-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathHISTORY
7046 lines (6041 loc) · 141 KB
/
HISTORY
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
TAG: qcreports_db-6-0-24-16
DATE: 01/16/2025
STAFF: liangh
wts2-1599/e4g-113/Do PMID search to find unevaluated experiments associated with papers...
# modified: pwi/pwireports.txt
# new file: pwi/GXD_HTExperimentPMID.py
TAG: qcreports_db-6-0-24-15
DATE: 11/19/2024
STAFF: lec
mirror_wget/bhmgiimsr01.jax.org.imsr_allStrains -> bhmgiimsr02lp.jax.org issue
# modified: Configuration.default
TAG: qcreports_db-6-0-24-14
DATE: 11/04/2024
STAFF: lec
wts2-1539/e4g-57/GXD RNA-Seq Type/Schema/Migration
# modified: pwi/GXD_HTSampleAnnotations.py
# new file: mgd/GXD_HTSampleNoRNAType.py
TAG: qcreports_db-6-0-24-13
DATE: 10/29/2024
STAFF: lec
wts2-1571/e4g-54/tweak WF_SupplementalData.rpt so that it excludes gxdht only papers
# modified: mgd/WF_SupplementalData.py
TAG: qcreports_db-6-0-24-13
TAG: qcreports_db-6-0-24-12
TAG: qcreports_db-6-0-24-11
TAG: qcreports_db-6-0-24-10
TAG: qcreports_db-6-0-24-9
TAG: qcreports_db-6-0-24-8
DATE: 10/25/2024
STAFF: lec
wts2-1565/e4g-39/GXD HT: Missing PMIDs
# new file: mgd/GXD_HTPubMed.py
TAG: qcreports_db-6-0-24-7
DATE: 10/22/2024
STAFF: lec
wts2-1567/e4g-42/change sort order of custom report: GXD HT Experiment notes displayed to the public
# modified: pwi/GXD_HTExperimentCuratedNote.py
TAG: qcreports_db-6-0-24-6
DATE: 10/08/2024
STAFF: lec
wts2-1563/e4g-29/tweak to existing Unused image panes from full coded references QC (GXD #8)
# modified: mgd/GXD_ImagesUnused.py
TAG: qcreports_db-6-0-24-5
DATE: 08/28/2024
STAFF: lec
wts2-1377/fl2-960/QC reports for MP-HP match tool
# new file: weekly/VOC_OntologyExactMatch.py
TAG: qcreports_db-6-0-24-4
DATE: 08/26/2024
STAFF: lec
wts2-1541/fl2-957/obsoletes showing in MP Ontology terms added in the last week report
# modified: weekly/VOC_MPNewTerms.py
TAG: qcreports_db-6-0-24-3
DATE: 08/19/2024
STAFF: lec
wts2-1536/fl2-950/QC report/GXD HT missing annotations to RNA seq experiment variants
# new file: mgd/GXD_HTRNASeq.py
TAG: qcreports_db-6-0-24-2
DATE: 07/12/2024
STAFF: lec
wts2-1521/fl2-924/Strain Check by Strain Repository ID; make case insensitive
# modified: PRB_StrainRepoCheck.py
TAG: qcreports_db-6-0-24-1
TAG: qcreports_db-6-0-23-29
DATE: 07/10/2024
STAFF: jer
wts2-1486/fl2-911 Don't display Reset button unless there is a form.
wts2-1486/fl2-911 Enable file upload. Required major rewrite.
TAG: qcreports_db-6-0-23-28
DATE: 07/02/2024
STAFF: lec
wts2-1512/fl2-913/emageload retire/qcr.shtml
TAG: qcreports_db-6-0-23-27
DATE: 06/27/2024
STAFF: lec
wts2-1486/fix reoombinase bug/GXD_IndexOverviewUber.py
TAG: qcreports_db-6-0-23-26
TAG: qcreports_db-6-0-23-25
DATE: 06/25/2024
STAFF: lec
fixed vocload; should use ldb=15 not ldb=191
wts2-1399/fl2-905/OMIM to MIM change broke 2 DO reports
# modified: VOC_OMIMDOMult.py
# modified: VOC_OMIMDOObsolete.py
TAG: qcreports_db-6-0-23-24
DATE: 06/12/2024
STAFF: lec
wts2-1492/fl2-861/change the run frequency of some GXD QC reports and rearrange list to reflect this new run frequency
# renamed: weekly/GXD_DupPrimers.sql -> mgd/GXD_DupPrimers.sql
# renamed: mgd/GXD_FullCodeable.py -> weekly/GXD_FullCodeable.py
# renamed: mgd/GXD_Images.py -> weekly/GXD_Images.py
# renamed: mgd/GXD_LackingImages.py -> weekly/GXD_LackingImages.py
# renamed: mgd/GXD_WithdrawnMarker.py -> weekly/GXD_WithdrawnMarker.py
TAG: qcreports_db-6-0-23-23
DATE: 06/06/2024
STAFF: lec
wts2-1483/fl2-894/more exclusions for References QC 5. J#s missing PDF’s
# modified: monthly/BIB_MissingPDFs.sql
TAG: qcreports_db-6-0-23-22
DATE: 05/29/2024
STAFF: lec
wts2-1480/fl2-876/move BIB Missing DOI from weekly to daily
# renamed: weekly/BIB_MissingDOI.sql -> mgd/BIB_MissingDOI.sql
TAG: qcreports_db-6-0-23-21
DATE: 05/28/2024
STAFF: lec
wts2-1403/fl2-732/Change of OMIM prefix to MIM in MGI: back end
TAG: qcreports_db-6-0-23-20
TAG: qcreports_db-6-0-23-19
DATE: 04/29/2024
STAFF: lec,jer
wts2-???/fl2-832/Move TR12977 custom report into qcreports_db/pwi
wts2-???/fl2-832/Move TR12977 custom report into qcreports_db/pwi - limit displayed rows to 1000.
