declutter by using default filenames

.dockerignore

@@ -5,9 +5,8 @@
 !app
 !migrations
 !tests
-!.flaskenv
 !boot.sh
 !config.py
 !docker-nopaque-entrypoint.sh
-!nopaque.py
 !requirements.txt
+!wsgi.py

.flaskenv

@@ -1 +0,0 @@
-FLASK_APP=nopaque.py

Dockerfile

@@ -46,7 +46,7 @@ COPY docker-nopaque-entrypoint.sh /usr/local/bin/
 COPY --chown=nopaque:nopaque app app
 COPY --chown=nopaque:nopaque migrations migrations
 COPY --chown=nopaque:nopaque tests tests
-COPY --chown=nopaque:nopaque .flaskenv boot.sh config.py nopaque.py requirements.txt ./
+COPY --chown=nopaque:nopaque boot.sh config.py wsgi.py requirements.txt ./
 
 RUN mkdir logs
 

app/__init__.py

@@ -33,6 +33,9 @@ scheduler = APScheduler()
 socketio = SocketIO()
 
 
+# TODO: Create export for lemmatized corpora
+
+
 def create_app(config: Config = Config) -> Flask:
     ''' Creates an initialized Flask (WSGI Application) object. '''
     app = Flask(__name__)

app/admin/json_routes.py

@@ -1,6 +1,6 @@
 from flask import abort, request
-from app import db
 from app.decorators import content_negotiation
+from app import db
 from app.models import User
 from . import bp
 

app/admin/routes.py

@@ -9,12 +9,12 @@ from app.users.settings.forms import (
     UpdateAccountInformationForm,
     UpdateProfileInformationForm
 )
-from . import bp
-from .forms import UpdateUserForm
 from app.users.utils import (
     user_endpoint_arguments_constructor as user_eac,
     user_dynamic_list_constructor as user_dlc
 )
+from . import bp
+from .forms import UpdateUserForm
 
 
 @bp.route('')

app/api/jobs.py

@@ -5,8 +5,8 @@ from flask import abort, Blueprint
 from werkzeug.exceptions import InternalServerError
 from app import db, hashids
 from app.models import Job, JobInput, JobStatus, TesseractOCRPipelineModel
-from .schemas import EmptySchema, JobSchema, SpaCyNLPPipelineJobSchema, TesseractOCRPipelineJobSchema, TesseractOCRPipelineModelSchema
 from .auth import auth_error_responses, token_auth
+from .schemas import EmptySchema, JobSchema, SpaCyNLPPipelineJobSchema, TesseractOCRPipelineJobSchema, TesseractOCRPipelineModelSchema
 
 
 bp = Blueprint('jobs', __name__)

app/api/users.py

@@ -3,11 +3,11 @@ from apifairy import authenticate, body, response
 from apifairy.decorators import other_responses
 from flask import abort, Blueprint
 from werkzeug.exceptions import InternalServerError
-from app import db
 from app.email import create_message, send
+from app import db
 from app.models import User
-from .schemas import EmptySchema, UserSchema
 from .auth import auth_error_responses, token_auth
+from .schemas import EmptySchema, UserSchema
 
 
 bp = Blueprint('users', __name__)

app/contributions/spacy_nlp_pipeline_models/json_routes.py

@@ -4,7 +4,7 @@ from threading import Thread
 from app import db
 from app.decorators import content_negotiation, permission_required
 from app.models import SpaCyNLPPipelineModel
-from .. import bp
+from . import bp
 
 
 @bp.route('/spacy-nlp-pipeline-models/<hashid:spacy_nlp_pipeline_model_id>', methods=['DELETE'])

app/contributions/spacy_nlp_pipeline_models/routes.py

@@ -8,9 +8,7 @@ from .forms import (
     CreateSpaCyNLPPipelineModelForm,
     UpdateSpaCyNLPPipelineModelForm
 )
-from .utils import (
-    spacy_nlp_pipeline_model_dlc as spacy_nlp_pipeline_model_dlc
-)
+from .utils import spacy_nlp_pipeline_model_dlc
 
