CHANGES.rst 26.3 KB
Newer Older
1
2
3
4
5
Changelog
=========

This is a record of changes made between each Mutalyzer release.

Mihai's avatar
Mihai committed
6
7
8
9
10
11
Version 2.0.33
---------------

Release date to be decided.


Mihai's avatar
Mihai committed
12
13
14
Version 2.0.32
---------------

Mihai's avatar
Mihai committed
15
Released on December 9th 2019.
Mihai's avatar
Mihai committed
16

Mihai's avatar
Mihai committed
17
18
19
20
21
22
23
24
25
- Update email address and wiki link (`#498
  <https://github.com/mutalyzer/mutalyzer/pull/498>`_).
- Fix erroneous message for mtDNA m. coordinate system (`#497
  <https://github.com/mutalyzer/mutalyzer/pull/497>`_).
- Update requirements (`#496
  <https://github.com/mutalyzer/mutalyzer/pull/496>`_).
- Fix invalid LRG record issue (`#495
  <https://github.com/mutalyzer/mutalyzer/pull/495>`_).

Mihai's avatar
Mihai committed
26

Mihai's avatar
Mihai committed
27
28
29
Version 2.0.31
---------------

Mihai's avatar
Mihai committed
30
Released on August 21st 2019.
Mihai's avatar
Mihai committed
31

Mihai's avatar
Mihai committed
32
33
34
35
36
37
38
39
40
41
42
- Update requirements (`#486
  <https://github.com/mutalyzer/mutalyzer/pull/486>`_).
- Add support for NCBI E-utilities API key (`#485
  <https://github.com/mutalyzer/mutalyzer/pull/485>`_).
- Update HGVS descriptions retrieval for SNP converter (`#482
  <https://github.com/mutalyzer/mutalyzer/issues/482>`_)
- Make file selection mandatory in the batch job web page  (`#481
  <https://github.com/mutalyzer/mutalyzer/issues/481>`_).
- Update Travis configuration (`#483
  <https://github.com/mutalyzer/mutalyzer/pull/483>`_)

Mihai's avatar
Mihai committed
43

Mihai's avatar
Mihai committed
44
45
46
Version 2.0.30
---------------

Mihai's avatar
Mihai committed
47
Released on May 24th 2019.
Mihai's avatar
Mihai committed
48

Mihai's avatar
Mihai committed
49
50
51
52
53
54
- Update requirements (`#475
  <https://github.com/mutalyzer/mutalyzer/pull/475>`_).
- Update documentation links (`#474
  <https://github.com/mutalyzer/mutalyzer/pull/474>`_).
- Fix the genbank parser to perform loci objects creation in two steps (`#468
  <https://github.com/mutalyzer/mutalyzer/issues/468>`_).
Mihai's avatar
Mihai committed
55

Mihai's avatar
Mihai committed
56

Mihai's avatar
Mihai committed
57
58
59
Version 2.0.29
---------------

Mihai's avatar
Mihai committed
60
Released on December 4th 2018.
Mihai's avatar
Mihai committed
61

Mihai's avatar
Mihai committed
62
63
64
65
66
67
68
69
70
71
72
- Improve user feedback for incorrect specific locus (`#459
  <https://github.com/mutalyzer/mutalyzer/pull/459>`_).
- Improve some position converter warning (`#458
  <https://github.com/mutalyzer/mutalyzer/pull/458>`_).
- Update requirements (`#457
  <https://github.com/mutalyzer/mutalyzer/pull/457>`_).
- Make API more consistent between UDs and NCs (`#456
  <https://github.com/mutalyzer/mutalyzer/pull/456>`_).
- Fix internal server error on IVS variant (`#452
  <https://github.com/mutalyzer/mutalyzer/pull/452>`_).

Mihai's avatar
Mihai committed
73
74
75
76

Version 2.0.28
---------------

Mihai's avatar
Mihai committed
77
Released on June 11th 2018.
Mihai's avatar
Mihai committed
78

Mihai's avatar
Mihai committed
79
80
- Support for LRG XML schema version 1.9 (`#449
  <https://github.com/mutalyzer/mutalyzer/pull/449>`_).
Mihai's avatar
Mihai committed
81

Mihai's avatar
Mihai committed
82

Mihai's avatar
Mihai committed
83
84
85
Version 2.0.27
---------------

Mihai's avatar
Mihai committed
86
Released on May 25th 2018.
Mihai's avatar
Mihai committed
87

