.gitlab-ci.yml 13 KB
Newer Older
1
2

before_script:
Mathieu Giraud's avatar
Mathieu Giraud committed
3
  - make demo
4
5
  - make data
  - make germline
6
  - make -C browser sha1
7
  - cp -p doc/analysis-example.vidjil browser/
8
9

stages:
10
  - test_tools
11
  - test_quality
12
  - test_unit
13
  - deploy_review
14
  - test_germlines
15
  - test_functional
16
  - test_shouldvdj
17
  - test_functional_external
18
  - coverage
19
  - prepare_release
20
  - tgz_release
Mathieu Giraud's avatar
Mathieu Giraud committed
21
22
  - valgrind_unit
  - valgrind_functional
23
  - multiple_tests
24
  - benchmark
25
  - publish_release
26
  - deploy_prod
27

28
29
# Anchors

30
31
.coverage_dependency:
  artifacts: &lcov_artifact
32
33
    paths:
      - algo/lcov_test_*.filtered
34
    expire_in: 1 week
35

36
37
38
39
40
41
# Tools

test_tools:
  stage: test_tools
  script: make -C tools/tests

42
43
44
45
46
47
48

# Germlines

test_germlines:
  stage: test_germlines
  script:
    - make -C germline get-all-data
49
    - make -C germline tests
50
  only:
51
    - /^feature-.*g.*\/.*$/
52
    - schedules
53

54
55
56
57
# Doc

include:
  - local: '/doc/.gitlab-ci.yml'
58
  - local: 'algo/.gitlab-ci-compilers.yml' # Stage multiple_tests
59

Mathieu Giraud's avatar
Mathieu Giraud committed
60
# Algorithm
61
62
63

test_algo_unit:
  stage: test_unit
64
  script: make -C algo unit_coverage
65
66
  artifacts:
    <<: *lcov_artifact
67
  only:
68
    - /^feature-.*a.*\/.*$/
69
    - schedules
70

71
72
test_algo_should:
  stage: test_functional
73
  script: make -C algo should_coverage
74
  artifacts:
75
    <<: *lcov_artifact
76
77
    reports:
      junit: algo/tests/should.xml
78
  only:
79
    - /^feature-.*a.*\/.*$/
80
    - schedules
81
82
83

test_algo_shouldvdj:
  stage: test_shouldvdj
84
  script: make -C algo shouldvdj_coverage
85
86
  artifacts:
    <<: *lcov_artifact
87
88
  only:
    - /^feature-.*a.*\/.*$/
89
90
    - schedules
  
91
92
algo_coverage:
  stage: coverage
93
  coverage: /^\s*lines\.*:\s+([0-9.]+\%)/
94
95
96
  script:
    - make -C algo lcov_reports
    - mv algo/reports/ coverage
97
98
  artifacts:
    paths:
99
      - coverage/
100
    expire_in: 1 week
101
  only:
102
    - /^feature-.*a.*\/.*$/
103
    - schedules
104

Mathieu Giraud's avatar
Mathieu Giraud committed
105
106
algo_valgrind_unit:
  stage: valgrind_unit
107
  script: make -C algo valgrind_unit
Mathieu Giraud's avatar
Mathieu Giraud committed
108
  only:
109
    - /^feature-.*a.*\/.*$/
110
    - schedules
111
112
  tags:
    - valgrind
Mathieu Giraud's avatar
Mathieu Giraud committed
113

114
.snip_valgrind_functional: &valgrind_functional
Mathieu Giraud's avatar
Mathieu Giraud committed
115
  stage: valgrind_functional
116
  script: make -C algo valgrind_should
117
118
119
120
121
  tags:
    - valgrind

algo_valgrind_functional:
  <<: *valgrind_functional
Mathieu Giraud's avatar
Mathieu Giraud committed
122
123
  when: manual
  only:
124
    - /^feature-.*a.*\/.*$/
125
    - schedules
126
127
128
129
130

release_valgrind_functional:
  <<: *valgrind_functional
  only:
    - /^feature-.*a.*\/release$/
Mathieu Giraud's avatar
Mathieu Giraud committed
131

132
133
134
135
136
prepare_release:
  stage: prepare_release
  script: make -C algo release RELEASE_TAG='rc'
  when: manual
  only:
137
    - /^feature-.*a.*\/.*$/
138

