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Merge pull request #14362 from xtrojak/sybila-tools-datatypes
Add datatypes for Sybila tools
This commit is contained in:
Marius van den Beek
@@ -925,6 +925,15 @@
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<!-- Povray script -->
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<datatype extension="pov" type="galaxy.datatypes.text:Text" subclass="true" display_in_upload="true"/>
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<!-- End Structural Materials datatypes -->
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<!-- Sybila types -->
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<datatype extension="pithya.result" type="galaxy.datatypes.text:PithyaResult" mimetype="application/json" display_in_upload="true"/>
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<datatype extension="pithya.property" type="galaxy.datatypes.text:PithyaProperty" display_in_upload="true" />
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<datatype extension="pithya.model" type="galaxy.datatypes.text:PithyaModel" display_in_upload="true" />
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<datatype extension="bcsl.ts" type="galaxy.datatypes.text:BCSLts" mimetype="application/json" display_in_upload="true"/>
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<datatype extension="bcsl.model" type="galaxy.datatypes.text:BCSLmodel" display_in_upload="true"/>
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<datatype extension="storm.sample" type="galaxy.datatypes.text:StormSample" display_in_upload="true"/>
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<datatype extension="storm.check" type="galaxy.datatypes.text:StormCheck" display_in_upload="true"/>
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<datatype extension="ctl.result" type="galaxy.datatypes.text:CTLresult" display_in_upload="true"/>
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<!-- CASTEP types -->
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<datatype extension="castep" type="galaxy.datatypes.text:Castep" display_in_upload="true"/>
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<datatype extension="param" type="galaxy.datatypes.text:Param" display_in_upload="true"/>
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@@ -1123,6 +1132,8 @@
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<sniffer type="galaxy.datatypes.text:Biom1"/>
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<sniffer type="galaxy.datatypes.text:ImgtJson"/>
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<sniffer type="galaxy.datatypes.text:GeoJson"/>
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<sniffer type="galaxy.datatypes.text:PithyaResult"/>
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<sniffer type="galaxy.datatypes.text:BCSLts"/>
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<sniffer type="galaxy.datatypes.text:Json"/>
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<sniffer type="galaxy.datatypes.genetics:GenotypeMatrix"/>
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<sniffer type="galaxy.datatypes.genetics:DataIn"/>
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@@ -1181,6 +1192,7 @@
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<sniffer type="galaxy.datatypes.speech:TextGrid" />
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<sniffer type="galaxy.datatypes.speech:BPF" />
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<sniffer type="galaxy.datatypes.text:Castep" />
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<sniffer type="galaxy.datatypes.text:CTLresult"/>
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<sniffer type="galaxy.datatypes.text:FormattedDensity" />
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<sniffer type="galaxy.datatypes.text:Param" />
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<sniffer type="galaxy.datatypes.text:Yaml" />
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@@ -1196,5 +1208,10 @@
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<sniffer type="galaxy.datatypes.binary:OxliSubset"/>
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<sniffer type="galaxy.datatypes.binary:OxliGraphLabels"/>
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<sniffer type="galaxy.datatypes.neo4j:Neo4jDBzip"/>
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<sniffer type="galaxy.datatypes.text:PithyaProperty"/>
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<sniffer type="galaxy.datatypes.text:PithyaModel"/>
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<sniffer type="galaxy.datatypes.text:BCSLmodel"/>
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<sniffer type="galaxy.datatypes.text:StormSample"/>
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<sniffer type="galaxy.datatypes.text:StormCheck"/>
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</sniffers>
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</datatypes>
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@@ -0,0 +1,13 @@
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VARS: pRB, E2F1
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PARAMS: y_pRB,0.001,1; y_E2F1,0.001,1
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CONSTS: a,0.04; kp,0.05; k2,1; k1,1
