19688: Fix @stubs decorator that was accidentally skipping tests
[arvados.git] / sdk / cwl / tests / arvados-tests.yml
1 # Copyright (C) The Arvados Authors. All rights reserved.
2 #
3 # SPDX-License-Identifier: Apache-2.0
4
5 - job: dir-job.yml
6   output:
7     "outlist": {
8         "size": 20,
9         "location": "output.txt",
10         "class": "File",
11         "checksum": "sha1$13cda8661796ae241da3a18668fb552161a72592"
12     }
13   tool: keep-dir-test-input.cwl
14   doc: Test directory in keep
15
16 - job: dir-job2.yml
17   output:
18     "outlist": {
19         "size": 20,
20         "location": "output.txt",
21         "class": "File",
22         "checksum": "sha1$13cda8661796ae241da3a18668fb552161a72592"
23     }
24   tool: keep-dir-test-input.cwl
25   doc: Test directory in keep
26
27 - job: null
28   output:
29     "outlist": {
30         "size": 20,
31         "location": "output.txt",
32         "class": "File",
33         "checksum": "sha1$13cda8661796ae241da3a18668fb552161a72592"
34     }
35   tool: keep-dir-test-input2.cwl
36   doc: Test default directory in keep
37
38 - job: null
39   output:
40     "outlist": {
41         "size": 20,
42         "location": "output.txt",
43         "class": "File",
44         "checksum": "sha1$13cda8661796ae241da3a18668fb552161a72592"
45     }
46   tool: keep-dir-test-input3.cwl
47   doc: Test default directory in keep
48
49 - job: octo.yml
50   output: {}
51   tool: cat.cwl
52   doc: Test hashes in filenames
53
54 - job: listing-job.yml
55   output: {
56     "out": {
57         "class": "File",
58         "location": "output.txt",
59         "size": 5,
60         "checksum": "sha1$724ba28f4a9a1b472057ff99511ed393a45552e1"
61     }
62   }
63   tool: wf/listing_shallow.cwl
64   doc: test shallow directory listing
65
66 - job: listing-job.yml
67   output: {
68     "out": {
69         "class": "File",
70         "location": "output.txt",
71         "size": 5,
72         "checksum": "sha1$724ba28f4a9a1b472057ff99511ed393a45552e1"
73     }
74   }
75   tool: wf/listing_none.cwl
76   doc: test no directory listing
77
78 - job: listing-job.yml
79   output: {
80     "out": {
81         "class": "File",
82         "location": "output.txt",
83         "size": 5,
84         "checksum": "sha1$724ba28f4a9a1b472057ff99511ed393a45552e1"
85     }
86   }
87   tool: wf/listing_deep.cwl
88   doc: test deep directory listing
89
90 - job: null
91   output: {}
92   tool: noreuse.cwl
93   doc: "Test arv:ReuseRequirement"
94
95 - job: 12213-keepref-job.yml
96   output: {
97     "out": [
98         {
99             "checksum": "sha1$1c78028c0d69163391eef89316b44a57bde3fead",
100             "location": "sample1_S01_R1_001.fastq.txt",
101             "class": "File",
102             "size": 32
103         },
104         {
105             "checksum": "sha1$5f3b4df1b0f7fdced751fc6079778600ad9fdb45",
106             "location": "sample2_S01_R1_001.fastq.txt",
107             "class": "File",
108             "size": 32
109         }
110     ]
111   }
112   tool: 12213-keepref-wf.cwl
113   doc: "Test manipulating keep references with expression tools"
114
115 - job: null
116   output:
117     out: null
118   tool: 12418-glob-empty-collection.cwl
119   doc: "Test glob output on empty collection"
120
121 - job: null
122   output:
123     "out": {
124         "location": "hello.out",
125         "class": "File",
126         "checksum": "sha1$ec5d3976351abab45a483a49ce714a8430cb203a",
127         "size": 24
128     }
129   tool: 13976-keepref-wf.cwl
130   doc: "Test issue 13976"
131
132 - job: null
133   output:
134     out: out
135   tool: wf/runin-wf.cwl
136   doc: "RunInSingleContainer cwl.input.json needs to be consistent with pathmapper manipulations"
137
138 - job: secondary/wf-job.yml
139   output: {}
140   tool: secondary/wf.cwl
141   doc: "RunInSingleContainer applies secondaryFile discovery & manipulation before generating cwl.input.yml"
142
143 - job: null
144   output:
145     out: out
146   tool: wf/runin-with-ttl-wf.cwl
147   doc: "RunInSingleContainer respects outputTTL"
148
149 - job: secret_test_job.yml
150   output: {
151     "out": {
152         "class": "File",
153         "location": "hashed_example.txt",
154         "size": 47,
155         "checksum": "sha1$f45341c7f03b4dd10646c402908d1aea0d580f5d"
156     }
157   }
158   tool: wf/secret_wf.cwl
159   doc: "Test secret input parameters"
160   tags: [ secrets ]
161
162 - job: null
163   output:
164     out: null
165   tool: wf/runin-reqs-wf.cwl
166   doc: "RunInSingleContainer handles dynamic resource requests on step"
167
168 - job: null
169   output:
170     out: null
171   tool: wf/runin-reqs-wf2.cwl
172   doc: "RunInSingleContainer handles dynamic resource requests on embedded subworkflow"
173
174 - job: null
175   output:
176     out: null
177   tool: wf/runin-reqs-wf3.cwl
178   should_fail: true
