aboutsummaryrefslogtreecommitdiff
path: root/gn3/db/traits.py
blob: f68609745880f36406414505de54da105b893c85 (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
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
"""This class contains functions relating to trait data manipulation"""
import os
from functools import reduce
from typing import Any, Dict, Union, Sequence

import MySQLdb

from gn3.settings import TMPDIR
from gn3.random import random_string
from gn3.function_helpers import compose
from gn3.db.datasets import retrieve_trait_dataset


def export_trait_data(
        trait_data: dict, samplelist: Sequence[str], dtype: str = "val",
        var_exists: bool = False, n_exists: bool = False):
    """
    Export data according to `samplelist`. Mostly used in calculating
    correlations.

    DESCRIPTION:
    Migrated from
    https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L166-L211

    PARAMETERS
    trait: (dict)
      The dictionary of key-value pairs representing a trait
    samplelist: (list)
      A list of sample names
    dtype: (str)
      ... verify what this is ...
    var_exists: (bool)
      A flag indicating existence of variance
    n_exists: (bool)
      A flag indicating existence of ndata
    """
    def __export_all_types(tdata, sample):
        sample_data = []
        if tdata[sample]["value"]:
            sample_data.append(tdata[sample]["value"])
            if var_exists:
                if tdata[sample]["variance"]:
                    sample_data.append(tdata[sample]["variance"])
                else:
                    sample_data.append(None)
            if n_exists:
                if tdata[sample]["ndata"]:
                    sample_data.append(tdata[sample]["ndata"])
                else:
                    sample_data.append(None)
        else:
            if var_exists and n_exists:
                sample_data += [None, None, None]
            elif var_exists or n_exists:
                sample_data += [None, None]
            else:
                sample_data.append(None)

        return tuple(sample_data)

    def __exporter(accumulator, sample):
        # pylint: disable=[R0911]
        if sample in trait_data["data"]:
            if dtype == "val":
                return accumulator + (trait_data["data"][sample]["value"], )
            if dtype == "var":
                return accumulator + (trait_data["data"][sample]["variance"], )
            if dtype == "N":
                return accumulator + (trait_data["data"][sample]["ndata"], )
            if dtype == "all":
                return accumulator + __export_all_types(trait_data["data"], sample)
            raise KeyError(f"Type `{dtype}` is incorrect")
        if var_exists and n_exists:
            return accumulator + (None, None, None)
        if var_exists or n_exists:
            return accumulator + (None, None)
        return accumulator + (None,)

    return reduce(__exporter, samplelist, tuple())


def get_trait_csv_sample_data(conn: Any,
                              trait_name: int, phenotype_id: int) -> str:
    """Fetch a trait and return it as a csv string"""
    __query = ("SELECT concat(st.Name, ',', ifnull(pd.value, 'x'), ',', "
               "ifnull(ps.error, 'x'), ',', ifnull(ns.count, 'x')) as 'Data' "
               "ifnull(ca.Name, 'x') as 'CaseAttr', "
               "ifnull(cxref.value, 'x') as 'Value' "
               "FROM PublishFreeze pf "
               "JOIN PublishXRef px ON px.InbredSetId = pf.InbredSetId "
               "JOIN PublishData pd ON pd.Id = px.DataId "
               "JOIN Strain st ON pd.StrainId = st.Id "
               "LEFT JOIN PublishSE ps ON ps.DataId = pd.Id "
               "AND ps.StrainId = pd.StrainId "
               "LEFT JOIN NStrain ns ON ns.DataId = pd.Id "
               "AND ns.StrainId = pd.StrainId "
               "LEFT JOIN CaseAttributeXRefNew cxref ON "
               "(cxref.InbredSetId = px.InbredSetId AND "
               "cxref.StrainId = st.Id) "
               "LEFT JOIN CaseAttribute ca ON ca.Id = cxref.CaseAttributeId"
               "WHERE px.Id = %s AND px.PhenotypeId = %s ORDER BY st.Name")
    case_attr_columns = set()
    csv_data = {}
    with conn.cursor() as cursor:
        cursor.execute(__query, (trait_name, phenotype_id))
        for data in cursor.fetchall():
            if data[1] == "x":
                csv_data[data[0]] = None
            else:
                sample, case_attr, value = data[0], data[1], data[2]
                if not csv_data.get(sample):
                    csv_data[sample] = {}
                csv_data[sample][case_attr] = None if value == "x" else value
                case_attr_columns.add(case_attr)
        if not case_attr_columns:
            return ("Strain Name,Value,SE,Count\n" +
                    "\n".join(csv_data.keys()))
        else:
            columns = sorted(case_attr_columns)
            csv = ("Strain Name,Value,SE,Count," +
                   ",".join(columns) + "\n")
            for key, value in csv_data.items():
                if not value:
                    csv += (key + (len(case_attr_columns) * ",x") + "\n")
                else:
                    vals = [str(value.get(column, "x")) for column in columns]
                    csv += (key + "," + ",".join(vals) + "\n")
            return csv
    return "No Sample Data Found"


