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comparison gmql_operators_tests.xml @ 0:a80c93182db3 draft default tip

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planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
author geco-team
date Tue, 26 Jun 2018 09:08:06 -0400
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1 <macros>
2 <xml name="query_intro" token_name="@NAME@">
3 <param name="authToken" value="guest2.gmql_user"/>
4 <param name="query_name" value="@NAME@"/>
5 <conditional name="query_create">
6 <param name="create" value="yes"/>
7 </conditional>
8 </xml>
9 <xml name="query_end" token_mat="@MAT@">
10 <conditional name="materialize">
11 <param name="materialize_result" value="@MAT@"/>
12 <yield />
13 </conditional>
14 </xml>
15 <xml name="simple_select" token_ds="@DS@">
16 <repeat name="operations">
17 <conditional name="operation">
18 <param name="operator" value="SELECT"/>
19 <conditional name="input">
20 <param name="input_type" value="i_ds"/>
21 <param name="gmql_datasets" value="rep.gmql_repository"/>
22 <param name="input_ds" value="@DS@"/>
23 <section name="region_predicates">
24 <conditional name="conditions">
25 <param name="ad_flags" value="strings"/>
26 <param name="conditions_string" value=""/>
27 </conditional>
28 </section>
29 <section name="metadata_predicates">
30 <conditional name="conditions">
31 <param name="ad_flags" value="strings"/>
32 <param name="conditions_string" value=""/>
33 </conditional>
34 </section>
35 <section name="semijoin_predicate">
36 <param name="condition" value="IN"/>
37 <param name="ds_ext" value=""/>
38 </section>
39 </conditional>
40 <yield />
41 </conditional>
42 </repeat>
43 </xml>
44 <xml name="composer_tests">
45 <tests>
46 <test>
47 <!-- TEST 1: Select (Simple Metadata Condition) -->
48 <expand macro="query_intro" name="test_select1"/>
49 <repeat name="operations">
50 <conditional name="operation" >
51 <param name="operator" value="SELECT"/>
52 <conditional name="input">
53 <param name="input_type" value="i_ds"/>
54 <param name="gmql_datasets" value="rep.gmql_repository"/>
55 <param name="input_ds" value="Example_Dataset_1"/>
56 <section name="metadata_predicates">
57 <conditional name="conditions">
58 <param name="ad_flags" value="steps"/>
59 <param name="negate" value="false"/>
60 <param name="attribute" value="grant"/>
61 <param name="condition" value="eq"/>
62 <param name="value" value="Stam"/>
63 </conditional>
64 </section>
65 <section name="region_predicates">
66 <conditional name="conditions">
67 <param name="ad_flags" value="strings"/>
68 <param name="conditions_string" value=""/>
69 </conditional>
70 </section>
71 <section name="semijoin_predicate">
72 <param name="condition" value="IN"/>
73 <param name="ds_ext" value=""/>
74 </section>
75 </conditional>
76 </conditional>
77 </repeat>
78 <param name="output_var" value="OUT"/>
79 <conditional name="m_stm">
80 <param name="materialize_stm" value="false" />
81 </conditional>
82 <expand macro="query_end" mat="false"/>
83 <output name="query" file="select1.gmql_query"/>
84 </test>
85 <test>
86 <!-- TEST 2: Select (Multiple Metadata, Region condition) -->
87 <expand macro="query_intro" name="test_select2"/>
88 <repeat name="operations">
89 <conditional name="operation" >
90 <param name="operator" value="SELECT"/>
91 <conditional name="input">
92 <param name="input_type" value="i_ds"/>
93 <param name="gmql_datasets" value="rep.gmql_repository"/>
94 <param name="input_ds" value="Example_Dataset_1" />
95 <section name="region_predicates">
96 <conditional name="conditions">
97 <param name="is_meta_value" value="false" />
98 <param name="ad_flag" value="steps" />
99 <param name="attribute" value="score" />
100 <param name="value" value="3" />
101 <param name="negate" value="false" />
102 <param name="condition" value="gt" />
103 </conditional>
104 </section>
105 <section name="metadata_predicates" >
106 <conditional name="conditions" >
107 <param name="ad_flag" value="steps" />