179   doc: "RunInSingleContainer disallows dynamic resource request on subworkflow steps"
180
181 - job: null
182   output:
183     out: null
184   tool: wf/runin-reqs-wf4.cwl
185   doc: "RunInSingleContainer discovers static resource request in subworkflow steps"
186
187 - job: null
188   output:
189     out: null
190   tool: wf/runin-reqs-wf5.cwl
191   doc: "RunInSingleContainer has minimum 128 MiB RAM"
192
193 - job: secondaryFiles/inp3.yml
194   output: {}
195   tool: secondaryFiles/example1.cwl
196   doc: Discover secondaryFiles at runtime if they are in keep
197
198 - job: null
199   output: {}
200   tool: secondaryFiles/example3.cwl
201   doc: Discover secondaryFiles on default values
202
203 - job: null
204   output:
205     out: null
206   tool: wf-defaults/wf1.cwl
207   doc: "Can have separate default parameters including directory and file inside same directory"
208
209 - job: null
210   output:
211     out: null
212   tool: wf-defaults/wf2.cwl
213   doc: "Can have a parameter default value that is a directory literal with a file literal"
214
215 - job: null
216   output:
217     out: null
218   tool: wf-defaults/wf3.cwl
219   doc: "Do not accept a directory literal without a basename"
220   should_fail: true
221
222 - job: null
223   output:
224     out: null
225   tool: wf-defaults/wf4.cwl
226   doc: default in embedded subworkflow missing 'id' field, v1.0
227   should_fail: true
228
229 - job: null
230   output:
231     out: null
232   tool: wf-defaults/wf8.cwl
233   doc: default in embedded subworkflow missing 'id' field, v1.1
234   should_fail: false
235
236 - job: null
237   output:
238     out: null
239   tool: wf-defaults/wf5.cwl
240   doc: default in embedded subworkflow
241
242 - job: null
243   output:
244     out: null
245   tool: wf-defaults/wf6.cwl
246   doc: default in RunInSingleContainer step
247
248 - job: null
249   output:
250     out: null
251   tool: wf-defaults/wf7.cwl
252   doc: workflow level default in RunInSingleContainer
253
254 - job: 13931-size-job.yml
255   output:
256     "out": {
257         "checksum": "sha1$5bf6e5357bd42a6b1d2a3a040e16a91490064d26",
258         "location": "size.txt",
259         "class": "File",
260         "size": 3
261     }
262   tool: 13931-size.cwl
263   doc: Test that size is set for files in Keep
264
265 - job: 15241-writable-dir-job.json
266   output: {
267     "results": {
268         "basename": "keep:6dd5fa20622d5a7a23c9147d0927da2a+180",
269         "class": "Directory",
270         "listing": [
271             {
272                 "basename": "d7514270f356df848477718d58308cc4+94",
273                 "class": "Directory",
274                 "listing": [
275                     {
276                         "basename": "a",
277                         "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
278                         "class": "File",
279                         "location": "a",
280                         "size": 0
281                     },
282                     {
283                         "basename": "blurg.txt",
284                         "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
285                         "class": "File",
286                         "location": "blurg.txt",
287                         "size": 0
288                     },
289                     {
290                         "basename": "c",
291                         "class": "Directory",
292                         "listing": [
293                             {
294                                 "basename": "d",
295                                 "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
296                                 "class": "File",
297                                 "location": "d",
298                                 "size": 0
299                             }
300                         ],
301                         "location": "c"
302                     },
303                     {
304                         "basename": "b",
305                         "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
306                         "class": "File",
307                         "location": "b",
308                         "size": 0
309                     }
310                 ],
311                 "location": "d7514270f356df848477718d58308cc4+94"
312             }
313         ],
314         "location": "keep:6dd5fa20622d5a7a23c9147d0927da2a+180"
315     }
316   }
317   tool: 15241-writable-dir.cwl
318   doc: Test for writable collections
319
320 - job: badkeep.yml
321   output: {}
322   should_fail: true
323   tool: 15295-bad-keep-ref.cwl
324   doc: Test checking for invalid keepref
325
326 - job: listing-job.yml
327   output: {
328     "out": {
329         "class": "File",
330         "location": "output.txt",
331         "size": 5,
332         "checksum": "sha1$724ba28f4a9a1b472057ff99511ed393a45552e1"
333     }
334   }
