aboutsummaryrefslogtreecommitdiff
path: root/bh20simplewebuploader/main.py
blob: 9132453d08f300af6d9bcf2a6bc6aa7efa18af97 (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
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
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
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
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
import collections
import itertools
import tempfile
import shutil
import subprocess
import logging
import os
import sys
import re
import string
import yaml
import pkg_resources
from flask import Flask, request, redirect, send_file, send_from_directory, render_template, jsonify
import os.path
import requests
import io
import arvados
from markupsafe import Markup

ARVADOS_API = 'lugli.arvadosapi.com'
ANONYMOUS_TOKEN = '5o42qdxpxp5cj15jqjf7vnxx5xduhm4ret703suuoa3ivfglfh'
UPLOADER_PROJECT = 'lugli-j7d0g-n5clictpuvwk8aa'
VALIDATED_PROJECT = 'lugli-j7d0g-5ct8p1i1wrgyjvp'

logging.basicConfig(level=logging.DEBUG)
log = logging.getLogger(__name__ )
log.debug("Entering web uploader")

if not os.path.isfile('bh20sequploader/main.py'):
    print("WARNING: run FLASK from the root of the source repository!", file=sys.stderr)

app = Flask(__name__, static_url_path='/static', static_folder='static')

# Limit file upload size. We shouldn't be working with anything over 1 MB; these are small genomes.
# We will enforce the limit ourselves and set a higher safety limit here.
app.config['MAX_CONTENT_LENGTH'] = 50 * 1024 * 1024

# When a file is too big we get a 413.
@app.errorhandler(413)
def handle_large_file(e):
    return (render_template('error.html',
        error_message="One of your files is too large. The maximum file size is 50 megabytes."), 413)


def type_to_heading(type_name):
    """
    Turn a type name like "sampleSchema" from the metadata schema into a human-readable heading.
    """

    # Remove camel case
    decamel = re.sub('([A-Z])', r' \1', type_name)
    # Split
    parts = decamel.split()
    # Capitalize words and remove unwanted components
    filtered = [part.capitalize() for part in parts if (part.lower() != 'schema' and part != '')]
    # Reassemble
    return ' '.join(filtered)

def name_to_label(field_name):
    """
    Turn a filed name like "host_health_status" from the metadata schema into a human-readable label.
    """

    # May end in a number, which should be set off by a space
    set_off_number = re.sub('([0-9]+)$', r' \1', field_name)

    return string.capwords(set_off_number.replace('_', ' '))

def is_iri(string):
    """
    Return True if the given string looks like an IRI, and False otherwise.

    Used for finding type IRIs in the schema.

    Right now only supports http(s) URLs because that's all we have in our schema.
    """

    return string.startswith('http')

def generate_form(schema, options):
    """
    Linearize the schema into a list of dicts.

    Each dict either has a 'heading' (in which case we put a heading for a
    form section in the template) or an 'id', 'label', 'type', and 'required'
    (in which case we make a form field in the template).

    Non-heading dicts with type 'select' will have an 'options' field, with a
    list of (name, value) tuples, and represent a form dropdown element.

    Non-heading dicts with type 'number' may have a 'step', which, if <1 or
    'any', allows the number to be a float.

    Non-heading dicts may have a human-readable 'docstring' field describing
    them.

    Takes the deserialized metadata schema YAML, and also a deserialized YAML
    of option values. The option values are keyed on (unscoped) field name in
    the schema, and each is a dict of human readable option -> corresponding
    IRI.
    """