TAG: qcreports_db-6-0-23-18
DATE: 04/02/2024
STAFF: lec
wts2-1155/GOC taking over GOA mouse, GOA human, etc.
# deleted: VOC_GOObsolete.py
wts2-1155/GOC taking over GOA mouse, GOA human, etc.
TAG: qcreports_db-6-0-23-17
DATE: 04/02/2024
STAFF: lec
wts2-1453/fl2-811/add curation state to existing custom report
TAG: qcreports_db-6-0-23-16
TAG: qcreports_db-6-0-23-15
DATE: 03/29/2024
STAFF: lec
wts2-1155/GOC taking over GOA mouse, GOA human, etc.
wts2-1450/Custom Report for GXD workflow tag
# new file: GXD_PriorityTags.py
mgd/GO_Combined_Report.py
mgd/GO_MGIGAF.py
mgd/GO_stats.py
mgd/GO_MGIGAF.py
monthly/MRK_GOSymbolChange.sql
qcgo_reports.csh
qcr.shtml
qcweekly_reports.csh
TAG: qcreports_db-6-0-23-14
DATE: 03/25/2024
STAFF: lec
wts2-1447/Lit triage: journals x year of publication (QC report to track journal usage in the MasterBib)
wts2-1448/Lit triage: journals x curatorial group (QC reports to track journal usage by group)
wts2-1449/Lit triage: journals' keep/discard numbers
# new file: monthly/BIB_JournalByYear.py
# new file: monthly/BIB_JournalByGroupYear.py
# new file: monthly/BIB_JournalByYearKD.py
TAG: qcreports_db-6-0-23-13
TAG: qcreports_db-6-0-23-12
DATE: 03/19/2024
STAFF: lec
wts2-1441/fl3-787/custom report listing HT Experiment Notes for experiments whose curation status = done
TAG: qcreports_db-6-0-23-11
TAG: qcreports_db-6-0-23-10
DATE: 03/14/2024
STAFF: lec
wts2-1439/fl2-784/HT/remove Raw Sample Count from PWI & QC
undo:
wts2-1430/fl2-778/add column to existing GXD_HTOverview
TAG: qcreports_db-6-0-23-9
DATE: 03/13/2024
STAFF: lec
wts2-1437/fl2-780/missing QC report 'New PubMed2Gene References for markers with no literature MP annot'
weird/looks ok on master/qcr.shtml
TAG: qcreports_db-6-0-23-8
DATE: 03/12/2024
STAFF: lec
wts2-1430/fl2-778/add column to existing GXD_HTOverview
TAG: qcreports_db-6-0-23-7
TAG: qcreports_db-6-0-23-6
DATE: 03/11/2024
STAFF: lec
wts2-1429/fl2-777/re-add weekly/BIB_Duplicates.sql
TAG: qcreports_db-6-0-23-5
TAG: qcreports_db-6-0-23-4
DATE: 03/1/2024
STAFF: lec
wts2-1419/fl2-761/Alicia Valenzuela QC, etc.
wts2-1421/obsolete QC reports
# deleted: mgd/PRB_Strain5.py
# deleted: mgd/PRB_Strain6.py
# deleted: mgd/PRB_StrainDup.sql
# deleted: mgd/PRB_StrainTrans.sql
# deleted: mgd/PRB_Strain_MultNoAlleles.sql
# deleted: mgd/PRB_Strain_NoAlleles1.sql
# deleted: mgd/PRB_Strain_NomenSyns.py
# deleted: mgd/PRB_Strain_OtherSyns.py
# deleted: mgd/PRB_Strain_SingleNoAlleles1.sql
# deleted: mgd/PRB_Strain_SingleNoAlleles2.sql
# deleted: mgd/PRB_Strain_Standard.sql
# deleted: weekly/BIB_Duplicates.sql
# deleted: weekly/GO_CurationMetrics.sql
# deleted: monthly/BIB_Dagger.sql
TAG: qcreports_db-6-0-23-3
DATE: 02/27/2024
STAFF: lec
wts2-1412/fl2-758/retire WF_GXD_secondary.rpt QC
# deleted: weekly/WF_GXD_secondary.py
TAG: qcreports_db-6-0-23-2
DATE: 02/01/2024
STAFF: lec
wts2-1382/fl2-717/add relevance
wts2-1381/fl2-721/New QC report: New PubMed2Gene References for markers with no literature MP annot.