def update_sample_data(conn: Any,  # pylint: disable=[R0913]
                       trait_name: str,
                       strain_name: str,
                       phenotype_id: int,
                       value: Union[int, float, str],
                       error: Union[int, float, str],
                       count: Union[int, str]):
    """Given the right parameters, update sample-data from the relevant
    table."""
    strain_id, data_id = "", ""

    with conn.cursor() as cursor:
        cursor.execute(
            ("SELECT Strain.Id, PublishData.Id FROM "
             "(PublishData, Strain, PublishXRef, PublishFreeze) "
             "LEFT JOIN PublishSE ON "
             "(PublishSE.DataId = PublishData.Id AND "
             "PublishSE.StrainId = PublishData.StrainId) "
             "LEFT JOIN NStrain ON "
             "(NStrain.DataId = PublishData.Id AND "
             "NStrain.StrainId = PublishData.StrainId) "
             "WHERE PublishXRef.InbredSetId = "
             "PublishFreeze.InbredSetId AND "
             "PublishData.Id = PublishXRef.DataId AND "
             "PublishXRef.Id = %s AND "
             "PublishXRef.PhenotypeId = %s "
             "AND PublishData.StrainId = Strain.Id "
             "AND Strain.Name = %s"),
            (trait_name, phenotype_id, str(strain_name)))
        strain_id, data_id = cursor.fetchone()
    updated_published_data: int = 0
    updated_se_data: int = 0
    updated_n_strains: int = 0

    with conn.cursor() as cursor:
        # Update the PublishData table
        if value == "x":
            cursor.execute(("DELETE FROM PublishData "
                            "WHERE StrainId = %s AND Id = %s"),
                           (strain_id, data_id))
            updated_published_data = cursor.rowcount
        else:
            cursor.execute(("UPDATE PublishData SET value = %s "
                        "WHERE StrainId = %s AND Id = %s"),
                       (value, strain_id, data_id))
            updated_published_data = cursor.rowcount

            if not updated_published_data:
                cursor.execute(
                    ("SELECT * FROM "
                     "PublishData WHERE StrainId = "
                     "%s AND Id = %s"),
                    (strain_id, data_id))
                if not cursor.fetchone():
                    cursor.execute(("INSERT INTO PublishData (Id, StrainId, "
                                    " value) VALUES (%s, %s, %s)"),
                                   (data_id, strain_id, value))
                    updated_published_data = cursor.rowcount

        # Update the PublishSE table
        if error == "x":
            cursor.execute(("DELETE FROM PublishSE "
                            "WHERE StrainId = %s AND DataId = %s"),
                           (strain_id, data_id))
            updated_se_data = cursor.rowcount
        else:
            cursor.execute(("UPDATE PublishSE SET error = %s "
                            "WHERE StrainId = %s AND DataId = %s"),
                           (None if error == "x" else error,
                            strain_id, data_id))
            updated_se_data = cursor.rowcount
            if not updated_se_data:
                cursor.execute(
                    ("SELECT * FROM "
                     "PublishSE WHERE StrainId = "
                     "%s AND DataId = %s"),
                    (strain_id, data_id))
                if not cursor.fetchone():
                    cursor.execute(
                        ("INSERT INTO PublishSE (StrainId, DataId, "
                         " error) VALUES (%s, %s, %s)"),
                        (strain_id, data_id, None if error == "x" else error))
                    updated_se_data = cursor.rowcount

        # Update the NStrain table
        if count == "x":
            cursor.execute(("DELETE FROM NStrain "
                            "WHERE StrainId = %s AND DataId = %s"),
                           (strain_id, data_id))
            updated_n_strains = cursor.rowcount
        else:
            cursor.execute(("UPDATE NStrain SET count = %s "
                            "WHERE StrainId = %s AND DataId = %s"),
                           (count, strain_id, data_id))
            updated_n_strains = cursor.rowcount
            if not updated_n_strains:
                cursor.execute(
                    ("SELECT * FROM "
                     "NStrain WHERE StrainId = "
                     "%s AND DataId = %s"),
                    (strain_id, data_id))
                if not cursor.fetchone():
                    cursor.execute(("INSERT INTO NStrain "
                                    "(StrainId, DataId, count) "
                                    "VALUES (%s, %s, %s)"),
                                   (strain_id, data_id, count))
                    updated_n_strains = cursor.rowcount
    return (updated_published_data,
            updated_se_data, updated_n_strains)


