From: Jim Procter Date: Fri, 7 Jun 2013 12:23:28 +0000 (+0100) Subject: JAL-724 JAL-715 refactor and create new test for RSBS framework and Multi-harmony... X-Git-Tag: Jalview_2_9~248^2~4 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=89fdf2b589aadf46000d58306e0b50dc9ef1af74;p=jalview.git JAL-724 JAL-715 refactor and create new test for RSBS framework and Multi-harmony service --- diff --git a/examples/testdata/smad.fa b/examples/testdata/smad.fa new file mode 100644 index 0000000..6a3b27b --- /dev/null +++ b/examples/testdata/smad.fa @@ -0,0 +1,132 @@ +>gi|7160686|emb|CAB76819.1|/1-465 +DVQAVAYEEPKHWCSIVYYELNNRVGEAFHASSTSILVDGFTDPSNNKNRFCLGLLSNVNRNSTIENTRRHI +GKGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHGFHPTTVCKIPSGCSLKIFNNQEF----AQLLAQSVNH +GFETVYELTKMCTLRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHNPISSVS +>gi|61967924|gb|AAX56944.1|/1-465 +DVQAVAYEEPKHWCSIVYYELNNRVGEAFHASSTSILVDGFTDPSNNKNRFCLGLLSNVNRNSTIENTRRHI +GKGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHGFHPTTVCKIPSGCSLKIFNNQEF----AQLLAQSVNH +GFETVYELTKMCTLRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHNPISSVS +>gi|11464653|gb|AAG35265.1|/1-455 +TMHPVNYQEPKYWCSIVYYELNNRVGEAFNASQLSIIIDGFTDPSNNSDRFCLGLLSNVNRNSTIENTRRHI +GKGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHNFHPTTVCKIPPGCSLKIFSNQEF----AHLLSRTVHH +GFEAVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWVEIHLNGPLQWLDRVLTQMGTPRNPISSVS +>gi|6273783|gb|AAF06361.1|/1-472 +DVHPVAYQEPKHWCSIVYYELNNRVGEAFLASSTSVLVDGFTDPSNNRNRFCLGLLSNVNRNSTIENTRRHI +GKGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHGFHPTTVCKIPSRCSLKIFNNQEF----AELLAQSVNH +GFEAVYELTKMCTIRMSFVKGWGAKYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHNPISSVS +>gi|11907945|gb|AAG41407.1|/1-465 +DVQAVAYEEPKHWCSIVYYELNNRVGEAFHASSTSVLVDGFTDPSNNKNRFCLGLLSNVNRNSTIENTRRHI +GKGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHGFHPTTVCKIPSGCSLKIFNNQEF----AQLLAQSVNH +GFETVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHNPISSVS +>gi|29725652|gb|AAO88909.1|/1-465 +DVQAVAYEEPKHWCSIVYYELNNRVGEAFHASSTSVLVDGFTDPSNNKNRFCLGLLSNVNRNSTIENTRRHI +GKGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHGFHPTTVCKIPSGCSLKIFNNQEF----AQLLAQSVNH +GFETVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHNPISSVS +>gi|1654323|gb|AAC50790.1|/1-465 +DVQAVAYEEPKHWCSIVYYELNNRVGEAFHASSTSVLVDGFTDPSNNKNRFCLGLLSNVNRNSTIENTRRHI +GKGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHGFHPTTVCKIPSGCSLKIFNNQEF----AQLLAQSVNH +GFETVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHNPISSVS +>gi|3192871|gb|AAC19116.1|/1-468 +DVQAVAYEEPKHWCSIVYYELNNRVGEAFHASSTSVLVDGFTDPSNNKNRFCLGLLSNVNRNSTIENTRRHI +GKGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHGFHPTTVCKIPSGCSLKIFNNQEF----AQLLAQSVNH +GFETVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHNPISSVS +>gi|55926152|ref|NP_001007481.1|/1-464 +DVQAVAYEEPKHWCSIVYYELNNRVGEAFHASSTSVLVDGFTDPSNNRNRFCLGLLSNVNRNSTIENTRRHI +GKGVHLYYVGGEVYAECLSDSSIFVQSRNCNFHHGFHPTTVCKIPSGCSLKIFNNQEF----AQLLAQSVNH +GFETVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHNPISSVS +>gi|61967926|gb|AAX56945.1|/1-465 +DVQPVAYEEPKHWCSIVYYELNNRVGEAFHASSTSVLVDGFTDPSNNKNRFCLGLLSNVNRNSTIENTRRHI +GKGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHGFHPTTVCKIPSGCSLKIFNNQEF----AQLLAQSVNH +GFEAVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPLNPISSVS +>gi|2360958|gb|AAB92396.1|/1-465 +DVQPVAYEEPKHWCSIVYYELNNRVGEAFHASSTSVLVDGFTDPSNNKSRFCLGLLSNVNRNSTIENTRRHI +GKGVHLYYVGGEVYAECLSDSSIFVQSRNCNFHHGFHPTTVCKIPSSCSLKIFNNQEF----AQLLAQSVNH +GFEAVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPLNPISSVS +>gi|5706366|dbj|BAA83093.1|/1-465 +DVQPVAYEEPKHWCSIVYYELNNRVGEAFHASSTSVLVDGFTDPANNKSRFCLGLLSNVNRNSTIENTRRHI +GKGVHLYYVGGEVYAECLSDSSIFVQSRNCNFHHGFHPTTVCKIPSSCSLKIFNNQEF----AQLLAQSVNH +GFEAVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPLNPISSVS +>gi|3982649|gb|AAC83580.1|/1-465 +DVQPVAYEEPKHWCSIVYYELNNRVGEAFHASSTSVLVDGFTDPSNNKSRFCLGLLSNVNRNSTIENTRRHI +GKGVHLYYVGGEVYAECLSDSSIFVQSRNCNFHHGFHPTTVCKIPSSCSLKIFNNQEF----AQLLAQSVNH +GFEAVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPLNPISSVS +>gi|6288777|gb|AAF06738.1|/1-464 +DVQPVEYQEPSHWCSIVYYELNNRVGEAYHASSTSVLVDGFTDPSNNKNRFCLGLLSNVNRNSTIENTRRHI +GKGVHLYYVGGEVYAECLSDTSIFVQSRNCNYHHGFHPTTVCKIPSGCSLKIFNNQEF----AQLLAQSVNH +GFEAVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEVHLHGPLQWLDKVLTQMGSPLNPISSVS +>gi|61967928|gb|AAX56946.1|/1-476 +NFRPVCYEEPQHWCSVAYYELNNRVGETFQASSRSILIDGFTDPSNNKNRFCLGLLSNVNRNSTIENTRRHI +GKGVHLYYVGGEVYAECVSDSSIFVQSRNCNYQHGFHPATVCKIPSGCSLKIFNNQLF----AQPLAQSVNH +GFEVVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHNPISSVS +>gi|2689629|gb|AAC53515.1|/1-434 +DFRPVCYEEPLHWCSVAYYELNNRVGETFQASSRSVLIDGFTDPSNNRNRFCLGLLSNVNRNSTIENTRRHI +GKGVHLYYVGGEVYAECVSDSSIFVQSRNCNYQHGFHPATVCKIPSGCSLKVFNNQLFAQLLAQLLAQSVHH +GFEVVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHNPISSVS +>gi|22532988|gb|AAF77079.2|/1-428 +DFRPVCYEEPQHWCSVAYYELNNRVGETFQASSRSVLIDGFTDPSNNRNRFCLGLLSNVNRNSTIENTRRHI +GKGVHLYYVGGEVYAECVSDSSIFVQSRNCNYQHGFHPATVCKIPSGCSLKVFNNQLF----AQLLAQSVHH +GFEVVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHNPISSVS +>gi|2967646|gb|AAC39657.1|/1-467 +DLQPVTYSEPAFWCSIAYYELNQRVGETFHASQPSLTVDGFTDPSNS-ERFCLGLLSNVNRNATVEMTRRHI +GRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEF----AALLAQSVNQ +GFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSVRCSSMS +>gi|45331050|gb|AAS57861.1|/1-468 +DLQPVTYSEPAFWCSIAYYELNQRVGETFHASQPSLTVDGFTDPSNS-ERFCLGLLSNVNRNATVEMTRRHI +GRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYDWHPATVCKIPPGCNLKIFNNQEF----AALLAQSVNQ +GFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSVRCSSMS +>gi|5360217|dbj|BAA81909.1|/1-467 +DLQPVTYSEPAFWCSIAYYELNQRVGETFHASQPSLTVDGFTDPSNS-ERFCLGLLSNVNRNATVEMTRRHI +GRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEF----AALLAQSVNQ +GFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSVRCSSMS +>gi|6288775|gb|AAF06737.1|/1-468 +DLQPVTYSEPAFWCSIAYYELNQRVGETFHASQPSLTVDGFTDPSNS-ERFCLCLLSNVNRNATVEMTRRHI +GRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEF----AALLAQSVNQ +GFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSVRCSSMS +>gi|58047721|gb|AAH89184.1|/1-467 +DLQPVTYSEPAFWCSIAYYELNQRVGETFHASQPSLTVDGFTDPSNS-ERFCLGLLSNVNRNATVEMTRRHI +GRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEF----AALLAQSVNQ +GFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSVRCSSMS +>gi|4009524|gb|AAD11458.1|/1-486 +DAAPVMYHEPAFWCSISYYELNTRVGETFHASQPSITVDGFTDPSNS-ERFCLGLLSNVNRNEVVEQTRRHI +GKGVRLYYIGGEVFAECLSDSSIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEF----AALLSQSVSQ +GFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDRVLTQMGSPRLPCSSMS +>gi|40254710|ref|NP_571441.2|/1-468 +DLQPVTYSEPAFWCSIAYYELNQRVGETFHASQPSLTVDGFTDPSNS-ERFCLGLLSNVNRNATVEMTRRHI +GRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEF----AALLAQSVNQ +GFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSVRCSSMS +>gi|18655485|pdb|1KHX|A|/22-227 +DLQPVTYSEPAFWCSIAYYELNQRVGETFHASQPSLTVDGFTDPSNS-ERFCLGLLSNVNRNATVEMTRRHI +GRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEF----AALLAQSVNQ +GFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSVRCSSMS +>gi|13992583|emb|CAC38118.1|/1-425 +DLQPVTYCEPAFWCSISYYELNQRVGETFHASQPSMTVDGFTDPSNS-ERFCLGLLSNVNRNAAVELTRRHI +GRGVRLYYIGGEVFAECLSDNAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEF----AALLAQSVNQ +GFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSIRCSSVS +>gi|11875329|dbj|BAB19634.1|/1-425 +DLQPVTYCEPAFWCSISYYELNQRVGETFHASQPSMTVDGFTDPSNS-ERFCLGLLSNVNRNAAVELTRRHI +GRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEF----AALLAQSVNQ +GFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSIRCSSVS +>gi|45331052|gb|AAS57862.1|/1-422 +DLQPVTYCESAFWCSISYYELNQRVGETFHASQPSLTVDGFTDPSNA-ERFCLGLLSNVNRNAAVELTRRHI +GRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEF----AALLAQSVNQ +GFEAVYRLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPNLRCSSVS +>gi|18418623|gb|AAL68976.1|/1-425 +DLQPVTYCEPAFWCSISYYELNQRVGETFHASQPSMTVDGFTDPSNS-ERFCLGLLSNVNRNAAVELTRRHI +GRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEF----AALLAQSVNQ +GFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSIRCSSVS +>gi|2564493|gb|AAB81755.1|/1-425 +DLQPVTYCEPAFWCSISYYELNQRVGETFHASQPSMTVDGFTDPSNS-ERLCLGLLSNVNRNAAVELTRRHI +GRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEF----AALLAQSVNQ +GFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSIRCSSVS +>gi|6981174|ref|NP_037227.1|/1-425 +DLQPVTYCEPAFWCSISYYELNQRVGETFHASQPSMTVDGFTDPSNS-ERFCLGLLSNVNRNAAVELTRRHI +GRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEF----AALLAQSVNQ +GFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSIRCSSVS +>gi|45383213|ref|NP_989806.1|/1-426 +DLQPVTYCEPAFWCSISYYELNQRVGETFHASQPSMTVDGFTDPSNS-ERFCLGLLSNVNRNAAVELTRRHI +GRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEF----AALLAQSVNQ +GFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSIRCSSVS +>gi|47523074|ref|NP_999302.1|/1-425 +DLQPVTYCEPAFWCSISYYELNQRVGETFHASQPSMTVDGFTDPSNS-ERFCLGLLSNVNRNAAVELTRRHI +GRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEF----AALLAQSVNQ +GFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSIRCSSVS diff --git a/examples/testdata/smad_groups.jva b/examples/testdata/smad_groups.jva new file mode 100644 index 0000000..ca5f507 --- /dev/null +++ b/examples/testdata/smad_groups.jva @@ -0,0 +1,19 @@ +JALVIEW_ANNOTATION +# Created: Tue Jun 04 16:56:03 BST 2013 + + +SEQUENCE_GROUP group1 1 211 -1 gi|7160686|emb|CAB76819.1| gi|61967924|gb|AAX56944.1| gi|11464653|gb|AAG35265.1| gi|6273783|gb|AAF06361.1| gi|11907945|gb|AAG41407.1| gi|29725652|gb|AAO88909.1| gi|1654323|gb|AAC50790.1| gi|3192871|gb|AAC19116.1| gi|55926152|ref|NP_001007481.1| +PROPERTIES group1 outlineColour=000000 displayBoxes=true displayText=true colourText=false showUnconserved=false textCol1=000000 textCol2=ffffff + +SEQUENCE_GROUP group2 1 211 -1 gi|61967926|gb|AAX56945.1| gi|2360958|gb|AAB92396.1| gi|5706366|dbj|BAA83093.1| gi|3982649|gb|AAC83580.1| gi|6288777|gb|AAF06738.1| +PROPERTIES group2 outlineColour=000000 displayBoxes=true displayText=true colourText=false showUnconserved=false textCol1=000000 textCol2=ffffff + +SEQUENCE_GROUP group3 1 211 -1 gi|61967928|gb|AAX56946.1| gi|2689629|gb|AAC53515.1| gi|22532988|gb|AAF77079.2| +PROPERTIES group3 outlineColour=000000 displayBoxes=true displayText=true colourText=false showUnconserved=false textCol1=000000 textCol2=ffffff + +SEQUENCE_GROUP group4 1 211 -1 gi|2967646|gb|AAC39657.1| gi|45331050|gb|AAS57861.1| gi|5360217|dbj|BAA81909.1| gi|6288775|gb|AAF06737.1| gi|58047721|gb|AAH89184.1| gi|4009524|gb|AAD11458.1| gi|40254710|ref|NP_571441.2| gi|18655485|pdb|1KHX|A| +PROPERTIES group4 outlineColour=000000 displayBoxes=true displayText=true colourText=false showUnconserved=false