    # Get the list of form components, one of which is the root
    components = schema.get('$graph', [])

    # Find the root
    root_name = None
    # And also index components by type name
    by_name = {}
    for component in components:
        # Get the name of each
        component_name = component.get('name', None)
        if isinstance(component_name, str):
            # And remember how to map back form it
            by_name[component_name] = component
        if component.get('documentRoot', False):
            # Find whichever one is the root
            root_name = component_name


    def walk_fields(type_name, parent_keys=['metadata'], subtree_optional=False):
        """
        Do a traversal of the component tree.
        Yield a bunch of form item dicts, in order.
        Form IDs are .-separated keypaths for where they are in the structure.
        parent_keys is the path of field names to where we are in the root record's document tree.
        """

        if len(parent_keys) > 1:
            # First make a heading, if we aren't the very root of the form
            yield {'heading': type_to_heading(type_name)}

        for field_name, field_type in by_name.get(type_name, {}).get('fields', {}).items():
            # For each field

            ref_iri = None
            docstring = None
            if not isinstance(field_type, str):
                # If the type isn't a string

                # It may have documentation
                docstring = field_type.get('doc', None)

                # See if it has a more info/what goes here URL
                predicate = field_type.get('jsonldPredicate', {})
                # Predicate may be a URL, a dict with a URL in _id, maybe a
                # dict with a URL in _type, or a dict with _id and _type but no
                # URLs anywhere. Some of these may not technically be allowed
                # by the format, but if they occur, we might as well try to
                # handle them.
                if isinstance(predicate, str):
                    if is_iri(predicate):
                        ref_iri = predicate
                else:
                    # Assume it's a dict. Look at the fields we know about.
                    for field in ['_id', 'type']:
                        field_value = predicate.get(field, None)
                        if isinstance(field_value, str) and is_iri(field_value) and ref_iri is None:
                            # Take the first URL-looking thing we find
                            ref_iri = field_value
                            break


                # Now overwrite the field type with the actual type string
                field_type = field_type.get('type', '')

            # Decide if the field is optional (type ends in ?)
            optional = False
            if field_type.endswith('?'):
                # It's optional
                optional = True
                # Drop the ?
                field_type = field_type[:-1]

            # Decide if the field is a list (type ends in [])
            is_list = False
            if field_type.endswith('[]'):
                # It's a list
                is_list = True
                # Reduce to the normal type
                field_type = field_type[:-2]

            if field_type in by_name:
                # This is a subrecord. We need to recurse
                for item in walk_fields(field_type, parent_keys + [field_name], subtree_optional or optional):
                    yield item
            else:
                # This is a leaf field. We need an input for it.
                record = {}
                record['id'] = '.'.join(parent_keys + [field_name])
                record['label'] = name_to_label(field_name)
                record['required'] = not optional and not subtree_optional
                record['list'] = is_list
                if ref_iri:
                    record['ref_iri'] = ref_iri
                if docstring:
                    record['docstring'] = docstring

                if field_name in options:
                    # The field will be a 'select' type no matter what its real
                    # data type is.
                    record['type'] = 'select' # Not a real HTML input type. It's its own tag.
                    # We have a set of values to present
                    record['options'] = []
                    for name, value in options[field_name].items():
                        # Make a tuple for each one
                        record['options'].append((name, value))
                elif field_type == 'string':
                    if field_name.endswith('date'):
                        # Use a date picker to generate a good string.
                        # Comes back YYYY-MM-DD.
                        record['type'] = 'date'
                    else:
                        # Normal text string
                        record['type'] = 'text'
                elif field_type == 'int':
                    record['type'] = 'number'
                elif field_type == 'float' or field_type == 'double':
                    record['type'] = 'number'
                    # Choose a reasonable precision for the control
                    record['step'] = '0.0001'
                else:
                    raise NotImplementedError('Unimplemented field type {} in {} in metadata schema'.format(field_type, type_name))
                yield record

    return list(walk_fields(root_name))


# At startup, we need to load the metadata schema from the uploader module, so we can make a form for it
METADATA_SCHEMA = yaml.safe_load(pkg_resources.resource_stream("bh20sequploader", "bh20seq-schema.yml"))
METADATA_OPTION_DEFINITIONS = yaml.safe_load(pkg_resources.resource_stream("bh20sequploader", "bh20seq-options.yml"))
FORM_ITEMS = generate_form(METADATA_SCHEMA, METADATA_OPTION_DEFINITIONS)

