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Merge branch 'visualizations-update' of gitlab.ub.uni-bielefeld.de:sfb1288inf/nopaque into visualizations-update

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This commit is contained in:
Inga Kirschnick 2023-07-11 09:33:22 +02:00
commit 22b43a689f
7 changed files with 147 additions and 84 deletions
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3
app/corpora/cli.py
View File

@ -19,6 +19,9 @@ def reset():
for corpus in [x for x in Corpus.query.all() if x.status in status]:
print(f'Resetting corpus {corpus}')
shutil.rmtree(os.path.join(corpus.path, 'cwb'), ignore_errors=True)
os.mkdir(os.path.join(corpus.path, 'cwb'))
os.mkdir(os.path.join(corpus.path, 'cwb', 'data'))
os.mkdir(os.path.join(corpus.path, 'cwb', 'registry'))
corpus.status = CorpusStatus.UNPREPARED
corpus.num_analysis_sessions = 0
db.session.commit()

3
app/corpora/cqi_over_sio/__init__.py
View File

@ -7,6 +7,7 @@ from threading import Lock
from app import db, hashids, socketio
from app.decorators import socketio_login_required
from app.models import Corpus, CorpusStatus
import math
'''
@ -83,7 +84,7 @@ def connect(auth):
socketio.sleep(3)
retry_counter -= 1
db.session.refresh(corpus)
cqi_client = CQiClient(f'cqpserver_{corpus_id}')
cqi_client = CQiClient(f'cqpserver_{corpus_id}', timeout=math.inf)
session['cqi_over_sio'] = {
'corpus_id': corpus_id,
'cqi_client': cqi_client,