 
 @bp.route('/spacy-nlp-pipeline-models')

app/contributions/tesseract_ocr_pipeline_models/routes.py

@@ -8,9 +8,7 @@ from .forms import (
     CreateTesseractOCRPipelineModelForm,
     UpdateTesseractOCRPipelineModelForm
 )
-from .utils import (
-    tesseract_ocr_pipeline_model_dlc as tesseract_ocr_pipeline_model_dlc
-)
+from .utils import tesseract_ocr_pipeline_model_dlc
 
 
 @bp.route('/tesseract-ocr-pipeline-models')

app/converters/sandpaper.py

@@ -1,11 +1,11 @@
-from flask import current_app
-from app import db
-from app.models import User, Corpus, CorpusFile
 from datetime import datetime
+from flask import current_app
 from pathlib import Path
 from typing import Dict, List
 import json
 import shutil
+from app import db
+from app.models import User, Corpus, CorpusFile
 
 
 class SandpaperConverter:

app/corpora/files/json_routes.py

@@ -1,7 +1,7 @@
-from flask import abort, current_app
+from flask import current_app
 from threading import Thread
-from app import db
 from app.decorators import content_negotiation
+from app import db
 from app.models import CorpusFile
 from ..decorators import corpus_follower_permission_required
 from . import bp

app/corpora/files/utils.py

@@ -1,6 +1,5 @@
 from flask import request, url_for
 from app.models import CorpusFile
-from ..utils import corpus_endpoint_arguments_constructor as corpus_eac
 
 
 def corpus_file_dynamic_list_constructor():

app/ext/flask_sqlalchemy/__init__.py

@@ -1,2 +0,0 @@
-from .container_column import ContainerColumn
-from .int_enum_column import IntEnumColumn

app/ext/flask_sqlalchemy/container_column.py

@@ -1,21 +0,0 @@
-import json
-from app import db
-
-
-class ContainerColumn(db.TypeDecorator):
-    impl = db.String
-
-    def __init__(self, container_type, *args, **kwargs):
-        super().__init__(*args, **kwargs)
-        self.container_type = container_type
-
-    def process_bind_param(self, value, dialect):
-        if isinstance(value, self.container_type):
-            return json.dumps(value)
-        elif isinstance(value, str) and isinstance(json.loads(value), self.container_type):
-            return value
-        else:
-            return TypeError()
-
-    def process_result_value(self, value, dialect):
-        return json.loads(value)

app/extensions/__init__.py

@@ -0,0 +1 @@
+

app/extensions/sqlalchemy/__init__.py

@@ -0,0 +1,2 @@
+from .types import ContainerColumn
+from .types import IntEnumColumn

app/extensions/sqlalchemy/types.py

@@ -1,6 +1,26 @@
+import json
 from app import db
 
 
+class ContainerColumn(db.TypeDecorator):
+    impl = db.String
+
+    def __init__(self, container_type, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.container_type = container_type
+
+    def process_bind_param(self, value, dialect):
+        if isinstance(value, self.container_type):
+            return json.dumps(value)
+        elif isinstance(value, str) and isinstance(json.loads(value), self.container_type):
+            return value
+        else:
+            return TypeError()
+
+    def process_result_value(self, value, dialect):
+        return json.loads(value)
+
+
 class IntEnumColumn(db.TypeDecorator):
     impl = db.Integer
 

app/models/corpus.py

@@ -9,7 +9,7 @@ import shutil
 import xml.etree.ElementTree as ET
 from app import db
 from app.converters.vrt import normalize_vrt_file
-from app.ext.flask_sqlalchemy import IntEnumColumn
+from app.extensions.sqlalchemy import IntEnumColumn
 from .corpus_follower_association import CorpusFollowerAssociation
 
 

app/models/job.py

@@ -7,7 +7,7 @@ from typing import Union
 from pathlib import Path
 import shutil
 from app import db
-from app.ext.flask_sqlalchemy import ContainerColumn, IntEnumColumn
+from app.extensions.sqlalchemy import ContainerColumn, IntEnumColumn
 
 
 class JobStatus(IntEnum):

app/models/spacy_nlp_pipeline_model.py

@@ -5,7 +5,7 @@ from pathlib import Path
 import requests
 import yaml
 from app import db
-from app.ext.flask_sqlalchemy import ContainerColumn
+from app.extensions.sqlalchemy import ContainerColumn
 from .file_mixin import FileMixin
 from .user import User
 

