integrate nopaque repo

This commit is contained in:
Patrick Jentsch
2020-06-05 14:42:04 +02:00
parent 450ddf69fc
commit cb2b64fa9d
164 changed files with 1212 additions and 168 deletions

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from flask import Blueprint
corpora = Blueprint('corpora', __name__)
from . import events, views # noqa

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from flask import current_app, request
from flask_login import current_user
from socket import gaierror
from .. import db, socketio
from ..decorators import socketio_login_required
from ..events import connected_sessions
from ..models import Corpus, User
import cqi
import math
from app import logger
from datetime import datetime
'''
' A dictionary containing lists of, with corpus ids associated, Socket.IO
' session ids (sid). {<corpus_id>: [<sid>, ...], ...}
'''
corpus_analysis_sessions = {}
'''
' A dictionary containing Socket.IO session id - CQi client pairs.
' {<sid>: CQiClient, ...}
'''
corpus_analysis_clients = {}
@socketio.on('corpus_analysis_init')
@socketio_login_required
def init_corpus_analysis(corpus_id):
socketio.start_background_task(corpus_analysis_session_handler,
current_app._get_current_object(),
corpus_id, current_user.id, request.sid)
@socketio.on('corpus_analysis_get_meta_data')
@socketio_login_required
def corpus_analysis_get_meta_data(corpus_id):
# get meta data from db
db_corpus = Corpus.query.get(corpus_id)
# TODO: Check if current user is actually the creator of the corpus?
metadata = {}
metadata['corpus_name'] = db_corpus.title
metadata['corpus_description'] = db_corpus.description
metadata['corpus_creation_date'] = db_corpus.creation_date.isoformat()
metadata['corpus_last_edited_date'] = db_corpus.last_edited_date.isoformat()
# get meta data from corpus in cqp server
client = corpus_analysis_clients.get(request.sid)
client_corpus = client.corpora.get('CORPUS')
metadata['corpus_properties'] = client_corpus.attrs['properties']
metadata['corpus_size_tokens'] = client_corpus.attrs['size']
text_attr = client_corpus.structural_attributes.get('text')
struct_attrs = client_corpus.structural_attributes.list(filters={'part_of': text_attr})
text_ids = range(0, (text_attr.attrs['size']))
texts_metadata = {}
for text_id in text_ids:
texts_metadata[text_id] = {}
for struct_attr in struct_attrs:
texts_metadata[text_id][struct_attr.attrs['name'][(len(text_attr.attrs['name']) + 1):]] = struct_attr.values_by_ids(list(range(struct_attr.attrs['size'])))[text_id]
metadata['corpus_all_texts'] = texts_metadata
metadata['corpus_analysis_date'] = datetime.utcnow().isoformat()
metadata['corpus_cqi_py_version'] = cqi.version
metadata['corpus_cqpserver_version'] = 'CQPserver v3.4.22' # TODO: make this dynamically
# write some metadata to the db
db_corpus.current_nr_of_tokens = metadata['corpus_size_tokens']
db.session.commit()
# emit data
payload = metadata
response = {'code': 200, 'desc': 'Corpus meta data', 'msg': 'OK', 'payload': payload}
socketio.emit('corpus_analysis_send_meta_data', response, room=request.sid)
@socketio.on('corpus_analysis_query')
@socketio_login_required
def corpus_analysis_query(query):
client = corpus_analysis_clients.get(request.sid)
if client is None:
response = {'code': 424, 'desc': 'No client found for this session',
'msg': 'Failed Dependency'}
socketio.emit('corpus_analysis_query', response, room=request.sid)
return
if client.status == 'running':
client.status = 'abort'
while client.status != 'ready':
socketio.sleep(0.1)
try:
corpus = client.corpora.get('CORPUS')
query_status = corpus.query(query)
results = corpus.subcorpora.get('Results')
except cqi.errors.CQiException as e:
payload = {'code': e.code, 'desc': e.description, 'msg': e.name}
response = {'code': 500, 'desc': None, 'msg': 'Internal Server Error',
