views.py 25.5 KB
Newer Older
1
from dgenies import app, app_title, app_folder, config_reader, mailer, APP_DATA, MODE
2

Floreal Cabanettes's avatar
Floreal Cabanettes committed
3
import os
4
5
import time
import datetime
6
import shutil
7
import re
8
import threading
Floreal Cabanettes's avatar
Floreal Cabanettes committed
9
from flask import render_template, request, url_for, jsonify, Response, abort, send_file, Markup
10
from pathlib import Path
11
12
13
14
15
from dgenies.lib.paf import Paf
from dgenies.lib.job_manager import JobManager
from dgenies.lib.functions import Functions, ALLOWED_EXTENSIONS
from dgenies.lib.upload_file import UploadFile
from dgenies.lib.fasta import Fasta
Floreal Cabanettes's avatar
Floreal Cabanettes committed
16
17
from markdown import Markdown
from markdown.extensions.toc import TocExtension
18
19
20
if MODE == "webserver":
    from dgenies.database import Session, Gallery
    from peewee import DoesNotExist
21

22

Floreal Cabanettes's avatar
Floreal Cabanettes committed
23
24
25
26
@app.context_processor
def global_templates_variables():
    return {
        "title": app_title,
27
28
        "mode": MODE,
        "all_jobs": Functions.get_list_all_jobs(MODE)
Floreal Cabanettes's avatar
Floreal Cabanettes committed
29
30
31
    }


32
33
34
# Main
@app.route("/", methods=['GET'])
def main():
35
36
37
38
39
40
    if MODE == "webserver":
        pict = Gallery.select().order_by("id")
        if len(pict) > 0:
            pict = pict[0].picture
        else:
            pict = None
Floreal Cabanettes's avatar
Floreal Cabanettes committed
41
42
    else:
        pict = None
Floreal Cabanettes's avatar
Floreal Cabanettes committed
43
    return render_template("index.html", menu="index", pict=pict)
Floreal Cabanettes's avatar
Floreal Cabanettes committed
44
45
46
47


@app.route("/run", methods=['GET'])
def run():
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
    if MODE == "webserver":
        with Session.connect():
            s_id = Session.new()
    else:
        upload_folder = Functions.random_string(20)
        tmp_dir = config_reader.upload_folder
        upload_folder_path = os.path.join(tmp_dir, upload_folder)
        while os.path.exists(upload_folder_path):
            upload_folder = Functions.random_string(20)
            upload_folder_path = os.path.join(tmp_dir, upload_folder)
        s_id = upload_folder
    id_job = Functions.random_string(5) + "_" + datetime.datetime.fromtimestamp(time.time()).strftime('%Y%m%d%H%M%S')
    if "id_job" in request.args:
        id_job = request.args["id_job"]
    email = ""
    if "email" in request.args:
        email = request.args["email"]
Floreal Cabanettes's avatar
Floreal Cabanettes committed
65
    return render_template("run.html", id_job=id_job, email=email,
66
                           menu="run", allowed_ext=ALLOWED_EXTENSIONS, s_id=s_id,
Floreal Cabanettes's avatar
Floreal Cabanettes committed
67
                           max_upload_file_size=config_reader.max_upload_file_size)
68
69


70
71
@app.route("/run-test", methods=['GET'])
def run_test():
72
73
74
75
76
77
78
    if MODE == "webserver":
        print(config_reader.allowed_ip_tests)
        if request.remote_addr not in config_reader.allowed_ip_tests:
            return abort(404)
        with Session.connect():
            return Session.new()
    return abort(500)
79
80


81
82
83
# Launch analysis
@app.route("/launch_analysis", methods=['POST'])
def launch_analysis():
84
85
86
87
88
89
90
91
92
93
94
95
    if MODE == "webserver":
        try:
            with Session.connect():
                session = Session.get(s_id=request.form["s_id"])
        except DoesNotExist:
            return jsonify({"success": False, "errors": ["Session has expired. Please refresh the page and try again"]})
        upload_folder = session.upload_folder
        # Delete session:
        session.delete_instance()
    else:
        upload_folder = request.form["s_id"]

96
97
    id_job = request.form["id_job"]
    email = request.form["email"]
98
99
100
101
    file_query = request.form["query"]
    file_query_type = request.form["query_type"]
    file_target = request.form["target"]
    file_target_type = request.form["target_type"]
102
103
104

