diff --git a/app/main/views.py b/app/main/views.py
index c238288183a75c55ec31d6373b3fc3e51d233d60..9a573a9f427ce7b2f105c43b85362e3fc79d52c9 100644
--- a/app/main/views.py
+++ b/app/main/views.py
@@ -5,7 +5,7 @@ from flask_login import current_user, login_required
from . import main
from .forms import CreateCorpusForm, QueryForm
from .. import db
-from ..models import Corpus, CorpusFile, Job
+from ..models import Corpus, CorpusFile, Job, JobInput, JobResult
from werkzeug.utils import secure_filename
import os
import threading
@@ -20,47 +20,30 @@ def index():
@main.route('/corpora/<int:corpus_id>')
@login_required
def corpus(corpus_id):
- if (current_user.is_administrator()):
- corpus = Corpus.query.get_or_404(corpus_id)
- else:
- corpus = current_user.corpora.filter_by(id=corpus_id).first()
- if not corpus:
- print('Corpus not found.')
- abort(404)
-
- dir = os.path.join(current_app.config['OPAQUE_STORAGE_DIRECTORY'],
- str(corpus.user_id),
- 'corpora',
- str(corpus.id))
- files = {}
- for file in sorted(os.listdir(dir)):
- files[file] = {}
- files[file]['path'] = os.path.join(file)
-
+ corpus = Corpus.query.get_or_404(corpus_id)
+ if not (corpus.creator == current_user
+ or current_user.is_administrator()):
+ abort(403)
return render_template('main/corpora/corpus.html.j2',
corpus=corpus,
- files=files,
- title='Corpus: ' + corpus.title)
+ title='Corpus')
@main.route('/corpora/<int:corpus_id>/download')
@login_required
def corpus_download(corpus_id):
- file = request.args.get('file')
- if (current_user.is_administrator()):
- corpus = Corpus.query.get_or_404(corpus_id)
- else:
- corpus = current_user.corpora.filter_by(id=corpus_id).first()
- if not file or not corpus:
- print('File not found.')
+ corpus_file_id = request.args.get('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['OPAQUE_STORAGE_DIRECTORY'],
- str(corpus.user_id),
- 'corpora',
- str(corpus.id))
+ corpus_file.dir)
return send_from_directory(as_attachment=True,
directory=dir,
- filename=file)
+ filename=corpus_file.filename)
@main.route('/corpora/<int:corpus_id>/analysis', methods=['GET', 'POST'])
@@ -83,20 +66,16 @@ def corpus_analysis(corpus_id):
@login_required
def dashboard():
create_corpus_form = CreateCorpusForm()
-
if create_corpus_form.validate_on_submit():
- app = current_app._get_current_object()
corpus = Corpus(creator=current_user._get_current_object(),
description=create_corpus_form.description.data,
title=create_corpus_form.title.data)
db.session.add(corpus)
db.session.commit()
-
- dir = os.path.join(app.config['OPAQUE_STORAGE_DIRECTORY'],
+ dir = os.path.join(current_app.config['OPAQUE_STORAGE_DIRECTORY'],
str(corpus.user_id),
'corpora',
str(corpus.id))
-
try:
os.makedirs(dir)
except OSError:
@@ -115,7 +94,6 @@ def dashboard():
db.session.commit()
flash('Corpus created!')
return redirect(url_for('main.dashboard'))
-
return render_template('main/dashboard.html.j2',
create_corpus_form=create_corpus_form,
title='Dashboard')
@@ -124,58 +102,33 @@ def dashboard():
@main.route('/jobs/<int:job_id>')
@login_required
def job(job_id):
- if (current_user.is_administrator()):
- job = Job.query.get_or_404(job_id)
- else:
- job = current_user.jobs.filter_by(id=job_id).first()
- if not job:
- print('Job not found.')