108 <param name="attribute" value="patient_age" />
109 <param name="value" value="64" />
110 <param name="negate" value="false" />
111 <param name="condition" value="eq" />
112 <repeat name="pm_additional" >
113 <param name="negate" value="false" />
114 <param name="attribute" value="cell" />
115 <param name="logCon" value="AND" />
116 <param name="value" value="8988T" />
117 <param name="condition" value="eq" />
118 </repeat>
119 </conditional>
120 </section>
121 <section name="semijoin_predicate">
122 <param name="condition" value="IN"/>
123 <param name="ds_ext" value=""/>
124 </section>
125 </conditional>
126 </conditional>
127 </repeat>
128 <param name="output_var" value="OUT"/>
129 <conditional name="m_stm">
130 <param name="materialize_stm" value="false" />
131 </conditional>
132 <expand macro="query_end" mat="false"/>
133 <output name="query" file="select2.gmql_query"/>
134 </test>
135 <test>
136 <!-- TEST 3: Select (TEST2 + Semijoin predicate) -->
137 <expand macro="query_intro" name="test_select3"/>
138 <repeat name="operations">
139 <conditional name="operation" >
140 <param name="operator" value="SELECT"/>
141 <conditional name="input">
142 <param name="input_type" value="i_ds"/>
143 <param name="gmql_datasets" value="rep.gmql_repository"/>
144 <param name="input_ds" value="Example_Dataset_1" />
145 <section name="region_predicates">
146 <conditional name="conditions">
147 <param name="is_meta_value" value="false" />
148 <param name="ad_flag" value="steps" />
149 <param name="attribute" value="score" />
150 <param name="value" value="3" />
151 <param name="negate" value="false" />
152 <param name="condition" value="gt" />
153 </conditional>
154 </section>
155 <section name="metadata_predicates" >
156 <conditional name="conditions" >
157 <param name="ad_flag" value="steps" />
158 <param name="attribute" value="patient_age" />
159 <param name="value" value="64" />
160 <param name="negate" value="false" />
161 <param name="condition" value="eq" />
162 <repeat name="pm_additional" >
163 <param name="negate" value="false" />
164 <param name="attribute" value="cell" />
165 <param name="logCon" value="AND" />
166 <param name="value" value="8988T" />
167 <param name="condition" value="eq" />
168 </repeat>
169 </conditional>
170 </section>
171 <section name="semijoin_predicate">
172 <param name="condition" value="IN"/>
173 <param name="ds_ext" value=""/>
174 </section>
175 </conditional>
176 </conditional>
177 </repeat>
178 <param name="output_var" value="OUT"/>
179 <conditional name="m_stm">
180 <param name="materialize_stm" value="false" />
181 </conditional>
182 <repeat name="operations">
183 <conditional name="operation">
184 <param name="operator" value="SELECT" />
185 <conditional name="input">
186 <param name="input_type" value="i_ds"/>
187 <param name="gmql_datasets" value="rep.gmql_repository"/>
188 <param name="input_ds" value="Example_Dataset_2" />
189 <section name="region_predicates">
190 <conditional name="conditions">
191 <param name="ad_flags" value="strings"/>
192 <param name="conditions_string" value=""/>
193 </conditional>
194 </section>
195 <section name="metadata_predicates">
196 <conditional name="conditions">
197 <param name="ad_flags" value="strings"/>
198 <param name="conditions_string" value=""/>
199 </conditional>
200 </section>
201 <section name="semijoin_predicate">
202 <repeat name="sj_attributes" >
203 <param name="sj_att" value="cell" />
204 </repeat>
205 <param name="ds_ext" value="OUT" />
206 </section>
207 </conditional>
208 <param name="output_var" value="OUT2"/>
209 </conditional>
210 </repeat>
211 <expand macro="query_end" mat="false"/>
212 <output name="query" file="select3.gmql_query"/>
213 </test>
214 <test>
215 <!-- TEST 4: PROJECT -->
216 <expand macro="query_intro" name="test_project1"/>
217 <expand macro="simple_select" ds="Example_Dataset_1" />
218 <param name="output_var" value="OUT"/>
219 <conditional name="m_stm">