def delete_sample_data(conn: Any,
                       trait_name: str,
                       strain_name: str,
                       phenotype_id: int):
    """Given the right parameters, delete sample-data from the relevant
    table."""
    strain_id, data_id = "", ""

    deleted_published_data: int = 0
    deleted_se_data: int = 0
    deleted_n_strains: int = 0

    with conn.cursor() as cursor:
        # Delete the PublishData table
        try:
            cursor.execute(
                ("SELECT Strain.Id, PublishData.Id FROM "
                 "(PublishData, Strain, PublishXRef, PublishFreeze) "
                 "LEFT JOIN PublishSE ON "
                 "(PublishSE.DataId = PublishData.Id AND "
                 "PublishSE.StrainId = PublishData.StrainId) "
                 "LEFT JOIN NStrain ON "
                 "(NStrain.DataId = PublishData.Id AND "
                 "NStrain.StrainId = PublishData.StrainId) "
                 "WHERE PublishXRef.InbredSetId = "
                 "PublishFreeze.InbredSetId AND "
                 "PublishData.Id = PublishXRef.DataId AND "
                 "PublishXRef.Id = %s AND "
                 "PublishXRef.PhenotypeId = %s "
                 "AND PublishData.StrainId = Strain.Id "
                 "AND Strain.Name = %s"),
                (trait_name, phenotype_id, str(strain_name)))

            # Check if it exists if the data was already deleted:
            if _result := cursor.fetchone():
                strain_id, data_id = _result

            # Only run if the strain_id and data_id exist
            if strain_id and data_id:
                cursor.execute(("DELETE FROM PublishData "
                                "WHERE StrainId = %s AND Id = %s"),
                               (strain_id, data_id))
                deleted_published_data = cursor.rowcount

                # Delete the PublishSE table
                cursor.execute(("DELETE FROM PublishSE "
                                "WHERE StrainId = %s AND DataId = %s"),
                               (strain_id, data_id))
                deleted_se_data = cursor.rowcount

                # Delete the NStrain table
                cursor.execute(("DELETE FROM NStrain "
                                "WHERE StrainId = %s AND DataId = %s"),
                               (strain_id, data_id))
                deleted_n_strains = cursor.rowcount
        except Exception as e:  #pylint: disable=[C0103, W0612]
            conn.rollback()
            raise MySQLdb.Error
        conn.commit()
        cursor.close()
        cursor.close()

    return (deleted_published_data,
            deleted_se_data, deleted_n_strains)


def insert_sample_data(conn: Any,  # pylint: disable=[R0913]
                       trait_name: str,
                       strain_name: str,
                       phenotype_id: int,
                       value: Union[int, float, str],
                       error: Union[int, float, str],
                       count: Union[int, str]):
    """Given the right parameters, insert sample-data to the relevant table.

    """

    inserted_published_data, inserted_se_data, inserted_n_strains = 0, 0, 0
    with conn.cursor() as cursor:
        try:
            cursor.execute("SELECT DataId FROM PublishXRef WHERE Id = %s AND "
                           "PhenotypeId = %s", (trait_name, phenotype_id))
            data_id = cursor.fetchone()

            cursor.execute("SELECT Id FROM Strain WHERE Name = %s",
                           (strain_name,))
            strain_id = cursor.fetchone()

            # Return early if an insert already exists!
            cursor.execute("SELECT Id FROM PublishData where Id = %s "
                           "AND StrainId = %s",
                           (data_id, strain_id))
            if cursor.fetchone():  # This strain already exists
                return (0, 0, 0)

            # Insert the PublishData table
            cursor.execute(("INSERT INTO PublishData (Id, StrainId, value)"
                            "VALUES (%s, %s, %s)"),
                           (data_id, strain_id, value))
            inserted_published_data = cursor.rowcount

            # Insert into the PublishSE table if error is specified
            if error and error != "x":
                cursor.execute(("INSERT INTO PublishSE (StrainId, DataId, "
                                " error) VALUES (%s, %s, %s)"),
                               (strain_id, data_id, error))
            inserted_se_data = cursor.rowcount

            # Insert into the NStrain table
            if count and count != "x":
                cursor.execute(("INSERT INTO NStrain "
                                "(StrainId, DataId, count) "
                                "VALUES (%s, %s, %s)"),
                               (strain_id, data_id, count))
            inserted_n_strains = cursor.rowcount
        except Exception:  # pylint: disable=[C0103, W0612]
            conn.rollback()
            raise MySQLdb.Error
    return (inserted_published_data,
            inserted_se_data, inserted_n_strains)


def retrieve_publish_trait_info(trait_data_source: Dict[str, Any], conn: Any):
    """Retrieve trait information for type `Publish` traits.