193
app/corpora/cqi_over_sio/extensions.py
View File

@ -1,9 +1,14 @@
from collections import Counter
from cqi import CQiClient
from cqi.models.corpora import Corpus
from cqi.status import StatusOk
from cqi.models.corpora import Corpus as CQiCorpus
from cqi.models.attributes import (
PositionalAttribute as CQiPositionalAttribute,
StructuralAttribute as CQiStructuralAttribute
)
from cqi.status import StatusOk as CQiStatusOk
from flask import session
from typing import Dict, List
import gzip
import json
import math
import os
@ -22,43 +27,28 @@ CQI_EXTENSION_FUNCTION_NAMES: List[str] = [
]
def ext_corpus_update_db(corpus: str):
def ext_corpus_update_db(corpus: str) -> CQiStatusOk:
db_corpus = Corpus.query.get(session['cqi_over_sio']['corpus_id'])
cqi_client: CQiClient = session['cqi_over_sio']['cqi_client']
cqi_corpus = cqi_client.corpora.get(corpus)
cqi_corpus: CQiCorpus = cqi_client.corpora.get(corpus)
db_corpus.num_tokens = cqi_corpus.size
db.session.commit()
return StatusOk()
return CQiStatusOk()
def ext_corpus_static_data(corpus: str) -> Dict:
db_corpus = Corpus.query.get(session['cqi_over_sio']['corpus_id'])
static_corpus_data_file = os.path.join(db_corpus.path, 'cwb', 'static.json')
static_corpus_data_file = os.path.join(db_corpus.path, 'cwb', 'static.json.gz')
if os.path.exists(static_corpus_data_file):
with open(static_corpus_data_file, 'r') as f:
return json.load(f)
with open(static_corpus_data_file, 'rb') as f:
return f.read()
cqi_client: CQiClient = session['cqi_over_sio']['cqi_client']
cqi_corpus = cqi_client.corpora.get(corpus)
##########################################################################
# A faster way to get cpos boundaries for smaller s_attrs #
##########################################################################
# cqi_corpus.query('Last', '<s> []* </s>;')
# cqi_subcorpus = cqi_corpus.subcorpora.get('Last')
# print(cqi_subcorpus.size)
# first_match = 0
# last_match = cqi_subcorpus.attrs['size'] - 1
# match_boundaries = zip(
# list(range(first_match, last_match + 1)),
# cqi_subcorpus.dump(cqi_subcorpus.attrs['fields']['match'], first_match, last_match),
# cqi_subcorpus.dump(cqi_subcorpus.attrs['fields']['matchend'], first_match, last_match)
# )
# for x in match_boundaries:
# print(x)
cqi_p_attrs = {
cqi_corpus: CQiCorpus = cqi_client.corpora.get(corpus)
cqi_p_attrs: Dict[str, CQiPositionalAttribute] = {
p_attr.name: p_attr
for p_attr in cqi_corpus.positional_attributes.list()
}
cqi_s_attrs = {
cqi_s_attrs: Dict[str, CQiStructuralAttribute] = {
s_attr.name: s_attr
for s_attr in cqi_corpus.structural_attributes.list()
}
@ -75,73 +65,121 @@ def ext_corpus_static_data(corpus: str) -> Dict:
'values': {'p_attrs': {}, 's_attrs': {}}
}
for p_attr in cqi_p_attrs.values():
static_corpus_data['corpus']['freqs'][p_attr.name] = dict(
zip(
range(0, p_attr.lexicon_size),
p_attr.freqs_by_ids(list(range(0, p_attr.lexicon_size)))
static_corpus_data['corpus']['freqs'][p_attr.name] = {}
chunk_size = 10000
p_attr_id_list = list(range(p_attr.lexicon_size))
chunks = [p_attr_id_list[i:i+chunk_size] for i in range(0, len(p_attr_id_list), chunk_size)]
del p_attr_id_list
for chunk in chunks:
# print(f'corpus.freqs.{p_attr.name}: {chunk[0]} - {chunk[-1]}')
static_corpus_data['corpus']['freqs'][p_attr.name].update(
dict(zip(chunk, p_attr.freqs_by_ids(chunk)))
)
)
static_corpus_data['p_attrs'][p_attr.name] = dict(
zip(
range(0, cqi_corpus.size),
p_attr.ids_by_cpos(list(range(0, cqi_corpus.size)))
del chunks
static_corpus_data['p_attrs'][p_attr.name] = {}
cpos_list = list(range(cqi_corpus.size))
chunks = [cpos_list[i:i+chunk_size] for i in range(0, len(cpos_list), chunk_size)]
del cpos_list
for chunk in chunks:
# print(f'p_attrs.{p_attr.name}: {chunk[0]} - {chunk[-1]}')
static_corpus_data['p_attrs'][p_attr.name].update(
dict(zip(chunk, p_attr.ids_by_cpos(chunk)))
)
)
static_corpus_data['values']['p_attrs'][p_attr.name] = dict(
zip(
range(0, p_attr.lexicon_size),
p_attr.values_by_ids(list(range(0, p_attr.lexicon_size)))
del chunks
static_corpus_data['values']['p_attrs'][p_attr.name] = {}
p_attr_id_list = list(range(p_attr.lexicon_size))
chunks = [p_attr_id_list[i:i+chunk_size] for i in range(0, len(p_attr_id_list), chunk_size)]
del p_attr_id_list
for chunk in chunks:
# print(f'values.p_attrs.{p_attr.name}: {chunk[0]} - {chunk[-1]}')
static_corpus_data['values']['p_attrs'][p_attr.name].update(
dict(zip(chunk, p_attr.values_by_ids(chunk)))
)
)
del chunks
for s_attr in cqi_s_attrs.values():
if s_attr.has_values:
continue
static_corpus_data['corpus']['counts'][s_attr.name] = s_attr.size
static_corpus_data['s_attrs'][s_attr.name] = {'lexicon': {}, 'values': None}
static_corpus_data['values']['s_attrs'][s_attr.name] = {}
if s_attr.name in ['s', 'ent']:
cqi_corpus.query('Last', f'<{s_attr.name}> []* </{s_attr.name}>;')
cqi_subcorpus = cqi_corpus.subcorpora.get('Last')
first_match = 0
last_match = cqi_subcorpus.size - 1
match_boundaries = zip(
range(first_match, last_match + 1),
cqi_subcorpus.dump(cqi_subcorpus.fields['match'], first_match, last_match),
cqi_subcorpus.dump(cqi_subcorpus.fields['matchend'], first_match, last_match)
)
for id, lbound, rbound in match_boundaries:
static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id] = {}