Mihai's avatar
Mihai committed
88
- Accept variant descriptions with NC files as references (`#445
Mihai's avatar
Mihai committed
89
  <https://github.com/mutalyzer/mutalyzer/pull/445>`_).
Mihai's avatar
Mihai committed
90
- Removed support for pending LRG reference files (`#444
Mihai's avatar
Mihai committed
91
  <https://github.com/mutalyzer/mutalyzer/pull/444>`_).
Mihai's avatar
Mihai committed
92
- Add link to wiki page with differences between Mutalyzer and HGVS (`#443
Mihai's avatar
Mihai committed
93
  <https://github.com/mutalyzer/mutalyzer/pull/443>`_).
Mihai's avatar
Mihai committed
94
- Fix for batch processor crash due to NCBI server timeout (`#442
Mihai's avatar
Mihai committed
95
  <https://github.com/mutalyzer/mutalyzer/pull/442>`_).
Mihai's avatar
Mihai committed
96
- Update genbank retriever parameters according to NCBI recommendations (`#439
Mihai's avatar
Mihai committed
97
  <https://github.com/mutalyzer/mutalyzer/pull/439>`_).
Mihai's avatar
Mihai committed
98
- Update getGeneLocation` to use standard strategy to select mapping (`#437
Mihai's avatar
Mihai committed
99
  <https://github.com/mutalyzer/mutalyzer/pull/437>`_).
Mihai's avatar
Mihai committed
100
- Add link to website changelog (`#434
Mihai's avatar
Mihai committed
101
102
  <https://github.com/mutalyzer/mutalyzer/pull/434>`_).

Mihai's avatar
Mihai committed
103

Mihai's avatar
Mihai committed
104
105
106
Version 2.0.26
---------------

Mihai's avatar
Mihai committed
107
Released on July 19th 2017.
Mihai's avatar
Mihai committed
108

109
- Description-extractor dependency updated to version 2.35 (`#429
Mihai's avatar
Mihai committed
110
  <https://github.com/mutalyzer/mutalyzer/pull/429>`_).
Mihai's avatar
Mihai committed
111
112
- Fix for negative cCDSStop due to wrong transcript to protein link (`#430
  <https://github.com/mutalyzer/mutalyzer/issues/430>`_).
Mihai's avatar
Mihai committed
113

114

Mihai's avatar
Mihai committed
115
116
117
Version 2.0.25
---------------

Mihai's avatar
Mihai committed
118
Released on May 17th 2017.
Mihai's avatar
Mihai committed
119

Mihai's avatar
Mihai committed
120
- Fix for batch processor crash when trying to alter an "item" column of the
Mihai's avatar
Mihai committed
121
  "batch_queue_items" database table (`#426
Mihai's avatar
Mihai committed
122
  <https://github.com/mutalyzer/mutalyzer/pull/426>`_).
Mihai's avatar
Mihai committed
123

Laros's avatar
Laros committed
124
125
126
Version 2.0.24
---------------

Mihai's avatar
Mihai committed
127
Released on April 12th 2017.
Laros's avatar
Laros committed
128

Mihai's avatar
Mihai committed
129
- Fix for SNP converter crash when called with 'rs0' as parameter.
Mihai's avatar
Mihai committed
130
  SNP converter displays now more warning messages (`#419
Mihai's avatar
Mihai committed
131
132
  <https://github.com/mutalyzer/mutalyzer/issues/419>`_).

Laros's avatar
Laros committed
133

mkroon's avatar
mkroon committed
134
135
136
Version 2.0.23
---------------

Laros's avatar
Laros committed
137
Released on November 9th 2016.
mkroon's avatar
mkroon committed
138

Laros's avatar
Laros committed
139
140
141
142
- Fix for internal server error in the position converter triggered by
  non-variant description (`#333
  <https://github.com/mutalyzer/mutalyzer/issues/333>`_).

mkroon's avatar
mkroon committed
143

Vermaat's avatar
Vermaat committed
144
145
146
Version 2.0.22
--------------

mkroon's avatar
mkroon committed
147
Released on September 20th 2016.
Vermaat's avatar
Vermaat committed
148

mkroon's avatar
mkroon committed
149
150
151
- Biopython dependency updated to version 1.68 (`#411
  <https://github.com/mutalyzer/mutalyzer/pull/411>`_).

Vermaat's avatar
Vermaat committed
152

Laros's avatar
Laros committed
153
154
155
Version 2.0.21
--------------

Vermaat's avatar
Vermaat committed
156
Released on June 24th 2016.
Laros's avatar
Laros committed
157

Vermaat's avatar
Vermaat committed
158
159
160
- Fix typo in batch SNP converter, causing all batch jobs to stall (`#409
  <https://github.com/mutalyzer/mutalyzer/pull/409>`_).

Laros's avatar
Laros committed
161

Vermaat's avatar
Vermaat committed
162
163
164
Version 2.0.20
--------------

Laros's avatar
Laros committed
165
166
167
168
169
170
171
172
Released on June 22th 2016.

- Accept accession number as transcript selector (`#405
  <https://github.com/mutalyzer/mutalyzer/pull/405>`_).
- Add legend to the output of runMutalyzer service (`#404
  <https://github.com/mutalyzer/mutalyzer/pull/404>`_).
- Remove support for GI numbers (`#396
  <https://github.com/mutalyzer/mutalyzer/pull/396>`_).
Vermaat's avatar
Vermaat committed
173
174


Vermaat's avatar
Vermaat committed
175
176
177
Version 2.0.19
--------------

Vermaat's avatar
Vermaat committed
178
Released on June 9th 2016.
Vermaat's avatar
Vermaat committed
179

Vermaat's avatar
Vermaat committed
180
181
182
183
184
- Fix reference file loading by URL (`#383
  <https://github.com/mutalyzer/mutalyzer/pull/383>`_).
- Consider accession version in `getGeneName` webservice method (`#390
  <https://github.com/mutalyzer/mutalyzer/pull/390>`_).