220 <param name="materialize_stm" value="false" />
221 </conditional>
222 <repeat name="operations">
223 <conditional name="operation">
224 <param name="operator" value="PROJECT"/>
225 <param name="input_var" value="OUT"/>
226 <section name="region_att">
227 <conditional name="allbut">
228 <param name="allbut_flag" value="exclude"/>
229 <repeat name="list_exclude">
230 <param name="attribute" value="name"/>
231 </repeat>
232 <repeat name="list_exclude">
233 <param name="attribute" value="frame"/>
234 </repeat>
235 </conditional>
236 </section>
237 <section name="meta_att">
238 <conditional name="allbut">
239 <param name="allbut_flag" value="keep"/>
240 <repeat name="list_keep">
241 <param name="attribute" value="cell"/>
242 </repeat>
243 </conditional>
244 </section>
245 <section name="project_new_meta"/>
246 <section name="project_new_regions">
247 <repeat name="new_region_att">
248 <param name="new_name" value="lengh"/>
249 <conditional name="gen_function">
250 <param name="expression" value="stop - start"/>
251 <param name="gen_type" value="arithmetic"/>
252 </conditional>
253 </repeat>
254 </section>
255 <param name="output_var" value="OUT2"/>
256 </conditional>
257 </repeat>
258 <output name="query" file="project1.gmql_query"/>
259 </test>
260 <test>
261 <!-- TEST 5: EXTEND -->
262 <expand macro="query_intro" name="test_extend1"/>
263 <expand macro="simple_select" ds="Example_Dataset_1"/>
264 <param name="output_var" value="OUT"/>
265 <conditional name="m_stm">
266 <param name="materialize_stm" value="false"/>
267 </conditional>
268 <repeat name="operations">
269 <conditional name="operation">
270 <param name="operator" value="EXTEND"/>
271 <section name="new_metadata_attributes">
272 <repeat name="new_attributes">
273 <param name="new_name" value="avg_score"/>
274 <param name="function" value="AVG"/>
275 <param name="argument" value="score"/>
276 </repeat>
277 <repeat name="new_attributes">
278 <param name="new_name" value="max_p"/>
279 <param name="function" value="MAX"/>
280 <param name="argument" value="pvalue"/>
281 </repeat>
282 </section>
283 <param name="input_var" value="OUT" />
284 <param name="output_var" value="OUT2"/>
285 </conditional>
286 </repeat>
287 <output name="query" file="extend1.gmql_query" />
288 </test>
289 <test>
290 <!-- TEST 6: ORDER -->
291 <expand macro="query_intro" name="test_order1" />
292 <expand macro="simple_select" ds="Example_Dataset_1" />
293 <param name="output_var" value="OUT" />
294 <repeat name="operations">
295 <conditional name="operation">
296 <param name="operator" value="ORDER"/>
297 <param name="output_var" value="OUT2"/>
298 <param name="input_var_ordering_ds" value="OUT"/>
299 <section name="ordering_attributes">
300 <repeat name="attributes">
301 <param name="attribute_name" value="score"/>
302 <param name="att_type" value="region"/>
303 <param name="order_type" value="desc"/>
304 </repeat>
305 <repeat name="attributes">
306 <param name="attribute_name" value="start"/>
307 <param name="att_type" value="region"/>
308 <param name="order_type" value="asc"/>
309 </repeat>
310 <repeat name="attributes">
311 <param name="attribute_name" value="ID"/>
312 <param name="att_type" value="metadata"/>
313 <param name="order_type" value="asc"/>
314 </repeat>
315 </section>
316 <section name="top_options">
317 <repeat name="to">
318 <param name="type" value="metadata"/>
319 <conditional name="opt">
320 <param name="k_type" value="n"/>
321 <param name="k" value="5"/>
322 </conditional>
323 </repeat>
324 </section>
325 </conditional>
326 </repeat>
327 <output name="query" file="order1.gmql_query" />
328 </test>
329 <test>
330 <!-- TEST 7: GROUP -->
331 <expand macro="query_intro" name="test_group1"/>
332 <expand macro="simple_select" ds="Example_Dataset_1"/>
333 <param name="output_var" value="OUT"/>
334 <repeat name="operations">
335 <conditional name="operation">
336 <param name="operator" value="GROUP"/>
337 <param name="output_var" value="OUT2"/>
338 <param name="input_var" value="OUT"/>