139
140
tgz_release:
  stage: tgz_release
141
142
  script: make -C algo release RELEASE_TAG=`cat algo/release`
  only:
143
    - /^feature-.*a.*\/release$/
144
  artifacts:
145
    paths:
146
147
    - algo/releases/vidjil-algo-`cat algo/release`.tar.gz
    - algo/releases/vidjil-algo-`cat algo/release`/vidjil-algo-`cat algo/release`_`uname -m`
148
    expire_in: 10 years
149
  allow_failure: false
150
151
  tags:
    - ubuntu-16.04-amd64
152

153
copy_release:
154
  stage: publish_release
155
156
157
158
159
160
161
162
  script:
    - |
      for repo in $ALGO_REPOSITORIES; do
        echo "Copying release to $repo"
        scp algo/releases/vidjil-algo*.tar.gz algo/releases/vidjil-algo*/vidjil-algo-*_* $repo
      done
      release_name=$(cat algo/release)
      ssh $VIDJIL_WWW "cd /var/www/html/releases; ln -sf vidjil-algo-${release_name}.tar.gz vidjil-latest.tgz; ln -sf vidjil-algo-${release_name}_x86_64 vidjil-latest_x86_64"
Mikaël Salson's avatar
Mikaël Salson committed
163
      ssh $VIDJIL_BONSAI "cd /bio1/www/html/vidjil; scp vidjil-algo-${release_name}* $VIDJIL_BONSAI_PROD:/bio1/www/html/vidjil"
164
  when: manual
165
166
167
  only:
    - /^feature-.*a.*\/release$/

168
169
deploy_release_prod:
  stage: deploy_prod
170
  when: manual
171
172
173
174
175
  only:
    - /^feature-.*a.*\/release$/
  script:
    - |
      release_name=$(cat algo/release)
176
      ssh $DEPLOY_SERVER "cd releases/vidjil;\
177
          tar xvzf vidjil-algo-${release_name}.tar.gz;\
178
179
          make -C vidjil-algo-${release_name};\
          ln -sfT vidjil-algo-${release_name} next"
180

Mathieu Giraud's avatar
Mathieu Giraud committed
181
# Client
182

183
test_browser_unit:
184
  stage: test_unit
Mathieu Giraud's avatar
Mathieu Giraud committed
185
  script: make unit_browser
186
187
188
  artifacts:
    paths:
    - browser/
189
  only:
190
191
    - /^feature-.*c.*\/.*$/
    - /^hotfix-.*c.*\/.*$/
Mathieu Giraud's avatar
Mathieu Giraud committed
192
    - prod-client
193
    - dev
194
    - schedules
195
196
  tags:
    - web
197

198
.browser-functional:
199
  stage: test_functional
200
  retry: 2
201
202
203
  script:
    - make -C browser
    - source /etc/profile.d/rvm.sh
204
    - rvm use 2.6.1
205
    - HEADLESS=1 make -C browser/test functional
206
207
208
  artifacts:
    paths:
    - browser/
209
210
    reports:
      junit: browser/test/test/TEST-*.xml
211
  only:
212
213
    - /^feature-.*c.*\/.*$/
    - /^hotfix-.*c.*\/.*$/
214
    - prod-client
215
    - schedules
216
217
  tags:
    - web
218

219
220
221
222
223
.browser-functional-chrome:
  extends: .browser-functional
  variables:
    WATIR_CHROME: "1"

224
.browser-functional-external:
225
  stage: test_functional_external
226
  retry: 2
227
228
229
  script:
    - make -C browser
    - source /etc/profile.d/rvm.sh
230
    - rvm use 2.6.1
231
    - HEADLESS=1 make -C browser/test external
232
233
234
  artifacts:
    paths:
    - browser/
235
236
    reports:
      junit: browser/test/test/TEST-*.xml
237
  only:
238
239
    - /^feature-.*c.*\/.*$/
    - /^hotfix-.*c.*\/.*$/
Mathieu Giraud's avatar
Mathieu Giraud committed
240
    - prod-client
241
    - schedules
242
243
  tags:
    - web
244

245
246
247
248
249
.browser-functional-external-chrome:
  extends: .browser-functional-external
  variables:
    WATIR_CHROME: "1"
    