'payload': payload}
socketio.emit('corpus_analysis_query', response, room=request.sid)
return
payload = {**query_status, 'match_count': results.attrs['size']}
response = {'code': 200, 'desc': None, 'msg': 'OK', 'payload': payload}
socketio.emit('corpus_analysis_query', response, room=request.sid)
# TODO: Stop here and add a new method for transmission
chunk_size = 100
chunk_start = 0
context = 50
progress = 0
client.status = 'running'
while chunk_start <= results.attrs['size']:
if client.status == 'abort':
break
chunk = results.export(context=context, cutoff=chunk_size,
expand_lists=False, offset=chunk_start)
chunk['cpos_ranges'] = True
if (results.attrs['size'] == 0):
progress = 100
else:
progress = ((chunk_start + chunk_size) / results.attrs['size']) * 100
progress = min(100, int(math.ceil(progress)))
response = {'code': 200, 'desc': None, 'msg': 'OK',
'payload': {'chunk': chunk, 'progress': progress}}
socketio.emit('corpus_analysis_query_results', response,
room=request.sid)
chunk_start += chunk_size
client.status = 'ready'
@socketio.on('corpus_analysis_inspect_match')
@socketio_login_required
def corpus_analysis_inspect_match(payload):
payload = payload["payload"]
client = corpus_analysis_clients.get(request.sid)
if client is None:
response = {'code': 424, 'desc': 'No client found for this session',
'msg': 'Failed Dependency'}
socketio.emit('corpus_analysis_inspect_match', response, room=request.sid)
return
try:
corpus = client.corpora.get('CORPUS')
s = corpus.structural_attributes.get('s')
payload = s.export(payload['first_cpos'], payload['last_cpos'], context=10)
payload['cpos_ranges'] = True
except cqi.errors.CQiException as e:
payload = {'code': e.code, 'desc': e.description, 'msg': e.name}
response = {'code': 500, 'desc': None, 'msg': 'Internal Server Error',
'payload': payload}
else:
response = {'code': 200, 'desc': None, 'msg': 'OK', 'payload': payload}
socketio.emit('corpus_analysis_inspect_match', response, room=request.sid)
def corpus_analysis_session_handler(app, corpus_id, user_id, session_id):
with app.app_context():
''' Setup analysis session '''
corpus = Corpus.query.get(corpus_id)
user = User.query.get(user_id)
if corpus is None:
response = {'code': 404, 'desc': None, 'msg': 'Not Found'}
socketio.emit('corpus_analysis_init', response, room=session_id)
return
elif not (corpus.creator == user or user.is_administrator()):
response = {'code': 403, 'desc': None, 'msg': 'Forbidden'}
socketio.emit('corpus_analysis_init', response, room=session_id)
return
elif corpus.status == 'unprepared':
response = {'code': 424, 'desc': 'Corpus is not prepared',
'msg': 'Failed Dependency'}
socketio.emit('corpus_analysis_init', response, room=request.sid)
return
while corpus.status != 'analysing':
db.session.refresh(corpus)
socketio.sleep(3)
client = cqi.CQiClient('cqpserver_{}'.format(corpus_id))
try:
payload = client.connect()
except cqi.errors.CQiException as e:
payload = {'code': e.code, 'desc': e.description, 'msg': e.name}
response = {'code': 500, 'desc': None,
'msg': 'Internal Server Error', 'payload': payload}
socketio.emit('corpus_analysis_init', response, room=session_id)
return
except gaierror:
response = {'code': 500, 'desc': None,
'msg': 'Internal Server Error'}
socketio.emit('corpus_analysis_init', response, room=session_id)
return
corpus_analysis_clients[session_id] = client
if corpus_id not in corpus_analysis_sessions:
corpus_analysis_sessions[corpus_id] = [session_id]
else:
corpus_analysis_sessions[corpus_id].append(session_id)
client.status = 'ready'
response = {'code': 200, 'desc': None, 'msg': 'OK', 'payload': payload}
socketio.emit('corpus_analysis_init', response, room=session_id)
''' Observe analysis session '''
while session_id in connected_sessions:
socketio.sleep(3)