app/models/tesseract_ocr_pipeline_model.py

@@ -5,7 +5,7 @@ from pathlib import Path
 import requests
 import yaml
 from app import db
-from app.ext.flask_sqlalchemy import ContainerColumn
+from app.extensions.sqlalchemy import ContainerColumn
 from .file_mixin import FileMixin
 from .user import User
 

app/models/user.py

@@ -12,7 +12,7 @@ import re
 import secrets
 import shutil
 from app import db, hashids
-from app.ext.flask_sqlalchemy import IntEnumColumn
+from app.extensions.sqlalchemy import IntEnumColumn
 from .corpus import Corpus
 from .corpus_follower_association import CorpusFollowerAssociation
 from .corpus_follower_role import CorpusFollowerRole

app/services/routes.py

@@ -6,7 +6,6 @@ from app import db, hashids
 from app.models import (
     Job,
     JobInput,
-    JobResult,
     JobStatus,
     TesseractOCRPipelineModel,
     SpaCyNLPPipelineModel
@@ -75,8 +74,6 @@ def tesseract_ocr_pipeline():
     version = request.args.get('version', service_manifest['latest_version'])
     if version not in service_manifest['versions']:
         abort(404)
-    job_results = JobResult.query.all()
-    choosable_job_ids = [job_result.job.hashid for job_result in job_results if job_result.job.service == "file-setup-pipeline" and job_result.filename.endswith('.pdf')]
     form = CreateTesseractOCRPipelineJobForm(prefix='create-job-form', version=version)
     if form.is_submitted():
         if not form.validate():
@@ -114,7 +111,6 @@ def tesseract_ocr_pipeline():
     return render_template(
         'services/tesseract_ocr_pipeline.html.j2',
         title=service_manifest['name'],
-        choosable_job_ids=choosable_job_ids,
         form=form,
         tesseract_ocr_pipeline_models=tesseract_ocr_pipeline_models,
         user_tesseract_ocr_pipeline_models_count=user_tesseract_ocr_pipeline_models_count

app/static/js/forms/base-form-new.js

@@ -0,0 +1,57 @@
+export class BaseForm {
+  constructor(formElement) {
+    this.element = formElement;
+
+    this.element.addEventListener('submit', (event) => {
+      event.preventDefault();
+      this.submit();
+    });
+    console.log("UsernamePostFormInitialized");
+  }
+
+  submit() {
+    let errorTextElements = this.element
+      .querySelectorAll('.supporting-text[data-supporting-text-type="error"]');
+    for (let errorTextElement of errorTextElements) {errorTextElement.remove();}
+
+    const body = new FormData(this.element);
+    const headers = {
+      'Accept': 'application/json',
+      'Content-Type': 'application/json'
+    };
+    const method = this.element.method;
+
+    const fetchPromise = new Promise((resolve, reject) => {
+      fetch(this.element.action, {body: body, headers: headers, method: method})
+        .then((response) => {
+          if (!response.ok) {
+            console.log("reject", response);
+            reject(response);
+            return;
+          }
+          console.log("resolve", response);
+          resolve(response);
+        });
+    });
+
+    fetchPromise
+      .then(
+        (response) => {console.log("Hello from resolve handler");return response.json();},
+        (response) => {
+          console.log("Hello from reject handler 1/2");
+          response.json()
+            .then((errors) => {
+              console.log("Hello from reject handler 2/2");
+              for (let [name, messages] of Object.entries(errors)) {
+                console.log(name, messages);
+                const inputFieldElement = this.element[name].closest('.input-field');
+                for (let message of messages) {
+                  const messageHTML = `<span class="supporting-text" data-supporting-text-type="error">${message}</span>`;
+                  inputFieldElement.insertAdjacentHTML('beforeend', messageHTML);
+                }
+              }
+            });
+        }
+      );
+  }
+};