    https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L399-L421"""
    keys = (
        "Id", "PubMed_ID", "Pre_publication_description",
        "Post_publication_description", "Original_description",
        "Pre_publication_abbreviation", "Post_publication_abbreviation",
        "Lab_code", "Submitter", "Owner", "Authorized_Users", "Authors",
        "Title", "Abstract", "Journal", "Volume", "Pages", "Month", "Year",
        "Sequence", "Units", "comments")
    columns = (
        "PublishXRef.Id, Publication.PubMed_ID, "
        "Phenotype.Pre_publication_description, "
        "Phenotype.Post_publication_description, "
        "Phenotype.Original_description, "
        "Phenotype.Pre_publication_abbreviation, "
        "Phenotype.Post_publication_abbreviation, "
        "Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, "
        "Phenotype.Authorized_Users, CAST(Publication.Authors AS BINARY), "
        "Publication.Title, Publication.Abstract, Publication.Journal, "
        "Publication.Volume, Publication.Pages, Publication.Month, "
        "Publication.Year, PublishXRef.Sequence, Phenotype.Units, "
        "PublishXRef.comments")
    query = (
        "SELECT "
        f"{columns} "
        "FROM "
        "PublishXRef, Publication, Phenotype "
        "WHERE "
        "PublishXRef.Id = %(trait_name)s AND "
        "Phenotype.Id = PublishXRef.PhenotypeId AND "
        "Publication.Id = PublishXRef.PublicationId AND "
        "PublishXRef.InbredSetId = %(trait_dataset_id)s")
    with conn.cursor() as cursor:
        cursor.execute(
            query,
            {
                k: v for k, v in trait_data_source.items()
                if k in ["trait_name", "trait_dataset_id"]
            })
        return dict(zip([k.lower() for k in keys], cursor.fetchone()))


def set_confidential_field(trait_type, trait_info):
    """Post processing function for 'Publish' trait types.

    It sets the value for the 'confidential' key."""
    if trait_type == "Publish":
        return {
            **trait_info,
            "confidential": 1 if (
                trait_info.get("pre_publication_description", None)
                and not trait_info.get("pubmed_id", None)) else 0}
    return trait_info


def retrieve_probeset_trait_info(trait_data_source: Dict[str, Any], conn: Any):
    """Retrieve trait information for type `ProbeSet` traits.

    https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L424-L435"""
    keys = (
        "name", "symbol", "description", "probe_target_description", "chr",
        "mb", "alias", "geneid", "genbankid", "unigeneid", "omim",
        "refseq_transcriptid", "blatseq", "targetseq", "chipid", "comments",
        "strand_probe", "strand_gene", "probe_set_target_region", "proteinid",
        "probe_set_specificity", "probe_set_blat_score",
        "probe_set_blat_mb_start", "probe_set_blat_mb_end", "probe_set_strand",
        "probe_set_note_by_rw", "flag")
    columns = (f"ProbeSet.{x}" for x in keys)
    query = (
        f"SELECT {', '.join(columns)} "
        "FROM "
        "ProbeSet, ProbeSetFreeze, ProbeSetXRef "
        "WHERE "
        "ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND "
        "ProbeSetXRef.ProbeSetId = ProbeSet.Id AND "
        "ProbeSetFreeze.Name = %(trait_dataset_name)s AND "
        "ProbeSet.Name = %(trait_name)s")
    with conn.cursor() as cursor:
        cursor.execute(
            query,
            {
                k: v for k, v in trait_data_source.items()
                if k in ["trait_name", "trait_dataset_name"]
            })
        return dict(zip(keys, cursor.fetchone()))


def retrieve_geno_trait_info(trait_data_source: Dict[str, Any], conn: Any):
    """Retrieve trait information for type `Geno` traits.

    https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L438-L449"""
    keys = ("name", "chr", "mb", "source2", "sequence")
    columns = ", ".join(f"Geno.{x}" for x in keys)
    query = (
        f"SELECT {columns} "
        "FROM "
        "Geno INNER JOIN GenoXRef ON GenoXRef.GenoId = Geno.Id "
        "INNER JOIN GenoFreeze ON GenoFreeze.Id = GenoXRef.GenoFreezeId "
        "WHERE "
        "GenoFreeze.Name = %(trait_dataset_name)s AND "
        "Geno.Name = %(trait_name)s")
    with conn.cursor() as cursor:
        cursor.execute(
            query,
            {
                k: v for k, v in trait_data_source.items()
                if k in ["trait_name", "trait_dataset_name"]
            })
        return dict(zip(keys, cursor.fetchone()))


def retrieve_temp_trait_info(trait_data_source: Dict[str, Any], conn: Any):
    """Retrieve trait information for type `Temp` traits.