@app.route('/')
def send_home():
    """
    Send the front page.
    """

    return render_template('home.html', menu='HOME')


@app.route('/upload')
def send_form():
    """
    Send the file upload form/front page.
    """

    return render_template('form.html', fields=FORM_ITEMS, menu='UPLOAD')

class FileTooBigError(RuntimeError):
    """
    Raised when the user gives a file that is too large.
    """
    pass

def copy_with_limit(in_file, out_file, limit=1024*1024):
    """
    Copy a file stream, and raise FileTooBigError if the file is too big.
    """

    bytes_used = 0
    buf_size = 65536

    buf = in_file.read(buf_size)
    bytes_used += len(buf)
    while buf:
        if bytes_used > limit:
            raise FileTooBigError('Hit file length limit')
        out_file.write(buf)
        buf = in_file.read(buf_size)
        bytes_used += len(buf)

def parse_input(input_string, html_type, number_step=None):
    """
    Parse an input from the given HTML input type into a useful Python type.
    Also needs the step we sent to distinguish int fields and float/double fields.

    Raise ValueError if something does not parse.
    Raise NotImplementedError if we forgot to implement a type.
    """

    if html_type == 'text' or html_type == 'select':
        return input_string
    elif html_type == 'number':
        # May be an int or a float.
        if number_step is None:
            # TODO: Assumes we only use the step for floats
            return int(input_string)
        else:
            return float(input_string)
    elif html_type == 'date':
        # Don't do our own date validation; pass it on as a string
        return input_string
    else:
        raise NotImplementedError('Unimplemented input type: {}'.format(html_type))

@app.route('/submit', methods=['POST'])
def receive_files():
    """
    Receive the uploaded files.
    """

    # We're going to work in one directory per request
    dest_dir = tempfile.mkdtemp()
    # The uploader will happily accept a FASTQ with this name
    fasta_dest = os.path.join(dest_dir, 'fasta.fa')
    metadata_dest = os.path.join(dest_dir, 'metadata.json')
    try:
        if 'fasta' not in request.files:
            return (render_template('error.html',
                error_message="You did not include a FASTA or FASTQ file."), 403)
        try:
            with open(fasta_dest, 'wb') as out_stream:
                # Use a plausible file size limit for a little FASTQ
                copy_with_limit(request.files.get('fasta').stream, out_stream, limit=50*1024*1024)
        except FileTooBigError as e:
            # Delegate to the 413 error handler
            return handle_large_file(e)

        if request.form.get('metadata_type', None) == 'upload':
            if 'metadata' not in request.files:
                return (render_template('error.html',
                    error_message="You did not include a metadata file."), 403)
            try:
                with open(metadata_dest, 'wb') as out_stream:
                    copy_with_limit(request.files.get('metadata').stream, out_stream)
            except FileTooBigError as e:
                # Delegate to the 413 error handler
                return handle_large_file(e)
        elif request.form.get('metadata_type', None) == 'fill':
            # Build a metadata dict
            metadata = {}

            # When we have metadata for an item, use this to set it.
            # If it is an item in a list, set is_list=True
            def set_metadata(item_id, value, is_list=False):
                # We have this thing. Make a place in the dict tree for it.
                parts = item_id.split('.')
                key = parts[-1]
                # Remove leading 'metadata'
                path = parts[1:-1]
                dest_dict = metadata
                for parent in path:
                    if parent not in dest_dict:
                        dest_dict[parent] = {}
                    dest_dict = dest_dict[parent]

                if not is_list:
                    dest_dict[key] = value
                else:
                    if key not in dest_dict:
                        dest_dict[key] = []
                    dest_dict[key].append(value)

            for item in FORM_ITEMS:
                # Pull all the field values we wanted from the form
                if 'heading' in item:
                    continue

                if item['list']:
                    # This is a list, serialized into form fields