    # Check form:
    form_pass = True
105
    errors = []
106
    if id_job == "":
107
        errors.append("Id of job not given")
108
109
        form_pass = False

110
111
112
113
    if MODE == "webserver":
        if email == "":
            errors.append("Email not given")
            form_pass = False
Floreal Cabanettes's avatar
Floreal Cabanettes committed
114
        elif not re.match(r"^[\w.\-]+@[\w\-.]{2,}\.[a-z]{2,4}$", email):
115
116
            errors.append("Email is invalid")
            form_pass = False
117
118
    if file_target == "":
        errors.append("No target fasta selected")
119
120
121
122
        form_pass = False

    # Form pass
    if form_pass:
123
        # Get final job id:
124
        id_job = re.sub('[^A-Za-z0-9_\-]+', '', id_job.replace(" ", "_"))
125
        id_job_orig = id_job
126
        i = 2
127
        while os.path.exists(os.path.join(APP_DATA, id_job)):
128
129
            id_job = id_job_orig + ("_%d" % i)
            i += 1
130

131
        folder_files = os.path.join(APP_DATA, id_job)
132
133
134
        os.makedirs(folder_files)

        # Save files:
135
136
137
        query = None
        if file_query != "":
            query_name = os.path.splitext(file_query.replace(".gz", ""))[0] if file_query_type == "local" else None
138
            query_path = os.path.join(app.config["UPLOAD_FOLDER"], upload_folder, file_query) \
139
                if file_query_type == "local" else file_query
140
141
142
            if file_query_type == "local" and not os.path.exists(query_path):
                errors.append("Query file not correct!")
                form_pass = False
143
144
            query = Fasta(name=query_name, path=query_path, type_f=file_query_type)
        target_name = os.path.splitext(file_target.replace(".gz", ""))[0] if file_target_type == "local" else None
145
        target_path = os.path.join(app.config["UPLOAD_FOLDER"], upload_folder, file_target) \
146
            if file_target_type == "local" else file_target
147
148
149
        if file_target_type == "local" and not os.path.exists(target_path):
            errors.append("Target file not correct!")
            form_pass = False
150
        target = Fasta(name=target_name, path=target_path, type_f=file_target_type)
151

152
153
154
155
156
157
158
159
160
        if form_pass:
            # Launch job:
            job = JobManager(id_job, email, query, target, mailer)
            if MODE == "webserver":
                job.launch()
            else:
                job.launch_standalone()
            return jsonify({"success": True, "redirect": url_for(".status", id_job=id_job)})
    if not form_pass:
161
        return jsonify({"success": False, "errors": errors})
162
163
164
165
166
167


# Status of a job
@app.route('/status/<id_job>', methods=['GET'])
def status(id_job):
    job = JobManager(id_job)
168
169
170
171
172
173
174
175
176
177
178
179
    j_status = job.status()
    mem_peak = j_status["mem_peak"] if "mem_peak" in j_status else None
    if mem_peak is not None:
        mem_peak = "%.1f G" % (mem_peak / 1024.0 / 1024.0)
    time_e = j_status["time_elapsed"] if "time_elapsed" in j_status else None
    if time_e is not None:
        if time_e < 60:
            time_e = "%d secs" % time_e
        else:
            minutes = time_e // 60
            seconds = time_e - minutes * 60
            time_e = "%d min %d secs" % (minutes, seconds)
180
181
182
183
184
185
186
187
188
    format = request.args.get("format")
    if format is not None and format == "json":
        return jsonify({
            "status": j_status["status"],
            "error": j_status["error"].replace("#ID#", ""),
            "id_job": id_job,
            "mem_peak": mem_peak,
            "time_elapsed": time_e
        })
Floreal Cabanettes's avatar
Floreal Cabanettes committed
189
    return render_template("status.html", status=j_status["status"],
190
191
                           error=j_status["error"].replace("#ID#", ""),
                           id_job=id_job, menu="results", mem_peak=mem_peak,
192
                           time_elapsed=time_e,
Floreal Cabanettes's avatar
Floreal Cabanettes committed
193
                           query_filtered=job.is_query_filtered(), target_filtered=job.is_target_filtered())
194
195


Floreal Cabanettes's avatar
Floreal Cabanettes committed
196
# Results path
197
@app.route("/result/<id_res>", methods=['GET'])
198
def result(id_res):
Floreal Cabanettes's avatar
Floreal Cabanettes committed
199
    return render_template("result.html", id=id_res, menu="result", current_result=id_res,
200
                           is_gallery=Functions.is_in_gallery(id_res, MODE))
201
202