''' Teardown analysis session '''
if client.status == 'running':
client.status = 'abort'
while client.status != 'ready':
socketio.sleep(0.1)
try:
client.disconnect()
except cqi.errors.CQiException:
pass
corpus_analysis_clients.pop(session_id, None)
corpus_analysis_sessions[corpus_id].remove(session_id)
if not corpus_analysis_sessions[corpus_id]:
corpus_analysis_sessions.pop(corpus_id, None)
corpus.status = 'stop analysis'
db.session.commit()

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from flask_wtf import FlaskForm
from werkzeug.utils import secure_filename
from wtforms import (BooleanField, FileField, StringField, SubmitField,
ValidationError, IntegerField, SelectField)
from wtforms.validators import DataRequired, Length, NumberRange
class AddCorpusFileForm(FlaskForm):
address = StringField('Adress', validators=[Length(0, 255)])
author = StringField('Author', validators=[DataRequired(), Length(1, 255)])
booktitle = StringField('Booktitle', validators=[Length(0, 255)])
chapter = StringField('Chapter', validators=[Length(0, 255)])
editor = StringField('Editor', validators=[Length(0, 255)])
file = FileField('File', validators=[DataRequired()])
institution = StringField('Institution', validators=[Length(0, 255)])
journal = StringField('Journal', validators=[Length(0, 255)])
pages = StringField('Pages', validators=[Length(0, 255)])
publisher = StringField('Publisher', validators=[Length(0, 255)])
publishing_year = IntegerField('Publishing year',
validators=[DataRequired()])
school = StringField('School', validators=[Length(0, 255)])
submit = SubmitField()
title = StringField('Title', validators=[DataRequired(), Length(1, 255)])
def __init__(self, corpus, *args, **kwargs):
super(AddCorpusFileForm, self).__init__(*args, **kwargs)
self.corpus = corpus
def validate_file(self, field):
if not field.data.filename.lower().endswith('.vrt'):
raise ValidationError('File does not have an approved extension: '
'.vrt')
field.data.filename = secure_filename(field.data.filename)
for corpus_file in self.corpus.files:
if field.data.filename == corpus_file.filename:
raise ValidationError('File already registered to corpus.')
class EditCorpusFileForm(FlaskForm):
address = StringField('Adress', validators=[Length(0, 255)])
author = StringField('Author', validators=[DataRequired(), Length(1, 255)])
booktitle = StringField('Booktitle', validators=[Length(0, 255)])
chapter = StringField('Chapter', validators=[Length(0, 255)])
editor = StringField('Editor', validators=[Length(0, 255)])
institution = StringField('Institution', validators=[Length(0, 255)])
journal = StringField('Journal', validators=[Length(0, 255)])
pages = StringField('Pages', validators=[Length(0, 255)])
publisher = StringField('Publisher', validators=[Length(0, 255)])
publishing_year = IntegerField('Publishing year',
validators=[DataRequired()])
school = StringField('School', validators=[Length(0, 255)])
submit = SubmitField()
title = StringField('Title', validators=[DataRequired(), Length(1, 255)])
class AddCorpusForm(FlaskForm):
description = StringField('Description',
validators=[DataRequired(), Length(1, 255)])
submit = SubmitField()
title = StringField('Title', validators=[DataRequired(), Length(1, 32)])
class QueryForm(FlaskForm):
query = StringField('Query',
validators=[DataRequired(), Length(1, 1024)])
submit = SubmitField('Send query')
class DisplayOptionsForm(FlaskForm):
expert_mode = BooleanField('Expert mode')
result_context = SelectField('Result context',
choices=[('', 'Choose your option'),
('10', '10'),
('20', '20'),
('30', '30'),
('40', '40'),
('50', '50')])
results_per_page = SelectField('Results per page',
choices=[('', 'Choose your option'),
('10', '10'),
('20', '20'),
('30', '30'),
('40', '40'),
('50', '50')])
class InspectDisplayOptionsForm(FlaskForm):