339 <conditional name="add_grouping">
340 <param name="group_type" value="both"/>
341 <section name="regions">
342 <repeat name="group_regions_atts">
343 <param name="attribute" value="score"/>
344 </repeat>
345 <repeat name="new_attributes">
346 <param name="new_name" value="min_signal"/>
347 <param name="function" value="MIN"/>
348 <param name="argument" value="signal"/>
349 </repeat>
350 </section>
351 <section name="metadata">
352 <conditional name="meta_agg">
353 <param name="meta_agg_flag" value="true"/>
354 <repeat name="new_attributes">
355 <param name="new_name" value="min_tier"/>
356 <param name="function" value="MIN"/>
357 <param name="argument" value="cell_tier"/>
358 </repeat>
359 </conditional>
360 <repeat name="group_meta_atts">
361 <param name="metajoin_match" value="SIMPLE"/>
362 <param name="j_att" value="cell_tissue"/>
363 </repeat>
364 </section>
365 </conditional>
366 </conditional>
367 </repeat>
368 <output name="query" file="group1.gmql_query" />
369 </test>
370 <test>
371 <!-- TEST 8: MERGE -->
372 <expand macro="query_intro" name="test_merge1"/>
373 <expand macro="simple_select" ds="Example_Dataset_1"/>
374 <param name="output_var" value="OUT"/>
375 <repeat name="operations">
376 <conditional name="operation">
377 <param name="operator" value="MERGE"/>
378 <param name="output_var" value="OUT2"/>
379 <param name="input_var" value="OUT"/>
380 <section name="groupby">
381 <repeat name="group_meta_atts">
382 <param name="metajoin_match" value="EXACT"/>
383 <param name="j_att" value="antibody_target"/>
384 </repeat>
385 </section>
386 </conditional>
387 </repeat>
388 </test>
389 <test>
390 <!-- TEST 9: UNION -->
391 <expand macro="query_intro" name="test_merge1"/>
392 <expand macro="simple_select" ds="Example_Dataset_1"/>
393 <param name="output_var" value="IN"/>
394 <expand macro="simple_select" ds="Example_Dataset_2" >
395 <param name="output_var" value="IN2" />
396 </expand>
397 <repeat name="operations">
398 <conditional name="operation" >
399 <param name="operator" value="UNION" />
400 <param name="output_var" value="OUT" />
401 <param name="input_var_second" value="IN2" />
402 <param name="input_var_first" value="IN" />
403 </conditional>
404 </repeat>
405 <output name="query" file="union1.gmql_query" />
406 </test>
407 <test>
408 <!-- TEST 10: DIFFERENCE -->
409 <expand macro="query_intro" name="test_merge1"/>
410 <expand macro="simple_select" ds="Example_Dataset_1"/>
411 <param name="output_var" value="IN"/>
412 <expand macro="simple_select" ds="Example_Dataset_2">
413 <param name="output_var" value="IN2"/>
414 </expand>
415 <repeat name="operations">
416 <conditional name="operation">
417 <param name="operator" value="DIFFERENCE"/>
418 <param name="output_var" value="OUT"/>
419 <param name="input_var_negative" value="IN2"/>
420 <param name="input_var_reference" value="IN"/>
421 <param name="exact_flag" value="true"/>
422 <section name="joinby">
423 <repeat name="group_meta_atts">
424 <param name="metajoin_match" value="SIMPLE"/>
425 <param name="j_att" value="cell"/>
426 </repeat>
427 </section>
428 </conditional>
429 </repeat>
430 <output name="query" file="difference1.gmql_query"/>
431 </test>
432 <test>
433 <!-- TEST 11: JOIN (Genomic Predicate + Joinby condition) -->
434 <expand macro="query_intro" name="test_join1"/>
435 <expand macro="simple_select" ds="Example_Dataset_1"/>
436 <param name="output_var" value="IN"/>
437 <expand macro="simple_select" ds="Example_Dataset_2">
438 <param name="output_var" value="IN2"/>
439 </expand>
440 <repeat name="operations">
441 <conditional name="operation">
442 <param name="operator" value="JOIN"/>
443 <param name="output_var" value="OUT"/>
444 <param name="input_var_anchor" value="IN"/>
445 <param name="input_var_experiment" value="IN2"/>
446 <section name="conditions_section">
447 <conditional name="conditions">
448 <param name="c_type" value="distance"/>
449 <repeat name="distance_conditions">