# new file: mgd/ALL_PM2GeneNoMP.py
# modified: mgd/GO_PM2GeneRefsNotInMGI.py
TAG: qcreports_db-6-0-23-1
DATE: 01/31/2024
STAFF: lec
# modified: mgd/VOC_InvalidProperties.py
fix bug
TAG: qcreports_db-6-0-22-76
DATE: 01/30/2024
STAFF: lec
wts2-1390/fl2-712/Custom report for batch allele retrieval
(qcreports/pwi/ALL_CheckByCreationDate.py)
TAG: qcreports_db-6-0-22-75
DATE: 12/05/2023
STAFF: sc
New report: weekly/HOM_MouseNoHuman.py
TAG: qcreports_db-6-0-22-74
DATE: 11/30/2023
STAFF: dbm
qcr.shtml: remove link to arrayexpload (retired)
TAG: qcreports_db-6-0-22-73
DATE: 11/28/2023
STAFF: lec
wts2-1343/fl2-653/Custom GXD report for highlight
TAG: qcreports_db-6-0-22-72
DATE: 11/21/2023
STAFF: lec
wts2-1342/fl2-649/one more for the PRB_Reference.sql.rpt/rename it
TAG: qcreports_db-6-0-22-70
DATE: 11/14/2023
STAFF: dbm
qcr.shtml: remove link to genmapload (retired)
TAG: qcreports_db-6-0-22-71
TAG: qcreports_db-6-0-22-69
DATE: 11/13/2023
STAFF: lec
wts2-1331/fl2-637/Update Images QC
# modified: mgd/GXD_Images.py
TAG: qcreports_db-6-0-22-68
DATE: 11/13/2023
STAFF: lec
wts2-1330/fl2-636/Duplicate RNAscope Probes (Mm-%)
# modified: monthly/PRB_Reference.sql
TAG: qcreports_db-6-0-22-67
TAG: qcreports_db-6-0-22-66
DATE: 11/09/2023
STAFF: lec
wts2-1328/fl2-633/Gene Expr Patterns papers to full code
# modified: weekly/GXD_FullCode.py
TAG: qcreports_db-6-0-22-65
DATE: 11/03/2023
STAFF: lec
wts2-1321/fl2-616/add PMID to Invalid Inferred From Values report
# modified: mgd/VOC_InvalidInferred.py
TAG: qcreports_db-6-0-22-64
DATE: 11/01/2023
STAFF: lec
wts2-1315/fl2-612/GXD HT Raw Sample Value Search: return by experiment (not sample)
# new file: GXD_HTRawSampleByValue2.py
# modified: pwireports.txt
TAG: qcreports_db-6-0-22-63
DATE: 10/25/2023
STAFF: dbm
wts2-1313/fl2-602/add sunday/inferred from linkout errors to GO/QC
TAG: qcreports_db-6-0-22-62
DATE: 10/19/2023
STAFF: dbm
qcr.shtml: remove link to TAL (retired)
TAG: qcreports_db-6-0-22-61
DATE: 10/17/2023
STAFF: sc
Fixed bug in MRK_Withdrawn.sql - never updated when MRK_Status terms
were moved to VOC_Term
TAG: qcreports_db-6-0-22-60
TAG: qcreports_db-6-0-22-59
DATE: 10/03/2023
STAFF: sc
fl2-568/move reports from targetedalleleload
1. weekly/TAL_check_superscript.py
2. weekly/TAL_dupe_allele.py
3. weekly/TAL_multiple_project_ids.py
4. added to qcr.shtml
TAG: qcreports_db-6-0-22-58
TAG: qcreports_db-6-0-22-57
DATE: 09/22/2023
STAFF: lec
wts2-1286/fl2-554/change GXD #39 and #40 from monthly runs to weekly
wts2-1285/tweak to two recent QCs
GXD_FullCodeableLargeScale.py
GXD_FullCodeableAdultSpecs.py
TAG: qcreports_db-6-0-22-56
DATE: 09/21/2023
STAFF: lec
wts2-1281/fl2-544/Add a column to the results of Strains report #14
mgd/MLP_Nomenclature.sql
TAG: qcreports_db-6-0-22-55
DATE: 09/06/2023
STAFF: lec
wts2-1268/fl2503/2 new GXD QC reports for fullcoding priority
# new file: monthly/GXD_FullCodeableLargeScale.py
# new file: monthly/GXD_FullCodeableAdultSpecs.py
TAG: qcreports_db-6-0-22-54
DATE: 07/11/2023
STAFF: lec
wts2-1228/fl2-437/GXD HT Raw Sample Key/Value Search--preferential return of predicted yes/no
GXD_HTRawSampleByKey.py,GXD_HTRawSampleByValue.py
TAG: qcreports_db-6-0-22-53
DATE: 06/27/2023
STAFF: jer
wts2-1177/fl2-412 Add fields to extracted text custom report.