app/static/js/resource-lists/job-output-list.js

@@ -1,137 +0,0 @@
-nopaque.resource_lists.JobOutputList = class JobOutputList extends nopaque.resource_lists.ResourceList {
-  static htmlClass = 'job-output-list';
-
-  constructor(listContainerElement, options = {}) {
-    super(listContainerElement, options);
-    this.listjs.list.addEventListener('click', (event) => {this.onClick(event)});
-    this.isInitialized = false;
-    this.userId = listContainerElement.dataset.userId;
-    this.jobOutput = listContainerElement.dataset.jobOutput;
-    this.jobIds = listContainerElement.dataset.jobIds;
-    if (this.userId === undefined) {return;}
-    app.subscribeUser(this.userId).then((response) => {
-      app.socket.on('PATCH', (patch) => {
-        if (this.isInitialized) {this.onPatch(patch);}
-      });
-    });
-    app.getUser(this.userId).then((user) => {
-      let jobIds = JSON.parse(this.jobIds.replace(/'/g, '"'));
-      let job_results = {};
-      for (let jobId of jobIds) {
-        for (let jobResult of Object.values(user.jobs[jobId].results)) {
-          if (jobResult.mimetype === 'application/pdf') {
-            job_results[jobResult.id] = jobResult;
-            job_results[jobResult.id].description = user.jobs[jobId].description;
-            job_results[jobResult.id].title = user.jobs[jobId].title;
-          }
-        }
-      }
-      this.add(Object.values(job_results));
-      this.isInitialized = true;
-    });
-  }
-
-  get item() {
-    return `
-      <tr class="list-item clickable hoverable">
-        <td><span class="title"></span></td>
-        <td><span class="description"></span></td>
-        <td><span class="filename"></span></td>
-        <td class="right-align">
-          <a class="list-action-trigger btn-flat waves-effect waves-light" data-list-action="add"><i class="material-icons">add</i></a>
-        </td>
-      </tr>
-    `.trim();
-  }
-
-  get valueNames() {
-    return [
-      {data: ['id']},
-      {data: ['creation-date']},
-      'title',
-      'description',
-      'filename'
-    ];
-  }
-
-  initListContainerElement() {
-    if (!this.listContainerElement.hasAttribute('id')) {
-      this.listContainerElement.id = nopaque.Utils.generateElementId('job-output-list-');
-    }
-    let listSearchElementId = nopaque.Utils.generateElementId(`${this.listContainerElement.id}-search-`);
-    this.listContainerElement.innerHTML = `
-      <div class="input-field">
-        <i class="material-icons prefix">search</i>
-        <input id="${listSearchElementId}" class="search" type="text"></input>
-        <label for="${listSearchElementId}">Search job output</label>
-      </div>
-      <table>
-        <thead>
-          <tr>
-            <th>Title</th>
-            <th>Description</th>
-            <th>Filename</th>
-            <th></th>
-          </tr>
-        </thead>
-        <tbody class="list"></tbody>
-      </table>
-      <ul class="pagination"></ul>
-    `;
-  }
-
-  mapResourceToValue(jobOutput) {
-    console.log(jobOutput);
-    return {
-      'id': jobOutput.id,
-      'creation-date': jobOutput.creationDate,
-      'title': jobOutput.title,
-      'description': jobOutput.description,
-      'filename': jobOutput.filename
-    };
-  }
-
-  sort() {
-    this.listjs.sort('title', {order: 'asc'});
-  }
-
-  onClick(event) {
-    let listItemElement = event.target.closest('.list-item[data-id]');
-    if (listItemElement === null) {return;}
-    let itemId = listItemElement.dataset.id;
-    let listActionElement = event.target.closest('.list-action-trigger[data-list-action]');
-    let listAction = listActionElement === null ? 'add' : listActionElement.dataset.listAction;
-    switch (listAction) {
-      case 'add': {
-        listActionElement.querySelector('i').textContent = 'done';
-        listActionElement.dataset.listAction = 'remove';
-        break;
-      }
-      case 'remove': {
-        listActionElement.querySelector('i').textContent = 'add';
-        listActionElement.dataset.listAction = 'add';
-        break;
-      }
-      default: {
-        break;
-      }
-    }
-  }
-
-  // onPatch(patch) {
-  //   let re = new RegExp(`^/users/${this.userId}/jobs/${this.jobId}/results/([A-Za-z0-9]*)`);
-  //   let filteredPatch = patch.filter(operation => re.test(operation.path));
-  //   for (let operation of filteredPatch) {
-  //     switch(operation.op) {
-  //       case 'add': {
-  //         let re = new RegExp(`^/users/${this.userId}/jobs/${this.jobId}/results/([A-Za-z0-9]*)$`);
-  //         if (re.test(operation.path)) {this.add(operation.value);}
-  //         break;
-  //       }
-  //       default: {
-  //         break;
-  //       }
-  //     }
-  //   }
-  // }
-};