    https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L450-452"""
    keys = ("name", "description")
    query = (
        f"SELECT {', '.join(keys)} FROM Temp "
        "WHERE Name = %(trait_name)s")
    with conn.cursor() as cursor:
        cursor.execute(
            query,
            {
                k: v for k, v in trait_data_source.items()
                if k in ["trait_name"]
            })
        return dict(zip(keys, cursor.fetchone()))


def set_haveinfo_field(trait_info):
    """
    Common postprocessing function for all trait types.

    Sets the value for the 'haveinfo' field."""
    return {**trait_info, "haveinfo": 1 if trait_info else 0}


def set_homologene_id_field_probeset(trait_info, conn):
    """
    Postprocessing function for 'ProbeSet' traits.

    Sets the value for the 'homologene' key.
    """
    query = (
        "SELECT HomologeneId FROM Homologene, Species, InbredSet"
        " WHERE Homologene.GeneId = %(geneid)s AND InbredSet.Name = %(group)s"
        " AND InbredSet.SpeciesId = Species.Id AND"
        " Species.TaxonomyId = Homologene.TaxonomyId")
    with conn.cursor() as cursor:
        cursor.execute(
            query,
            {
                k: v for k, v in trait_info.items()
                if k in ["geneid", "group"]
            })
        res = cursor.fetchone()
        if res:
            return {**trait_info, "homologeneid": res[0]}
    return {**trait_info, "homologeneid": None}


def set_homologene_id_field(trait_type, trait_info, conn):
    """
    Common postprocessing function for all trait types.

    Sets the value for the 'homologene' key."""
    def set_to_null(ti): return {**ti, "homologeneid": None} # pylint: disable=[C0103, C0321]
    functions_table = {
        "Temp": set_to_null,
        "Geno": set_to_null,
        "Publish": set_to_null,
        "ProbeSet": lambda ti: set_homologene_id_field_probeset(ti, conn)
    }
    return functions_table[trait_type](trait_info)


def load_publish_qtl_info(trait_info, conn):
    """
    Load extra QTL information for `Publish` traits
    """
    query = (
        "SELECT PublishXRef.Locus, PublishXRef.LRS, PublishXRef.additive "
        "FROM PublishXRef, PublishFreeze "
        "WHERE PublishXRef.Id = %(trait_name)s "
        "AND PublishXRef.InbredSetId = PublishFreeze.InbredSetId "
        "AND PublishFreeze.Id = %(dataset_id)s")
    with conn.cursor() as cursor:
        cursor.execute(
            query,
            {
                "trait_name": trait_info["trait_name"],
                "dataset_id": trait_info["db"]["dataset_id"]
            })
        return dict(zip(["locus", "lrs", "additive"], cursor.fetchone()))
    return {"locus": "", "lrs": "", "additive": ""}


def load_probeset_qtl_info(trait_info, conn):
    """
    Load extra QTL information for `ProbeSet` traits
    """
    query = (
        "SELECT ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, "
        "ProbeSetXRef.mean, ProbeSetXRef.additive "
        "FROM ProbeSetXRef, ProbeSet "
        "WHERE ProbeSetXRef.ProbeSetId = ProbeSet.Id "
        " AND ProbeSet.Name = %(trait_name)s "
        "AND ProbeSetXRef.ProbeSetFreezeId = %(dataset_id)s")
    with conn.cursor() as cursor:
        cursor.execute(
            query,
            {
                "trait_name": trait_info["trait_name"],
                "dataset_id": trait_info["db"]["dataset_id"]
            })
        return dict(zip(
            ["locus", "lrs", "pvalue", "mean", "additive"], cursor.fetchone()))
    return {"locus": "", "lrs": "", "pvalue": "", "mean": "", "additive": ""}


def load_qtl_info(qtl, trait_type, trait_info, conn):
    """
    Load extra QTL information for traits

    DESCRIPTION:
    Migrated from
    https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L500-L534