expert_mode_inspect = BooleanField('Expert mode')
highlight_sentences = BooleanField('Split sentences')
context_sentences = IntegerField('Context sentences',
validators=[NumberRange(min=0, max=10)],
default=3)
class QueryDownloadForm(FlaskForm):
file_type = SelectField('File type',
choices=[('', 'Choose file type'),
('csv', 'csv'),
('json', 'json'),
('excel', 'excel'),
('html', 'html-table')],
validators=[DataRequired()])

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from datetime import datetime
from .. import db
from ..decorators import background
from ..models import Corpus, CorpusFile
import xml.etree.ElementTree as ET
import os
import shutil
@background
def build_corpus(corpus_id, *args, **kwargs):
app = kwargs['app']
with app.app_context():
corpus = Corpus.query.get(corpus_id)
if corpus is None:
return
corpus.status = 'File processing'
db.session.commit()
corpus_dir = os.path.join(app.config['NOPAQUE_STORAGE'],
str(corpus.user_id), 'corpora',
str(corpus.id))
output_dir = os.path.join(corpus_dir, 'merged')
shutil.rmtree(output_dir, ignore_errors=True)
os.mkdir(output_dir)
master_element_tree = ET.ElementTree(
ET.fromstring('<corpus>\n</corpus>'))
for corpus_file in corpus.files:
file = os.path.join(corpus_dir, corpus_file.filename)
element_tree = ET.parse(file)
text_node = element_tree.find('text')
text_node.set('address', corpus_file.address or "NULL")
text_node.set('author', corpus_file.author)
text_node.set('booktitle', corpus_file.booktitle or "NULL")
text_node.set('chapter', corpus_file.chapter or "NULL")
text_node.set('editor', corpus_file.editor or "NULL")
text_node.set('institution', corpus_file.institution or "NULL")
text_node.set('journal', corpus_file.journal or "NULL")
text_node.set('pages', corpus_file.pages or "NULL")
text_node.set('publisher', corpus_file.publisher or "NULL")
text_node.set('publishing_year', str(corpus_file.publishing_year))
text_node.set('school', corpus_file.school or "NULL")
text_node.set('title', corpus_file.title)
element_tree.write(file)
master_element_tree.getroot().insert(1, text_node)
output_file = os.path.join(output_dir, 'corpus.vrt')
master_element_tree.write(output_file, xml_declaration=True,
encoding='utf-8')
corpus.status = 'submitted'
corpus.last_edited_date = datetime.utcnow()
db.session.commit()
@background
def delete_corpus(corpus_id, *args, **kwargs):
app = kwargs['app']
with app.app_context():
corpus = Corpus.query.get(corpus_id)
if corpus is None:
return
path = os.path.join(app.config['NOPAQUE_STORAGE'], str(corpus.user_id),
'corpora', str(corpus.id))
shutil.rmtree(path, ignore_errors=True)
corpus.delete()
@background
def delete_corpus_file(corpus_file_id, *args, **kwargs):
app = kwargs['app']
with app.app_context():
corpus_file = CorpusFile.query.get(corpus_file_id)
if corpus_file is None:
return
path = os.path.join(app.config['NOPAQUE_STORAGE'], corpus_file.dir,
corpus_file.filename)
try:
os.remove(path)
except Exception:
pass
else:
corpus_file.delete()

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from flask import (abort, current_app, flash, make_response, redirect, request,
render_template, url_for, send_from_directory)
from flask_login import current_user, login_required
from . import corpora
from . import tasks
from .forms import (AddCorpusFileForm, AddCorpusForm, EditCorpusFileForm,
QueryDownloadForm, QueryForm, DisplayOptionsForm,
InspectDisplayOptionsForm)
from .. import db
from ..models import Corpus, CorpusFile
import os
@corpora.route('/add', methods=['GET', 'POST'])
@login_required
def add_corpus():
add_corpus_form = AddCorpusForm()
if add_corpus_form.validate_on_submit():
corpus = Corpus(creator=current_user,
description=add_corpus_form.description.data,
status='unprepared', title=add_corpus_form.title.data)