203
204
@app.route("/gallery", methods=['GET'])
def gallery():
205
    if MODE == "webserver":
Floreal Cabanettes's avatar
Floreal Cabanettes committed
206
        return render_template("gallery.html", items=Functions.get_gallery_items(), menu="gallery")
207
    return abort(404)
208
209
210
211


@app.route("/gallery/<filename>", methods=['GET'])
def gallery_file(filename):
212
213
214
215
216
217
    if MODE == "webserver":
        try:
            return send_file(os.path.join(config_reader.app_data, "gallery", filename))
        except FileNotFoundError:
            abort(404)
    return abort(404)
218
219


220
def get_file(file, gzip=False):  # pragma: no cover
Floreal Cabanettes's avatar
Floreal Cabanettes committed
221
222
223
224
225
226
    try:
        # Figure out how flask returns static files
        # Tried:
        # - render_template
        # - send_file
        # This should not be so non-obvious
227
        return open(file, "rb" if gzip else "r").read()
228
229
    except FileNotFoundError:
        abort(404)
Floreal Cabanettes's avatar
Floreal Cabanettes committed
230
    except IOError as exc:
231
        print(exc.__traceback__)
232
        abort(500)
Floreal Cabanettes's avatar
Floreal Cabanettes committed
233
234


Floreal Cabanettes's avatar
Floreal Cabanettes committed
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
@app.route("/documentation/run", methods=['GET'])
def documentation_run():
    with open(os.path.join(app_folder, "doc_run.md" if MODE == "webserver" else "doc_run_standalone.md"), "r",
              encoding='utf-8') as install_instr:
        content = install_instr.read()
    md = Markdown(extensions=[TocExtension(baselevel=1)])
    max_upload_file_size = config_reader.max_upload_file_size
    if max_upload_file_size == -1:
        max_upload_file_size = "no limit"
    else:
        max_upload_file_size = Functions.get_readable_size(max_upload_file_size, 0)
    max_upload_size = config_reader.max_upload_size
    if max_upload_size == -1:
        max_upload_size = "no limit"
    else:
        max_upload_size = Functions.get_readable_size(max_upload_size, 0)
    max_upload_size_ava = config_reader.max_upload_size_ava
    if max_upload_size_ava == -1:
        max_upload_size_ava = "no limit"
    else:
        max_upload_size_ava = Functions.get_readable_size(max_upload_size_ava, 0)
    content = Markup(md.convert(content)).replace("###size###", max_upload_file_size)\
                                         .replace("###size_unc###", max_upload_size)\
                                         .replace("###size_ava###", max_upload_size_ava)
    toc = Markup(md.toc)
Floreal Cabanettes's avatar
Floreal Cabanettes committed
260
    return render_template("documentation.html", menu="documentation", content=content, toc=toc)
Floreal Cabanettes's avatar
Floreal Cabanettes committed
261
262


Floreal Cabanettes's avatar
Floreal Cabanettes committed
263
264
@app.route("/install", methods=['GET'])
def install():
265
    with open(os.path.join(app_folder, "INSTALL.md"), "r", encoding='utf-8') as install_instr:
Floreal Cabanettes's avatar
Floreal Cabanettes committed
266
267
268
269
        content = install_instr.read()
    md = Markdown(extensions=[TocExtension(baselevel=1)])
    content = Markup(md.convert(content))
    toc = Markup(md.toc)
Floreal Cabanettes's avatar
Floreal Cabanettes committed
270
    return render_template("documentation.html", menu="install", content=content, toc=toc)
Floreal Cabanettes's avatar
Floreal Cabanettes committed
271
272


Floreal Cabanettes's avatar
Floreal Cabanettes committed
273
274
275
276
277
278
279
280
281
282
283
@app.route("/paf/<id_res>", methods=['GET'])
def download_paf(id_res):
    map_file = os.path.join(APP_DATA, id_res, "map.paf.sorted")
    if not os.path.exists(map_file):
        map_file = os.path.join(APP_DATA, id_res, "map.paf")
    if not os.path.exists(map_file):
        abort(404)
    content = get_file(map_file)
    return Response(content, mimetype="text/plain")


