diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample index 77e40e7f253..f0b6878311f 100644 --- a/lib/galaxy/config/sample/datatypes_conf.xml.sample +++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample @@ -925,6 +925,15 @@ + + + + + + + + + @@ -1123,6 +1132,8 @@ + + @@ -1181,6 +1192,7 @@ + @@ -1196,5 +1208,10 @@ + + + + + diff --git a/lib/galaxy/datatypes/test/test_file1.pithya.model b/lib/galaxy/datatypes/test/test_file1.pithya.model new file mode 100644 index 00000000000..06e66614d15 --- /dev/null +++ b/lib/galaxy/datatypes/test/test_file1.pithya.model @@ -0,0 +1,13 @@ +VARS: pRB, E2F1 + +PARAMS: y_pRB,0.001,1; y_E2F1,0.001,1 + +CONSTS: a,0.04; kp,0.05; k2,1; k1,1 + +VAR_POINTS: pRB: 1500, 20; E2F1: 1500, 20 + +EQ: pRB = k1*Hillp(E2F1,0.5,1,0,1)*Hillm(pRB,0.5,1,1,0) - y_pRB*pRB +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 + +THRES: pRB: 0, 15 +THRES: E2F1: 0, 3, 15 diff --git a/lib/galaxy/datatypes/test/test_file1.pithya.property b/lib/galaxy/datatypes/test/test_file1.pithya.property new file mode 100644 index 00000000000..d96ba7f1211 --- /dev/null +++ b/lib/galaxy/datatypes/test/test_file1.pithya.property @@ -0,0 +1,10 @@ +# high state of E2F1 (observed in cancer cells) +high = E2F1 > 3 +# low state of E2F1 (observed in healthy cells) +low = E2F1 < 3 + +:?stay_low = AG low +:?stay_high = AG high +:?reach_high = EF high +:?reach_low = EF low +:?bistability = reach_and_stay_high && reach_and_stay_low diff --git a/lib/galaxy/datatypes/test/test_file1.pithya.result b/lib/galaxy/datatypes/test/test_file1.pithya.result new file mode 100644 index 00000000000..9c07ae1a06f --- /dev/null +++ b/lib/galaxy/datatypes/test/test_file1.pithya.result @@ -0,0 +1 @@ +{"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]]}]} diff --git a/lib/galaxy/datatypes/test/test_file2.storm.check b/lib/galaxy/datatypes/test/test_file2.storm.check new file mode 100644 index 00000000000..ca72cfcd0db --- /dev/null +++ b/lib/galaxy/datatypes/test/test_file2.storm.check @@ -0,0 +1,24 @@ +Storm 1.5.2 (dev) + +Date: Tue Aug 31 11:52:43 2021 +Command line arguments: --explicit /tmp/exp_transitions.tra /tmp/exp_labels.lab --prop 'P <= 0.2 [F "property_0"]' +Current working directory: /home/biodivine + + WARN (DeterministicSparseTransitionParser.cpp:114): Warning while parsing /tmp/exp_transitions.tra: state 0 has no outgoing transitions. A self-loop was inserted. +Time for model construction: 0.003s. + +-------------------------------------------------------------- +Model type: DTMC (sparse) +States: 36 +Transitions: 73 +Reward Models: none +State Labels: 2 labels + * property_0 -> 7 item(s) + * init -> 1 item(s) +Choice Labels: none +-------------------------------------------------------------- + +Model checking property "1": P<=1/5 [F "property_0"] ... +Result (for initial states): true + +Time for model checking: 0.004s. diff --git a/lib/galaxy/datatypes/test/test_file2.storm.sample b/lib/galaxy/datatypes/test/test_file2.storm.sample new file mode 100644 index 00000000000..eecd28df08d --- /dev/null +++ b/lib/galaxy/datatypes/test/test_file2.storm.sample @@ -0,0 +1,26 @@ +Storm-pars 1.5.2 (dev) + +Date: Tue Aug 31 11:54:33 2021 +Command line arguments: --prism /tmp/prism-parametric.pm --prop 'P=? [F VAR_13 > 0]' +Current working directory: /home/biodivine + +Time for model input parsing: 0.054s. + +Time for model construction: 0.060s. + +-------------------------------------------------------------- +Model type: DTMC (sparse) +States: 31 +Transitions: 60 +Reward Models: none +State Labels: 3 labels + * deadlock -> 0 item(s) + * init -> 1 item(s) + * (VAR_13 > 0) -> 3 item(s) +Choice Labels: none +-------------------------------------------------------------- + +Model