250
ff32-browser-functional:
251
252
  extends: .browser-functional
  variables:
253
    FIREFOX_VERSION: 32
254

255
ff45-browser-functional:
256
257
  extends: .browser-functional
  variables:
258
259
    FIREFOX_VERSION: 45

260
chrome-browser-functional:
261
262
  extends: .browser-functional-chrome
        
263
old-chrome-browser-functional:
264
  extends: .browser-functional-chrome
265
266
267
  tags:
    - legacy

268
ff32-browser-functional-external:
269
270
  extends: .browser-functional-external
  variables:
271
    FIREFOX_VERSION: 32
272

273
ff45-browser-functional-external:
274
275
  extends: .browser-functional-external
  variables:
276
    FIREFOX_VERSION: 45
277

278
chrome-browser-functional-external:
279
280
  extends: .browser-functional-external-chrome
    
281
old-chrome-browser-functional-external-chrome:
282
283
284
  extends: .browser-functional-external-chrome
  tags:
    - legacy
285

286
287
code_quality:
  stage: test_quality
288
  script: make -C browser quality
289
  only:
290
291
    - /^feature-.*c.*\/.*$/
    - /^hotfix-.*c.*\/.*$/
292
    - prod-client
293
    - dev
294
    - schedules
295
296
  tags:
    - web
297

Ryan Herbert's avatar
Ryan Herbert committed
298
299
300
301
302
# Server

test_server_unit:
    stage: test_unit
    script:
303
304
      - virtualenv $CI_BUILD_REF_SLUG
      - source $CI_BUILD_REF_SLUG/bin/activate
305
      - pip install -r requirements.txt
Ryan Herbert's avatar
Ryan Herbert committed
306
      - make -C server install_web2py_standalone
307
      - make -C server launch_fuse_server
308
      - make unit_server || (make -C server kill_fuse_server; deactivate; false)
Ryan Herbert's avatar
Ryan Herbert committed
309
      - make -C server kill_fuse_server
310
      - deactivate
311
312
313
    artifacts:
      reports:
        junit: server/web2py/test-reports/TEST*xml
Ryan Herbert's avatar
Ryan Herbert committed
314
    only:
315
316
      - /^feature-.*s.*\/.*$/
      - /^hotfix-.*s.*\/.*$/
Ryan Herbert's avatar
Ryan Herbert committed
317
318
      - prod-server
      - dev
319
      - schedules
Ryan Herbert's avatar
Ryan Herbert committed
320
321
322
    tags:
      - web

323
.test_server_functional:
324
325
  stage: test_functional
  script:
326
327
    - docker build --no-cache --build-arg git_branch=$CI_COMMIT_REF_NAME --build-arg build_env=TEST -t "vidjil/server:test" docker/vidjil-server
    - docker build --no-cache --build-arg git_branch=$CI_COMMIT_REF_NAME --build-arg build_env=TEST -t "vidjil/client:test" docker/vidjil-client
328
    - sed -i '/\:\/etc\/nginx\/ssl/d' ./docker/docker-compose.yml
329
330
331
    - sed -i '/\/var\/lib\/mysql/d' ./docker/docker-compose.yml
    - sed -i 's/\/opt\/vidjil\/databases/databases/' ./docker/docker-compose.yml
    - echo -e "volumes:\n    databases:" >> ./docker/docker-compose.yml
332
    - sed -i 's/\:latest/\:test/g' ./docker/docker-compose.yml
333
    - cd docker/vidjil-server/conf/ && mv defs.py defs_https.py && mv defs_http.py defs.py && cd ../../..
334
    - make germline && cp browser/js/germline.js docker/vidjil-client/conf
335
    - cd docker && docker-compose up -d && cd ..
336
    - sed -i "s/^python\ \.\.\/\.\.\/\.\./docker\ exec\ docker_uwsgi_1\ python\ \/usr\/share\/vidjil\/server\/web2py/" server/web2py/applications/vidjil/tests/init_tests.sh
337
    - docker exec docker_uwsgi_1 sed -i "s/^\(FILE_SOURCE .*\)/FILE_SOURCE = '\/usr\/share\/vidjil\/demo'/" /usr/share/vidjil/server/web2py/applications/vidjil/modules/defs.py
338
    - docker exec docker_nginx_1 make -C /usr/share/vidjil browser
339
    - source /etc/profile.d/rvm.sh
340
    - rvm use 2.6.1
341
342
    - HEADLESS=1 make functional_server
  after_script:
343
    - cd docker && docker-compose down -v
344
    - docker rmi "vidjil/server:test" "vidjil/client:test" reporter:test
345
346
347
  artifacts:
    reports:
      junit: server/web2py/applications/vidjil/tests/test/TEST-*.xml
348
349
350
351
352
  only:
    - /^feature-.*s.*\/.*$/
    - /^hotfix-.*s.*\/.*$/
    - prod-server
    - dev
353
    - schedules
354
  tags:
355
    - x86_64
356
    - docker
357