Vermaat's avatar
Vermaat committed
185

Vermaat's avatar
Vermaat committed
186
187
188
Version 2.0.18
--------------

Vermaat's avatar
Vermaat committed
189
Released on May 23rd 2016.
Vermaat's avatar
Vermaat committed
190

Vermaat's avatar
Vermaat committed
191
192
193
194
195
196
197
198
199
- Fixed installation on CentOS 6 (`#358
  <https://github.com/mutalyzer/mutalyzer/pull/358>`_).
- Auto focus primary form input on page load (`#363
  <https://github.com/mutalyzer/mutalyzer/pull/363>`_).
- Check optional argument for ``dup`` (`#369
  <https://github.com/mutalyzer/mutalyzer/pull/369>`_).
- Fixes for chromosome slicing by gene symbol (`#371
  <https://github.com/mutalyzer/mutalyzer/pull/371>`_).

Vermaat's avatar
Vermaat committed
200

Vermaat's avatar
Vermaat committed
201
202
203
Version 2.0.17
--------------

Vermaat's avatar
Vermaat committed
204
Released on March 24th 2016.
Vermaat's avatar
Vermaat committed
205

Vermaat's avatar
Vermaat committed
206
207
208
209
210
211
212
213
- Position converter now checks for selection of gene/transcript (`#346
  <https://github.com/mutalyzer/mutalyzer/pull/346>`_).
- Update about page and link to `new mailing list
  <https://groups.google.com/forum/#!forum/mutalyzer>`_ (`#353
  <https://github.com/mutalyzer/mutalyzer/pull/353>`_).
- Batch jobs processor is more robust on errors (`#356
  <https://github.com/mutalyzer/mutalyzer/pull/356>`_).

Vermaat's avatar
Vermaat committed
214

Vermaat's avatar
Vermaat committed
215
216
217
Version 2.0.16
--------------

Vermaat's avatar
Vermaat committed
218
Released on February 25th 2016.
Vermaat's avatar
Vermaat committed
219

Vermaat's avatar
Vermaat committed
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
- Fixed transcript naming in mapping webservices (`#147
  <https://github.com/mutalyzer/mutalyzer/pull/147>`_). See below for
  :ref:`details <changelog_2016_details>`.
- Support LRG transcripts in the position converter (`#147
  <https://github.com/mutalyzer/mutalyzer/pull/147>`_).
- Don't report ``ext*?`` when variant RNA has stop codon (`#146
  <https://github.com/mutalyzer/mutalyzer/pull/146>`_).

.. _changelog_2016_details:

The following three webservice methods return a list of transcript identifiers
for some query:

- `getTranscriptsRange`
- `getTranscripts`
- `getTranscriptsByGeneName`

Previously they didn't work correctly for LRG transcripts (a bogus version was
included and no transcript was selected) and RefSeq transcripts on mtDNA (no
transcript was selected).

Additionally, the `getTranscriptsMapping` webservice method didn't return
enough information to construct a complete transcript name. This is now
reported in a new `transcript` field.

Finally, the `getTranscriptsRange` method now optionally includes version
numbers with the boolean `versions` argument (default `false`).

Vermaat's avatar
Vermaat committed
248

Vermaat's avatar
Vermaat committed
249
250
251
Version 2.0.15
--------------

Vermaat's avatar
Vermaat committed
252
Released on January 6th 2016.
Vermaat's avatar
Vermaat committed
253

Vermaat's avatar
Vermaat committed
254
255
256
257
258
259
260
261
262
263
- Speedup NCBI mapview file import (`#124
  <https://github.com/mutalyzer/mutalyzer/pull/124>`_).
- Parse genbank file without VERSION field (`#126
  <https://github.com/mutalyzer/mutalyzer/pull/126>`_).
- Fix issue where some transcripts would not show in the legend (`#136
  <https://github.com/mutalyzer/mutalyzer/pull/136>`_).
- Don't discard complete gene from GenBank file when it has incomplete but
  also complete features annotated (`#138
  <https://github.com/mutalyzer/mutalyzer/pull/138>`_)

Vermaat's avatar
Vermaat committed
264

Vermaat's avatar
Vermaat committed
265
266
267
Version 2.0.14
--------------

Vermaat's avatar
Vermaat committed
268
Released on November 9th 2015.
Vermaat's avatar
Vermaat committed
269

Vermaat's avatar
Vermaat committed
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
- E-mail address is now optional in batch job website interface (`#119
  <https://github.com/mutalyzer/mutalyzer/pull/119>`_).
- Use Mailcheck in the batch jobs form (`#107
  <https://github.com/mutalyzer/mutalyzer/pull/107>`_).
- Optional email for batch jobs from webservices (`#104
  <https://github.com/mutalyzer/mutalyzer/pull/104>`_).
- Process batch jobs grouped by email address (`#101
  <https://github.com/mutalyzer/mutalyzer/pull/101>`_).
- Use interval binning scheme on transcript mappings (`#100
  <https://github.com/mutalyzer/mutalyzer/pull/100>`_).
- Back translator interface (`#74
  <https://github.com/mutalyzer/mutalyzer/pull/74>`_).
- Transcript-protein links are now cached in Redis (`#94
  <https://github.com/mutalyzer/mutalyzer/pull/94>`_).
- Added `Ter` as a valid amino acid in the HGVS grammar (`#90
  <https://github.com/mutalyzer/mutalyzer/pull/90>`_).
- Refactoring of unit tests (`#88
  <https://github.com/mutalyzer/mutalyzer/pull/88>`_, `#89
  <https://github.com/mutalyzer/mutalyzer/pull/89>`_).