TAG: qcreports_db-6-0-22-52
DATE: 06/14/2023
STAFF: lec
wts2-1210/fl2-411/GXD QC: add another excluded assay type
TAG: qcreports_db-6-0-22-51
TAG: qcreports_db-6-0-22-50
DATE: 06/12/2023
STAFF: lec
wts2-1208/fl2-402/add PMID id to GXD HT Experiment Note Search
pwi/GXD_HTExperimentByNote.py
TAG: qcreports_db-6-0-22-49
DATE: 06/08/2023
STAFF: jer
wts2-1195/fl2-399/Custom report alleles with "mut =" in Nomenclature note
TAG: qcreports_db-6-0-22-48
DATE: 06/08/2023
STAFF: dbm
wts2-1201/fl2-400/Various QC report changes (retire, change frequency, reorder)
TAG: qcreports_db-6-0-22-47
DATE: 05/30/2023
STAFF: lec
wts2-1194/fl2-385/Adding columns to Strain Check by Strain Nomenclature report
PRB_StrainNomenCheck.py
TAG: qcreports_db-6-0-22-46
DATE: 05/24/2023
STAFF: lec
wts2-1187/fl2-362/Missing driver QC report
wts2-1190/fl2-465/new custom report: GXD Assay Note Search
TAG: qcreports_db-6-0-22-45
TAG: qcreports_db-6-0-22-44
DATE: 05/23/2023
STAFF: lec
wts2-1185/fl2-355/Variant Curation Activity Report
TAG: qcreports_db-6-0-22-43
DATE: 05/12/2023
STAFF: lec
wts2-1132/fl2-343/Define MGI staff contacts for unassigned Sequence Group QC reports
TAG: qcreports_db-6-0-22-42
DATE: 05/12/2023
STAFF: lec
wts2-1115/fl2-206/QC reports/wiki/etc. changes due to retiring in MGI (part 2)
TAG: qcreports_db-6-0-22-41
DATE: 05/09/2023
STAFF: lec
wts2-1171/fl2-335/new custom report: GXD Specimen Note Search
TAG: qcreports_db-6-0-22-40
DATE: 04/26/2023
STAFF: sc
wts2-1050/Florida Too Project
TAG: qcreports_db-6-0-22-39
DATE: 04/11/2023
STAFF: dbm
fl2-278/Clean up bhmgiapp14ld (scrum server) /data/downloads (includes Test and Prod)
qcr.html: removed gensatload link (retired)
TAG: qcreports_db-6-0-22-38
DATE: 03/01/2023
STAFF: lec
wts2-1093/fl2-233/Missing DOI QC report
weekly/BIB_MissingDOI.sql
TAG: qcreports_db-6-0-22-37
TAG: qcreports_db-6-0-22-36
DATE: 02/28/2023
STAFF: lec
wts2-556/fl2-210/Request for additional GO QC report: under-annotated genes (TR13434)
monthly/GO_Unannotationed.py
TAG: qcreports_db-6-0-22-35
DATE: 02/22/2023
STAFF: lec
wts2-1115/fl2-178/QC reports/wiki/etc. changes due to retiring in MGI (part 1)
TAG: qcreports_db-6-0-22-34
DATE: 02/10/2023
STAFF: sc
WTS2-1114 - report of symbols with GO NOCTUA annotations that have
symbol, merger, or withdrawal, delete in the last month
TAG: qcreports_db-6-0-22-33
DATE: 02/09/2023
STAFF: lec
wts2-1097/fl2-203/add Experiments where Curation State=Done and Evaluation !=Yes
mgd/GXD_HTExpCuration.py
TAG: no tag
DATE: 02/07/2023
STAFF: lec
ok to install on production at next tag
florida too/fl2b/expresses-component
weekly/MRK_NonMouseNotInEG.py
TAG: qcreports_db-6-0-22-32
TAG: qcreports_db-6-0-22-31
DATE: 02/02/2023
STAFF: sc
Added MP HP Relationship Load and MP HPO Header mapping load to the index page
TAG: qcreports_db-6-0-22-30
DATE: 02/02/2023
STAFF: lec
wts2-1198/fl2-171/exclude cell line, deleted and certain other alleles
weekly/ALL_MolNotesNoMP.py
TAG: qcreports_db-6-0-22-29
DATE: 01/23/2022
STAFF: sc
wts2-1100/fl2-146/New custom report for extracted text
pwi/BIB_ExtractedTextByMGIIDs.py
TAG: qcreports_db-6-0-22-28