static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['bounds'] = [lbound, rbound]
static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['counts'] = {}
static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['counts']['token'] = rbound - lbound + 1
cqi_subcorpus.drop()
##########################################################################
# A faster way to get cpos boundaries for smaller s_attrs #
##########################################################################
# if s_attr.name in ['s', 'ent']:
# cqi_corpus.query('Last', f'<{s_attr.name}> []* </{s_attr.name}>;')
# cqi_subcorpus = cqi_corpus.subcorpora.get('Last')
# first_match = 0
# last_match = cqi_subcorpus.size - 1
# match_boundaries = zip(
# range(first_match, last_match + 1),
# cqi_subcorpus.dump(cqi_subcorpus.fields['match'], first_match, last_match),
# cqi_subcorpus.dump(cqi_subcorpus.fields['matchend'], first_match, last_match)
# )
# for id, lbound, rbound in match_boundaries:
# static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id] = {}
# static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['bounds'] = [lbound, rbound]
# static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['counts'] = {}
# static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['counts']['token'] = rbound - lbound + 1
# cqi_subcorpus.drop()
for id in range(0, s_attr.size):
if s_attr.name not in ['s', 'ent']:
static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id] = {}
lbound, rbound = s_attr.cpos_by_id(id)
static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['bounds'] = [lbound, rbound]
static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['counts'] = {}
static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['counts']['token'] = rbound - lbound + 1
if s_attr.name not in ['text', 's']:
continue
cpos_range = range(lbound, rbound + 1)
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})
# print(f's_attrs.{s_attr.name}.lexicon.{id}')
static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id] = {
'bounds': None,
'counts': None,
'freqs': None
}
if s_attr.name != 'text':
continue
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})
lbound, rbound = s_attr.cpos_by_id(id)
# print(f's_attrs.{s_attr.name}.lexicon.{id}.bounds')
static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['bounds'] = [lbound, rbound]
# print(f's_attrs.{s_attr.name}.lexicon.{id}.counts')
static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['counts'] = {}
static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['counts']['token'] = rbound - lbound + 1
cpos_list = list(range(lbound, rbound + 1))
chunks = [cpos_list[i:i+chunk_size] for i in range(0, len(cpos_list), chunk_size)]
del cpos_list
ent_ids = set()
for chunk in chunks:
# print(f'Gather ent_ids from cpos: {chunk[0]} - {chunk[-1]}')
ent_ids.update({x for x in cqi_s_attrs['ent'].ids_by_cpos(chunk) if x != -1})
static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['counts']['ent'] = len(ent_ids)
del ent_ids
s_ids = set()
for chunk in chunks:
# print(f'Gather s_ids from cpos: {chunk[0]} - {chunk[-1]}')
s_ids.update({x for x in cqi_s_attrs['s'].ids_by_cpos(chunk) if x != -1})
static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['counts']['s'] = len(s_ids)
del s_ids
# print(f's_attrs.{s_attr.name}.lexicon.{id}.freqs')
static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['freqs'] = {}
for p_attr in cqi_p_attrs.values():
static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['freqs'][p_attr.name] = dict(Counter(p_attr.ids_by_cpos(list(cpos_range))))
p_attr_ids = []
for chunk in chunks:
# print(f'Gather p_attr_ids from cpos: {chunk[0]} - {chunk[-1]}')
p_attr_ids.extend(p_attr.ids_by_cpos(chunk))
static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['freqs'][p_attr.name] = dict(Counter(p_attr_ids))
del p_attr_ids
del chunks
sub_s_attrs = cqi_corpus.structural_attributes.list(filters={'part_of': s_attr})
s_attr_value_names = [
s_attr_value_names: List[str] = [
sub_s_attr.name[(len(s_attr.name) + 1):]
for sub_s_attr in sub_s_attrs
]
sub_s_attr_values = [
sub_s_attr.values_by_ids(list(range(0, s_attr.size)))
for sub_s_attr in sub_s_attrs
]
s_attr_id_list = list(range(s_attr.size))
chunks = [s_attr_id_list[i:i+chunk_size] for i in range(0, len(s_attr_id_list), chunk_size)]
del s_attr_id_list
sub_s_attr_values = []
for sub_s_attr in sub_s_attrs:
tmp = []
for chunk in chunks:
tmp.extend(sub_s_attr.values_by_ids(chunk))
sub_s_attr_values.append(tmp)
del tmp
del chunks
# print(f's_attrs.{s_attr.name}.values')
static_corpus_data['s_attrs'][s_attr.name]['values'] = s_attr_value_names
# print(f'values.s_attrs.{s_attr.name}')
static_corpus_data['values']['s_attrs'][s_attr.name] = {
s_attr_id: {
s_attr_value_name: sub_s_attr_values[s_attr_value_name_idx][s_attr_id_idx]
@ -150,9 +188,12 @@ def ext_corpus_static_data(corpus: str) -> Dict:
)
} for s_attr_id_idx, s_attr_id in enumerate(range(0, s_attr.size))
}
with open(static_corpus_data_file, 'w') as f:
del sub_s_attr_values
with gzip.open(static_corpus_data_file, 'wt') as f:
json.dump(static_corpus_data, f)
return static_corpus_data
del static_corpus_data
with open(static_corpus_data_file, 'rb') as f:
return f.read()
def ext_corpus_paginate_corpus(

