
|
||||
normalized_vrt_path = os.path.join(self.path, 'cwb', f'{corpus_file.id}.norm.vrt')
|
||||
normalized_vrt_path = os.path.join(build_dir, f'{corpus_file.id}.norm.vrt')
|
||||
try:
|
||||
normalize_vrt_file(corpus_file.path, normalized_vrt_path)
|
||||
except:
|
||||
@ -1636,7 +1641,7 @@ class Corpus(HashidMixin, db.Model):
|
||||
# corpus_element.insert(1, text_element)
|
||||
corpus_element.append(text_element)
|
||||
ET.ElementTree(corpus_element).write(
|
||||
os.path.join(self.path, 'cwb', 'corpus.vrt'),
|
||||
os.path.join(build_dir, 'corpus.vrt'),
|
||||
encoding='utf-8'
|
||||
)
|
||||
self.status = CorpusStatus.SUBMITTED
|
||||
|
||||
@ -138,7 +138,15 @@ cqi.models.corpora.CorpusCollection = class CorpusCollection extends cqi.models.
|
||||
/************************************************************************
|
||||
* Custom additions for nopaque *
|
||||
************************************************************************/
|
||||
returnValue.static_data = await this.client.api.ext_corpus_static_data(corpusName);
|
||||
// returnValue.static_data = await this.client.api.ext_corpus_static_data(corpusName);
|
||||
let tmp = await this.client.api.ext_corpus_static_data(corpusName);
|
||||
console.log(tmp);
|
||||
let inflated = pako.inflate(tmp);
|
||||
console.log(inflated);
|
||||
let decoder = new TextDecoder('utf-8');
|
||||
console.log(decoder);
|
||||
let decoded = decoder.decode(inflated);
|
||||
returnValue.static_data = JSON.parse(decoded);
|
||||
return returnValue;
|
||||
}
|
||||
|
||||
|
||||
@ -2,6 +2,7 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/list.js/2.3.1/list.min.js" integrity="sha512-93wYgwrIFL+b+P3RvYxi/WUFRXXUDSLCT2JQk9zhVGXuS2mHl2axj6d+R6pP+gcU5isMHRj1u0oYE/mWyt/RjA==" crossorigin="anonymous" referrerpolicy="no-referrer"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/socket.io/4.5.4/socket.io.min.js" integrity="sha512-HTENHrkQ/P0NGDFd5nk6ibVtCkcM7jhr2c7GyvXp5O+4X6O5cQO9AhqFzM+MdeBivsX7Hoys2J7pp2wdgMpCvw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/plotly.js/2.24.2/plotly.min.js" integrity="sha512-dAXqGCq94D0kgLSPnfvd/pZpCMoJQpGj2S2XQmFQ9Ay1+96kbjss02ISEh+TBNXMggGg/1qoMcOHcxg+Op/Jmw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/pako/2.1.0/pako_inflate.min.js" integrity="sha512-mlnC6JeOvg9V4vBpWMxGKscsCdScB6yvGVCeFF2plnQMRmwH69s9F8SHPbC0oirqfePmRBhqx2s3Bx7WIvHfWg==" crossorigin="anonymous" referrerpolicy="no-referrer"></script>
|
||||
|
||||
{%- assets
|
||||
filters='rjsmin',
|
||||
|
||||
Loading…
Reference in New Issue
Block a user