- abort(404)
-
- dir = os.path.join(current_app.config['OPAQUE_STORAGE_DIRECTORY'],
- str(job.user_id),
- 'jobs',
- str(job.id))
- files = {}
- for file in sorted(os.listdir(dir)):
- if file == 'output':
- continue
- files[file] = {}
- files[file]['path'] = os.path.join(file)
- if job.status == 'complete':
- files[file]['results'] = {}
- results_dir = os.path.join(dir, 'output', file)
- for result in sorted(os.listdir(results_dir)):
- result_type = result.rsplit(".", 1)[1]
- files[file]['results'][result_type] = {}
- files[file]['results'][result_type]['path'] = os.path.join(
- 'output', files[file]['path'], result
- )
-
- return render_template('main/jobs/job.html.j2',
- files=files,
- job=job,
- title='Job')
+ job = Job.query.get_or_404(job_id)
+ if not (job.creator == current_user or current_user.is_administrator()):
+ abort(403)
+ return render_template('main/jobs/job.html.j2', job=job, title='Job')
@main.route('/jobs/<int:job_id>/download')
@login_required
def job_download(job_id):
- file = request.args.get('file')
- if (current_user.is_administrator()):
- job = Job.query.get_or_404(job_id)
+ ressource_id = request.args.get('ressource_id')
+ ressource_type = request.args.get('ressource_type')
+ if ressource_type == 'input':
+ ressource = JobInput.query.get_or_404(ressource_id)
+ elif ressource_type == 'result':
+ ressource = JobResult.query.get_or_404(ressource_id)
else:
- job = current_user.jobs.filter_by(id=job_id).first()
- if not file or not job:
- print('File not found.')
+ abort(400)
+ if not ressource.job_id == job_id:
abort(404)
+ if not (ressource.job.creator == current_user
+ or current_user.is_administrator()):
+ abort(403)
dir = os.path.join(current_app.config['OPAQUE_STORAGE_DIRECTORY'],
- str(job.user_id),
- 'jobs',
- str(job.id))
+ ressource.dir)
return send_from_directory(as_attachment=True,
directory=dir,
- filename=file)
+ filename=ressource.filename)
@main.route('/jobs/<int:job_id>/delete')
diff --git a/app/templates/main/corpora/corpus.html.j2 b/app/templates/main/corpora/corpus.html.j2
index 321f9c284e0739ceb0e9daa9b598d2d176733fa4..1e47854c755b12f595c316a421142a10a7bd8428 100644
--- a/app/templates/main/corpora/corpus.html.j2
+++ b/app/templates/main/corpora/corpus.html.j2
@@ -1,85 +1,9 @@
{% extends "limited_width.html.j2" %}
{% block page_content %}
-<script>
- var corpus_user_id = {{ corpus.user_id|tojson|safe }}
- socket.emit('inspect_user', {{ corpus_user_id }});
-</script>
-<script>
- var CORPUS_ID = {{ corpus.id|tojson|safe }}
- var foreignCorpusFlag;
- {% if current_user.id == corpus.user_id %}
- foreignCorpusFlag = false;
- {% else %}
- foreignCorpusFlag = true;
- {% endif %}
-
- class InformationUpdater {
- constructor(corpusId) {
- this.corpusId = corpusId;
- if (foreignCorpusFlag) {
- foreignCorpusSubscribers.push(this);
- } else {
- corporaSubscribers.push(this);
- }
- }
-
- _init() {
- var creationDateElement, descriptionElement, titleElement;
-
- if (foreignCorpusFlag) {
- this.corpus = foreignCorpora[this.corpusId];
- } else {
- this.corpus = corpora[this.corpusId];
- }
- creationDateElement = document.getElementById("creation-date");
- creationDateElement.value = (new Date(this.corpus.creation_date * 1000)).toLocaleString();
- descriptionElement = document.getElementById("description");
- descriptionElement.innerHTML = this.corpus.description;
- titleElement = document.getElementById("title");
- titleElement.innerHTML = this.corpus.title;
-
- M.updateTextFields();
- }
-
- _update(patch) {
- var newStatusColor, operation, pathArray, status, statusColor,