Floreal Cabanettes's avatar
Floreal Cabanettes committed
284
# Get graph (ajax request)
285
286
287
@app.route('/get_graph', methods=['POST'])
def get_graph():
    id_f = request.form["id"]
288
289
290
    paf = os.path.join(APP_DATA, id_f, "map.paf")
    idx1 = os.path.join(APP_DATA, id_f, "query.idx")
    idx2 = os.path.join(APP_DATA, id_f, "target.idx")
291

292
    paf = Paf(paf, idx1, idx2)
293

294
295
    if paf.parsed:
        res = paf.get_d3js_data()
296
        res["success"] = True
297
298
299
300
301
302
        return jsonify(res)
    return jsonify({"success": False, "message": paf.error})


@app.route('/sort/<id_res>', methods=['POST'])
def sort_graph(id_res):
303
    if not os.path.exists(os.path.join(APP_DATA, id_res, ".all-vs-all")):
304
305
306
        paf_file = os.path.join(APP_DATA, id_res, "map.paf")
        idx1 = os.path.join(APP_DATA, id_res, "query.idx")
        idx2 = os.path.join(APP_DATA, id_res, "target.idx")
307
        paf = Paf(paf_file, idx1, idx2, False)
308
309
310
311
312
313
314
        paf.sort()
        if paf.parsed:
            res = paf.get_d3js_data()
            res["success"] = True
            return jsonify(res)
        return jsonify({"success": False, "message": paf.error})
    return jsonify({"success": False, "message": "Sort is not available for All-vs-All mode"})
Floreal Cabanettes's avatar
Floreal Cabanettes committed
315

Floréal Cabanettes's avatar
Floréal Cabanettes committed
316

317
318
319
320
@app.route('/reverse-contig/<id_res>', methods=['POST'])
def reverse_contig(id_res):
    contig_name = request.form["contig"]
    if not os.path.exists(os.path.join(APP_DATA, id_res, ".all-vs-all")):
321
322
323
        paf_file = os.path.join(APP_DATA, id_res, "map.paf")
        idx1 = os.path.join(APP_DATA, id_res, "query.idx")
        idx2 = os.path.join(APP_DATA, id_res, "target.idx")
324
325
326
327
328
329
330
331
332
333
        paf = Paf(paf_file, idx1, idx2, False)
        paf.reverse_contig(contig_name)
        if paf.parsed:
            res = paf.get_d3js_data()
            res["success"] = True
            return jsonify(res)
        return jsonify({"success": False, "message": paf.error})
    return jsonify({"success": False, "message": "Sort is not available for All-vs-All mode"})


334
335
@app.route('/freenoise/<id_res>', methods=['POST'])
def free_noise(id_res):
336
337
338
    paf_file = os.path.join(APP_DATA, id_res, "map.paf")
    idx1 = os.path.join(APP_DATA, id_res, "query.idx")
    idx2 = os.path.join(APP_DATA, id_res, "target.idx")
339
340
341
342
343
344
345
346
347
    paf = Paf(paf_file, idx1, idx2, False)
    paf.parse_paf(noise=request.form["noise"] == "1")
    if paf.parsed:
        res = paf.get_d3js_data()
        res["success"] = True
        return jsonify(res)
    return jsonify({"success": False, "message": paf.error})