db.session.add(corpus)
db.session.commit()
dir = os.path.join(current_app.config['NOPAQUE_STORAGE'],
str(corpus.user_id), 'corpora', str(corpus.id))
try:
os.makedirs(dir)
except OSError:
flash('[ERROR]: Could not add corpus!', 'corpus')
corpus.delete()
else:
url = url_for('corpora.corpus', corpus_id=corpus.id)
flash('[<a href="{}">{}</a>] added'.format(url, corpus.title),
'corpus')
return redirect(url_for('corpora.corpus', corpus_id=corpus.id))
return render_template('corpora/add_corpus.html.j2',
add_corpus_form=add_corpus_form,
title='Add corpus')
@corpora.route('/<int:corpus_id>')
@login_required
def corpus(corpus_id):
corpus = Corpus.query.get_or_404(corpus_id)
if not (corpus.creator == current_user or current_user.is_administrator()):
abort(403)
return render_template('corpora/corpus.html.j2', corpus=corpus,
title='Corpus')
@corpora.route('/<int:corpus_id>/analyse')
@login_required
def analyse_corpus(corpus_id):
corpus = Corpus.query.get_or_404(corpus_id)
if corpus.status == 'prepared':
corpus.status = 'start analysis'
db.session.commit()
display_options_form = DisplayOptionsForm(
prefix='display-options-form',
result_context=request.args.get('context', 20),
results_per_page=request.args.get('results_per_page', 30))
query_form = QueryForm(prefix='query-form',
query=request.args.get('query'))
query_download_form = QueryDownloadForm(prefix='query-download-form')
inspect_display_options_form = InspectDisplayOptionsForm(
prefix='inspect-display-options-form')
return render_template(
'corpora/analyse_corpus.html.j2',
corpus_id=corpus_id,
display_options_form=display_options_form,
query_form=query_form,
query_download_form=query_download_form,
inspect_display_options_form=inspect_display_options_form,
title='Corpus analysis')
@corpora.route('/<int:corpus_id>/delete')
@login_required
def delete_corpus(corpus_id):
corpus = Corpus.query.get_or_404(corpus_id)
if not (corpus.creator == current_user or current_user.is_administrator()):
abort(403)
tasks.delete_corpus(corpus_id)
flash('Corpus deleted!', 'corpus')
return redirect(url_for('main.dashboard'))
@corpora.route('/<int:corpus_id>/files/add', methods=['GET', 'POST'])
@login_required
def add_corpus_file(corpus_id):
corpus = Corpus.query.get_or_404(corpus_id)
if not (corpus.creator == current_user or current_user.is_administrator()):
abort(403)
add_corpus_file_form = AddCorpusFileForm(corpus,
prefix='add-corpus-file-form')
if add_corpus_file_form.is_submitted():
if not add_corpus_file_form.validate():
return make_response(add_corpus_file_form.errors, 400)
# Save the file
dir = os.path.join(str(corpus.user_id), 'corpora', str(corpus.id))
add_corpus_file_form.file.data.save(
os.path.join(current_app.config['NOPAQUE_STORAGE'], dir,
add_corpus_file_form.file.data.filename))
corpus_file = CorpusFile(
address=add_corpus_file_form.address.data,
author=add_corpus_file_form.author.data,
booktitle=add_corpus_file_form.booktitle.data,
chapter=add_corpus_file_form.chapter.data,
corpus=corpus,
dir=dir,
editor=add_corpus_file_form.editor.data,
filename=add_corpus_file_form.file.data.filename,
institution=add_corpus_file_form.institution.data,
journal=add_corpus_file_form.journal.data,
pages=add_corpus_file_form.pages.data,
publisher=add_corpus_file_form.publisher.data,
publishing_year=add_corpus_file_form.publishing_year.data,
school=add_corpus_file_form.school.data,
title=add_corpus_file_form.title.data)
db.session.add(corpus_file)
corpus.status = 'unprepared'
db.session.commit()
flash('Corpus file added!', 'corpus')
return make_response(
{'redirect_url': url_for('corpora.corpus', corpus_id=corpus.id)},
201)
return render_template('corpora/add_corpus_file.html.j2',
corpus=corpus,
add_corpus_file_form=add_corpus_file_form,
title='Add corpus file')