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VAR_POINTS: pRB: 1500, 20; E2F1: 1500, 20
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EQ: pRB = k1*Hillp(E2F1,0.5,1,0,1)*Hillm(pRB,0.5,1,1,0) - y_pRB*pRB
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EQ: E2F1 = kp + k2*a*a*0.0625*Hillm(E2F1,4,2,1,0)*Hillm(pRB,5,1,1,0) + k2*Hillp(E2F1,4,2,0,1)*Hillm(pRB,5,1,1,0) - y_E2F1*E2F1
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THRES: pRB: 0, 15
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THRES: E2F1: 0, 3, 15
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@@ -0,0 +1,10 @@
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# high state of E2F1 (observed in cancer cells)
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high = E2F1 > 3
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# low state of E2F1 (observed in healthy cells)
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low = E2F1 < 3
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:?stay_low = AG low
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:?stay_high = AG high
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:?reach_high = EF high
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:?reach_low = EF low
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:?bistability = reach_and_stay_high && reach_and_stay_low
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@@ -0,0 +1 @@
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{"variables":["pRB","E2F1"],"parameters":["y_pRB"],"thresholds":[[0.0,0.02334889926617745,0.0466977985323549,0.07004669779853236,0.0933955970647098,0.11674449633088725,0.1400933955970647,0.16344229486324216,0.1867911941294196,0.21014009339559706,0.2334889926617745,0.256837891927952,0.2801867911941294,0.3035356904603069,0.35023348899266177,0.39693128752501666]],"parameter_bounds":[[0.0,1.0]],"states":[{"id":8717,"bounds":[[1.3308872581721147,1.4242828552368245],[11.227484989993329,11.587725150100066]]},{"id":8718,"bounds":[[1.4242828552368245,1.5176784523015343],[11.227484989993329,11.587725150100066]]},{"id":8719,"bounds":[[1.5176784523015343,1.611074049366244],[11.227484989993329,11.587725150100066]]},{"id":8720,"bounds":[[1.611074049366244,1.7044696464309539],[11.227484989993329,11.587725150100066]]},{"id":8721,"bounds":[[1.7044696464309539,1.8212141427618411],[11.227484989993329,11.587725150100066]]}],"type":"rectangular","parameter_values":[[[[0.174655571734003,0.17511282157273875]]],[[[0.15632047914681707,0.17511282157273875]]],[[[0.14055859185879657,0.1567297275502395]]],[[[0.12705696870430946,0.14093038684771772]]],[[[0.12705696870430946,0.1275646137723884]]],[[[0.08037989357199904,0.0807182318621894]]],[[[0.07171486575321386,0.0807182318621894]]],[[[0.06437073836837151,0.07202650145489457]]],[[[0.06437073836837151,0.06465910081655664]]],[[[0.0039941330464278125,0.004253357302638203]]],[[[0.003677177243966719,0.004253357302638203]]]],"results":[{"formula":"1 attractor(s)","data":[[0,0],[1,1],[2,2],[3,3],[4,4],[5,5],[6,6],[7,7],[8,8],[9,9],[10,10],[11,11],[12,12],[13,13],[14,14],[15,15],[16,16],[17,17],[18,18],[19,19],[20,20],[21,21],[22,22],[23,23],[24,24],[25,25],[26,26],[27,27],[28,28],[29,29],[30,30],[31,31],[32,32],[33,33],[34,34],[35,35]]},{"formula":"2 attractor(s)","data":[[197,131],[198,132],[199,133],[33,134],[109,135],[200,136],[111,137]]}]}
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@@ -0,0 +1,24 @@
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Storm 1.5.2 (dev)
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Date: Tue Aug 31 11:52:43 2021
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Command line arguments: --explicit /tmp/exp_transitions.tra /tmp/exp_labels.lab --prop 'P <= 0.2 [F "property_0"]'
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Current working directory: /home/biodivine
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WARN (DeterministicSparseTransitionParser.cpp:114): Warning while parsing /tmp/exp_transitions.tra: state 0 has no outgoing transitions. A self-loop was inserted.
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Time for model construction: 0.003s.
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--------------------------------------------------------------
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Model type: DTMC (sparse)
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States: 36
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Transitions: 73
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Reward Models: none
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State Labels: 2 labels
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* property_0 -> 7 item(s)
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* init -> 1 item(s)
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Choice Labels: none
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--------------------------------------------------------------
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Model checking property "1": P<=1/5 [F "property_0"] ...
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Result (for initial states): true
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Time for model checking: 0.004s.