                    # We count how many values we got
                    value_count = 0

                    for index in itertools.count():
                        # Get [0] through [n], until something isn't there.
                        entry_id = '{}[{}]'.format(item['id'], index)

                        if index == 1000:
                            # Don't let them provide too much stuff.
                            return (render_template('error.html',
                                    error_message="You provided an extremely large number of values for the metadata item {}".format(item['id'])), 403)

                        if entry_id in request.form:
                            if len(request.form[entry_id]) > 0:
                                # Put an entry in the list
                                try:
                                    # Parse the item
                                    parsed = parse_input(request.form[entry_id], item['type'], item.get('step', None))
                                except ValueError:
                                    # We don't like that input
                                    return (render_template('error.html',
                                            error_message="You provided an unacceptable value for the metadata item {}".format(entry_id)), 403)
                                # Save it
                                set_metadata(item['id'], parsed, is_list=True)
                                value_count += 1
                            else:
                                # Empty items are silently skipped.
                                pass
                        else:
                            # We have run out of form fields for this list.
                            break

                        if item['required'] and value_count == 0:
                            # They forgot a required item. Maybe all entries were empty.
                            return (render_template('error.html',
                                    error_message="You omitted any values for the required metadata item {}".format(item['id'])), 403)

                elif item['id'] in request.form and len(request.form[item['id']]) > 0:
                    # Not a list, but a single item which is present.
                    try:
                        # Parse the item
                        parsed = parse_input(request.form[item['id']], item['type'], item.get('step', None))
                    except ValueError:
                        # We don't like that input
                        return (render_template('error.html',
                            error_message="You provided an unacceptable value for the metadata item {}".format(item['id'])), 403)
                    # Save it
                    set_metadata(item['id'], parsed)
                elif item['required']:
                    return (render_template('error.html',
                            error_message="You omitted the required metadata item {}".format(item['id'])), 403)

            # Now serialize the file with all the items
            with open(metadata_dest, 'w') as out_stream:
                yaml.dump(metadata, out_stream)
        else:
            return (render_template('error.html',
                    error_message="You did not include metadata."), 403)

        # Try and upload files to Arvados using the sequence uploader CLI

        cmd = ['python3','bh20sequploader/main.py', metadata_dest, fasta_dest]
        print(" ".join(cmd),file=sys.stderr)
        result = subprocess.run(cmd,
            stdout=subprocess.PIPE, stderr=subprocess.PIPE)

        if result.returncode != 0:
            # It didn't work. Complain.
            error_message="Uploader returned value {} and said:".format(result.returncode) + str(result.stderr.decode('utf-8'))
            print(error_message, file=sys.stderr)
            return (render_template('error.html', error_message=error_message), 403)
        else:
            # It worked. Say so.
            return render_template('success.html', log=result.stdout.decode('utf-8', errors='replace'))
    finally:
        shutil.rmtree(dest_dir)

def get_html_body(fn):
    buf = ""
    in_body = False
    begin_body = re.compile(r"<body>",re.IGNORECASE)
    end_body = re.compile(r"(</body>|.*=\"postamble\")",re.IGNORECASE)
    with open(fn) as f:
        for line in f:
            if end_body.match(line):
                break
            if in_body:
                buf += line
            elif begin_body.match(line):
                in_body = True
    return buf