Vermaat's avatar
Vermaat committed
290

Vermaat's avatar
Vermaat committed
291
292
293
Version 2.0.13
--------------

Vermaat's avatar
Vermaat committed
294
Released on October 1st 2015.
Vermaat's avatar
Vermaat committed
295

Vermaat's avatar
Vermaat committed
296
297
298
- Fix query bug in update transcript-protein links (`#85
  <https://github.com/mutalyzer/mutalyzer/pull/85>`_).

Vermaat's avatar
Vermaat committed
299

Vermaat's avatar
Vermaat committed
300
301
302
Version 2.0.12
--------------

Vermaat's avatar
Vermaat committed
303
Released on September 30th 2015.
Vermaat's avatar
Vermaat committed
304

Vermaat's avatar
Vermaat committed
305
306
307
308
309
310
311
312
313
314
315
316
317
- Fix off-by-one in slicing chromosome by gene name (`#79
  <https://github.com/mutalyzer/mutalyzer/pull/79>`_).
- Document scheme used for all positions and ranges (`#79
  <https://github.com/mutalyzer/mutalyzer/pull/79>`_).
- Show diff for variant protein from non-reference start codon (`#78
  <https://github.com/mutalyzer/mutalyzer/pull/78>`_).
- Visualise protein change, also with alternative start (`#72
  <https://github.com/mutalyzer/mutalyzer/pull/72>`_).
- Translate alternative start to M, also in variant (`#72
  <https://github.com/mutalyzer/mutalyzer/pull/72>`_).
- Added Baker's yeast (SacCer_Apr2011/sacCer3) assembly (`#73
  <https://github.com/mutalyzer/mutalyzer/pull/73>`_).

Vermaat's avatar
Vermaat committed
318

Vermaat's avatar
Vermaat committed
319
320
321
Version 2.0.11
--------------

Vermaat's avatar
Vermaat committed
322
Released on August 6th 2015.
Vermaat's avatar
Vermaat committed
323

Vermaat's avatar
Vermaat committed
324
- Fix bug in recognizing ``p.(=)`` (was reported as ``p.?``) (`#65
Vermaat's avatar
Vermaat committed
325
326
  <https://github.com/mutalyzer/mutalyzer/pull/65>`_).

Vermaat's avatar
Vermaat committed
327

Vermaat's avatar
Vermaat committed
328
329
330
Version 2.0.10
--------------

Vermaat's avatar
Vermaat committed
331
Released on July 21st 2015.
Vermaat's avatar
Vermaat committed
332

Vermaat's avatar
Vermaat committed
333
334
335
- Don't crash the position converter on transcript mappings containing no
  exons (`#63
  <https://github.com/mutalyzer/mutalyzer/pull/63>`_).
Vermaat's avatar
Vermaat committed
336
337
- Use the notation for an uncertain stop codon, e.g., ``p.(Gln730Profs*?)``
  instead of ``p.(Gln730Profs*96)`` when a variant results in a frame shift or
Vermaat's avatar
Vermaat committed
338
339
340
341
342
  extension and we don't see a new stop codon in the RNA (`#57
  <https://github.com/mutalyzer/mutalyzer/pull/57>`_).
- Added Dog (Broad CanFam3.1/canFam3) assembly for position converter (`#56
  <https://github.com/mutalyzer/mutalyzer/pull/56>`_).

Vermaat's avatar
Vermaat committed
343

Vermaat's avatar
Vermaat committed
344
345
346
Version 2.0.9
-------------

Vermaat's avatar
Vermaat committed
347
Released on July 9th 2015.
Vermaat's avatar
Vermaat committed
348

Vermaat's avatar
Vermaat committed
349
350
351
352
353
354
- Improvements in encoding detection of uploaded batch files (`#52
  <https://github.com/LUMC/mutalyzer/pull/52>`_, `#53
  <https://github.com/LUMC/mutalyzer/pull/53>`_).
- Usability improvements in reading DNA for description extractor (`#54
  <https://github.com/mutalyzer/mutalyzer/pull/54>`_).

Vermaat's avatar
Vermaat committed
355

Vermaat's avatar
Vermaat committed
356
357
358
Version 2.0.8
-------------

Vermaat's avatar
Vermaat committed
359
Released on May 27th 2015.
Vermaat's avatar
Vermaat committed
360

Vermaat's avatar
Vermaat committed
361
362
- The `HGVS variant description extractor
  <https://github.com/mutalyzer/description-extractor>`_ package is available
Vermaat's avatar
Vermaat committed
363
  through the Description Extractor interface (`#1
Vermaat's avatar
Vermaat committed
364
365
366
367
368
  <https://github.com/LUMC/mutalyzer/pull/1>`_).
- GitHub project moved from `LUMC/mutalyzer
  <https://github.com/LUMC/mutalyzer>`_ to `mutalyzer/mutalyzer
  <https://github.com/LUMC/mutalyzer>`_.