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@@ -0,0 +1,26 @@
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Storm-pars 1.5.2 (dev)
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Date: Tue Aug 31 11:54:33 2021
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Command line arguments: --prism /tmp/prism-parametric.pm --prop 'P=? [F VAR_13 > 0]'
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Current working directory: /home/biodivine
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Time for model input parsing: 0.054s.
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Time for model construction: 0.060s.
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--------------------------------------------------------------
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Model type: DTMC (sparse)
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States: 31
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Transitions: 60
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Reward Models: none
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State Labels: 3 labels
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* deadlock -> 0 item(s)
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* init -> 1 item(s)
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* (VAR_13 > 0) -> 3 item(s)
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Choice Labels: none
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--------------------------------------------------------------
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Model checking property "1": P=? [F (VAR_13 > 0)] ...
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Result (initial states): ((param_sig) * (2981688543185870087663495150126244302243211334125913130541472787739802879829617808110453272217978374073720397249812500000000000000000000000000000000*param_block^2*param_sig^4+21333081000995441881478481888623294608561432837600286741218656884283620692512542203861605829532226092102934969442322694750000000000000000000000000000*param_block^2+39132416603004844706196842373313272958271263050686725335537624140954554083030939648762564370066208263332252673796791507500000000000000000000000000000*param_block^3+22725999490705377615041471133908386334886227218171410438914202044860955570751027688763780193895740093693277310924369400000000000000000000000000000000*param_block^4+4245231150311364342612854790676605418253049153545896232307346492306252682008919270223849752504307504320664247517188723800000000000000000000000000000*param_block+3208978818800247399506763118470536036989385423591596173967281127328788493228035015636535956506569555711016320577817679061497326203211080000000000000*param_sig+61337241783765857891013320525639798082527501818023156733982938906674645568072155420853118954216213548904852362777061738609148204736454500000000000000*param_block^2*param_sig+74369918766404647592913928656863192667117420889433781173107741721170856650611346506277604830614523491564585562186305128156035141329240000000000000000*param_block^3*param_sig+29292019838238331850968165043795743170409577972626036193644124317339136456350216875337061516525802454304327791722750500000000000000000000000000000000*param_block^4*param_sig+19902622481499489037239723031085884009390738986142582753983084280681700808413379128470957648933080862881426158617714463694327731092463850000000000000*param_block*param_sig+4988231807874665106368003757977042997192179259217166529296729711205229419890270158470421379470061661981037187602312836044526074892761100000000000000*param_sig^2+59601551364347403569696046187070921651122929428946390382552332230109692835887798717812528775399049540520370596585742609690208728119308750000000000000*param_block^2*param_sig^2+46192170164668265056819074737333877291295544847929182558994672251565820597224197376450246544898952754998090489639395163646243621415550000000000000000*param_block^3*param_sig^2+9377194403932374268124660332452806355725761378949846467347269487253715794857888095086660972929117334709214264218094973175220501423772464357643884000*param_block^3*param_sig^3+8921144215261864428692689196891058971406744515998644847029720979796682460863133143839669201013739000242824402488269161846556804540000000000000000000*param_block^4*param_sig^2+23082287092982285261521833710527899304094126172081965804252830610430812603140429782139624302429880262001526161428768219750503507187973495927296538450*param_block^2*param_sig^3+3033543996110841631945273977359607825154524619770251161191749427292223175220501433419497881797347290488662407111607750000000000000000000000000000000*param_block*param_sig^4+15647645284008923066441148084578465388470746425309070323293366934293856928604775268701474119262030255126624306747492267357542190429822247353486849285*param_block*param_sig^3+28020885305453682349511300346585293159400120608409114630098547684193006645719467786525298339687114470730745853782276038939665742329926375000000000000*param_block*param_sig^2+606060606060606086243026136074268382137648447809459208926545824967618746672222608708252887932032337859781929300646200000000000000000000000000000000*param_sig^4+2976310726310726390537465491247021999587550355313910009812905878666014279171723787491799172194130205204794727808478779511424404472526262240433363428*param_sig^3+549594155844155832063941940412527773883976317799876825897631779983932196027501909876829090909090908960000000000000000000000000000000000000000000000))/(450000000000000000000000000000000000000000000000000000000000000000 * ((5*param_block+4) * (10*param_block+1) * (250000000000000000*param_block+66666666666666663) * (7*param_sig+9) * (2272727272727273*param_sig+5000000000000000*param_block) * (2857142857142857*param_sig+750000000000000) * (3333333333333333*param_sig+4357142857142857) * (33333333333333335*param_sig+68518518518518518)))
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Time for model checking: 0.061s.