450 <conditional name="type_dc">
451 <param name="type_dc_value" value="dist"/>
452 <param name="dc" value="MD"/>
453 <param name="n" value="1"/>
454 </conditional>
455 </repeat>
456 <repeat name="distance_conditions">
457 <conditional name="type_dc">
458 <param name="type_dc_value" value="stream"/>
459 <param name="ds" value="UP"/>
460 </conditional>
461 </repeat>
462 <param name="output_opt" value="RIGHT"/>
463 </conditional>
464 </section>
465 <section name="joinby">
466 <repeat name="joinby_clause">
467 <param name="metajoin_match" value="SIMPLE"/>
468 <param name="j_att" value="cell"/>
469 </repeat>
470 </section>
471 </conditional>
472 </repeat>
473 <output name="query" file="join1.gmql_query"/>
474 </test>
475 <test>
476 <!-- TEST 12: JOIN (Genomic Predicate, Region Conditions, Joinby) -->
477 <expand macro="query_intro" name="test_join2"/>
478 <expand macro="simple_select" ds="Example_Dataset_1"/>
479 <param name="output_var" value="IN"/>
480 <expand macro="simple_select" ds="Example_Dataset_2">
481 <param name="output_var" value="IN2"/>
482 </expand>
483 <repeat name="operations">
484 <conditional name="operation">
485 <param name="operator" value="JOIN"/>
486 <param name="input_var_anchor" value="IN"/>
487 <param name="output_var" value="OUT"/>
488 <param name="input_var_experiment" value="IN2"/>
489 <section name="conditions_section">
490 <conditional name="conditions">
491 <param name="c_type" value="both"/>
492 <repeat name="distance_conditions">
493 <conditional name="type_dc">
494 <param name="type_dc_value" value="dist"/>
495 <param name="dc" value="DL"/>
496 <param name="n" value="0"/>
497 </conditional>
498 </repeat>
499 <param name="output_opt" value="INT"/>
500 <repeat name="region_attributes">
501 <param name="attribute" value="score" />
502 </repeat>
503 <repeat name="region_attributes">
504 <param name="attribute" value="chr" />
505 </repeat>
506 </conditional>
507 </section>
508 <section name="joinby">
509 <repeat name="joinby_clause">
510 <param name="metajoin_match" value="SIMPLE"/>
511 <param name="j_att" value="cell"/>
512 </repeat>
513 <repeat name="joinby_clause">
514 <param name="metajoin_match" value="SIMPLE"/>
515 <param name="j_att" value="provider"/>
516 </repeat>
517 </section>
518 </conditional>
519 </repeat>
520 <output name="query" file="join2.gmql_query"/>
521 </test>
522 <test>
523 <!-- TEST 13: MAP -->
524 <expand macro="query_intro" name="test_map1"/>
525 <expand macro="simple_select" ds="Example_Dataset_1"/>
526 <param name="output_var" value="IN"/>
527 <expand macro="simple_select" ds="Example_Dataset_2">
528 <param name="output_var" value="IN2"/>
529 </expand>
530 <repeat name="operations">
531 <conditional name="operation">
532 <param name="input_var_reference" value="IN"/>
533 <param name="output_var" value="OUT"/>
534 <param name="count_result" value="mapped_n"/>
535 <param name="input_var_experiment" value="IN2"/>
536 <param name="operator" value="MAP"/>
537 <section name="new_regions_attributes">
538 <repeat name="new_regions">
539 <param name="new_name" value="avg_score"/>
540 <param name="function" value="AVG"/>
541 <param name="argument" value="score"/>
542 </repeat>
543 <repeat name="new_regions">
544 <param name="new_name" value="min_score"/>
545 <param name="function" value="MIN"/>
546 <param name="argument" value="score"/>
547 </repeat>
548 <repeat name="new_regions">
549 <param name="new_name" value="chr_list"/>
550 <param name="function" value="BAG"/>
551 <param name="argument" value="chr"/>
552 </repeat>
553 </section>
554 <section name="joinby">
555 <repeat name="joinby_clause">
556 <param name="metajoin_match" value="SIMPLE"/>
557 <param name="j_att" value="cell_tissue"/>
558 </repeat>
559 </section>
560 </conditional>
561 </repeat>
562 <output name="query" file="map1.gmql_query"/>
563 </test>
564 <test>
565 <!-- TEST 13: COVER (Base Variant) -->
566 <expand macro="query_intro" name="test_cover1"/>
567 <expand macro="simple_select" ds="Example_Dataset_1"/>