Vermaat's avatar
Vermaat committed
369

Vermaat's avatar
Vermaat committed
370
371
372
Version 2.0.7
-------------

Vermaat's avatar
Vermaat committed
373
Released on March 27th 2015.
Vermaat's avatar
Vermaat committed
374

Vermaat's avatar
Vermaat committed
375
- Return fault code and description on RPC service errors (`#31
Vermaat's avatar
Vermaat committed
376
  <https://github.com/LUMC/mutalyzer/pull/31>`_).
Vermaat's avatar
Vermaat committed
377
- Use esummary 2.0 response format (`#32
Vermaat's avatar
Vermaat committed
378
379
  <https://github.com/LUMC/mutalyzer/pull/32>`_).

Vermaat's avatar
Vermaat committed
380

Vermaat's avatar
Vermaat committed
381
382
383
Version 2.0.6
-------------

Vermaat's avatar
Vermaat committed
384
Released on February 10th 2015.
Vermaat's avatar
Vermaat committed
385

386
- Added `getGeneLocation` webservice method. Given a gene symbol and optional
Vermaat's avatar
Vermaat committed
387
  genome build, it returns the location of the gene (`#28
388
  <https://github.com/LUMC/mutalyzer/pull/28>`_).
Vermaat's avatar
Vermaat committed
389
- Discard incomplete genes in genbank reference files (`#26
390
  <https://github.com/LUMC/mutalyzer/pull/26>`_).
391

Vermaat's avatar
Vermaat committed
392

Vermaat's avatar
Vermaat committed
393
394
395
Version 2.0.5
-------------

Vermaat's avatar
Vermaat committed
396
Released on December 16th 2014.
Vermaat's avatar
Vermaat committed
397

Vermaat's avatar
Vermaat committed
398
399
400
401
402
- New website layout by `Landscape <http://wearelandscape.nl/>`_ (`GitLab!26
  <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/26>`_).
- Source code moved from `GitLab <https://git.lumc.nl/mutalyzer/mutalyzer>`_
  to `GitHub <https://github.com/LUMC/mutalyzer>`_.
- Automated unit tests `on Travis CI <https://travis-ci.org/LUMC/mutalyzer>`_
Vermaat's avatar
Vermaat committed
403
  (`#16 <https://github.com/LUMC/mutalyzer/pull/16>`_).
Vermaat's avatar
Vermaat committed
404
- Developer documentation `hosted on Read the Docs
Vermaat's avatar
Vermaat committed
405
  <http://mutalyzer.readthedocs.org/en/latest/>`_ (`#17
Vermaat's avatar
Vermaat committed
406
407
  <https://github.com/LUMC/mutalyzer/pull/18>`_).

Vermaat's avatar
Vermaat committed
408

Vermaat's avatar
Vermaat committed
409
Version 2.0.4
Vermaat's avatar
Vermaat committed
410
411
-------------

Vermaat's avatar
Vermaat committed
412
Released on November 19th 2014.
Vermaat's avatar
Vermaat committed
413

Vermaat's avatar
Vermaat committed
414
415
416
417
418
419
420
421
- Many string encoding related fixes. Summarizing, Mutalyzer should now be
  completely aware of input and output string encodings, in all
  interfaces. Internally, all strings are unicode strings. This comes with
  minor changes in the webservice definitions, which most clients will
  probably not notice (`GitLab!25
  <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/25>`_).
- Don't crash on mail errors in the batch scheduler (`GitLab#30
  <https://git.lumc.nl/mutalyzer/mutalyzer/issues/30>`_).
422
423
- Fix importing transcript mappings from UCSC database (`GitLab#9
  <https://git.lumc.nl/mutalyzer/mutalyzer/issues/9>`_).
Vermaat's avatar
Vermaat committed
424
425
- Rename GRCh36 to NCBI36 (`GitLab#8
  <https://git.lumc.nl/mutalyzer/mutalyzer/issues/8>`_).
Vermaat's avatar
Vermaat committed
426
427
428
- Updated all Python dependencies to their latest versions.
- Mutalyzer is now Open Source! Source code is available under the AGPL and
  documentation under the CC-by-sa license.
Vermaat's avatar
Vermaat committed
429

Vermaat's avatar
Vermaat committed
430
431
432
433
434
435

Version 2.0.3
-------------

Released on September 20th 2014.

Vermaat's avatar
Vermaat committed
436
437
- Fix several error cases in LOVD2 view on the name checker.

Vermaat's avatar
Vermaat committed
438

Vermaat's avatar
Vermaat committed
439
440
441
Version 2.0.2
-------------

Vermaat's avatar
Vermaat committed
442
Released on October 9th 2014.
Vermaat's avatar
Vermaat committed
443

Vermaat's avatar
Vermaat committed
444
445
446
447
448
449
- Fix incorrect GRCm38 chromosome accession number versions.
- Fix crash in position converter batch jobs.
- Upgrade the webservice library we use (Spyne, from 2.10.10 to 2.11.0). This
  potentially affects behaviour of both our SOAP and HTTP/RPC+JSON
  webservices, although our tests did not show any problems.