@app.route('/download')
def download_page():
    buf = get_html_body('doc/web/download.html')
    return render_template('resource.html',menu='DOWNLOAD',embed=buf)

def pending_table(output, items):
    output.write(
"""
<table>
<tr><th>Collection</th>
<th>Sequence label</th></tr>
""")
    for r in items:
        if r["status"] != "pending":
            continue
        output.write("<tr>")
        output.write("<td><a href='https://workbench.lugli.arvadosapi.com/collections/%s'>%s</a></td>" % (r["uuid"], r["uuid"]))
        output.write("<td>%s</td>" % Markup.escape(r["sequence_label"]))
        output.write("</tr>")
    output.write(
"""
</table>
""")

def rejected_table(output, items):
    output.write(
"""
<table>
<tr><th>Collection</th>
<th>Sequence label</th>
<th>Errors</th></tr>
""")
    for r in items:
        if r["status"] != "rejected":
            continue
        output.write("<tr>")
        output.write("<td><a href='https://workbench.lugli.arvadosapi.com/collections/%s'>%s</a></td>" % (r["uuid"], r["uuid"]))
        output.write("<td>%s</td>" % Markup.escape(r["sequence_label"]))
        output.write("<td><pre>%s</pre></td>" % Markup.escape("\n".join(r.get("errors", []))))
        output.write("</tr>")
    output.write(
"""
</table>
""")


@app.route('/status')
def status_page():
    """
    Processing status
    """

    api = arvados.api(host=ARVADOS_API, token=ANONYMOUS_TOKEN)
    pending = arvados.util.list_all(api.collections().list, filters=[["owner_uuid", "=", UPLOADER_PROJECT]])
    out = []
    status = {}
    for p in pending:
        prop = p["properties"]
        out.append(prop)
        if "status" not in prop:
            prop["status"] = "pending"
        prop["created_at"] = p["created_at"]
        prop["uuid"] = p["uuid"]
        status[prop["status"]] = status.get(prop["status"], 0) + 1

    output = io.StringIO()

    validated = api.collections().list(filters=[["owner_uuid", "=", VALIDATED_PROJECT]], limit=1).execute()
    status["passed"] = validated["items_available"]

    for s in (("passed", "/download"), ("pending", "#pending"), ("rejected", "#rejected")):
        output.write("<p><a href='%s'>%s sequences QC %s</a></p>" % (s[1], status.get(s[0], 0), s[0]))

    output.write("<a id='pending'><h1>Pending</h1>")
    pending_table(output, out)

    output.write("<a id='rejected'><h1>Rejected</h1>")
    rejected_table(output, out)

    return render_template('status.html', table=Markup(output.getvalue()), menu='STATUS')

@app.route('/demo')
def demo_page():
    return render_template('demo.html',menu='DEMO')

@app.route('/blog',methods=['GET'])
def blog_page():
    blog_content = request.args.get('id') # e.g. using-covid-19-pubseq-part3
    buf = None;
    if blog_content:
        buf = get_html_body('doc/blog/'+blog_content+'.html')
    return render_template('blog.html',menu='BLOG',embed=buf,blog=blog_content)


@app.route('/about')
def about_page():
    buf = get_html_body('doc/web/about.html')
    return render_template('about.html',menu='ABOUT',embed=buf)

##
@app.route('/map')
def map_page():
    return render_template('map.html',menu='DEMO')



## Dynamic API functions starting here
## This is quick and dirty for now, just to get something out and demonstrate the queries
## Feel free to rename the functions/endpoints, feel free to process result so we get nicer JSON
## but most likley you don't want to touch the queries, Cheers.
baseURL='http://sparql.genenetwork.org/sparql/'

@app.route('/api/getCount', methods=['GET'])
def getCount():
    api = arvados.api(host=ARVADOS_API, token=ANONYMOUS_TOKEN)
    c = api.collections().list(filters=[["owner_uuid", "=", VALIDATED_PROJECT]], limit=1).execute()

    return jsonify({'sequences': c["items_available"]})

@app.route('/api/getAllaccessions', methods=['GET'])
def getAllaccessions():
    query="""SELECT DISTINCT ?fasta ?value WHERE {?fasta ?x[ <http://edamontology.org/data_2091> ?value ]}"""
    payload = {'query': query, 'format': 'json'}
    r = requests.get(baseURL, params=payload)
    result = r.json()['results']['bindings']
    return jsonify([{'uri': x['fasta']['value'],
                     'value': x['value']['value']} for x in result])