348
349
@app.route('/get-fasta-query/<id_res>', methods=['POST'])
def build_fasta(id_res):
350
    res_dir = os.path.join(APP_DATA, id_res)
351
352
    lock_query = os.path.join(res_dir, ".query-fasta-build")
    is_sorted = os.path.exists(os.path.join(res_dir, ".sorted"))
353
    compressed = request.form["gzip"].lower() == "true"
354
355
356
357
358
    query_fasta = Functions.get_fasta_file(res_dir, "query", is_sorted)
    if query_fasta is not None:
        if is_sorted and not query_fasta.endswith(".sorted"):
            # Do the sort
            Path(lock_query).touch()
359
            if not compressed or MODE == "standalone":  # If compressed, it will took a long time, so not wait
360
                Path(lock_query + ".pending").touch()
361
362
363
364
365
            thread = threading.Timer(1, Functions.sort_fasta, kwargs={
                "job_name": id_res,
                "fasta_file": query_fasta,
                "index_file": os.path.join(res_dir, "query.idx.sorted"),
                "lock_file": lock_query,
366
                "compress": compressed,
367
368
369
                "mailer": mailer
            })
            thread.start()
370
            if not compressed or MODE == "standalone":
371
372
                i = 0
                time.sleep(5)
373
                while os.path.exists(lock_query) and (i < 2 or MODE == "standalone"):
374
375
                    i += 1
                    time.sleep(5)
Floreal Cabanettes's avatar
Floreal Cabanettes committed
376
                os.remove(lock_query + ".pending")
377
378
379
                if os.path.exists(lock_query):
                    return jsonify({"success": True, "status": 1, "status_message": "In progress"})
                return jsonify({"success": True, "status": 2, "status_message": "Done",
380
                                "gzip": compressed})
381
382
            else:
                return jsonify({"success": True, "status": 1, "status_message": "In progress"})
383
384
385
386
387
        elif is_sorted and os.path.exists(lock_query):
            # Sort is already in progress
            return jsonify({"success": True, "status": 1, "status_message": "In progress"})
        else:
            # No sort to do or sort done
388
389
390
391
392
393
394
            if compressed and not query_fasta.endswith(".gz.fasta"):
                # If compressed file is asked, we must compress it now if not done before...
                Path(lock_query).touch()
                thread = threading.Timer(1, Functions.compress_and_send_mail, kwargs={
                    "job_name": id_res,
                    "fasta_file": query_fasta,
                    "index_file": os.path.join(res_dir, "query.idx.sorted"),
395
                    "lock_file": lock_query,
396
397
398
399
400
                    "compressed": compressed,
                    "mailer": mailer
                })
                thread.start()
                return jsonify({"success": True, "status": 1, "status_message": "In progress"})
401
402
403
404
405
406
407
            return jsonify({"success": True, "status": 2, "status_message": "Done",
                            "gzip": query_fasta.endswith(".gz") or query_fasta.endswith(".gz.sorted")})
    else:
        return jsonify({"success": False,
                        "message": "Unable to get fasta file for query. Please contact us to report the bug"})


408
def build_query_as_reference(id_res):
409
410
411
412
413
    paf_file = os.path.join(APP_DATA, id_res, "map.paf")
    idx1 = os.path.join(APP_DATA, id_res, "query.idx")
    idx2 = os.path.join(APP_DATA, id_res, "target.idx")
    paf = Paf(paf_file, idx1, idx2, False, mailer=mailer, id_job=id_res)
    paf.parse_paf(False, True)
414
415
416
417
418
419
420
421
422
423
    if MODE == "webserver":
        thread = threading.Timer(0, paf.build_query_chr_as_reference)
        thread.start()
        return True
    return paf.build_query_chr_as_reference()


@app.route('/build-query-as-reference/<id_res>', methods=['POST'])
def post_query_as_reference(id_res):
    build_query_as_reference(id_res)
424
425
426
    return jsonify({"success": True})


427
428
429
430
431
432
433
@app.route('/get-query-as-reference/<id_res>', methods=['GET'])
def get_query_as_reference(id_res):
    if MODE != "standalone":
        return abort(404)
    return send_file(build_query_as_reference(id_res))


434
435
436
437
438
439
440
441
@app.route('/download/<id_res>/<filename>')
def download_file(id_res, filename):
    file_dl = os.path.join(APP_DATA, id_res, filename)
    if os.path.isfile(file_dl):
        return send_file(file_dl)
    return abort(404)


442
443
444
@app.route('/fasta-query/<id_res>', defaults={'filename': ""}, methods=['GET'])
@app.route('/fasta-query/<id_res>/<filename>', methods=['GET'])  # Use fake URL in mail to set download file name
def dl_fasta(id_res, filename):
445
    res_dir = os.path.join(APP_DATA, id_res)
446
447
448
449
450
451
452
453
454
455
456
457
458
    lock_query = os.path.join(res_dir, ".query-fasta-build")
    is_sorted = os.path.exists(os.path.join(res_dir, ".sorted"))
    if not os.path.exists(lock_query) or not is_sorted:
        query_fasta = Functions.get_fasta_file(res_dir, "query", is_sorted)
        if query_fasta is not None:
            if query_fasta.endswith(".gz") or query_fasta.endswith(".gz.sorted"):
                content = get_file(query_fasta, True)
                return Response(content, mimetype="application/gzip")
            content = get_file(query_fasta)
            return Response(content, mimetype="text/plain")
    abort(404)