checking property "1": P=? [F (VAR_13 > 0)] ... +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))) +Time for model checking: 0.061s. + diff --git a/lib/galaxy/datatypes/test/test_file3.bcsl.model b/lib/galaxy/datatypes/test/test_file3.bcsl.model new file mode 100644 index 00000000000..925375baeb1 --- /dev/null +++ b/lib/galaxy/datatypes/test/test_file3.bcsl.model @@ -0,0 +1,34 @@ +#! rules +// signal changes +sig{i}::ext => sig{a}::ext @ k_sig_1 +sig{a}::ext => sig{a}::cell @ (k_sig_2*[sig{a}::ext])/(1 + [block{a}::cell]) + +block{i}::ext => block{a}::ext @ k_block_1 +block{a}::ext => block{a}::cell @ (k_block_2*[block{a}::ext])/(1 + [sig{a}::cell]) + +sig{a}::cell + P1()::cell => sig{a}.P1()::cell @ param_sig*[sig{a}::cell]*[P1()::cell] +sig{_}.P1()::cell => sig{_}::cell + P1()::cell @ k_deg*[sig{_}.P1()::cell] +sig{a}.P1(active{off})::cell => sig{a}.P1(active{on})::cell @ 0.5*[sig{a}.P1(active{off})::cell] +sig{a}.P1()::cell => sig{a}::cell + P1()::cell @ k_deg*[sig{a}.P1()::cell] + +block{a}::cell + P1()::cell => block{a}.P1()::cell @ param_block*[block{a}::cell]*[P1()::cell] + +P1(active{on})::cell + P2()::cell => P1(active{on}).P2()::cell @ 0.4*[P1(active{on})::cell]*[P2()::cell] +P1().P2()::cell => P1()::cell + P2()::cell @ k_deg*[P1().P2()::cell] +P1().P2(active{off})::cell => P1().P2(active{on})::cell @ k_prod*[P1().P2(active{off})::cell] + +#! inits +sig{i}::ext +block{i}::ext +P1(active{off})::cell +P2(active{off})::cell + +#! definitions +k_sig_1 = 0.8 +k_sig_2 = 0.2 +k_block_1 = 0.9 +k_block_2 = 0.3 +k_deg = 0.3 +k_prod = 0.6 +param_sig = 0.3 +param_block = 0.4 diff --git a/lib/galaxy/datatypes/test/test_file3.bcsl.ts b/lib/galaxy/datatypes/test/test_file3.bcsl.ts new file mode 100644 index 00000000000..caa80f95841 --- /dev/null +++ b/lib/galaxy/datatypes/test/test_file3.bcsl.ts @@ -0,0 +1,155 @@ +{ + "edges": [ + { + "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)" + } +} diff --git a/lib/galaxy/datatypes/test/test_file3.ctl.result b/lib/galaxy/datatypes/test/test_file3.ctl.result new file mode 100644 index 00000000000..63ef18885f2 --- /dev/null +++ b/lib/galaxy/datatypes/test/test_file3.ctl.result @@ -0,0 +1,2 @@ +Result: True +Number of satisfying states: 31 diff --git a/lib/galaxy/datatypes/text.py b/lib/galaxy/datatypes/text.py index 9ffa741f327..18badf79c8f 100644 --- a/lib/galaxy/datatypes/text.py +++ b/lib/galaxy/datatypes/text.py @@ -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""" diff --git a/mypy.ini b/mypy.ini index bfca49825f8..d36ec043ce8 100644 --- a/mypy.ini +++ b/mypy.ini @@ -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 diff --git a/test/unit/data/datatypes/test_bcsl.py b/test/unit/data/datatypes/test_bcsl.py new file mode 100644 index 00000000000..fcc60a08609 --- /dev/null +++ b/test/unit/data/datatypes/test_bcsl.py @@ -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 diff --git a/test/unit/data/datatypes/test_pithya.py b/test/unit/data/datatypes/test_pithya.py new file mode 100644 index 00000000000..950345feca1 --- /dev/null +++ b/test/unit/data/datatypes/test_pithya.py @@ -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 diff --git a/test/unit/data/datatypes/test_storm.py b/test/unit/data/datatypes/test_storm.py new file mode 100644 index 00000000000..32a2269a7dc --- /dev/null +++ b/test/unit/data/datatypes/test_storm.py @@ -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 diff --git a/test/unit/data/datatypes/util.py b/test/unit/data/datatypes/util.py index 87a66a027c5..b77b2513541 100644 --- a/test/unit/data/datatypes/util.py +++ b/test/unit/data/datatypes/util.py @@ -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