# parameter must be encoded e.g. http://arvados.org/keep:6e6276698ed8b0e6cd21f523e4f91179+123/sequence.fasta must become
# http%3A%2F%2Fcollections.lugli.arvadosapi.com%2Fc%3D00a6af865453564f6a59b3d2c81cc7c1%2B123%2Fsequence.fasta
@app.route('/api/getDetailsForSeq', methods=['GET'])
def getDetailsForSeq():
    seq_id = request.args.get('seq')
    query="""SELECT DISTINCT ?key ?key_label ?value WHERE {
    <placeholder> ?x [?key ?value] .
    OPTIONAL {?key <http://www.w3.org/2000/01/rdf-schema#label> ?key_tmp_label } .
    BIND(IF(BOUND(?key_tmp_label),?key_tmp_label, ?key) as ?key_label)}"""
    query=query.replace("placeholder", seq_id)
    payload = {'query': query, 'format': 'json'}
    r = requests.get(baseURL, params=payload)
    result = r.json()['results']['bindings']
    return jsonify([{'uri': x['key']['value'], 'key_label': x['key_label']['value'],
                     'value': x['value']['value']} for x in result])

# Endpoint should provide all necessary information to draw a map (!)
@app.route('/api/getCountByGPS', methods=['GET'])
def getCountByGPS():
    query="""SELECT DISTINCT ?location ?location_label ?GPS (count(?fasta) as ?fastaCount) WHERE {
    ?fasta ?x[ <http://purl.obolibrary.org/obo/GAZ_00000448> ?location] .
    ?location <http://www.wikidata.org/prop/direct/P625> ?GPS .
    OPTIONAL { ?location rdfs:label ?key_tmp_label }
    BIND(IF(BOUND(?key_tmp_label),?key_tmp_label, ?location) as ?location_label)
    }
    GROUP BY ?location ?location_label ?GPS
    """
    payload = {'query': query, 'format': 'json'}
    r = requests.get(baseURL, params=payload)
    result = r.json()['results']['bindings']
    return jsonify([{'count': x['fastaCount']['value'],
                     'Location': x['location']['value'],
                     'LocationLabel': x['location_label']['value'],
                     'GPS' :x['GPS']['value'][6:-1]} for x in result])


@app.route('/api/getSEQCountbytech', methods=['GET'])
def getSEQCountbytech():
    query="""SELECT ?tech ?tech_label (count(?fasta) as ?fastaCount) WHERE
    {?fasta ?x [<http://purl.obolibrary.org/obo/OBI_0600047>  ?tech] .
     OPTIONAL {?tech <http://www.w3.org/2000/01/rdf-schema#label> ?tech_tmp_label } .
     BIND(IF(BOUND(?tech_tmp_label), ?tech_tmp_label,?tech) as ?tech_label)}
    GROUP BY ?tech ?tech_label ORDER BY DESC (?fastaCount)
    """
    payload = {'query': query, 'format': 'json'}
    r = requests.get(baseURL, params=payload)
    result = r.json()['results']['bindings']
    return jsonify([{'count': x['fastaCount']['value'],
                     'key': x['tech']['value'],
                     'label': x['tech_label']['value']} for x in result])

## List all Sequences/submissions by a given tech, as example e.g. http://purl.obolibrary.org/obo/OBI_0000759
## Has to be encoded again so should be --> http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0000759
@app.route('/api/getSEQbytech', methods=['GET'])
def getSEQbytech():
    query="""SELECT ?fasta WHERE
    {?fasta ?x [<http://purl.obolibrary.org/obo/OBI_0600047>  <placeholder>] }
    """
    tech = request.args.get('tech')
    query=query.replace("placeholder", tech)
    payload = {'query': query, 'format': 'json'}
    r = requests.get(baseURL, params=payload)
    result = r.json()['results']['bindings']
    return str(result)