TAG: qcreports_db-6-0-22-27
DATE: 01/13/2022
STAFF: sc
wts2-1091 - weekly/ALL_NomenCheck.py
TAG: qcreports_db-6-0-22-26
DATE: 12/22/2022
STAFF: sc
WTS2-1077 add PubMed ids to HT overview report
mgd/GXD_HTOverview.py
TAG: qcreports_db-6-0-22-25
TAG: qcreports_db-6-0-22-24
TAG: qcreports_db-6-0-22-23
DATE: 12/14/2022, 12/15/2022
STAFF: lec
wts2-1073/Titles come in from pubmed that say 'dagger'"
monthly/BIB_Dagger.sql
TAG: qcreports_db-6-0-22-22
TAG: qcreports_db-6-0-22-21
TAG: qcreports_db-6-0-22-20
TAG: qcreports_db-6-0-22-19
DATE: 12/01/2022, 12/07/2022
STAFF: lec
fl2/gxd secondary triage
monthly/GXD_NotRouted.py
weekly/WF_GXD_secondary.py
TAG: qcreports_db-6-0-22-18
DATE: 11/30/2022
STAFF: lec
fl2/gxd secondary triage
weekly/WF_GXD_secondary.py
TAG: qcreports_db-6-0-22-17
DATE: 11/25/2022
STAFF: lec
wts2-1046/Move PWI/GO/Potential GO Reference Report to qcreports_db/pwi
TAG: qcreports_db-6-0-22-16
TAG: qcreports_db-6-0-22-15
TAG: qcreports_db-6-0-22-14
TAG: qcreports_db-6-0-22-13
TAG: qcreports_db-6-0-22-12
TAG: qcreports_db-6-0-22-11
TAG: qcreports_db-6-0-22-10
TAG: qcreports_db-6-0-22-9
DATE: 11/10/2022, 11/14/2022
STAFF: lec
wts2-888/SQA: PWI/Custom Reports/new pwi folder
wts2-1031/Divide data in nomen QC reports
modified: mgd/HMD_SymbolDiffs.py
TAG: qcreports_db-6-0-22-8
DATE: 11/08/2022
STAFF: lec
wts2-1031/Divide data in nomen QC reports
modified: mgd/HMD_SymbolDiffs.py
TAG: qcreports_db-6-0-22-7
DATE: 10/14/2022
STAFF: lec
wts2-1009/Additional GXD QC report for Probes
mgd/GXD_ProbeAntibody.sql
monthly/PRB_Reference.sql
TAG: qcreports_db-6-0-22-6
DATE: 10/04/2022
STAFF: lec
wts2-992/identify HT index experiments with associated PMID used by GXD in MasterBib
weekly/GXD_HTExpPubMedID.sql
TAG: qcreports_db-6-0-22-5
DATE: 09/09/2022
STAFF: lec
wts2-977/Add SynGO annotation tracking to GO stats report
TAG: qcreports_db-6-0-22-4
DATE: 09/09/2022
STAFF: lec
wts2-976/Tweaks to GO Stats report
TAG: qcreports_db-6-0-22-3
TAG: qcreports_db-6-0-22-2
TAG: qcreports_db-6-0-22-1
DATE: 08/25/2022, 08/31/2022
STAFF: lec
wts2-761/MGD db cleanup - gxd vocabs -> voc_vocab/voc_term
wts2-761/use keys for Absent/Not Applicable query
TAG: qcreports_db-6-0-21-5
TAG: qcreports_db-6-0-21-4
DATE: 07/21/2022
STAFF: sc
wts2-944 created ondemand directory
converted the WTS2-673 customSQL report to an on demand QC report:
BIB_ArticlesByYear.csh/BIB_ArticlesByYear.py
TAG: qcreports_db-6-0-21-3
TAG: qcreports_db-6-0-21-2
DATE: 07/19/2022
STAFF: sc
wts2-896/crm-306
weekly/MRK_QTLCandidateGene.py
TAG: qcreports_db-6-0-21-1
DATE: 07/18/2022
STAFF: lec
wts2-938/Non-Recombinase allele with driver gene check
RECOMB_NoDriver.py
TAG: qcreports_db-6-0-20-2
DATE: 06/30/2022
STAFF: lec
wts2-918/Tweek for reporting invalid properties
TAG: qcreports_db-6-0-20-1
DATE: 06/27/2022
STAFF: lec
wts2-791/cell type annotations to obsolete CL terms/GXD_CellLine_Obsolete.sql
TAG: qcreports_db-6-0-18-14
DATE: 05/12/2022
STAFF: sc
mgd/GXD_ChildExpNotParent.py - bug fix
WTS2-868 - something is scrambled on the GXD_ChildExpNotParent.rpt
TAG: qcreports_db-6-0-18-13
TAG: qcreports_db-6-0-18-12
DATE: 04/07/2022
STAFF: lec