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@@ -0,0 +1,34 @@
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#! rules
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// signal changes
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sig{i}::ext => sig{a}::ext @ k_sig_1
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sig{a}::ext => sig{a}::cell @ (k_sig_2*[sig{a}::ext])/(1 + [block{a}::cell])
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block{i}::ext => block{a}::ext @ k_block_1
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block{a}::ext => block{a}::cell @ (k_block_2*[block{a}::ext])/(1 + [sig{a}::cell])
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sig{a}::cell + P1()::cell => sig{a}.P1()::cell @ param_sig*[sig{a}::cell]*[P1()::cell]
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sig{_}.P1()::cell => sig{_}::cell + P1()::cell @ k_deg*[sig{_}.P1()::cell]
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sig{a}.P1(active{off})::cell => sig{a}.P1(active{on})::cell @ 0.5*[sig{a}.P1(active{off})::cell]
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sig{a}.P1()::cell => sig{a}::cell + P1()::cell @ k_deg*[sig{a}.P1()::cell]
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block{a}::cell + P1()::cell => block{a}.P1()::cell @ param_block*[block{a}::cell]*[P1()::cell]
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P1(active{on})::cell + P2()::cell => P1(active{on}).P2()::cell @ 0.4*[P1(active{on})::cell]*[P2()::cell]
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P1().P2()::cell => P1()::cell + P2()::cell @ k_deg*[P1().P2()::cell]
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P1().P2(active{off})::cell => P1().P2(active{on})::cell @ k_prod*[P1().P2(active{off})::cell]
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#! inits
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sig{i}::ext
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block{i}::ext
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P1(active{off})::cell
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P2(active{off})::cell
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#! definitions
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k_sig_1 = 0.8
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k_sig_2 = 0.2
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k_block_1 = 0.9
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k_block_2 = 0.3
|
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k_deg = 0.3
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k_prod = 0.6
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param_sig = 0.3
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param_block = 0.4
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@@ -0,0 +1,155 @@
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{
|
||||
"edges": [
|
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{
|
||||
"p": 0.22222222222222227,
|
||||
"t": 9,
|
||||
"s": 2
|
||||
},
|
||||
{
|
||||
"p": 0.5,
|
||||
"t": 8,
|
||||
"s": 4
|
||||
},
|
||||
{
|
||||
"p": 0.25,
|
||||
"t": 7,
|
||||
"s": 1
|
||||
},
|
||||
{
|
||||
"p": 0.37499999999999994,
|
||||
"t": 2,
|
||||
"s": 1
|
||||
},