Vermaat's avatar
Vermaat committed
450

Vermaat's avatar
Vermaat committed
451
452
453
Version 2.0.1
-------------

Vermaat's avatar
Vermaat committed
454
Released on September 27th 2014.
Vermaat's avatar
Vermaat committed
455

456
457
458
- Fix POST requests to the HTTP/RPC+JSON webservice. This was a regression
  from version 2.0.beta-33. Thanks to Ken Doig for reporting the issue.

Vermaat's avatar
Vermaat committed
459

Vermaat's avatar
Vermaat committed
460
461
462
Version 2.0.0
-------------

Vermaat's avatar
Vermaat committed
463
Released on September 26th 2014.
Vermaat's avatar
Vermaat committed
464
465

This release does not bring many new features, but comes with significant
Vermaat's avatar
Vermaat committed
466
changes to the technical infrastructure. `GitLab!6
Vermaat's avatar
Vermaat committed
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
<https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/6>`_ tracks most of
this.

Some highlights especially users of the webservices should be aware of:

- HTTP/RPC+JSON webservice has changed response format (wrapper object
  removed). See below for an :ref:`example <changelog_200_example>`.
- No more plain HTTP access, only redirects to HTTPS.
- Many website entrypoints have changed URLs and form parameter names (the old
  ones have HTTP redirects).
- Removed old redirects from paths starting with ``/2.0/``.
- In maintenance mode, all requests get a *Service Temporarily Unavailable*
  response with status code 503.

Other changes:

Vermaat's avatar
Vermaat committed
483
- Upload a genbank file using the SOAP webservice (`uploadGenBankLocalFile`).
Vermaat's avatar
Vermaat committed
484
- Do not cleanup the cache during request handling (`GitLab#18
Vermaat's avatar
Vermaat committed
485
  <https://git.lumc.nl/mutalyzer/mutalyzer/issues/18>`_).
Vermaat's avatar
Vermaat committed
486
- Add GRCh38 (hg38) assembly (`GitLab!20
Vermaat's avatar
Vermaat committed
487
  <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/20>`_).
Vermaat's avatar
Vermaat committed
488
- Move from nose to `pytest <http://pytest.org/>`_ for unit tests (`GitLab!23
Vermaat's avatar
Vermaat committed
489
  <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/23>`_).
Vermaat's avatar
Vermaat committed
490
491
- Fix running Mutalyzer in a `virtual environment
  <http://virtualenv.readthedocs.org/>`_ and have an up-to-date
Vermaat's avatar
Vermaat committed
492
  ``requirements.txt`` for `pip <http://pip.readthedocs.org/>`_ (`GitLab!4
Vermaat's avatar
Vermaat committed
493
  <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/4>`_).
Vermaat's avatar
Vermaat committed
494
- Switch from TAL to Jinja2 (`GitLab!3
Vermaat's avatar
Vermaat committed
495
  <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/3>`_).
Vermaat's avatar
Vermaat committed
496
- Refactor user interfaces (`GitLab!5
Vermaat's avatar
Vermaat committed
497
  <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/5>`_).
Vermaat's avatar
Vermaat committed
498
- Move from configobj to Python module based config (`GitLab!7
Vermaat's avatar
Vermaat committed
499
  <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/7>`_).
Vermaat's avatar
Vermaat committed
500
- Use SQLAlchemy as ORM (`GitLab!8
Vermaat's avatar
Vermaat committed
501
  <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/8>`_).
Vermaat's avatar
Vermaat committed
502
- Use Redis for stat counters (`GitLab!10
Vermaat's avatar
Vermaat committed
503
  <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/10>`_).
Vermaat's avatar
Vermaat committed
504
- Port website from web.py to Flask (`GitLab!11
Vermaat's avatar
Vermaat committed
505
  <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/11>`_).
Vermaat's avatar
Vermaat committed
506
- Isolated unit tests using fixtures and an in-memory database (`GitLab!12
Vermaat's avatar
Vermaat committed
507
  <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/12>`_).
Vermaat's avatar
Vermaat committed
508
- Display announcement on website (`GitLab!14
Vermaat's avatar
Vermaat committed
509
  <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/14>`_).
Vermaat's avatar
Vermaat committed
510
- Database migrations with Alembic (`GitLab!15
Vermaat's avatar
Vermaat committed
511
  <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/15>`_).
Vermaat's avatar
Vermaat committed
512
- Update documentation and use Sphinx (`GitLab!16
Vermaat's avatar
Vermaat committed
513
514
  <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/16>`_).
- Move to `semantic versioning <http://semver.org/>`_, starting with version
Vermaat's avatar
Vermaat committed
515
516
  2.0.0 (`GitLab!22
  <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/22>`_).
Vermaat's avatar
Vermaat committed
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
- Add 404 not found page.
- Don't auto remove comma characters in syntax checker.
- Add a dash (``-``) as an allowed character in the gene name.
- Range, reverse complement range, and compound
  insertions/insertion-deletions.