568 <param name="output_var" value="IN"/>
569 <repeat name="operations">
570 <conditional name="operation">
571 <param name="output_var" value="OUT"/>
572 <param name="cover_variant" value="COVER"/>
573 <param name="input_var" value="IN"/>
574 <param name="operator" value="COVER"/>
575 <conditional name="minAcc">
576 <param name="min_type" value="value"/>
577 <param name="value" value="1"/>
578 </conditional>
579 <conditional name="maxAcc">
580 <param name="max_type" value="ANY"/>
581 </conditional>
582 <section name="new_regions_attributes">
583 <repeat name="new_regions">
584 <param name="new_name" value="min_pvalue"/>
585 <param name="function" value="MIN"/>
586 <param name="argument" value="pvalue"/>
587 </repeat>
588 </section>
589 <section name="groupby">
590 <repeat name="groupby_clause">
591 <param name="metajoin_match" value="SIMPLE"/>
592 <param name="j_att" value="cell"/>
593 </repeat>
594 <repeat name="groupby_clause">
595 <param name="metajoin_match" value="SIMPLE"/>
596 <param name="j_att" value="antibody_target"/>
597 </repeat>
598 </section>
599 </conditional>
600 </repeat>
601 <output name="query" file="cover1.gmql_query"/>
602 </test>
603 <test>
604 <!-- TEST 14: COVER (Variants) -->
605 <expand macro="query_intro" name="test_cover2"/>
606 <expand macro="simple_select" ds="Example_Dataset_1"/>
607 <param name="output_var" value="IN"/>
608 <repeat name="operations">
609 <conditional name="operation">
610 <param name="operator" value="COVER"/>
611 <param name="output_var" value="OUT1"/>
612 <param name="cover_variant" value="FLAT"/>
613 <param name="input_var" value="IN"/>
614 <conditional name="minAcc">
615 <param name="min_type" value="value"/>
616 <param name="value" value="2"/>
617 </conditional>
618 <conditional name="maxAcc">
619 <param name="max_type" value="value"/>
620 <param name="value" value="4"/>
621 </conditional>
622 <section name="groupby">
623 <repeat name="groupby_clause">
624 <param name="metajoin_match" value="SIMPLE"/>
625 <param name="j_att" value="cell"/>
626 </repeat>
627 </section>
628 </conditional>
629 </repeat>
630 <repeat name="operations">
631 <conditional name="operation">
632 <param name="operator" value="COVER"/>
633 <param name="output_var" value="OUT2"/>
634 <param name="cover_variant" value="SUMMIT"/>
635 <param name="input_var" value="IN"/>
636 <conditional name="minAcc">
637 <param name="min_type" value="value"/>
638 <param name="value" value="2"/>
639 </conditional>
640 <conditional name="maxAcc">
641 <param name="max_type" value="value"/>
642 <param name="value" value="4"/>
643 </conditional>
644 <section name="groupby">
645 <repeat name="groupby_clause">
646 <param name="metajoin_match" value="SIMPLE"/>
647 <param name="j_att" value="cell"/>
648 </repeat>
649 </section>
650 </conditional>
651 </repeat>
652 <repeat name="operations">
653 <conditional name="operation">
654 <param name="operator" value="COVER"/>
655 <param name="output_var" value="OUT3"/>
656 <param name="cover_variant" value="HISTOGRAM"/>
657 <param name="input_var" value="IN"/>
658 <conditional name="minAcc">
659 <param name="min_type" value="ALL_n"/>
660 <param name="n" value="2"/>
661 </conditional>
662 <conditional name="maxAcc">
663 <param name="max_type" value="ALL_n_k"/>
664 <param name="k" value="1"/>
665 <param name="n" value="2"/>
666 </conditional>
667 <section name="groupby">
668 <repeat name="groupby_clause">
669 <param name="metajoin_match" value="SIMPLE"/>
670 <param name="j_att" value="antibody_target"/>
671 </repeat>
672 </section>
673 </conditional>
674 </repeat>
675 <output name="query" file="cover2.gmql_query"/>
676 </test>
677 <test>
678 <!-- TEST 15: Query Compilation -->
679 <expand macro="query_intro" name="test_compile"/>
680 <repeat name="operations">
681 <conditional name="operation">
682 <param name="operator" value="SELECT"/>
683 <conditional name="input">
684 <param name="input_type" value="i_ds"/>
685 <param name="gmql_datasets" value="rep.gmql_repository"/>