textCol1=000000 textCol2=ffffff + +SEQUENCE_GROUP group5 1 211 -1 gi|13992583|emb|CAC38118.1| gi|11875329|dbj|BAB19634.1| gi|45331052|gb|AAS57862.1| gi|18418623|gb|AAL68976.1| gi|2564493|gb|AAB81755.1| gi|6981174|ref|NP_037227.1| gi|45383213|ref|NP_989806.1| gi|47523074|ref|NP_999302.1| +PROPERTIES group5 outlineColour=000000 displayBoxes=true displayText=true colourText=false showUnconserved=false textCol1=000000 textCol2=ffffff + diff --git a/src/jalview/ws/rest/RestServiceDescription.java b/src/jalview/ws/rest/RestServiceDescription.java index 6828f2d..fd9e3b4 100644 --- a/src/jalview/ws/rest/RestServiceDescription.java +++ b/src/jalview/ws/rest/RestServiceDescription.java @@ -873,100 +873,6 @@ public class RestServiceDescription return valid; } - public static void main(String argv[]) - { - // test separator list - try - { - assert (separatorListToArray("foo=',',min='foo',max='1,2,3',fa=','", - ",").length == 4); - if (separatorListToArray("minsize='2', sep=','", ",").length == 2) - { - assert (false); - } - - } catch (AssertionError x) - { - System.err.println("separatorListToArray is faulty."); - } - if (argv.length == 0) - { - if (!testRsdExchange("Test using default Shmmr service", - RestClient.makeShmmrRestClient().service)) - { - System.err.println("default test failed."); - } - else - { - System.err.println("default test passed."); - } - } - else - { - int i = 0, p = 0; - for (String svc : argv) - { - p += testRsdExchange("Test " + (++i), svc) ? 1 : 0; - } - System.err.println("" + p + " out of " + i + " tests passed."); - - } - } - - private static boolean testRsdExchange(String desc, String servicestring) - { - try - { - RestServiceDescription newService = new RestServiceDescription( - servicestring); - if (!newService.isValid()) - { - throw new Error("Failed to create service from '" + servicestring - + "'.\n" + newService.getInvalidMessage()); - } - return testRsdExchange(desc, newService); - } catch (Throwable x) - { - System.err.println("Failed for service (" + desc + "): " - + servicestring); - x.printStackTrace(); - return false; - } - } - - private static boolean testRsdExchange(String desc, - RestServiceDescription service) - { - try - { - String fromservicetostring = service.toString(); - RestServiceDescription newService = new RestServiceDescription( - fromservicetostring); - if (!newService.isValid()) - { - throw new Error("Failed to create service from '" - + fromservicetostring + "'.\n" - + newService.getInvalidMessage()); - } - - if (!service.equals(newService)) - { - System.err.println("Failed for service (" + desc + ")."); - System.err.println("Original service and parsed service differ."); - System.err.println("Original: " + fromservicetostring); - System.err.println("Parsed : " + newService.toString()); - return false; - } - } catch (Throwable x) - { - System.err.println("Failed for service (" + desc + "): " - + service.toString()); - x.printStackTrace(); - return false; - } - return true; - } - /** * covenience method to generate the id and sequence string vector from a set * of seuqences using each sequence's getName() and getSequenceAsString() diff --git a/test/jalview/ws/rest/ShmmrRSBSService.java b/test/jalview/ws/rest/ShmmrRSBSService.java new file mode 100644 index 0000000..05f7cd0 --- /dev/null +++ b/test/jalview/ws/rest/ShmmrRSBSService.java @@ -0,0 +1,132 @@ +/** + * + */ +package jalview.ws.rest; + +import static org.junit.Assert.