459
460
@app.route('/qt-assoc/<id_res>', methods=['GET'])
def qt_assoc(id_res):
461
    res_dir = os.path.join(APP_DATA, id_res)
462
    if os.path.exists(res_dir) and os.path.isdir(res_dir):
463
464
465
        paf_file = os.path.join(APP_DATA, id_res, "map.paf")
        idx1 = os.path.join(APP_DATA, id_res, "query.idx")
        idx2 = os.path.join(APP_DATA, id_res, "target.idx")
466
467
468
469
470
471
472
473
474
475
476
477
        try:
            paf = Paf(paf_file, idx1, idx2, False)
            paf.parse_paf(False)
        except FileNotFoundError:
            print("Unable to load data!")
            abort(404)
            return False
        csv_content = paf.build_query_on_target_association_file()
        return Response(csv_content, mimetype="text/plain")
    abort(404)


478
479
480
481
482
483
@app.route('/no-assoc/<id_res>', methods=['POST'])
def no_assoc(id_res):
    """
    Get contigs that match with None target
    :param id_res: id of the result
    """
484
    res_dir = os.path.join(APP_DATA, id_res)
485
    if os.path.exists(res_dir) and os.path.isdir(res_dir):
486
487
488
        paf_file = os.path.join(APP_DATA, id_res, "map.paf")
        idx1 = os.path.join(APP_DATA, id_res, "query.idx")
        idx2 = os.path.join(APP_DATA, id_res, "target.idx")
489
490
491
492
493
494
        try:
            paf = Paf(paf_file, idx1, idx2, False)
        except FileNotFoundError:
            print("Unable to load data!")
            abort(404)
            return False
495
        file_content = paf.build_list_no_assoc(request.form["to"])
496
497
498
499
500
501
502
503
        empty = file_content == "\n"
        return jsonify({
            "file_content": file_content,
            "empty": empty
        })
    abort(404)


Floreal Cabanettes's avatar
Floreal Cabanettes committed
504
505
@app.route('/summary/<id_res>', methods=['POST'])
def summary(id_res):
506
507
508
509
510
511
512
513
514
515
    paf_file = os.path.join(APP_DATA, id_res, "map.paf")
    idx1 = os.path.join(APP_DATA, id_res, "query.idx")
    idx2 = os.path.join(APP_DATA, id_res, "target.idx")
    try:
        paf = Paf(paf_file, idx1, idx2, False)
    except FileNotFoundError:
        return jsonify({
            "success": False,
            "message": "Unable to load data!"
        })
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
    percents = None
    s_status = "waiting"  # Accepted values: waiting, done, fail
    status_file = os.path.join(APP_DATA, id_res, ".summarize")
    fail_file = status_file + ".fail"
    if not os.path.exists(status_file):  # The job is finished or not started
        if not os.path.exists(fail_file):  # The job has not started yet or has successfully ended
            percents = paf.get_summary_stats()
            if percents is None:  # The job has not started yet
                Path(status_file).touch()
                thread = threading.Timer(0, paf.build_summary_stats, kwargs={"status_file": status_file})
                thread.start()
            else:  # The job has successfully ended
                s_status = "done"
        else:  # The job has failed
            s_status = "fail"

    if s_status == "waiting":  # The job is running
        # Check if the job end in the next 30 seconds
        nb_iter = 0
        while os.path.exists(status_file) and not os.path.exists(fail_file) and nb_iter < 10:
            time.sleep(3)
            nb_iter += 1
        if not os.path.exists(status_file):  # The job has ended
            percents = paf.get_summary_stats()
            if percents is None:  # The job has failed
                s_status = "fail"
            else:  # The job has successfully ended
                s_status = "done"

    if s_status == "fail":
546
547
548
549
550
551
        return jsonify({
            "success": False,
            "message": "Build of summary failed. Please contact us to report the bug"
        })
    return jsonify({
        "success": True,
552
553
        "percents": percents,
        "status": s_status
554
    })
Floreal Cabanettes's avatar
Floreal Cabanettes committed
555
556


557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
def get_filter_out(id_res, type_f):
    filter_file = os.path.join(APP_DATA, id_res, ".filter-" + type_f)
    return Response(get_file(filter_file), mimetype="text/plain")


@app.route('/filter-out/<id_res>/query')
def get_filter_out_query(id_res):
    return get_filter_out(id_res=id_res, type_f="query")


@app.route('/filter-out/<id_res>/target')
def get_filter_out_target(id_res):
    return get_filter_out(id_res=id_res, type_f="target")