    PARAMETERS:
    qtl: boolean
    trait_type: string
      The type of the trait in consideration
    trait_info: map/dictionary
      A dictionary of the trait's key-value pairs
    conn:
      A database connection object
    """
    if not qtl:
        return trait_info
    qtl_info_functions = {
        "Publish": load_publish_qtl_info,
        "ProbeSet": load_probeset_qtl_info
    }
    if trait_info["name"] not in qtl_info_functions:
        return trait_info

    return qtl_info_functions[trait_type](trait_info, conn)


def build_trait_name(trait_fullname):
    """
    Initialises the trait's name, and other values from the search data provided
    """
    def dataset_type(dset_name):
        if dset_name.find('Temp') >= 0:
            return "Temp"
        if dset_name.find('Geno') >= 0:
            return "Geno"
        if dset_name.find('Publish') >= 0:
            return "Publish"
        return "ProbeSet"

    name_parts = trait_fullname.split("::")
    assert len(name_parts) >= 2, f"Name format error: '{trait_fullname}'"
    dataset_name = name_parts[0]
    dataset_type = dataset_type(dataset_name)
    return {
        "db": {
            "dataset_name": dataset_name,
            "dataset_type": dataset_type},
        "trait_fullname": trait_fullname,
        "trait_name": name_parts[1],
        "cellid": name_parts[2] if len(name_parts) == 3 else ""
    }


def retrieve_probeset_sequence(trait, conn):
    """
    Retrieve a 'ProbeSet' trait's sequence information
    """
    query = (
        "SELECT ProbeSet.BlatSeq "
        "FROM ProbeSet, ProbeSetFreeze, ProbeSetXRef "
        "WHERE ProbeSet.Id=ProbeSetXRef.ProbeSetId "
        "AND ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId "
        "AND ProbeSet.Name = %(trait_name)s "
        "AND ProbeSetFreeze.Name = %(dataset_name)s")
    with conn.cursor() as cursor:
        cursor.execute(
            query,
            {
                "trait_name": trait["trait_name"],
                "dataset_name": trait["db"]["dataset_name"]
            })
        seq = cursor.fetchone()
        return {**trait, "sequence": seq[0] if seq else ""}


def retrieve_trait_info(
        threshold: int, trait_full_name: str, conn: Any,
        qtl=None):
    """Retrieves the trait information.

    https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L397-L456

    This function, or the dependent functions, might be incomplete as they are
    currently."""
    trait = build_trait_name(trait_full_name)
    trait_dataset_type = trait["db"]["dataset_type"]
    trait_info_function_table = {
        "Publish": retrieve_publish_trait_info,
        "ProbeSet": retrieve_probeset_trait_info,
        "Geno": retrieve_geno_trait_info,
        "Temp": retrieve_temp_trait_info
    }

    common_post_processing_fn = compose(
        lambda ti: load_qtl_info(qtl, trait_dataset_type, ti, conn),
        lambda ti: set_homologene_id_field(trait_dataset_type, ti, conn),
        lambda ti: {"trait_type": trait_dataset_type, **ti},
        lambda ti: {**trait, **ti})

    trait_post_processing_functions_table = {
        "Publish": compose(
            lambda ti: set_confidential_field(trait_dataset_type, ti),
            common_post_processing_fn),
        "ProbeSet": compose(
            lambda ti: retrieve_probeset_sequence(ti, conn),
            common_post_processing_fn),
        "Geno": common_post_processing_fn,
        "Temp": common_post_processing_fn
    }

    retrieve_info = compose(
        set_haveinfo_field, trait_info_function_table[trait_dataset_type])

    trait_dataset = retrieve_trait_dataset(
        trait_dataset_type, trait, threshold, conn)
    trait_info = retrieve_info(
        {
            "trait_name": trait["trait_name"],
            "trait_dataset_id": trait_dataset["dataset_id"],
            "trait_dataset_name": trait_dataset["dataset_name"]
        },
        conn)
    if trait_info["haveinfo"]:
        return {
            **trait_post_processing_functions_table[trait_dataset_type](
                {**trait_info, "group": trait_dataset["group"]}),
            "db": {**trait["db"], **trait_dataset}
        }
    return trait_info


def retrieve_temp_trait_data(trait_info: dict, conn: Any):
    """
    Retrieve trait data for `Temp` traits.
    """
    query = (
        "SELECT "
        "Strain.Name, TempData.value, TempData.SE, TempData.NStrain, "
        "TempData.Id "
        "FROM TempData, Temp, Strain "
        "WHERE TempData.StrainId = Strain.Id "
        "AND TempData.Id = Temp.DataId "
        "AND Temp.name = %(trait_name)s "
        "ORDER BY Strain.Name")
    with conn.cursor() as cursor:
        cursor.execute(
            query,
            {"trait_name": trait_info["trait_name"]})
        return [dict(zip(
            ["sample_name", "value", "se_error", "nstrain", "id"],
            row))
                for row in cursor.fetchall()]
    return []