fixed link to /data/loads/go/goamouse/output/pubmed.error
TAG: qcreports_db-6-0-18-11
TAG: qcreports_db-6-0-18-10
DATE: 04/06/2022
STAFF: lec
wts2-802/HT index custom & QC reports don't work with GEO primary ids
added logicaldb = 190
# modified: GXD_HTExpCuration.py
# modified: GXD_HTSampleGenotypeNA.py
# modified: GXD_HTSampleNoAge.sql
# modified: GXD_HTSampleNoStructure.py
# modified: GXD_HTSampleTheilerAge.py
wts2-792/QC for GXD & Cre: specimens/gel lanes lacking an age min/max
# modified: mgd/GXD_SpecNoAge.sql
# modified: mgd/RECOMB_SpecNoAge.sql
TAG: qcreports_db-6-0-18-9
TAG: qcreports_db-6-0-18-8
DATE: 03/23/2022
STAFF: lec
wts2-703/new Noctua -> GO Annotation pipeline
# modified: qcnightly_reports.csh
remove: mgidbmigration/tr13272/go_cam.csh
remove: weekly/PHENO_Features.py per Allele Relationship PWI
wts2-804/modify BIB_Duplicates.sql.rpt to "ignore" period at end of title
TAG: qcreports_db-6-0-18-7
TAG: qcreports_db-6-0-18-6
DATE: 02/21/2022
STAFF: lec
CHANGES:
wts2-767/mgi_notechunk/mgi_note merge
TAG: not tag
DATE: 01/31/2022
STAFF: lec
monthly/ALL_RefCounts.py; added [email protected]
TAG: qcreports_db-6-0-18-5
DATE: 02/09/2020
STAFF: lec
wts2-773/Adding curator column to New Allele Report
# modified: weekly/ALL_NewAllele.py
TAG: qcreports_db-6-0-18-4
TAG: qcreports_db-6-0-18-3
TAG: qcreports_db-6-0-18-2
TAG: qcreports_db-6-0-18-1
DATE: 01/10/2022
STAFF: sc
Merge YAKS branch to trunk
lec - monthly/ALL_RefCounts.py; added [email protected]
TAG: qcreports_db-6-0-17-27
TAG: qcreports_db-6-0-17-26
DATE: 12/27/2021
STAFF: lec
wts2-750/Allele report "Review for AP:NewAlleleNomenclature tag" not finding all relevant "routed" pdfs
mgd/WF_AP_NewAlleleNomenTag.py
sym link removed: weeklyGO_stats.py
TAG: qcreports_db-6-0-17-25
TAG: qcreports_db-6-0-17-24
TAG: qcreports_db-6-0-17-23
DATE: 12/20/2021, 12/21/2021
STAFF: lec
wts2-752/add all root section to GO Stats report/GO_stats.py
wts2-747/add resonsible person to Allele QC reports
wts2-746/discontinue selected 'Allele' and 'Strain' QC reports
remove:
ALL_NoMutantSentence.py
ALL_SequenceReference.sql
ALL_UncodedReference.py
ALL_NoPhenoRef.py
ALL_MCLAllele.sql
ALL_NoOrigRef.sql
GXD_OrphanGenotype.sql
WF_AP_Routed.py
BIB_StatusMismatch_AP.sql
PRB_StrainJAX8.sql
remove mmrrc piece only:
PRB_StrainJAX2.py
PRB_StrainJAX3.py
TAG: qcreports_db-6-0-17-22
DATE: 12/09/2021
STAFF: lec
wts2-739/add references = discard used in Annotations to existing MRK_BIB_Discard.py report
# deleted: mgd/MRK_BIB_Discard.py
# new file: mgd/MRK_BIB_Discard.sql
TAG: qcreports_db-6-0-17-21
DATE: 12/01/2021
STAFF: lec
wts2-735/WF_AP_Discard obsolete/removed
TAG: qcreports_db-6-0-17-20
DATE: 11/30/2021
STAFF: dbm
yaks-394/exclude recombinase reporter assays
TAG: qcreports_db-6-0-17-19
TAG: qcreports_db-6-0-17-18
TAG: qcreports_db-6-0-17-17
TAG: qcreports_db-6-0-17-16
TAG: qcreports_db-6-0-17-15
DATE: 10/29/2021
STAFF: sc
yaks-319 Cell Type QC Report - all CL terms with synonyms
new: mgd/GXD_CellType_Terms.py
tweaks:
exclude obsolete
include only exact synonyms
change syn col hdr to ExactSynonyms
TAG: qcreports_db-6-0-17-14