572
573
@app.route("/ask-upload", methods=['POST'])
def ask_upload():
574
575
576
577
578
    if MODE == "standalone":
        return jsonify({
            "success": True,
            "allowed": True
        })
579
580
    try:
        s_id = request.form['s_id']
Floreal Cabanettes's avatar
Floreal Cabanettes committed
581
582
583
        with Session.connect():
            session = Session.get(s_id=s_id)
            allowed = session.ask_for_upload(True)
584
585
        return jsonify({
            "success": True,
Floreal Cabanettes's avatar
Floreal Cabanettes committed
586
            "allowed": allowed
587
588
589
        })
    except DoesNotExist:
        return jsonify({"success": False, "message": "Session not initialized. Please refresh the page."})
590
591


592
593
@app.route("/ping-upload", methods=['POST'])
def ping_upload():
594
595
596
597
598
    if MODE == "webserver":
        s_id = request.form['s_id']
        with Session.connect():
            session = Session.get(s_id=s_id)
            session.ping()
599
    return "OK"
600
601


602
603
604
605
@app.route("/upload", methods=['POST'])
def upload():
    try:
        s_id = request.form['s_id']
606
607
608
609
610
611
        if MODE == "webserver":
            try:
                with Session.connect():
                    session = Session.get(s_id=s_id)
                    if session.ask_for_upload(False):
                        folder = session.upload_folder
Floreal Cabanettes's avatar
Floreal Cabanettes committed
612
                    else:
613
614
615
616
617
618
                        return jsonify({"files": [], "success": "ERR", "message": "Not allowed to upload!"})
            except DoesNotExist:
                return jsonify(
                    {"files": [], "success": "ERR", "message": "Session not initialized. Please refresh the page."})
        else:
            folder = s_id
Floreal Cabanettes's avatar
Floreal Cabanettes committed
619

620
        files = request.files[list(request.files.keys())[0]]
Floreal Cabanettes's avatar
Floreal Cabanettes committed
621

622
623
624
625
626
627
628
        if files:
            filename = files.filename
            folder_files = os.path.join(app.config["UPLOAD_FOLDER"], folder)
            if not os.path.exists(folder_files):
                os.makedirs(folder_files)
            filename = Functions.get_valid_uploaded_filename(filename, folder_files)
            mime_type = files.content_type
Floreal Cabanettes's avatar
Floreal Cabanettes committed
629

630
631
632
            if not Functions.allowed_file(files.filename):
                result = UploadFile(name=filename, type_f=mime_type, size=0, not_allowed_msg="File type not allowed")
                shutil.rmtree(folder_files)
Floreal Cabanettes's avatar
Floreal Cabanettes committed
633

634
635
636
637
638
639
640
641
642
643
644
645
646
647
            else:
                # save file to disk
                uploaded_file_path = os.path.join(folder_files, filename)
                files.save(uploaded_file_path)

                # get file size after saving
                size = os.path.getsize(uploaded_file_path)

                # return json for js call back
                result = UploadFile(name=filename, type_f=mime_type, size=size)

            return jsonify({"files": [result.get_file()], "success": "OK"})

        return jsonify({"files": [], "success": "404", "message": "No file provided"})
648
649
650
    except:  # Except all possible exceptions to prevent crashes
        return jsonify({"files": [], "success": "ERR", "message": "An unexpected error has occurred on upload. "
                                                                  "Please contact the support."})
651
652


653
654
655
656
657
658
@app.route("/send-mail/<id_res>", methods=['POST'])
def send_mail(id_res):
    allowed = False
    key_file = None
    if "key" in request.form:
        key = request.form["key"]
659
        res_dir = os.path.join(APP_DATA, id_res)
660
661
662
663
664
665
666
667
668
669
670
671
        key_file = os.path.join(res_dir, ".key")
        if os.path.exists(key_file):
            with open(key_file) as k_f:
                true_key = k_f.readline().strip("\n")
                allowed = key == true_key
    if allowed:
        os.remove(key_file)
        job_mng = JobManager(id_job=id_res, mailer=mailer)
        job_mng.set_inputs_from_res_dir()
        job_mng.send_mail()
        return "OK"
    else:
672
        abort(403)
673
674
675
676
677
678
679
680
681
682


@app.route("/delete/<id_res>", methods=['POST'])
def delete_job(id_res):
    job = JobManager(id_job=id_res)
    success, error = job.delete()
    return jsonify({
        "success": success,
        "error": error
    })