## Example location, encoded http%3A%2F%2Fwww.wikidata.org%2Fentity%2FQ1223
@app.route('/api/getSEQbyLocation', methods=['GET'])
def getSEQbyLocation():
    query="""SELECT ?fasta WHERE {?fasta ?x[ <http://purl.obolibrary.org/obo/GAZ_00000448> <placeholder>]}"""
    location=request.args.get('location')
    query=query.replace("placeholder", location)
    print(query)
    payload = {'query': query, 'format': 'json'}
    r = requests.get(baseURL, params=payload)
    result = r.json()['results']['bindings']
    return str(result)


@app.route('/api/getSEQCountbyLocation', methods=['GET'])
def getSEQCountbyLocation():
    query="""SELECT ?geoLocation ?geoLocation_label (count(?fasta) as ?fastaCount)  WHERE
    {?fasta ?x [<http://purl.obolibrary.org/obo/GAZ_00000448> ?geoLocation] .
    Optional {?geoLocation <http://www.w3.org/2000/01/rdf-schema#label> ?geoLocation_tmp_label}
    BIND(IF(BOUND(?geoLocation_tmp_label), ?geoLocation_tmp_label, ?geoLocation) as ?geoLocation_label)}
    GROUP BY ?geoLocation ?geoLocation_label ORDER BY DESC (?fastaCount)
    """
    payload = {'query': query, 'format': 'json'}
    r = requests.get(baseURL, params=payload)
    result = r.json()['results']['bindings']
    return jsonify([{'count': x['fastaCount']['value'],
                     'key': x['geoLocation']['value'],
                     'label': x['geoLocation_label']['value']} for x in result])


@app.route('/api/getSEQCountbyContinent', methods=['GET'])
def getSEQCountbyContinent():
    query="""SELECT DISTINCT ?continent ?continent_label (count(?fasta) as ?fastaCount) WHERE {
    ?fasta ?x[ <http://purl.obolibrary.org/obo/GAZ_00000448> ?location] .
   ?location <http://www.wikidata.org/prop/direct/P17> ?country .
    ?country <http://www.wikidata.org/prop/direct/P30> ?continent .
    OPTIONAL { ?continent rdfs:label ?key_tmp_label }
    BIND(IF(BOUND(?key_tmp_label),?key_tmp_label, ?location) as ?continent_label)
    }
    GROUP BY ?continent ?continent_label
    """
    payload = {'query': query, 'format': 'json'}
    r = requests.get(baseURL, params=payload)
    result = r.json()['results']['bindings']
    return jsonify([{'count': x['fastaCount']['value'],
                     'key': x['continent']['value'],
                     'label': x['continent_label']['value']} for x in result])



@app.route('/api/getSEQCountbyCountryContinent', methods=['GET'])
def getSEQCountbyCountryContinent():
    query="""SELECT DISTINCT ?location ?location_label (count(?fasta) as ?fastaCount) WHERE {
    ?fasta ?x[ <http://purl.obolibrary.org/obo/GAZ_00000448> ?location] .
    ?location <http://www.wikidata.org/prop/direct/P30> <placeholder> .
    OPTIONAL { ?location rdfs:label ?key_tmp_label }
    BIND(IF(BOUND(?key_tmp_label),?key_tmp_label, ?location) as ?location_label)
    }
    GROUP BY ?location ?location_label
    """
    continent = request.args.get('continent')
    query = query.replace("placeholder", continent)
    payload = {'query': query, 'format': 'json'}
    r = requests.get(baseURL, params=payload)
    result = r.json()['results']['bindings']
    return jsonify([{'count': x['fastaCount']['value'],
                     'key': x['location']['value'],
                     'label': x['location_label']['value']} for x in result])