.. _changelog_200_example:

The wrapper object has been removed from the HTTP/RPC+JSON webservice response
format. As an example, consider an old response format for the `checkSyntax`
method:

.. code-block:: json

    {
      "checkSyntaxResponse": {
        "checkSyntaxResult": {
          "valid": true,
          "messages": {
            "SoapMessage": []
          }
        }
      }
    }

The new response format is:

.. code-block:: json

    {
      "valid": true,
      "messages": []
    }


Vermaat's avatar
Vermaat committed
552
553
554
555
556
557
Version 2.0.beta-33
-------------------

Released on August 19th 2014.

- Link to `Upcoming server update
Vermaat's avatar
Vermaat committed
558
  <https://humgenprojects.lumc.nl/trac/mutalyzer/wiki/News/2014-08-19-upcoming-server-update>`_
Vermaat's avatar
Vermaat committed
559
560
  announcement.

Vermaat's avatar
Vermaat committed
561
562
563
564
565
566

Version 2.0.beta-32
-------------------

Released on June 26th 2014.

Vermaat's avatar
Vermaat committed
567
568
569
- Link to `Visual interface for Variant Description Extractor
  <https://humgenprojects.lumc.nl/trac/mutalyzer/wiki/News/2014-06-26-visual-interface>`_
  announcement.
Vermaat's avatar
Vermaat committed
570
571


572
573
574
Version 2.0.beta-31
-------------------

Vermaat's avatar
Vermaat committed
575
576
577
578
579
580
Released on March 27th 2014.

- Due to incorrect interpretation, temporarily only support one CDS per
  transcript (ignore all others) in LRG.
- Due to incorrect interpretation, temporarily ignore transcripts without a
  fixed id.
581
582
583
584
585
586
587
588


Version 2.0.beta-30
-------------------

Released on February 18th 2014.

- Handle NCBI Entrez response validation errors (fixes, among other things,
Vermaat's avatar
Vermaat committed
589
  `LOVD Trac#29 <https://humgenprojects.lumc.nl/trac/LOVD3/ticket/29>`_).
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
- Loosen error severity when CDS cannot be translated.
- Mutalyzer development migrated from Subversion to Git for version control.


Version 2.0.beta-29
-------------------

Released on October 11th 2013.

- Add Jonathan Vis attribution and COMMIT logo to about page.


Version 2.0.beta-28
-------------------

Released on September 18th 2013.

- Enable the HTTP/RPC+JSON web service to be used with POST requests.


Version 2.0.beta-27
-------------------

Released on June 18th 2013.

- Fix caching transcript-protein links from NCBI, reducing impact of NCBI
  communication problems.


Version 2.0.beta-26
-------------------

Released on April 9th 2013.

- Added mm10 (Mouse) transcript mappings to position converter.
Vermaat's avatar
Vermaat committed
625
- LRG parser updated to LRG 1.7 schema (`Trac#127
626
627
628
629
630
631
632
633
634
635
636
637
  <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/127>`_).


Version 2.0.beta-25
-------------------

Released on March 25th 2013.

- Detect incorrect exon annotation in transcript references.
- Move documentation to Trac.
- Exon table is included in `runMutalyzer` webservice results.
- Temporarily disable frameshift detection in experimental description
Vermaat's avatar
Vermaat committed
638
  extractor (`Trac#124
639
640
641
642
643
644
645
646
647
648
  <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/124>`_).
- Allow selectors on transcript references in position converter.
- Syntax checker now supports protein level variant descriptions.


Version 2.0.beta-24
-------------------

Released on December 10th 2012.

Vermaat's avatar
Vermaat committed
649
- Rename some warning codes (webservice API) (`Trac#98
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
  <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/98>`_).
- Variants on mtDNA in position converter.


Version 2.0.beta-23
-------------------

Released on November 8th 2012.

No user-visible changes.


Version 2.0.beta-22
-------------------

Released on November 2nd 2012.

Vermaat's avatar
Vermaat committed
667
- Submitting batch jobs via the web services (`Trac#115
668
  <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/115>`_).
Vermaat's avatar
Vermaat committed
669
- Allow for leading whitespace in batch job input (`Trac#107
670
671
672
673
674
  <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/107>`_).
- New `descriptionExtract` webservice function.
- Name checker now includes description extractor output as an experimental
  service.
- Slice chromosome by gene name in reference file loader is now case
Vermaat's avatar
Vermaat committed
675
  insensitive (`Trac#118
676
  <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/118>`_).
Vermaat's avatar
Vermaat committed
677
- Warn on missing positioning scheme (`Trac#114
678
679
680
681
682
683
684
685
686
  <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/114>`_).


Version 2.0.beta-21
-------------------

Released on July 23rd 2012.

- Support compound variants in position converter.
Vermaat's avatar
Vermaat committed
687
- Support non-coding transcripts in position converter (`Trac#102
688
689
  <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/102>`_).
- Move to new RPC library version, causing slight change in HTTP/RPC+JSON
Vermaat's avatar
Vermaat committed
690
691
  webservice output (more wrappers around output), but fixes `Trac#104
  <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/104>`_.
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
- Fix position converter for delins with explicit deleted sequence.
- Fix description update from Version 2.0.beta-20 to use- notation instead of
  counting.