DATE: 10/28/2021
STAFF: lec
wts2-556/Request for additional GO QC report: under-annotated genes (TR13434)
TAG: qcreports_db-6-0-17-13
DATE: 10/8/2021
STAFF: dbm
wts2-675/changes to GXD_Images.py
TAG: qcreports_db-6-0-17-12
DATE: 10/7/2021
STAFF: dbm
wts2-682/added BIB_COVRefTagCounts.py and updated qcr.shtml
TAG: qcreports_db-6-0-17-11
DATE: 10/7/2021
STAFF: dbm
wts2-684/changes to GXD_Images.py, GXD_FullCode.py and qcr.shtml
TAG: qcreports_db-6-0-17-10
DATE: 06/21/2021
STAFF: lec
yaks-39/Identify curator contacts for all loads
qcr.shtml updates
TAG: qcreports_db-6-0-17-9
DATE: 06/10/2021
STAFF: lec
b39/451/TR13463/changes to GO QC/MRK_GOIEA.py
got overwritten by TR13349/merge
TAG: qcreports_db-6-0-17-8
TAG: qcreports_db-6-0-17-7
TAG: qcreports_db-6-0-17-6
TAG: qcreports_db-6-0-17-5
DATE: 06/03/2021
STAFF: sc
WTS2-615 - mgd/WF_AP_NewAlleleNomenTag.py - new column: indexed genes
WTS2-614 - mgd/WF_AP_NewAlleleNomenTag.py - new exclusions
WTS2-616 - weekly/WF_AP_Tags.py - new column: indexed genes
WTS2-619 - mgd/WF_AP_IndexingNeeded.py - new report
TAG: qcreports_db-6-0-17-4
TAG: qcreports_db-6-0-17-3
TAG: qcreports_db-6-0-17-2
TAG: qcreports_db-6-0-17-1
DATE: 05/11/2021, 05/20/2021
STAFF: lec
TR13349/Genome Build 39
TAG: qcreports_db-6-0-16-31
DATE: 04/29/2021
STAFF: lec
b39/451/TR13463/changes to GO QC/MRK_GOIEA.py
TAG: qcreports_db-6-0-16-30
DATE: 04/27/2021
STAFF: lec
b39-467/GO-Done report/GO_done.py
TAG: qcreports_db-6-0-16-29
DATE: 04/27/2021
STAFF: dbm
1) Remove assocload directory: move reports to assocload product
TAG: qcreports_db-6-0-16-28
DATE: 04/26/2021
STAFF: dbm
1) Remove egload directory: not used
2) Remove pirsfload directory: moved script to pirsfload product
3) qcr.shtml: Removed link to Unigene load (retired)
TAG: qcreports_db-6-0-16-27
DATE: 04/21/2021
STAFF: sc
WTS2-569 - updates to:
mgd/GXD_HTSampleNoAge.sql
mgd/GXD_SpecNoAge.sql
mgd/RECOMB_SpecNoAge.sql
TAG: qcreports_db-6-0-?-?
DATE: ?
STAFF: lec
TR13349/Genome Build 39 project
obsolete reports:
WF_AP_Routed.py
changes:
MRK_BIB_Discard.py
GXD_Referenes.sql
GXD_Triage.py
WF_SupplimentalData.py
WF_GXD_Secondary.py
WF_AP_Discard.py
WF_AP_NewAlleleNomenTag.py
WF_AP_Tags.py
QTL_Triage.py
allstrain/Allele Strain of Origin vs. Parent Cell Line Strain (see allcacheload/allstrain.py)
changes:
mgd/GXD_ImageCheck.sql
mgd/GXD_Images.py
mgd/GXD_LackingImages.py
weekly/PHENO_ImageCheck.sql
Alliance Homology Report changes:
MRK_RatNoGO.sql
GO_Combined_Report.py
MRK_Homology_Class1.py
HMD_SymbolDiffs.py
obsolete homology reports:
MRK_Homology_Class2.py - uses homologene to determine homology clusters with no mouse genes - REMOVED OBSOLETE
MRK_Homology_Class3.py - uses homologene to determine homology classes with > n genes from a single species - REMOVED OBSOLETE
>>>>>>> tr13349
TAG: qcreports_db-6-0-16-25
TAG: qcreports_db-6-0-16-24
DATE: 04/21/2021
STAFF: lec
WTS2-600/mgd/GXD_ImageCheck.sql
also removed egload/dummy.py : obsolete/not used
TAG: qcreports_db-6-0-16-23
>>>>>>> master
TAG: qcreports_db-6-0-16-22
DATE: 04/14/2021, 04/21/2021
STAFF: lec
add go_cam.csh to qcnightly_reports.csh