|
||||
{
|
||||
"p": 0.5,
|
||||
"t": 9,
|
||||
"s": 4
|
||||
},
|
||||
{
|
||||
"p": 1.0,
|
||||
"t": 5,
|
||||
"s": 10
|
||||
},
|
||||
{
|
||||
"p": 0.6666666666666667,
|
||||
"t": 9,
|
||||
"s": 7
|
||||
},
|
||||
{
|
||||
"p": 0.44444444444444453,
|
||||
"t": 1,
|
||||
"s": 2
|
||||
},
|
||||
{
|
||||
"p": 1,
|
||||
"t": 6,
|
||||
"s": 6
|
||||
},
|
||||
{
|
||||
"p": 0.37499999999999994,
|
||||
"t": 3,
|
||||
"s": 1
|
||||
},
|
||||
{
|
||||
"p": 0.4444444444444445,
|
||||
"t": 12,
|
||||
"s": 11
|
||||
},
|
||||
{
|
||||
"p": 0.1764705882352941,
|
||||
"t": 5,
|
||||
"s": 9
|
||||
},
|
||||
{
|
||||
"p": 0.36363636363636365,
|
||||
"t": 10,
|
||||
"s": 5
|
||||
},
|
||||
{
|
||||
"p": 0.3529411764705882,
|
||||
"t": 4,
|
||||
"s": 9
|
||||
},
|
||||
{
|
||||
"p": 0.11111111111111112,
|
||||
"t": 5,
|
||||
"s": 11
|
||||
},
|
||||
{
|
||||
"p": 0.25,
|
||||
"t": 10,
|
||||
"s": 3
|
||||
},
|
||||
{
|
||||
"p": 0.4444444444444445,
|
||||
"t": 3,
|
||||
"s": 11
|
||||
},
|
||||
{
|
||||
"p": 0.47058823529411764,
|
||||
"t": 7,
|
||||
"s": 9
|
||||
},
|
||||
{
|
||||
"p": 0.7499999999999999,
|
||||
"t": 11,
|
||||
"s": 3
|
||||
},
|
||||
{
|
||||
"p": 0.33333333333333337,
|
||||
"t": 10,
|
||||
"s": 7
|
||||
},
|
||||
{
|
||||
"p": 0.36363636363636365,
|
||||
"t": 6,
|
||||
"s": 5
|
||||
},
|
||||
{
|
||||
"p": 1.0,
|
||||
"t": 5,
|
||||
"s": 8
|
||||
},
|
||||
{
|
||||
"p": 1.0,
|
||||
"t": 6,
|
||||
"s": 12
|
||||
},
|
||||
{
|
||||
"p": 0.2727272727272727,
|
||||
"t": 8,
|
||||
"s": 5
|
||||
},
|
||||
{
|
||||
"p": 0.33333333333333337,
|
||||
"t": 11,
|
||||
"s": 2
|
||||
}
|
||||
],
|
||||
"ordering": [
|
||||
"P1().P2()::cell",
|
||||
"P1()::cell",
|
||||
"P2()::cell",
|
||||
"block{_}.P1()::cell",
|
||||
"block{_}::cell",
|
||||
"block{_}::ext",
|
||||
"sig{_}.P1()::cell",
|
||||
"sig{_}::cell",
|
||||
"sig{_}::ext"
|
||||
],
|
||||
"initial": 2,
|
||||
"nodes": {
|
||||
"1": "(1, 0, 0, 0, 0, 1, 0, 0, 1)",
|
||||
"2": "(0, 1, 1, 0, 0, 1, 0, 0, 1)",
|
||||
"3": "(1, 0, 0, 0, 1, 0, 0, 0, 1)",
|
||||
"4": "(0, 0, 1, 0, 0, 1, 1, 0, 0)",
|
||||
"5": "(0, 1, 1, 0, 1, 0, 0, 1, 0)",
|
||||
"6": "(0, 0, 1, 1, 0, 0, 0, 1, 0)",
|
||||
"7": "(1, 0, 0, 0, 0, 1, 0, 1, 0)",
|
||||
"8": "(0, 0, 1, 0, 1, 0, 1, 0, 0)",
|
||||
"9": "(0, 1, 1, 0, 0, 1, 0, 1, 0)",
|
||||
"10": "(1, 0, 0, 0, 1, 0, 0, 1, 0)",
|
||||
"11": "(0, 1, 1, 0, 1, 0, 0, 0, 1)",
|
||||
"12": "(0, 0, 1, 1, 0, 0, 0, 0, 1)"
|
||||
}
|
||||
}
|
||||
@@ -0,0 +1,2 @@
|
||||
Result: True
|
||||
Number of satisfying states: 31
|
||||
@@ -1093,6 +1093,186 @@ class Yaml(Text):
|
||||
return False
|
||||
|
||||
|
||||
@build_sniff_from_prefix
|
||||
class BCSLmodel(Text):
|
||||
"""BioChemical Space Language model file"""
|
||||
|
||||
file_ext = "bcsl.model"
|
||||
|
||||
def sniff_prefix(self, file_prefix: FilePrefix):
|
||||
"""
|
||||
Determines whether the file is in .bcsl.model format
|
||||
"""
|
||||
reg = r"^#! rules|^#! inits|^#! definitions"
|
||||
return re.search(reg, file_prefix.contents_header, re.MULTILINE) is not None
|
||||
|
||||
|
||||
@build_sniff_from_prefix
|
||||
class BCSLts(Json):
|
||||
"""BioChemical Space Language transition system file"""
|
||||
|
||||
file_ext = "bcsl.ts"
|
||||
|