335   tool: 16169-no-listing-hint.cwl
336   doc: "Test cwltool:LoadListingRequirement propagation"
337
338 - job: hello.yml
339   output:
340     "out": {
341         "location": "hello.out",
342         "class": "File",
343         "checksum": "sha1$ec5d3976351abab45a483a49ce714a8430cb203a",
344         "size": 24
345     }
346   tool: 16377-missing-default.cwl
347   doc: "Test issue 16377 - missing default fails even when it should be overridden by valid input"
348
349 - job: hello.yml
350   output:
351     "out":
352       "checksum": "sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15"
353       "class": "File"
354       "location": "foo.txt"
355       "size": 4
356   tool: 17267-broken-schemas.cwl
357   doc: "Test issue 17267 - inaccessible $schemas URL is not a fatal error"
358
359 - job: null
360   output: {}
361   tool: wf/trick_defaults2.cwl
362   doc: "Test issue 17462 - secondary file objects on file defaults are not resolved"
363
364 - job: null
365   output: {
366     "stuff": {
367         "location": "bar.txt",
368         "basename": "bar.txt",
369         "class": "File",
370         "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
371         "size": 0
372     }
373   }
374   tool: 17521-dot-slash-glob.cwl
375   doc: "Test issue 17521 - bug with leading './' capturing files in subdirectories"
376
377 - job: null
378   output: {
379     "stuff": {
380         "basename": "foo",
381         "class": "Directory",
382         "listing": [
383             {
384                 "basename": "bar.txt",
385                 "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
386                 "class": "File",
387                 "location": "foo/bar.txt",
388                 "size": 0
389             }
390         ],
391         "location": "foo"
392     }
393   }
394   tool: 10380-trailing-slash-dir.cwl
395   doc: "Test issue 10380 - bug with trailing slash when capturing an output directory"
396
397 - job: null
398   output: {
399     "stuff": {
400         "basename": "78f3957c41d044352303a3fa326dff1e+102",
401         "class": "Directory",
402         "listing": [
403             {
404                 "basename": "baz.txt",
405                 "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
406                 "class": "File",
407                 "location": "78f3957c41d044352303a3fa326dff1e+102/baz.txt",
408                 "size": 0
409             },
410             {
411                 "basename": "foo",
412                 "class": "Directory",
413                 "listing": [
414                     {
415                         "basename": "bar.txt",
416                         "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
417                         "class": "File",
418                         "location": "78f3957c41d044352303a3fa326dff1e+102/foo/bar.txt",
419                         "size": 0
420                     }
421                 ],
422                 "location": "78f3957c41d044352303a3fa326dff1e+102/foo"
423             }
424         ],
425         "location": "78f3957c41d044352303a3fa326dff1e+102"
426     }
427   }
428   tool: 17801-runtime-outdir.cwl
429   doc: "Test issue 17801 - bug using $(runtime.outdir) to capture the output directory"
430
431 - job: null
432   output:
433     "val": "keep:f225e6259bdd63bc7240599648dde9f1+97/hg19.fa"
434   tool: 17858-pack-visit-crash.cwl
435   doc: "Test issue 17858 - keep ref default inputs on ExpressionTool"
436
437 - job: 17879-ignore-sbg-fields-job.yml
438   output:
439     "outstr": "foo woble bar"
440   tool: 17879-ignore-sbg-fields.cwl
441   doc: "Test issue 17879 - ignores sbg fields"
442
443 - job: chipseq/chip-seq-single.json
444   output: {}
445   tool: chipseq/cwl-packed.json
446   doc: "Test issue 18723 - correctly upload two directories with the same basename"
447
448 - job: null
449   output: {}
450   tool: 18994-basename/wf_ren.cwl
451   doc: "Test issue 18994 - correctly stage file with modified basename"
452
453 - job: 19109-upload-secondary.yml
454   output: {
455     "out": {
456         "basename": "file1.catted",
457         "class": "File",
458         "location": "file1.catted",
459         "size": 20,
460         "checksum": "sha1$c4cead17cebdd829f38c48e18a28f1da72339ef7"
461     },
462     "out2": {
463         "basename": "file2.catted",
464         "checksum": "sha1$6f71c5d1512519ede45bedfdd624e05fd8037b0d",
465         "class": "File",
466         "location": "file2.catted",
467         "size": 12
468     }
469   }
470   tool: 19109-upload-secondary.cwl
471   doc: "Test issue 19109 - correctly discover & upload secondary files"
472
473 - job: 19678-name-id.yml
474   output: {
475     "processed_name": {
476         "first": "foo",
477         "last": "bar"
478     }
479   }
480   tool: 19678-name-id.cwl
481   doc: "Test issue 19678 - non-string type input parameter called 'name'"