def retrieve_species_id(group, conn: Any):
    """
    Retrieve a species id given the Group value
    """
    with conn.cursor as cursor:
        cursor.execute(
            "SELECT SpeciesId from InbredSet WHERE Name = %(group)s",
            {"group": group})
        return cursor.fetchone()[0]
    return None


def retrieve_geno_trait_data(trait_info: Dict, conn: Any):
    """
    Retrieve trait data for `Geno` traits.
    """
    query = (
        "SELECT Strain.Name, GenoData.value, GenoSE.error, GenoData.Id "
        "FROM (GenoData, GenoFreeze, Strain, Geno, GenoXRef) "
        "LEFT JOIN GenoSE ON "
        "(GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId) "
        "WHERE Geno.SpeciesId = %(species_id)s "
        "AND Geno.Name = %(trait_name)s AND GenoXRef.GenoId = Geno.Id "
        "AND GenoXRef.GenoFreezeId = GenoFreeze.Id "
        "AND GenoFreeze.Name = %(dataset_name)s "
        "AND GenoXRef.DataId = GenoData.Id "
        "AND GenoData.StrainId = Strain.Id "
        "ORDER BY Strain.Name")
    with conn.cursor() as cursor:
        cursor.execute(
            query,
            {"trait_name": trait_info["trait_name"],
             "dataset_name": trait_info["db"]["dataset_name"],
             "species_id": retrieve_species_id(
                 trait_info["db"]["group"], conn)})
        return [
            dict(zip(
                ["sample_name", "value", "se_error", "id"],
                row))
            for row in cursor.fetchall()]
    return []


def retrieve_publish_trait_data(trait_info: Dict, conn: Any):
    """
    Retrieve trait data for `Publish` traits.
    """
    query = (
        "SELECT "
        "Strain.Name, PublishData.value, PublishSE.error, NStrain.count, "
        "PublishData.Id "
        "FROM (PublishData, Strain, PublishXRef) "
        "LEFT JOIN PublishSE ON "
        "(PublishSE.DataId = PublishData.Id "
        "AND PublishSE.StrainId = PublishData.StrainId) "
        "LEFT JOIN NStrain ON "
        "(NStrain.DataId = PublishData.Id "
        "AND NStrain.StrainId = PublishData.StrainId) "
        "WHERE PublishData.Id = PublishXRef.DataId "
        "AND PublishXRef.Id = %(trait_name)s "
        "AND PublishXRef.InbredSetId = %(dataset_id)s "
        "AND PublishData.StrainId = Strain.Id "
        "ORDER BY Strain.Name")
    with conn.cursor() as cursor:
        cursor.execute(
            query,
            {"trait_name": trait_info["trait_name"],
             "dataset_id": trait_info["db"]["dataset_id"]})
        return [
            dict(zip(
                ["sample_name", "value", "se_error", "nstrain", "id"], row))
            for row in cursor.fetchall()]
    return []


def retrieve_cellid_trait_data(trait_info: Dict, conn: Any):
    """
    Retrieve trait data for `Probe Data` types.
    """
    query = (
        "SELECT "
        "Strain.Name, ProbeData.value, ProbeSE.error, ProbeData.Id "
        "FROM (ProbeData, ProbeFreeze, ProbeSetFreeze, ProbeXRef, Strain,"
        " Probe, ProbeSet) "
        "LEFT JOIN ProbeSE ON "
        "(ProbeSE.DataId = ProbeData.Id "
        " AND ProbeSE.StrainId = ProbeData.StrainId) "
        "WHERE Probe.Name = %(cellid)s "
        "AND ProbeSet.Name = %(trait_name)s "
        "AND Probe.ProbeSetId = ProbeSet.Id "
        "AND ProbeXRef.ProbeId = Probe.Id "
        "AND ProbeXRef.ProbeFreezeId = ProbeFreeze.Id "
        "AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id "
        "AND ProbeSetFreeze.Name = %(dataset_name)s "
        "AND ProbeXRef.DataId = ProbeData.Id "
        "AND ProbeData.StrainId = Strain.Id "
        "ORDER BY Strain.Name")
    with conn.cursor() as cursor:
        cursor.execute(
            query,
            {"cellid": trait_info["cellid"],
             "trait_name": trait_info["trait_name"],
             "dataset_id": trait_info["db"]["dataset_id"]})
        return [
            dict(zip(
                ["sample_name", "value", "se_error", "id"], row))
            for row in cursor.fetchall()]
    return []