- updatedElement;
-
- for (operation of patch) {
- /* "/corpusId/valueName" -> ["corpusId", "valueName"] */
- pathArray = operation.path.split("/").slice(1);
- if (pathArray[0] != this.jobId) {continue;}
- switch(operation.op) {
- case "delete":
- location.reload();
- break;
- case "replace":
- switch(pathArray[1]) {
- case "description":
- updatedElement = document.getElementById("description");
- updatedElement.innerHTML = operation.value;
- break;
- case "title":
- updatedElement = document.getElementById("title");
- updatedElement.innerHTML = operation.value;
- break;
- default:
- break;
- }
- break;
- default:
- break;
- }
- }
- }
- }
- var informationUpdater = new InformationUpdater(CORPUS_ID);
-</script>
-
<div class="col s12 m4">
- <h3 id="title"></h3>
- <p id="description"></p>
+ <h3 id="title">{{ corpus.title }}</h3>
+ <p id="description">{{ corpus.description }}</p>
<h2>Actions:</h2>
<!-- Confirm deletion of job with modal dialogue
Modal Trigger-->
@@ -106,29 +30,33 @@
<div class="row">
<div class="col s12 m6">
<div class="input-field">
- <input disabled value="" id="creation-date" type="text" class="validate">
+ <input disabled value="{{ corpus.creation_date.strftime('%m/%d/%Y, %H:%M:%S %p') }}" id="creation-date" type="text" class="validate">
<label for="creation-date">Creation date</label>
</div>
</div>
</div>
<span class="card-title">Files</span>
- <table>
+ <table class="highlight responsive-table">
<thead>
<tr>
- <th style="width: 50%;">Inputs</th>
+ <th>Filename</th>
+ <th>Download</th>
</tr>
</thead>
<tbody>
- {% for file in files %}
+ {% for file in corpus.files %}
<tr>
- <td>
- <a href="{{ url_for('main.corpus_download', corpus_id=corpus.id, file=files[file]['path']) }}" class="waves-effect waves-light btn-small"><i class="material-icons left">file_download</i>{{ file }}</a>
+ <td id="file-{{ file.id }}-filename">{{ file.filename }}</td>
+ <td id="file-{{ file.id }}-download">
+ <a class="waves-effect waves-light btn-small" download href="{{ url_for('main.corpus_download', corpus_id=corpus.id, corpus_file_id=file.id) }}">
+ <i class="material-icons">file_download</i>
+ </a>
</td>
</tr>
{% endfor %}
</tbody>
</table>
+ </div>
</div>
</div>
-
{% endblock %}
diff --git a/app/templates/main/jobs/job.html.j2 b/app/templates/main/jobs/job.html.j2
index 1a43d9dbf5615f82f9ebf3db597d421d6035d6ca..3cdf3933816849ea118c7dd2d53dd6da93d73511 100644
--- a/app/templates/main/jobs/job.html.j2
+++ b/app/templates/main/jobs/job.html.j2
@@ -2,16 +2,16 @@
{% block page_content %}
<script>
- var job_user_id = {{ job.user_id|tojson|safe }}
+ var job_user_id = {{ job.user_id }}
socket.emit('inspect_user', job_user_id);
</script>
<script>
- var JOB_ID = {{ job.id|tojson|safe }}
+ var JOB_ID = {{ job.id }}
var foreignJobFlag;
{% if current_user.id == job.user_id %}
- foreignJobFlag = false;
+ foreignJobFlag = false;
{% else %}
- foreignJobFlag = true;
+ foreignJobFlag = true;
{% endif %}
class InformationUpdater {
@@ -25,111 +25,45 @@
}
_init() {
- var creationDateElement, descriptionElement, endDateElement,
- memMbElement, nCoresElement, serviceElement, serviceArgsElement,
- serviceVersionElement, statusColor, statusElement, titleElement;
-
if (foreignJobFlag) {
this.job = foreignJobs[this.jobId];
} else {
this.job = jobs[this.jobId];
}
- // Title
- this.setTitle(this.job.title);
- // Description
- this.setDescription(this.job.description);
// Status
this.setStatus(this.job.status);
- // Creation date
- this.setCreationDate(this.job.creation_date);
// End date