||||
def sniff_prefix(self, file_prefix: FilePrefix):
|
||||
"""
|
||||
Determines whether the file is in .bcsl.ts format
|
||||
"""
|
||||
is_bcsl_ts = False
|
||||
if self._looks_like_json(file_prefix):
|
||||
is_bcsl_ts = self._looks_like_bcsl_ts(file_prefix)
|
||||
return is_bcsl_ts
|
||||
|
||||
def set_peek(self, dataset):
|
||||
if not dataset.dataset.purged:
|
||||
lines = "States: {}\nTransitions: {}\nUnique agents: {}\nInitial state: {}"
|
||||
ts = json.load(open(dataset.file_name, "r"))
|
||||
dataset.peek = lines.format(len(ts["nodes"]), len(ts["edges"]), len(ts["ordering"]), ts["initial"])
|
||||
dataset.blurb = nice_size(dataset.get_size())
|
||||
else:
|
||||
dataset.peek = "file does not exist"
|
||||
dataset.blurb = "file purged from disk"
|
||||
|
||||
def _looks_like_bcsl_ts(self, file_prefix: FilePrefix):
|
||||
content = open(file_prefix.filename, "r").read()
|
||||
keywords = ['"edges":', '"nodes":', '"ordering":', '"initial":']
|
||||
if all(keyword in content for keyword in keywords):
|
||||
return self._looks_like_json(file_prefix)
|
||||
return False
|
||||
|
||||
|
||||
@build_sniff_from_prefix
|
||||
class StormSample(Text):
|
||||
"""
|
||||
Storm PCTL parameter synthesis result file
|
||||
containing probability function of parameters.
|
||||
"""
|
||||
|
||||
file_ext = "storm.sample"
|
||||
|
||||
def sniff_prefix(self, file_prefix: FilePrefix):
|
||||
"""
|
||||
Determines whether the file is in .storm.sample format
|
||||
"""
|
||||
keywords = ["Storm-pars", "Result (initial states)"]
|
||||
return all(keyword in file_prefix.contents_header for keyword in keywords)
|
||||
|
||||
def set_peek(self, dataset):
|
||||
if not dataset.dataset.purged:
|
||||
dataset.peek = "Storm-pars sample results."
|
||||
dataset.blurb = nice_size(dataset.get_size())
|
||||
else:
|
||||
dataset.peek = "file does not exist"
|
||||
dataset.blurb = "file purged from disk"
|
||||
|
||||
|
||||
@build_sniff_from_prefix
|
||||
class StormCheck(Text):
|
||||
"""
|
||||
Storm PCTL model checking result file
|
||||
containing boolean or numerical result.
|
||||
"""
|
||||
|
||||
file_ext = "storm.check"
|
||||
|
||||
def sniff_prefix(self, file_prefix: FilePrefix):
|
||||
"""
|
||||
Determines whether the file is in .storm.check format
|
||||
"""
|
||||
keywords = ["Storm ", "Result (for initial states)"]
|
||||
return all(keyword in file_prefix.contents_header for keyword in keywords)
|
||||
|
||||
def set_peek(self, dataset):
|
||||
if not dataset.dataset.purged:
|
||||
with open(dataset.file_name, "r") as result:
|
||||
answer = ""
|
||||
for line in result:
|
||||
if "Result (for initial states):" in line:
|
||||
answer = line.split()[-1]
|
||||
break
|
||||
dataset.peek = "Model checking result: {}".format(answer)
|
||||
dataset.blurb = nice_size(dataset.get_size())
|
||||
else:
|
||||
dataset.peek = "file does not exist"
|
||||
dataset.blurb = "file purged from disk"
|
||||
|
||||
|
||||
@build_sniff_from_prefix
|
||||
class CTLresult(Text):
|
||||
"""CTL model checking result"""
|
||||
|
||||
file_ext = "ctl.result"
|
||||
|
||||
def sniff_prefix(self, file_prefix: FilePrefix):
|
||||
"""
|
||||
Determines whether the file is in .ctl.result format
|