Version 2.0.beta-20
-------------------

Released on July 21st 2012.

- Disabled the ``-u`` and ``+d`` convention in favour of the official HGVS
  recommendations.


Version 2.0.beta-19
-------------------

Released on June 21st 2012.

Vermaat's avatar
Vermaat committed
711
- Fix crash on inversions (`Trac#99
712
713
714
715
716
717
718
719
  <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/99>`_).


Version 2.0.beta-18
-------------------

Released on June 7th 2012.

Vermaat's avatar
Vermaat committed
720
- Moved from soaplib to rpclib for webservices (`Trac#66
721
  <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/66>`_).
Vermaat's avatar
Vermaat committed
722
- Added HTTP/RPC+JSON webservice (`Trac#18
723
  <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/18>`_).
Vermaat's avatar
Vermaat committed
724
- Fixed name checker errors in some adjacent variants (`Trac#83
725
726
727
  <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/83>`_).
- Name checker form now uses GET requests to support easier linking to result
  pages.
Vermaat's avatar
Vermaat committed
728
729
730
- You can now specify chromosomes by name in the reference file loader
  (`Trac#92 <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/92>`_).
- Made batch daemon not crash on MySQL restarts (`Trac#91
731
  <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/91>`_).
Vermaat's avatar
Vermaat committed
732
- Position converter now detects incorrect order in position ranges (`Trac#95
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
  <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/95>`_).
- Added NBIC logo to 'about' page.


Version 2.0.beta-17
-------------------

Released on April 2nd 2012.

- Fixed crossmapping bug for some transcripts.
- Fixes for NCBI Entrez EFetch Version 2.0 release.
- Better chromosomal variant descriptions.
- Various smaller features and bugfixes.


Version 2.0.beta-16
-------------------

Released on March 1st 2012.

- Fixed position converter mapping info for some transcripts.
- Fixed deletion with deleted sequence length as argument.


Version 2.0.beta-15
-------------------

Released on February 20th 2012.

- Added 'Description Extractor' (see the main menu).
- Fixes for NCBI Entrez EFetch Version 2.0 release.
- Added chromosomal positions to `getTranscriptsAndInfo` webservice.
- Fixed chromosome slicing on reverse complement
- Fixed describing NOP variants with ``=``.
- Added Reference sequence info in `runMutalyzer` SOAP function response.
- Fixed mapping info for genes mapped to more than one chromosome.
- Various smaller features and bugfixes.


Version 2.0.beta-14
-------------------

Released on January 26th 2012.

- Added a SOAP service `getTranscriptsMapping`.
- Various smaller features and bugfixes.


Version 2.0.beta-13
-------------------

Released on January 25th 2012.

- Accept EX positioning scheme.
- Fix handling of LRG reference sequences.
- Various smaller features and bugfixes.


Version 2.0.beta-12
-------------------

Released on November 25th 2011.

- Accept plasmid reference sequences.
- View variant position in UCSC Genome Browser (only for transcript
  references).
- Retry querying dbSNP if it does not respond the first time.
- Support reference GenBank files built from contigs.
- Add optional argument to SOAP service `numberConversion` to map chromosomal
  locations to any gene.
- Various smaller features and bugfixes.


Version 2.0.beta-11
-------------------

Released on September 30st 2011.

- Major code refactoring:

  - Mutalyzer is now structured as a proper Python package.
  - Reworked installation and upgrade procedure.
  - Remote installation using Fabric.
  - Batch scheduler is now a proper system daemon.
  - Use mod_wsgi (with web.py) instead of the deprecated mod_python.
  - Added a lot of internal documentation.
  - Introduce unit tests.
  - Handle deletions of entire exons.
  - Added a SOAP service `info`.
  - Handle unknown (fuzzy) intronic positions.
  - Automatic synchronization of database and cache between Mutalyzer
    installations.
  - Use NCBI instead of UCSC for transcript mapping info.
  - Added a SOAP service `getdbSNPDescriptions`.
  - Moved Trac and Subversion repository to new server.
  - Implement HTTP HEAD method for ``/Reference/*`` locations.

- Added a SOAP service `ping`.
- Added an optional versions parameter to the SOAP service `getTranscripts`.
- Various smaller features and bugfixes.


Version 2.0.beta-10
-------------------

Released on July 21st 2011.

- Greatly reduce runtime for large batch jobs.


Version 2.0.beta-9
------------------

Released on June 27th 2011.

- Reworked the calculation of new splice site positions.
- Optionally restrict SOAP service `getTranscriptsAndInfo` transcripts to a
  gene.
- Add raw variants to SOAP service `runMutalyzer` results.
- Provide webservice client examples.
- Various smaller features and bugfixes.


Older versions
--------------

Vermaat's avatar
Typo    
Vermaat committed
859
The first lines of code for Mutalyzer 2.0 were written July 28th 2009, and
860
861
version 2.0.beta-8 was released on January 31st 2011. As far as Mutalyzer 1 is
concerned, archaeology is not really our field of research.