${DBUTILS}/mgidbmigration/tr13272/go_cam.csh
TAG: qcreports_db-6-0-16-21
TAG: qcreports_db-6-0-16-20
DATE: 04/14/2021
STAFF: sc
WTS2-497 new report weekly/VOC_DODups.sql
TAG: qcreports_db-6-0-16-19
DATE: 04/13/2021
STAFF: dbm
TR13481/New GO Text Load
>>>>>>> master
TAG: qcreports_db-6-0-16-18
DATE: 04/08/2021
STAFF: lec
TR13307/Adding PMIDS from Noctua load into MGI
TAG: qcreports_db-6-0-16-17
DATE: 03/30/2021
STAFF: sc
TR13485/Fix bug in mgd/VOC_InvalidInferred.py - see TR
TAG: qcreports_db-6-0-16-16
DATE: 03/12/2021
STAFF: dbm
TR13379/Modifications to GO Stats
TAG: qcreports_db-6-0-16-15
DATE: 03/02/2021
STAFF: lec
TR13469/proisoformload/GAF2.2 changes
TAG: qcreports_db-6-0-16-14
DATE: 01/28/2021
STAFF: sc
TR13433 - New GO report: pm2gene Refs not in MGI
mgd/GO_PM2GeneRefsNotInMGI.py
TAG: qcreports_db-6-0-16-13
DATE: 01/26/2026
STAFF: dbm
1) MRK_GOUnknown.py: Exclude references tagged with GO:QC1_GOunknown_exclude
2) MRK_NoGO.py: Exclude references tagged with GO:QC4_NoGO_exclude
3) MRK_GOIEA.py: Exclude references tagged with GO:QC5_IEA-only_exclude
TAG: qcreports_db-6-0-16-12
DATE: 10/23/2020
STAFF: dbm
python3 fix: mgd/GO_InvalidInferredFrom.py, mgd/MRK_GOIEA.py
TAG: qcreports_db-6-0-16-11
DATE: 10/14/2020
STAFF: sc
but fix: mgd/GXD_ImagePanes.py
TAG: qcreports_db-6-0-16-10
DATE: 09/23/2020
STAFF: lec
TR13327/AP group weekly reference QC reports/WF_AP_Tags.py
TAG: qcreports_db-6-0-16-9
DATE: 09/09/2020
STAFF: sc
TR13374 - New MRK_C4AM.rpt
TAG: qcreports_db-6-0-16-8
DATE: 09/04/2020
STAFF: lec
TR13327/AP group weekly reference QC reports/WF_AP_Tags.py
TAG: qcreports_db-6-0-16-7
DATE: 09/04/2020
STAFF: lec
TR13277/change short citation to longer citation on journal QC reports
TR13356/re-label and re-sort GO QC reports
TR13357/removal of GO QC report (mgd/MGI_GenotypeDescriptions.py)
TAG: qcreports_db-6-0-16-6
DATE: 09/04/2020
STAFF: lec
TR13186/add auto copyright for Cell Rep
TR13363/add J# to list of GXD electronic references
TAG: qcreports_db-6-0-16-5
DATE: 08/27/2020
STAFF: sc
TR13204/Infrastructure Release
pirsfloadRpt.csh calls python report scripts, but was not updated to use ${PYTHON}
TAG: qcreports_db-6-0-16-4
DATE: 08/26/2020
STAFF: lec
TR13204/Infrastructure Release
re-add http://wts.informatics.jax.org/wts_projects/11100/11105/GXD_EarlyEmbPapers.py
TAG: qcreports_db-6-0-16-3
DATE: 08/25/2020
STAFF: lec
mgd/GO_InvalidInferredFrom.py : check if inferredFrom = None
TAG: qcreports_db-6-0-16-2
DATE: 08/24/2020
STAFF: lec
TR13369/QC report of COV: tagged papers/weekly/BIB_Covid.py
TAG: qcreports_db-6-0-16-1
DATE: 08/21/2020
STAFF: lec
TR13204/Infrastructure Release
TAG: qcreports_db-6-0-15-9
DATE: 07/10/2020
STAFF: dbm
CHANGES:TR13348 - Move GXD_References.sql from weekly to daily
TAG: qcreports_db-6-0-15-8
TAG: qcreports_db-6-0-15-7
TAG: qcreports_db-6-0-15-6
TAG: qcreports_db-6-0-15-5
DATE: 05/13/2020
STAFF: sc
CHANGES:TR13265 - Variants QC reports: add checking for ref = var
TAG: qcreports_db-6-0-?
DATE:
STAFF:
CHANGES:
TR13204/Infrastructure/python 3
re-add http://wts.informatics.jax.org/wts_projects/11100/11105/GXD_EarlyEmbPapers.py
TAG: qcreports_db-6-0-15-4