if (this.job.end_date) {this.setEndDate(this.job.end_date);}
- // Memory
- this.setMemMb(this.job.mem_mb);
- // CPU cores
- this.setNCores(this.job.n_cores);
- // Service
- this.setService(this.job.service);
- // Service arguments
- this.setServiceArgs(this.job.service_args);
- // Service version
- this.setServiceVersion(this.job.service_version);
-
- var filesElement, input, inputDownloadElement, inputElement,
- inputFilenameElement, inputResultsElement;
-
- filesElement = document.getElementById("files");
- for (input of this.job.inputs) {
- // Data row
- inputElement = document.createElement("tr");
- filesElement.append(inputElement);
- // Input filename
- inputFilenameElement = document.createElement("td");
- inputFilenameElement.id = `input-${input.id}-filename`;
- inputElement.append(inputFilenameElement);
- // Input download
- inputDownloadElement = document.createElement("td");
- inputDownloadElement.id = `input-${input.id}-download`;
- inputElement.append(inputDownloadElement);
- // Third column for input result file download buttons
- inputResultsElement = document.createElement("td");
- inputResultsElement.id = `input-${input.id}-results`;
- inputElement.append(inputResultsElement);
- this.setInputFilename(input);
- this.setInputDownload(input);
- this.setInputResults(input);
+ // Input results
+ for (let input of this.job.inputs) {
+ for (let result of input.results) {
+ this.setResult(result);
+ }
}
}
- setInputDownload(input) {
- var inputDownloadButtonElement, inputDownloadButtonIconElement,
- inputDownloadElement;
- inputDownloadElement = document.getElementById(`input-${input.id}-download`);
- inputDownloadButtonElement = document.createElement("a");
- inputDownloadButtonElement.classList.add("waves-effect", "waves-light", "btn-small");
- inputDownloadButtonElement.href = `${this.jobId}/download?file=${input.filename}`;
- inputDownloadButtonElement.setAttribute("download", "");
- inputDownloadButtonIconElement = document.createElement("i");
- inputDownloadButtonIconElement.classList.add("material-icons");
- inputDownloadButtonIconElement.innerText = "file_download";
- inputDownloadButtonElement.append(inputDownloadButtonIconElement);
- inputDownloadElement.append(inputDownloadButtonElement);
- }
-
- setInputFilename(input) {
- var inputFilenameElement;
- inputFilenameElement = document.getElementById(`input-${input.id}-filename`);
- inputFilenameElement.innerText = input.filename;
- }
-
_update(patch) {
- var input, operation, pathArray;
+ var pathArray;
- for (operation of patch) {
+ for (let operation of patch) {
/* "/jobId/valueName" -> ["jobId", "valueName"] */
pathArray = operation.path.split("/").slice(1);
if (pathArray[0] != this.jobId) {continue;}
switch(operation.op) {
case "add":
if (pathArray[1] === "inputs" && pathArray[3] === "results") {
- console.log(operation.value);
- this.setInputResult(operation.value);
+ this.setResult(operation.value);
}
break;
case "delete":
location.reload();
break;
case "replace":
- switch(pathArray[1]) {
- case "end_date":
- this.setEndDate(operation.value);
- break;
- case "status":
- this.setStatus(operation.value);
- break;
- default:
- break;
+ if (pathArray[1] === "end_date") {
+ this.setEndDate(operation.value);
+ } else if (pathArray[1] === "status") {
+ this.setStatus(operation.value);
}
break;
default:
@@ -138,109 +72,43 @@
}
}
- setTitle(title) {
- var titleElement;
- titleElement = document.getElementById("title");
- titleElement.innerText = title;
- }
-
- setDescription(description) {
- var descriptionElement;