12
app/daemon/corpus_utils.py
View File

@ -28,19 +28,19 @@ def _create_build_corpus_service(corpus):
''' ## Command ## '''
command = ['bash', '-c']
command.append(
f'mkdir /corpora/data/nopaque_{corpus.id}'
f'mkdir /corpora/data/nopaque-{corpus.hashid.lower()}'
' && '
'cwb-encode'
' -c utf8'
f' -d /corpora/data/nopaque_{corpus.id}'
f' -d /corpora/data/nopaque-{corpus.hashid.lower()}'
' -f /root/files/corpus.vrt'
f' -R /usr/local/share/cwb/registry/nopaque_{corpus.id}'
f' -R /usr/local/share/cwb/registry/nopaque-{corpus.hashid.lower()}'
' -P pos -P lemma -P simple_pos'
' -S ent:0+type -S s:0'
' -S text:0+address+author+booktitle+chapter+editor+institution+journal+pages+publisher+publishing_year+school+title'
' -xsB -9'
' && '
f'cwb-make -V NOPAQUE_{corpus.id}'
f'cwb-make -V NOPAQUE-{corpus.hashid.upper()}'
)
''' ## Constraints ## '''
constraints = ['node.role==worker']
@ -149,11 +149,15 @@ def _create_cqpserver_container(corpus):
''' ### Corpus data volume ### '''
data_volume_source = os.path.join(corpus.path, 'cwb', 'data')
data_volume_target = '/corpora/data'
# data_volume_source = os.path.join(corpus.path, 'cwb', 'data', f'nopaque_{corpus.id}')
# data_volume_target = f'/corpora/data/nopaque_{corpus.hashid.lower()}'
data_volume = f'{data_volume_source}:{data_volume_target}:rw'
volumes.append(data_volume)
''' ### Corpus registry volume ### '''
registry_volume_source = os.path.join(corpus.path, 'cwb', 'registry')
registry_volume_target = '/usr/local/share/cwb/registry'
# registry_volume_source = os.path.join(corpus.path, 'cwb', 'registry', f'nopaque_{corpus.id}')
# registry_volume_target = f'/usr/local/share/cwb/registry/nopaque_{corpus.hashid.lower()}'
registry_volume = f'{registry_volume_source}:{registry_volume_target}:rw'
volumes.append(registry_volume)
# Check if a cqpserver container already exists. If this is the case,

9
app/models.py
View File

@ -1607,9 +1607,14 @@ class Corpus(HashidMixin, db.Model):
return corpus
def build(self):
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

10
app/static/js/cqi/models/corpora.js
View File

@ -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;
}

1
app/templates/_scripts.html.j2
View File

@ -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',