||||
"""
|
||||
keywords = ["Result:", "Number of satisfying states:"]
|
||||
return all(keyword in file_prefix.contents_header for keyword in keywords)
|
||||
|
||||
def set_peek(self, dataset):
|
||||
if not dataset.dataset.purged:
|
||||
with open(dataset.file_name, "r") as result:
|
||||
answer = ""
|
||||
for line in result:
|
||||
if "Result:" in line:
|
||||
answer = line.split()[-1]
|
||||
dataset.peek = "Model checking result: {}".format(answer)
|
||||
dataset.blurb = nice_size(dataset.get_size())
|
||||
else:
|
||||
dataset.peek = "file does not exist"
|
||||
dataset.blurb = "file purged from disk"
|
||||
|
||||
|
||||
@build_sniff_from_prefix
|
||||
class PithyaProperty(Text):
|
||||
"""Pithya CTL property format"""
|
||||
|
||||
file_ext = "pithya.property"
|
||||
|
||||
def sniff_prefix(self, file_prefix: FilePrefix):
|
||||
"""
|
||||
Determines whether the file is in .pithya.property format
|
||||
"""
|
||||
return re.search(r":\?[a-zA-Z0-9_]+[ ]*=", file_prefix.contents_header) is not None
|
||||
|
||||
|
||||
@build_sniff_from_prefix
|
||||
class PithyaModel(Text):
|
||||
"""Pithya model format"""
|
||||
|
||||
file_ext = "pithya.model"
|
||||
|
||||
def sniff_prefix(self, file_prefix: FilePrefix):
|
||||
"""
|
||||
Determines whether the file is in .pithya.model format
|
||||
"""
|
||||
keywords = ["VARS", "EQ", "THRES"]
|
||||
return all(keyword in file_prefix.contents_header for keyword in keywords)
|
||||
|
||||
|
||||
@build_sniff_from_prefix
|
||||
class PithyaResult(Json):
|
||||
"""Pithya result format"""
|
||||
|
||||
file_ext = "pithya.result"
|
||||
|
||||
def sniff_prefix(self, file_prefix: FilePrefix):
|
||||
"""
|
||||
Determines whether the file is in .pithya.result format
|
||||
"""
|
||||
is_pithya_result = False
|
||||
if self._looks_like_json(file_prefix):
|
||||
is_pithya_result = self._looks_like_pithya_result(file_prefix)
|
||||
return is_pithya_result
|
||||
|
||||
def _looks_like_pithya_result(self, file_prefix: FilePrefix):
|
||||
content = open(file_prefix.filename, "r").read()
|
||||
keywords = ['"variables":', '"states":', '"parameter_values":', '"results":']
|
||||
if all(keyword in content for keyword in keywords):
|
||||
return self._looks_like_json(file_prefix)
|
||||
return False
|
||||
|
||||
|
||||
@build_sniff_from_prefix
|
||||
class Castep(Text):
|
||||
"""Report on a CASTEP calculation"""
|
||||
|
||||
@@ -862,3 +862,7 @@ check_untyped_defs = False
|
||||
check_untyped_defs = False
|
||||
[mypy-*.config.test_config_values]
|
||||
check_untyped_defs = False
|
||||
[mypy-*.datatypes.test_storm]
|
||||
check_untyped_defs = False
|
||||
[mypy-*.datatypes.test_bcsl]
|
||||
check_untyped_defs = False
|
||||
|
||||
@@ -0,0 +1,39 @@
|
||||
import pytest
|
||||
|
||||
from galaxy.datatypes.text import (
|
||||
BCSLmodel,
|
||||
BCSLts,
|
||||
CTLresult,
|
||||
)
|
||||
from .util import (
|
||||
get_input_files,
|
||||
MockDataset,
|
||||
MockDatasetDataset,
|
||||
)
|
||||
|
||||
|
||||
@pytest.mark.parametrize(
|
||||
"bcsl_loader, input_file",
|
||||
[[BCSLmodel, "test_file3.bcsl.model"], [BCSLts, "test_file3.bcsl.ts"], [CTLresult, "test_file3.ctl.result"]],
|
||||
)
|
||||
def test_bcsl_sniff(bcsl_loader, input_file):