@corpora.route('/<int:corpus_id>/files/<int:corpus_file_id>/delete')
@login_required
def delete_corpus_file(corpus_id, corpus_file_id):
corpus_file = CorpusFile.query.get_or_404(corpus_file_id)
if not corpus_file.corpus_id == corpus_id:
abort(404)
if not (corpus_file.corpus.creator == current_user
or current_user.is_administrator()):
abort(403)
tasks.delete_corpus_file(corpus_file_id)
flash('Corpus file deleted!', 'corpus')
return redirect(url_for('corpora.corpus', corpus_id=corpus_id))
@corpora.route('/<int:corpus_id>/files/<int:corpus_file_id>/download')
@login_required
def download_corpus_file(corpus_id, corpus_file_id):
corpus_file = CorpusFile.query.get_or_404(corpus_file_id)
if not corpus_file.corpus_id == corpus_id:
abort(404)
if not (corpus_file.corpus.creator == current_user
or current_user.is_administrator()):
abort(403)
dir = os.path.join(current_app.config['NOPAQUE_STORAGE'],
corpus_file.dir)
return send_from_directory(as_attachment=True, directory=dir,
filename=corpus_file.filename)
@corpora.route('/<int:corpus_id>/files/<int:corpus_file_id>/edit',
methods=['GET', 'POST'])
@login_required
def edit_corpus_file(corpus_id, corpus_file_id):
corpus = Corpus.query.get_or_404(corpus_id)
corpus_file = CorpusFile.query.get_or_404(corpus_file_id)
if not corpus_file.corpus_id == corpus_id:
abort(404)
if not (corpus_file.corpus.creator == current_user
or current_user.is_administrator()):
abort(403)
edit_corpus_file_form = EditCorpusFileForm(prefix='edit-corpus-file-form')
if edit_corpus_file_form.validate_on_submit():
corpus_file.address = edit_corpus_file_form.address.data
corpus_file.author = edit_corpus_file_form.author.data
corpus_file.booktitle = edit_corpus_file_form.booktitle.data
corpus_file.chapter = edit_corpus_file_form.chapter.data
corpus_file.editor = edit_corpus_file_form.editor.data
corpus_file.institution = edit_corpus_file_form.institution.data
corpus_file.journal = edit_corpus_file_form.journal.data
corpus_file.pages = edit_corpus_file_form.pages.data
corpus_file.publisher = edit_corpus_file_form.publisher.data
corpus_file.publishing_year = \
edit_corpus_file_form.publishing_year.data
corpus_file.school = edit_corpus_file_form.school.data
corpus_file.title = edit_corpus_file_form.title.data
corpus.status = 'unprepared'
db.session.commit()
flash('Corpus file edited!', 'corpus')
return redirect(url_for('corpora.corpus', corpus_id=corpus_id))
# If no form is submitted or valid, fill out fields with current values
edit_corpus_file_form.address.data = corpus_file.address
edit_corpus_file_form.author.data = corpus_file.author
edit_corpus_file_form.booktitle.data = corpus_file.booktitle
edit_corpus_file_form.chapter.data = corpus_file.chapter
edit_corpus_file_form.editor.data = corpus_file.editor
edit_corpus_file_form.institution.data = corpus_file.institution
edit_corpus_file_form.journal.data = corpus_file.journal
edit_corpus_file_form.pages.data = corpus_file.pages
edit_corpus_file_form.publisher.data = corpus_file.publisher
edit_corpus_file_form.publishing_year.data = corpus_file.publishing_year
edit_corpus_file_form.school.data = corpus_file.school
edit_corpus_file_form.title.data = corpus_file.title
return render_template('corpora/edit_corpus_file.html.j2',
corpus_file=corpus_file, corpus=corpus,
edit_corpus_file_form=edit_corpus_file_form,
title='Edit corpus file')
@corpora.route('/<int:corpus_id>/prepare')
@login_required
def prepare_corpus(corpus_id):
corpus = Corpus.query.get_or_404(corpus_id)
if not (corpus.creator == current_user or current_user.is_administrator()):
abort(403)
if corpus.files.all():
tasks.build_corpus(corpus_id)
flash('Corpus gets build now.', 'corpus')
else:
flash('Can not build corpus, please add corpus file(s).', 'corpus')
return redirect(url_for('corpora.corpus', corpus_id=corpus_id))