- descriptionElement = document.getElementById("description");
- descriptionElement.innerText = description;
- }
-
- setStatus(status) {
- var statusColor, statusElement;
- statusElement = document.getElementById("status");
- for (statusColor of Object.values(JobList.STATUS_COLORS)) {
- statusElement.classList.remove(statusColor);
- }
- statusElement.classList.add(JobList.STATUS_COLORS[status] || JobList.STATUS_COLORS['default']);
- statusElement.innerText = status;
- }
-
- setCreationDate(timestamp) {
- var creationDateElement;
- creationDateElement = document.getElementById("creation-date");
- creationDateElement.value = new Date(timestamp * 1000).toLocaleString();
- M.updateTextFields();
- }
-
setEndDate(timestamp) {
- var endDateElement;
- endDateElement = document.getElementById("end-date");
- endDateElement.value = new Date(timestamp * 1000).toLocaleString();
- M.updateTextFields();
- }
-
- setMemMb(memMb) {
- var memMbElement;
- memMbElement = document.getElementById("mem-mb");
- memMbElement.value = memMb;
+ document.getElementById("end-date").value = new Date(timestamp * 1000).toLocaleString();
M.updateTextFields();
}
- setNCores(nCores) {
- var nCoresElement;
- nCoresElement = document.getElementById("n-cores");
- nCoresElement.value = nCores;
- M.updateTextFields();
- }
-
- setService(service) {
- var serviceElement;
- serviceElement = document.getElementById("service");
- serviceElement.value = service;
- M.updateTextFields();
- }
-
- setServiceArgs(serviceArgs) {
- var serviceArgsElement;
- serviceArgsElement = document.getElementById("service-args");
- serviceArgsElement.value = serviceArgs;
- M.updateTextFields();
- }
-
- setServiceVersion(serviceVersion) {
- var serviceVersionElement;
- serviceVersionElement = document.getElementById("service-version");
- serviceVersionElement.value = serviceVersion;
- M.updateTextFields();
- }
-
- setInputResults(input) {
- var result;
- for (result of input.results) {
- this.setInputResult(result);
- }
- }
-
- setInputResult(result) {
- var inputResultsElement, resultDownloadButtonElement,
+ setResult(result) {
+ var resultsElement, resultDownloadButtonElement,
resultDownloadButtonIconElement;
- inputResultsElement = document.getElementById(`input-${result.job_input_id}-results`);
+ resultsElement = document.getElementById(`input-${result.job_input_id}-results`);
resultDownloadButtonElement = document.createElement("a");
resultDownloadButtonElement.classList.add("waves-effect", "waves-light", "btn-small");
- var resultFile = `${result.dir}/${result.filename}`;
- resultFile = resultFile.substring(resultFile.indexOf("output/"));
- resultDownloadButtonElement.href = `${this.jobId}/download?file=${resultFile}`;
+ resultDownloadButtonElement.href = `/jobs/${this.jobId}/download?ressource_id=${result.id}&ressource_type=result`;
resultDownloadButtonElement.innerText = result.filename.split(".").reverse()[0];
resultDownloadButtonElement.setAttribute("download", "");
resultDownloadButtonIconElement = document.createElement("i");
resultDownloadButtonIconElement.classList.add("material-icons", "left");
resultDownloadButtonIconElement.innerText = "file_download";
resultDownloadButtonElement.prepend(resultDownloadButtonIconElement);
- inputResultsElement.append(resultDownloadButtonElement);
- inputResultsElement.append(" ");
+ resultsElement.append(resultDownloadButtonElement);
+ resultsElement.append(" ");
+ }
+
+ setStatus(status) {
+ var statusElement;
+ statusElement = document.getElementById("status");
+ statusElement.classList.remove(...Object.values(JobList.STATUS_COLORS));