|
||||
loader = bcsl_loader()
|
||||
with get_input_files(input_file) as input_files:
|
||||
assert loader.sniff(input_files[0]) is True
|
||||
|
||||
|
||||
@pytest.mark.parametrize(
|
||||
"bcsl_loader, input_file, expected_peek",
|
||||
[
|
||||
[BCSLts, "test_file3.bcsl.ts", "States: 12\nTransitions: 25\nUnique agents: 9\nInitial state: 2"],
|
||||
[CTLresult, "test_file3.ctl.result", """Model checking result: True"""],
|
||||
],
|
||||
)
|
||||
def test_bcsl_set_peek(bcsl_loader, input_file, expected_peek):
|
||||
loader = bcsl_loader()
|
||||
with get_input_files(input_file) as input_files:
|
||||
dataset = MockDataset(1)
|
||||
dataset.file_name = input_files[0]
|
||||
dataset.dataset = MockDatasetDataset(dataset.file_name)
|
||||
loader.set_peek(dataset)
|
||||
assert dataset.peek == expected_peek
|
||||
@@ -0,0 +1,22 @@
|
||||
import pytest
|
||||
|
||||
from galaxy.datatypes.text import (
|
||||
PithyaModel,
|
||||
PithyaProperty,
|
||||
PithyaResult,
|
||||
)
|
||||
from .util import get_input_files
|
||||
|
||||
|
||||
@pytest.mark.parametrize(
|
||||
"pithya_loader, input_file",
|
||||
[
|
||||
[PithyaModel, "test_file1.pithya.model"],
|
||||
[PithyaProperty, "test_file1.pithya.property"],
|
||||
[PithyaResult, "test_file1.pithya.result"],
|
||||
],
|
||||
)
|
||||
def test_pithya_sniff(pithya_loader, input_file):
|
||||
loader = pithya_loader()
|
||||
with get_input_files(input_file) as input_files:
|
||||
assert loader.sniff(input_files[0]) is True
|
||||
@@ -0,0 +1,41 @@
|
||||
import pytest
|
||||
|
||||
from galaxy.datatypes.text import (
|
||||
StormCheck,
|
||||
StormSample,
|
||||
)
|
||||
from .util import (
|
||||
get_input_files,
|
||||
MockDataset,
|
||||
MockDatasetDataset,
|
||||
)
|
||||
|
||||
|
||||
@pytest.mark.parametrize(
|
||||
"storm_loader, input_file",
|
||||
[
|
||||
[StormSample, "test_file2.storm.sample"],
|
||||
[StormCheck, "test_file2.storm.check"],
|
||||
],
|
||||
)
|
||||
def test_storm_sniff(storm_loader, input_file):
|
||||
loader = storm_loader()
|
||||
with get_input_files(input_file) as input_files:
|
||||
assert loader.sniff(input_files[0]) is True
|
||||
|
||||
|
||||
@pytest.mark.parametrize(
|
||||
"storm_loader, input_file, expected_peek",
|
||||
[
|
||||
[StormSample, "test_file2.storm.sample", """Storm-pars sample results."""],
|
||||
[StormCheck, "test_file2.storm.check", """Model checking result: true"""],
|
||||
],
|
||||
)
|
||||
def test_storm_set_peek(storm_loader, input_file, expected_peek):
|
||||
loader = storm_loader()
|
||||
with get_input_files(input_file) as input_files:
|
||||
dataset = MockDataset(1)
|
||||
dataset.file_name = input_files[0]
|
||||
dataset.dataset = MockDatasetDataset(dataset.file_name)
|
||||
loader.set_peek(dataset)
|
||||
assert dataset.peek == expected_peek
|
||||
@@ -8,6 +8,12 @@ from galaxy.datatypes.sniff import get_test_fname
|
||||
from galaxy.util.hash_util import md5_hash_file
|
||||
|
||||
|
||||
class MockDatasetDataset:
|
||||
def __init__(self, file_name):
|
||||
self.file_name = file_name
|
||||
self.purged = False
|
||||
|
||||
|
||||
class MockMetadata:
|
||||
file_name: Optional[str] = None
|
||||
|
||||
|
||||
Reference in New Issue
Block a user