def retrieve_probeset_trait_data(trait_info: Dict, conn: Any):
    """
    Retrieve trait data for `ProbeSet` traits.
    """
    query = (
        "SELECT Strain.Name, ProbeSetData.value, ProbeSetSE.error, "
        "ProbeSetData.Id "
        "FROM (ProbeSetData, ProbeSetFreeze, Strain, ProbeSet, ProbeSetXRef) "
        "LEFT JOIN ProbeSetSE ON "
        "(ProbeSetSE.DataId = ProbeSetData.Id "
        "AND ProbeSetSE.StrainId = ProbeSetData.StrainId) "
        "WHERE ProbeSet.Name = %(trait_name)s "
        "AND ProbeSetXRef.ProbeSetId = ProbeSet.Id "
        "AND ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id "
        "AND ProbeSetFreeze.Name = %(dataset_name)s "
        "AND ProbeSetXRef.DataId = ProbeSetData.Id "
        "AND ProbeSetData.StrainId = Strain.Id "
        "ORDER BY Strain.Name")

    with conn.cursor() as cursor:
        cursor.execute(
            query,
            {"trait_name": trait_info["trait_name"],
             "dataset_name": trait_info["db"]["dataset_name"]})
        return [
            dict(zip(
                ["sample_name", "value", "se_error", "id"], row))
            for row in cursor.fetchall()]
    return []


def with_samplelist_data_setup(samplelist: Sequence[str]):
    """
    Build function that computes the trait data from provided list of samples.

    PARAMETERS
    samplelist: (list)
      A list of sample names

    RETURNS:
      Returns a function that given some data from the database, computes the
      sample's value, variance and ndata values, only if the sample is present
      in the provided `samplelist` variable.
    """
    def setup_fn(tdata):
        if tdata["sample_name"] in samplelist:
            val = tdata["value"]
            if val is not None:
                return {
                    "sample_name": tdata["sample_name"],
                    "value": val,
                    "variance": tdata["se_error"],
                    "ndata": tdata.get("nstrain", None)
                }
        return None
    return setup_fn


def without_samplelist_data_setup():
    """
    Build function that computes the trait data.

    RETURNS:
      Returns a function that given some data from the database, computes the
      sample's value, variance and ndata values.
    """
    def setup_fn(tdata):
        val = tdata["value"]
        if val is not None:
            return {
                "sample_name": tdata["sample_name"],
                "value": val,
                "variance": tdata["se_error"],
                "ndata": tdata.get("nstrain", None)
            }
        return None
    return setup_fn


def retrieve_trait_data(trait: dict, conn: Any, samplelist: Sequence[str] = tuple()):
    """
    Retrieve trait data

    DESCRIPTION
    Retrieve trait data as is done in
    https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L258-L386
    """
    # I do not like this section, but it retains the flow in the old codebase
    if trait["db"]["dataset_type"] == "Temp":
        results = retrieve_temp_trait_data(trait, conn)
    elif trait["db"]["dataset_type"] == "Publish":
        results = retrieve_publish_trait_data(trait, conn)
    elif trait["cellid"]:
        results = retrieve_cellid_trait_data(trait, conn)
    elif trait["db"]["dataset_type"] == "ProbeSet":
        results = retrieve_probeset_trait_data(trait, conn)
    else:
        results = retrieve_geno_trait_data(trait, conn)

    if results:
        # do something with mysqlid
        mysqlid = results[0]["id"]
        if samplelist:
            data = [
                item for item in
                map(with_samplelist_data_setup(samplelist), results)
                if item is not None]
        else:
            data = [
                item for item in
                map(without_samplelist_data_setup(), results)
                if item is not None]

        return {
            "mysqlid": mysqlid,
            "data": dict(map(
                lambda x: (
                    x["sample_name"],
                    {k: v for k, v in x.items() if x != "sample_name"}),
                data))}
    return {}


def generate_traits_filename(base_path: str = TMPDIR):
    """Generate a unique filename for use with generated traits files."""
    return (
        f"{os.path.abspath(base_path)}/traits_test_file_{random_string(10)}.txt")


def export_informative(trait_data: dict, inc_var: bool = False) -> tuple:
    """
    Export informative strain

    This is a migration of the `exportInformative` function in
    web/webqtl/base/webqtlTrait.py module in GeneNetwork1.

    There is a chance that the original implementation has a bug, especially
    dealing with the `inc_var` value. It the `inc_var` value is meant to control
    the inclusion of the `variance` value, then the current implementation, and
    that one in GN1 have a bug.
    """
    def __exporter__(acc, data_item):
        if not inc_var or data_item["variance"] is not None:
            return (
                acc[0] + (data_item["sample_name"],),
                acc[1] + (data_item["value"],),
                acc[2] + (data_item["variance"],))
        return acc
    return reduce(
        __exporter__,
        filter(lambda td: td["value"] is not None,
               trait_data["data"].values()),
        (tuple(), tuple(), tuple()))