358
ff32-server-functional:
359
360
361
362
  extends: .test_server_functional
  variables:
    FIREFOX_VERSION: 32

363
ff45-server-functional:
364
365
366
367
368
  extends: .test_server_functional
  variables:
    FIREFOX_VERSION: 45


369
370
371
372
373
374

# Benchmark

benchmark_algo:
  stage: benchmark
  script:
375
    - cd algo/tests ; python3 benchmark-releases.py -bic
376
377
378
379
380
381
382
  when: manual
  only:
    - /^feature-.*a.*\/.*$/
  tags:
    - several-compilers


Ryan Herbert's avatar
Ryan Herbert committed
383
384
# Deployment

385
386
deploy_review:
  stage: deploy_review
387
  script:
388
    - make -C browser icons
389
    - echo "$REVIEW_CONFIG_JS" > browser/js/conf.js
390
    - rsync -av --delete browser $REVIEW_SERVER:$REVIEW_SERVER_PATH$CI_BUILD_REF_SLUG
391
  environment:
392
    name: review/$CI_BUILD_REF_NAME
Mikaël Salson's avatar
Mikaël Salson committed
393
    url: http://$CI_BUILD_REF_SLUG.ci.vidjil.org/?data=analysis-example.vidjil
Mathieu Giraud's avatar
Mathieu Giraud committed
394
    on_stop: stop_deploy_review
395
  only:
396
397
    - /^feature-.*c.*\/.*$/
    - /^hotfix-.*c.*\/.*$/
398
399
  tags:
    - web
400

401
402
403
deploy_review_server:
  stage: deploy_review
  script:
404
405
    - make -C browser icons
    - cp ./docker/vidjil-client/conf/conf.js ./browser/js/conf.js
406
    - sed -i -r "s/localhost/${CI_BUILD_REF_SLUG}.server.ci.vidjil.org/g" ./browser/js/conf.js
407
    - sed -r 's/^.*FILE_SOURCE.*$/FILE_SOURCE="\/usr\/share\/vidjil\/demo"/' ./docker/vidjil-server/conf/defs.py > ./server/web2py/applications/vidjil/modules/defs.py
408
409
    - mv docker docker_${CI_BUILD_REF_SLUG}
    - cd docker_${CI_BUILD_REF_SLUG}
410
411
    - TMP_DOCKER=$(tempfile)
    - cp docker-compose.yml $TMP_DOCKER
412
413
414
    - awk -f ci/for-review.awk $TMP_DOCKER > docker-compose.yml
    - sed -i '$e cat ci/fuse-entrypoint.sh' vidjil-server/scripts/fuse-entrypoint.sh
    - rm -f $TMP_DOCKER
415
    - sed -i -r "s/WEB2PY_ADMIN_PASSWORD=/WEB2PY_ADMIN_PASSWORD=$REVIEW_SERVER_ADMIN_PASSWORD/" docker-compose.yml
416
    - cd ..
417
    - rsync -av --exclude .git . $REVIEW_SERVER:$REVIEW_SERVER_PATH_SERVER$CI_BUILD_REF_SLUG || $(case "$?" in 0|23) exit 0 ;; *) exit $?; esac)
418
    - ssh $REVIEW_SERVER "cd $REVIEW_SERVER_PATH_SERVER; ./install_certs.sh ${CI_BUILD_REF_SLUG}; cd ${CI_BUILD_REF_SLUG}/docker_${CI_BUILD_REF_SLUG}; ls -lnd ../browser | cut -d ' ' -f 3 > ../uid; docker-compose up -d mysql fuse uwsgi nginx workers"
419
420
  environment:
    name: review_server/$CI_BUILD_REF_NAME
421
    url: http://$CI_BUILD_REF_SLUG.server.ci.vidjil.org/browser/
422
    on_stop: stop_deploy_review_server
423
    auto_stop_in: 2 months
424
425
426
427
  only:
    - /^feature-.*s.*\/.*$/
    - /^hotfix-.*s.*\/.*$/