*; + +import java.io.BufferedReader; +import java.io.IOException; +import java.util.ArrayList; +import java.util.Hashtable; +import java.util.List; +import java.util.Map; + +import jalview.datamodel.AlignmentI; +import jalview.datamodel.AlignmentView; +import jalview.gui.AlignFrame; +import jalview.io.FileParse; +import jalview.ws.rest.InputType; +import jalview.ws.rest.params.SeqGroupIndexVector; + +import org.junit.AfterClass; +import org.junit.BeforeClass; +import org.junit.Test; + +/** + * @author jimp + * + */ +public class ShmmrRSBSService +{ + + @Test + public void testSeparatorListToArrayForRestServiceDescriptions() + { + assertTrue( + "separatorListToArray is faulty.", + RestServiceDescription.separatorListToArray( + "foo=',',min='foo',max='1,2,3',fa=','", ",").length == 4); + assertTrue("separatorListToArray is faulty.", + RestServiceDescription.separatorListToArray( + "minsize='2', sep=','", ",").length != 2); // probably should come as 2 + } + + @Test + public void testShmmrService() + { + + assertTrue( + "Test Rsd Exchange using using default Shmmr service failed.", + testRsdExchange("Test using default Shmmr service", + RestClient.makeShmmrRestClient().service)); + } + @Test + public void testShmmrServiceDataprep() throws Exception + { + RestClient _rc = RestClient.makeShmmrRestClient(); + assertNotNull(_rc); + AlignFrame alf = new jalview.io.FileLoader(false).LoadFileWaitTillLoaded("examples/testdata/smad.fa", jalview.io.FormatAdapter.FILE); + assertNotNull("Couldn't find test data.",alf); + alf.loadJalviewDataFile("examples/testdata/smad_groups.jva", + jalview.io.FormatAdapter.FILE, null, null); + assertTrue("Couldn't load the test data's annotation file (should be 5 groups but found "+alf.getViewport().getAlignment().getGroups().size()+").", alf.getViewport().getAlignment().getGroups().size()==5); + + RestClient rc = new RestClient(_rc.service, alf, true); + + + + assertNotNull("Couldn't creat RestClient job.",rc); + jalview.bin.Cache.initLogger(); + RestJob rjb = new RestJob(0, new RestJobThread(rc),rc.av.getAlignment(),null); + rjb.setAlignmentForInputs(rc.service.getInputParams().values(), rc.av.getAlignment()); + for (Map.Entry e:rc.service.getInputParams().entrySet()) { + System.out.println("For Input '"+e.getKey()+":\n"+e.getValue().formatForInput(rjb).getContentLength()); + } + } + + private static boolean testRsdExchange(String desc, String servicestring) + { + try + { + RestServiceDescription newService = new RestServiceDescription( + servicestring); + if (!newService.isValid()) + { + throw new Error("Failed to create service from '" + servicestring + + "'.\n" + newService.getInvalidMessage()); + } + return testRsdExchange(desc, newService); + } catch (Throwable x) + { + System.err.println("Failed for service (" + desc + "): " + + servicestring); + x.printStackTrace(); + return false; + } + } + + private static boolean testRsdExchange(String desc, + RestServiceDescription service) + { + try + { + String fromservicetostring = service.toString(); + RestServiceDescription newService = new RestServiceDescription( + fromservicetostring); + if (!newService.isValid()) + { + throw new Error("Failed to create service from '" + + fromservicetostring + "'.\n" + + newService.getInvalidMessage()); + } + + if (!service.equals(newService)) + { + System.err.println("Failed for service (" + desc + ")."); + System.err.println("Original service and parsed service differ."); + System.err.println("Original: " + fromservicetostring); + System.err.println("Parsed : " + newService.toString()); + return false; + } + } catch (Throwable x) + { + System.err.println("Failed for service (" + desc + "): " + + service.toString()); + x.printStackTrace(); + return false; + } + return true; + } + +}