+ statusElement.classList.add(JobList.STATUS_COLORS[status] || JobList.STATUS_COLORS['default']);
+ statusElement.innerText = status;
}
}
+
var informationUpdater = new InformationUpdater(JOB_ID);
</script>
<div class="col s12 m4">
- <h3 id="title"></h3>
- <p id="description"></p>
+ <h3 id="title">{{ job.title }}</h3>
+ <p id="description">{{ job.description }}</p>
<a class="waves-effect waves-light btn" id="status"></a>
<h2>Actions:</h2>
<!-- Confirm deletion of job with modal dialogue
@@ -269,7 +137,7 @@
<div class="row">
<div class="col s12 m6">
<div class="input-field">
- <input disabled value="" id="creation-date" type="text" class="validate">
+ <input disabled value="{{ job.creation_date.strftime('%m/%d/%Y, %H:%M:%S %p') }}" id="creation-date" type="text" class="validate">
<label for="creation-date">Creation date</label>
</div>
</div>
@@ -285,13 +153,13 @@
<div class="row">
<div class="col s12 m6">
<div class="input-field">
- <input disabled value="" id="mem-mb" type="text" class="validate">
+ <input disabled value="{{ job.mem_mb }}" id="mem-mb" type="text" class="validate">
<label for="mem-mb">Memory</label>
</div>
</div>
<div class="col s12 m6">
<div class="input-field">
- <input disabled value="" id="n-cores" type="text" class="validate">
+ <input disabled value="{{ job.n_cores }}" id="n-cores" type="text" class="validate">
<label for="n-cores">CPU cores</label>
</div>
</div>
@@ -301,19 +169,19 @@
<div class="row">
<div class="col s12 m4">
<div class="input-field">
- <input disabled value="" id="service" type="text" class="validate">
+ <input disabled value="{{ job.service }}" id="service" type="text" class="validate">
<label for="service">Service</label>
</div>
</div>
<div class="col s12 m4">
<div class="input-field">
- <input disabled value="" id="service-args" type="text" class="validate">
+ <input disabled value="{{ job.service_args|e }}" id="service-args" type="text" class="validate">
<label for="service-args">Service arguments</label>
</div>
</div>
<div class="col s12 m4">
<div class="input-field">
- <input disabled value="" id="service-version" type="text" class="validate">
+ <input disabled value="{{ job.service_version }}" id="service-version" type="text" class="validate">
<label for="service-version">Service version</label>
</div>
</div>
@@ -329,12 +197,24 @@
<table class="highlight responsive-table">
<thead>
<tr>
- <th>File</th>
- <th>Input</th>
+ <th>Filename</th>
+ <th>Download</th>
<th>Results</th>
</tr>
</thead>
- <tbody id="files"></tbody>
+ <tbody>
+ {% for input in job.inputs %}
+ <tr>
+ <td id="input-{{ input.id }}-filename">{{ input.filename }}</td>
+ <td id="input-{{ input.id }}-download">
+ <a class="waves-effect waves-light btn-small" download href="{{ url_for('main.job_download', job_id=job.id, ressource_id=input.id, ressource_type='input') }}">
+ <i class="material-icons">file_download</i>
+ </a>
+ </td>
+ <td id="input-{{ input.id }}-results"></td>
+ </tr>
+ {% endfor %}
+ </tbody>
</table>
</div>
</div>
diff --git a/docker-entrypoint.sh b/docker-entrypoint.sh
index af07577710e6c286f86e5d9b6b7b6a4ee7849143..85c9486d43bbef53474ff197d38223a67ceb38de 100755
--- a/docker-entrypoint.sh
+++ b/docker-entrypoint.sh
@@ -1,6 +1,10 @@
#!/bin/sh
-./wait-for-it/wait-for-it.sh db:5432 --strict --timeout=0
+echo "Waiting for db..."
+wait-for-it/wait-for-it.sh db:5432 --strict --timeout=0
+echo "Waiting for redis..."
+wait-for-it/wait-for-it.sh redis:6379 --strict --timeout=0
+
if [ $# -eq 0 ]
then
venv/bin/python -u opaque.py