428
deploy_docker:
429
  stage: deploy_prod
430
  script:
431
    - export CUR_DATE=`date +%Y-%m-%d`
432
    - export TYPE=`echo $CI_COMMIT_REF_NAME | awk '{ gsub(/prod-/, "") }{ print $1 }'`
433
434
    - export SHA=`echo $CI_COMMIT_SHA | awk '{ print substr($0, 0, 8) }'`
    - export TAG="vidjil/$TYPE:$CUR_DATE-$SHA"
435
    - docker login -u "$CI_REGISTRY_USER" -p "$CI_REGISTRY_PASSWORD" $CI_REGISTRY
436
    - docker build --no-cache --build-arg git_branch=$CI_COMMIT_REF_NAME --build-arg build_env=PRODUCTION -t $TAG docker/vidjil-$TYPE
437
438
439
440
    - docker push $TAG
    - docker tag $TAG "vidjil/$TYPE:latest"
    - docker push "vidjil/$TYPE:latest"
    - docker rmi $TAG "vidjil/$TYPE:latest"
441
442
443
  when: manual
  only:
    - prod-server
444
    - prod-client
445
446
  tags:
    - web
447
    - docker
448

449
deploy_prod:
450
  stage: deploy_prod
451
  script:
452
453
454
455
456
457
458
    - ssh $PROD_CLIENT_SERVER "
         cd $PROD_CLIENT_PATH;
         git fetch
         && git reset --hard origin/prod-client
         && make -C browser
         && make -C browser sha1
         && cp doc/analysis-example.vidjil browser/"
459
460
  environment:
    name: production
461
    url: http://$PROD_CLIENT_SERVER/?data=analysis-example.vidjil
462
463
  only:
    - prod-client
464
465
  tags:
    - web
466

467
468
469
470
471
deploy_germlines:
  stage: deploy_prod
  script:
    - make -C germline get-all-data
    - make -C germline js
472
    - date=$(date +%Y-%m-%d)
473
474
475
476
477
478
479
480
    - tar cvzf germline-$date.tar.gz germline/*/*.fa germline/IMGT_RELEASE browser/js/germline.js
    - scp germline-$date.tar.gz $VIDJIL_WWW:$REMOTE_GERMLINE_DIR
  only:
    - manual
    - /^feature-.*g.*\/.*$/
    


481
482
stop_deploy_review:
  stage: deploy_review
483
484
485
  variables:
    GIT_STRATEGY: none
  script:
486
    - ssh $REVIEW_SERVER "rm -rf $REVIEW_SERVER_PATH$CI_BUILD_REF_SLUG"
487
488
  when: manual
  environment:
489
    name: review/$CI_BUILD_REF_NAME
490
    action: stop
491
  only:
492
493
    - /^feature-.*c.*\/.*$/
    - /^hotfix-.*c.*\/.*$/
494
  tags:
495
    - web
496
497
498
499

stop_deploy_review_server:
  stage: deploy_review
  script:
500
    - ssh $REVIEW_SERVER "set -o xtrace; docker-compose -f $REVIEW_SERVER_PATH_SERVER$CI_BUILD_REF_SLUG/docker_$CI_BUILD_REF_SLUG/docker-compose.yml down -v ; rm -rf $REVIEW_SERVER_PATH_SERVER$CI_BUILD_REF_SLUG; $REVIEW_SERVER_PATH_SERVER/uninstall_certs.sh $CI_BUILD_REF_SLUG"
501
502
503
504
505
506
507
  when: manual
  environment:
    name: review_server/$CI_BUILD_REF_NAME
    action: stop
  only:
    - /^feature-.*s.*\/.*$/
    - /^hotfix-.*s.*\/.*$/