686 <param name="input_ds" value="Example_Dataset_1"/>
687 <section name="metadata_predicates">
688 <conditional name="conditions">
689 <param name="ad_flags" value="steps"/>
690 <param name="negate" value="false"/>
691 <param name="attribute" value="grant"/>
692 <param name="condition" value="eq"/>
693 <param name="value" value="Stam"/>
694 </conditional>
695 </section>
696 <section name="region_predicates">
697 <conditional name="conditions">
698 <param name="ad_flags" value="strings"/>
699 <param name="conditions_string" value=""/>
700 </conditional>
701 </section>
702 <section name="semijoin_predicate">
703 <param name="condition" value="IN"/>
704 <param name="ds_ext" value=""/>
705 </section>
706 </conditional>
707 </conditional>
708 </repeat>
709 <param name="output_var" value="VAR"/>
710 <conditional name="materialize">
711 <param name="file_name" value="TG"/>
712 <param name="materialize_result" value="true"/>
713 <conditional name="choose_op">
714 <param name="op" value="compile"/>
715 </conditional>
716 </conditional>
717 <output name="query" file="query.gmql_query"/>
718 <output name="log" ftype="txt">
719 <assert_contents>
720 <has_text text="COMPILE_SUCCESS"/>
721 </assert_contents>
722 </output>
723 </test>
724 <test>
725 <!-- TEST 16: Query Execution -->
726 <param name="authToken" value="guest2.gmql_user"/>
727 <param name="query_name" value="testexec"/>
728 <conditional name="query_create">
729 <param name="create" value="yes"/>
730 </conditional>
731 <repeat name="operations">
732 <conditional name="operation">
733 <param name="operator" value="SELECT"/>
734 <conditional name="input">
735 <param name="input_type" value="i_ds"/>
736 <param name="gmql_datasets" value="rep.gmql_repository"/>
737 <param name="input_ds" value="Example_Dataset_1"/>
738 <section name="metadata_predicates">
739 <conditional name="conditions">
740 <param name="ad_flags" value="steps"/>
741 <param name="negate" value="false"/>
742 <param name="attribute" value="grant"/>
743 <param name="condition" value="eq"/>
744 <param name="value" value="Stam"/>
745 </conditional>
746 </section>
747 <section name="region_predicates">
748 <conditional name="conditions">
749 <param name="ad_flags" value="strings"/>
750 <param name="conditions_string" value=""/>
751 </conditional>
752 </section>
753 <section name="semijoin_predicate">
754 <param name="condition" value="IN"/>
755 <param name="ds_ext" value=""/>
756 </section>
757 </conditional>
758 </conditional>
759 </repeat>
760 <param name="output_var" value="VAR"/>
761 <conditional name="materialize">
762 <param name="file_name" value="TG"/>
763 <param name="materialize_result" value="true"/>
764 <conditional name="choose_op">
765 <param name="op" value="run"/>
766 <param name="out_format" value="gdm"/>
767 <param name="import" value="true"/>
768 </conditional>
769 </conditional>
770 <output name="query" file="query.gmql_query"/>
771 <output name="log" ftype="txt">
772 <assert_contents>
773 <has_text text="SUCCESS"/>
774 </assert_contents>
775 </output>
776 <output name="updated_list" ftype="gmql_repository">
777 <assert_contents>
778 <has_text_matching expression="testexec_\d+_\d+_TG"/>
779 </assert_contents>
780 </output>
781 <collection name="query_results_s" type="list">
782 <metadata name="name" value="testexec results"/>
783 <discovered_dataset designation="S00000" file="TG/S_00000.gdm"/>
784 <discovered_dataset designation="S00001" file="TG/S_00001.gdm"/>
785 <discovered_dataset designation="S00002" file="TG/S_00002.gdm"/>
786 </collection>
787 <collection name="query_results_m" type="list">
788 <metadata name="name" value="testexec results metadata"/>
789 <discovered_dataset designation="S00000" file="TG/S_00000.gdm.meta"/>
790 <discovered_dataset designation="S00001" file="TG/S_00001.gdm.meta"/>
791 <discovered_dataset designation="S00002" file="TG/S_00002.gdm.meta"/>
792 </collection>
793 </test>
794 </tests>
795 </xml>
796 </macros>