@app.route('/api/getSEQCountbySpecimenSource', methods=['GET'])
def getSEQCountbySpecimenSource():
    query="""SELECT ?specimen_source ?specimen_source_label (count(?fasta) as ?fastaCount)  WHERE
    {?fasta ?x [<http://purl.obolibrary.org/obo/OBI_0001479>  ?specimen_source]
     Optional { ?specimen_source <http://www.w3.org/2000/01/rdf-schema#label> ?specimen_source_tmp_label}
     BIND(IF(BOUND(?specimen_source_tmp_label), ?specimen_source_tmp_label ,?specimen_source) as ?specimen_source_label)}
     GROUP BY ?specimen_source ?specimen_source_label
     ORDER BY DESC (?fastaCount)
    """
    payload = {'query': query, 'format': 'json'}
    r = requests.get(baseURL, params=payload)
    result = r.json()['results']['bindings']
    return jsonify([{'count': x['fastaCount']['value'],
                     'key': x['specimen_source']['value'],
                     'label': x['specimen_source_label']['value']} for x in result])

# Example specimen http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C155831
@app.route('/api/getSEQbySpecimenSource', methods=['GET'])
def getSEQBySpecimenSource():
    query="""SELECT ?fasta ?specimen_source ?specimen_source_label  WHERE
    {?fasta ?x [<http://purl.obolibrary.org/obo/OBI_0001479> <placeholder>]
    BIND (concat(?specimen_source,"_label") as ?specimen_source_label)}
    """
    specimen=request.args.get('specimen')
    query = query.replace("placeholder", specimen)
    payload = {'query': query, 'format': 'json'}
    r = requests.get(baseURL, params=payload)
    result = r.json()['results']['bindings']
    return str(result)

#No data for this atm
@app.route('/api/getSEQCountbyHostHealthStatus', methods=['GET'])
def getSEQCountbyHostHealthStatus():
    query="""SELECT ?health_status ?health_status_label (count(?fasta) as ?fastaCount)  WHERE
    {?fasta ?x [<http://purl.obolibrary.org/obo/NCIT_C25688> ?health_status]
    BIND (concat(?health_status,"_label") as ?health_status_label)}
    GROUP BY ?health_status ?health_status_label
    ORDER BY DESC (?fastaCount)
    """
    payload = {'query': query, 'format': 'json'}
    r = requests.get(baseURL, params=payload)
    result = r.json()['results']['bindings']
    return str(result)

@app.route('/api/getSEQbyLocationAndTech', methods=['GET'])
def getSEQbyLocationAndTech():
    query="""SELECT ?fasta WHERE { ?fasta ?x [
        <http://purl.obolibrary.org/obo/GAZ_00000448> <placeholderLoc>; <http://purl.obolibrary.org/obo/OBI_0600047>  <placeholderTech> ]}"""
    location=request.args.get('location')
    tech=request.args.get('tech')
    query=query.replace("placeholderLoc", location)
    query = query.replace("placeholderTech", tech)
    print(query)
    payload = {'query': query, 'format': 'json'}
    r = requests.get(baseURL, params=payload)
    result = r.json()['results']['bindings']
    return str(result)


# Example Location http%3A%2F%2Fwww.wikidata.org%2Fentity%2FQ1223
# Example specimen http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C155831
@app.route('/api/getSEQbyLocationAndSpecimenSource', methods=['GET'])
def getSEQbyLocationAndSpecimenSource():
    query="""SELECT ?fasta WHERE { ?fasta ?x [
        <http://purl.obolibrary.org/obo/GAZ_00000448> <placeholderLoc>; <http://purl.obolibrary.org/obo/OBI_0001479>  <placeholderSpecimen> ]}
    """
    location = request.args.get('location')
    specimen = request.args.get('specimen')
    query = query.replace("placeholderLoc", location)
    query = query.replace("placeholderSpecimen", specimen)
    print(query)
    payload = {'query': query, 'format': 'json'}
    r = requests.get(baseURL, params=payload)
    result = r.json()['results']['bindings']
    return str(result)