app/templates/_base/scripts.html.j2

@@ -52,7 +52,6 @@
   'js/resource-lists/job-input-list.js',
   'js/resource-lists/job-list.js',
   'js/resource-lists/job-result-list.js',
-  'js/resource-lists/job-output-list.js',
   'js/resource-lists/public-corpus-list.js',
   'js/resource-lists/public-user-list.js',
   'js/resource-lists/spacy-nlp-pipeline-model-list.js',

app/templates/services/tesseract_ocr_pipeline.html.j2

@@ -37,15 +37,6 @@
 
     <div class="col s12">
       <h2>Submit a job</h2>
-      <div class="card">
-        <div class="card-content">
-          <p>Add an existing file from your workflow or add a new one below.</p>
-          <div class="job-output-list" data-user-id="{{ current_user.hashid}}" data-job-ids="{{ choosable_job_ids }}"></div>
-        </div>
-        <div class="card-action right-align">
-          <a class="waves-effect waves-light btn"><i class="material-icons right">send</i>Submit</a>
-        </div>
-      </div>
       <div class="card">
         <form class="create-job-form" enctype="multipart/form-data" method="POST">
           <div class="card-content">
@@ -60,8 +51,6 @@
               <div class="col s12 l5">
                 {{ wtf.render_field(form.pdf, accept='application/pdf', placeholder='Choose a PDF file') }}
               </div>
-            </div>
-            <div class="row">
               <div class="col s12 l4">
                 <div class="input-field">
                   <i class="material-icons prefix">language</i>

app/users/settings/forms.py

@@ -1,4 +1,3 @@
-from flask_login import current_user
 from flask_wtf import FlaskForm
 from flask_wtf.file import FileField, FileRequired
 from wtforms import (
@@ -17,7 +16,7 @@ from wtforms.validators import (
     Regexp
 )
 from app.models import User, UserSettingJobStatusMailNotificationLevel
-from app.wtforms.validators import FileSize
+from app.extensions.wtforms.validators import FileSize
 
 
 class UpdateAccountInformationForm(FlaskForm):

boot.sh

@@ -24,7 +24,7 @@ if [[ "${#}" == "0" ]]; then
             sleep 5
         done
     fi
-    python3 nopaque.py
+    python3 wsgi.py
 elif [[ "${1}" == "flask" ]]; then
     flask ${@:2}
 elif [[ "${1}" == "--help" || "${1}" == "-h" ]]; then

docker-compose.yml

@@ -1,5 +1,3 @@
-version: "3.5"
-
 # The docker-compose.yml file is not meant to be modified itself. 
 # Instead use the following files for configurations:
 # - .env: Environment variables for the docker-compose.yml file.

docker-compose/docker-compose.development.yml

@@ -1,5 +1,3 @@
-version: "3.5"
-
 services:
   nopaque:
     environment:
@@ -13,6 +11,6 @@ services:
       - "./config.py:/home/nopaque/config.py"
       - "./docker-entrypoint.sh:/usr/local/bin/docker-entrypoint.sh"
       - "./migrations:/home/nopaque/migrations"
-      - "./nopaque.py:/home/nopaque/nopaque.py"
       - "./requirements.txt:/home/nopaque/requirements.txt"
       - "./tests:/home/nopaque/tests"
+      - "./wsgi.py:/home/nopaque/wsgi.py"

docker-compose/docker-compose.scale.yml

@@ -1,5 +1,3 @@
-version: "3.5"
-
 services:
   nopaque:
     environment:

docker-compose/docker-compose.traefik.yml

@@ -1,5 +1,3 @@
-version: "3.5"
-
 networks:
   traefik:
     external: true

requirements.txt

@@ -15,7 +15,7 @@ Flask-Marshmallow==0.14.0
 Flask-Menu==0.7.2
 Flask-Migrate
 Flask-Paranoid
-Flask-SocketIO
+Flask-SocketIO==5.3.6
 Flask-SQLAlchemy==2.5.1
 Flask-WTF
 hiredis