From 7e625752237ee07e815bfb28048bb0b1193b45c5 Mon Sep 17 00:00:00 2001 From: pvtroshin Date: Wed, 9 Feb 2011 15:49:35 +0000 Subject: [PATCH] new services are registered in wsbuild git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3728 e3abac25-378b-4346-85de-24260fe3988d --- TODO.txt | 10 + datamodel/compbio/data/sequence/Score.java | 29 +- datamodel/compbio/data/sequence/SequenceUtil.java | 15 +- how_to_add_new_webservice.txt | 8 + webservices/compbio/data/msa/jaxws/CancelJob.java | 4 +- .../compbio/data/msa/jaxws/CancelJobResponse.java | 4 +- .../compbio/data/msa/jaxws/GetJobStatus.java | 4 +- .../data/msa/jaxws/GetJobStatusResponse.java | 4 +- webservices/compbio/data/msa/jaxws/GetLimit.java | 4 +- .../compbio/data/msa/jaxws/GetLimitResponse.java | 4 +- webservices/compbio/data/msa/jaxws/GetLimits.java | 4 +- .../compbio/data/msa/jaxws/GetLimitsResponse.java | 4 +- webservices/compbio/data/msa/jaxws/GetPresets.java | 4 +- .../compbio/data/msa/jaxws/GetPresetsResponse.java | 4 +- .../compbio/data/msa/jaxws/GetRunnerOptions.java | 4 +- .../data/msa/jaxws/GetRunnerOptionsResponse.java | 4 +- .../data/msa/jaxws/JobSubmissionExceptionBean.java | 4 +- .../data/msa/jaxws/LimitExceededExceptionBean.java | 4 +- .../compbio/data/msa/jaxws/PullExecStatistics.java | 4 +- .../data/msa/jaxws/PullExecStatisticsResponse.java | 4 +- .../msa/jaxws/ResultNotAvailableExceptionBean.java | 4 +- .../msa/jaxws/UnsupportedRuntimeExceptionBean.java | 4 +- .../msa/jaxws/WrongParameterExceptionBean.java | 4 +- webservices/compbio/ws/client/Jws2Client.java | 13 +- .../compbio/ws/server/resource/AAConWS.wsdl | 118 +++---- .../compbio/ws/server/resource/AAConWS_schema1.xsd | 147 ++++---- .../ws/server/resource/ClustalWS_schema1.xsd | 93 ++++-- .../compbio/ws/server/resource/DisemblWS.wsdl | 292 ++++++++++++++++ .../ws/server/resource/DisemblWS_schema1.xsd | 350 ++++++++++++++++++++ .../compbio/ws/server/resource/GlobPlotWS.wsdl | 292 ++++++++++++++++ .../ws/server/resource/GlobPlotWS_schema1.xsd | 350 ++++++++++++++++++++ .../compbio/ws/server/resource/JronnWS.wsdl | 292 ++++++++++++++++ .../compbio/ws/server/resource/JronnWS_schema1.xsd | 350 ++++++++++++++++++++ .../compbio/ws/server/resource/MafftWS_schema1.xsd | 93 ++++-- .../ws/server/resource/MuscleWS_schema1.xsd | 87 +++-- .../ws/server/resource/TcoffeeWS_schema1.xsd | 87 +++-- wsbuild.xml | 41 ++- 37 files changed, 2468 insertions(+), 275 deletions(-) create mode 100644 webservices/compbio/ws/server/resource/DisemblWS.wsdl create mode 100644 webservices/compbio/ws/server/resource/DisemblWS_schema1.xsd create mode 100644 webservices/compbio/ws/server/resource/GlobPlotWS.wsdl create mode 100644 webservices/compbio/ws/server/resource/GlobPlotWS_schema1.xsd create mode 100644 webservices/compbio/ws/server/resource/JronnWS.wsdl create mode 100644 webservices/compbio/ws/server/resource/JronnWS_schema1.xsd diff --git a/TODO.txt b/TODO.txt index 7493df2..0acbf85 100644 --- a/TODO.txt +++ b/TODO.txt @@ -1,5 +1,15 @@ TODO: +FIXME: +Conecting to JABAWS version 2 service +09-Feb-2011 15:27:53 compbio.ws.client.Jws2Client connect +INFO: Connected successfully! +Exception in thread "main" java.lang.NullPointerException + at compbio.ws.client.MetadataHelper.getParametersList(MetadataHelper.java:30) + at compbio.ws.client.Jws2Client.(Jws2Client.java:179) + at compbio.ws.client.Jws2Client.main(Jws2Client.java:483) + + Need to pass predicted ranges to the client too - some are not straightforward to devise. This may require changes to SequenceAnnotation diff --git a/datamodel/compbio/data/sequence/Score.java b/datamodel/compbio/data/sequence/Score.java index 39bb398..b61c74e 100644 --- a/datamodel/compbio/data/sequence/Score.java +++ b/datamodel/compbio/data/sequence/Score.java @@ -6,15 +6,14 @@ import java.io.OutputStream; import java.io.OutputStreamWriter; import java.text.NumberFormat; import java.util.ArrayList; -import java.util.Collections; -import java.util.List; import java.util.Locale; import java.util.Set; -import java.util.SortedSet; import java.util.TreeSet; import javax.xml.bind.annotation.XmlAccessType; import javax.xml.bind.annotation.XmlAccessorType; +import javax.xml.bind.annotation.XmlElement; +import javax.xml.bind.annotation.XmlTransient; import compbio.util.annotation.Immutable; @@ -29,6 +28,7 @@ import compbio.util.annotation.Immutable; @Immutable public class Score { + @XmlTransient static final NumberFormat NUMBER_FORMAT = NumberFormat .getNumberInstance(Locale.UK); static { @@ -37,10 +37,13 @@ public class Score { } private Enum method; + // private String method; - private SortedSet ranges = new TreeSet(); + @XmlElement + private TreeSet ranges = new TreeSet(); - private List scores = Collections.emptyList(); + @XmlElement + private ArrayList scores = new ArrayList(0); private Score() { // JaXB default constructor @@ -56,7 +59,7 @@ public class Score { * the actual conservation values for each column of the * alignment */ - public Score(Enum method, List scores) { + public Score(Enum method, ArrayList scores) { this.method = method; this.scores = new ArrayList(scores); } @@ -72,13 +75,13 @@ public class Score { * The set of ranges i.e. parts of the sequence with specific * function, usually can be calculated based on scores */ - public Score(Enum method, List scores, SortedSet ranges) { + public Score(Enum method, ArrayList scores, TreeSet ranges) { this.method = method; this.ranges = ranges; this.scores = scores; } - public Score(Enum method, SortedSet ranges) { + public Score(Enum method, TreeSet ranges) { this.method = method; this.ranges = ranges; } @@ -88,8 +91,8 @@ public class Score { this.scores = toList(scores); } - private List toList(float[] values) { - List vlist = new ArrayList(); + private ArrayList toList(float[] values) { + ArrayList vlist = new ArrayList(); for (float v : values) { vlist.add(new Float(v)); } @@ -109,7 +112,7 @@ public class Score { * * @return the column scores for the alignment */ - public List getScores() { + public ArrayList getScores() { return scores; } @@ -118,11 +121,11 @@ public class Score { * * @return */ - public SortedSet getRanges() { + public TreeSet getRanges() { return ranges; } - public void setRanges(SortedSet ranges) { + public void setRanges(TreeSet ranges) { this.ranges = ranges; } diff --git a/datamodel/compbio/data/sequence/SequenceUtil.java b/datamodel/compbio/data/sequence/SequenceUtil.java index 3990f8f..c4e1def 100644 --- a/datamodel/compbio/data/sequence/SequenceUtil.java +++ b/datamodel/compbio/data/sequence/SequenceUtil.java @@ -30,7 +30,6 @@ import java.util.HashSet; import java.util.List; import java.util.Map; import java.util.Scanner; -import java.util.SortedSet; import java.util.TreeSet; import java.util.logging.Level; import java.util.regex.Matcher; @@ -459,11 +458,11 @@ public final class SequenceUtil { ArrayList hotloops = new ArrayList(); String sequenceName = scansingle.nextLine().trim(); - SortedSet coilsR = parseRanges(DisemblResult.COILS, + TreeSet coilsR = parseRanges(DisemblResult.COILS, scansingle.nextLine()); - SortedSet rem465R = parseRanges(DisemblResult.REM465, + TreeSet rem465R = parseRanges(DisemblResult.REM465, scansingle.nextLine()); - SortedSet loopsR = parseRanges(DisemblResult.HOTLOOPS, + TreeSet loopsR = parseRanges(DisemblResult.HOTLOOPS, scansingle.nextLine()); String title = scansingle.nextLine(); @@ -503,8 +502,8 @@ public final class SequenceUtil { * @param lines * @return */ - private static SortedSet parseRanges(Enum resultType, String lines) { - SortedSet ranges = new TreeSet(); + private static TreeSet parseRanges(Enum resultType, String lines) { + TreeSet ranges = new TreeSet(); Scanner scan = new Scanner(lines); @@ -589,9 +588,9 @@ public final class SequenceUtil { ArrayList smoothedScore = new ArrayList(); String sequenceName = scansingle.nextLine().trim(); - SortedSet domsR = parseRanges(GlobProtResult.GlobDoms, + TreeSet domsR = parseRanges(GlobProtResult.GlobDoms, scansingle.nextLine()); - SortedSet disorderR = parseRanges(GlobProtResult.Disorder, + TreeSet disorderR = parseRanges(GlobProtResult.Disorder, scansingle.nextLine()); String title = scansingle.nextLine(); diff --git a/how_to_add_new_webservice.txt b/how_to_add_new_webservice.txt index 8d7e7cc..7df641e 100644 --- a/how_to_add_new_webservice.txt +++ b/how_to_add_new_webservice.txt @@ -30,6 +30,14 @@ Edit binaries/src setexecutableflag.sh and compilebin.sh scripts accordingly. 12) Register web service in WEB-INF/ web.xml and sun-jaxws.xml +13) Add generated wsdl to wsbuild.xml ant script to generate the stubs + +14) Run build-server task in wsbuild file. Watch for errors. If cannot compile that means +that JAXB cannot serialize some of the data structures. Add appropriate annotations to your data types. +Check that + - you do not have interfaces as fields + - you have a default no args constructor (can be private if you do not need it) + 13) Modify the client to work with your web service. 14) Test. diff --git a/webservices/compbio/data/msa/jaxws/CancelJob.java b/webservices/compbio/data/msa/jaxws/CancelJob.java index 32660d9..9b1f062 100644 --- a/webservices/compbio/data/msa/jaxws/CancelJob.java +++ b/webservices/compbio/data/msa/jaxws/CancelJob.java @@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlType; -@XmlRootElement(name = "cancelJob", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlRootElement(name = "cancelJob", namespace = "http://msa.data.compbio/01/12/2010/") @XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "cancelJob", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlType(name = "cancelJob", namespace = "http://msa.data.compbio/01/12/2010/") public class CancelJob { @XmlElement(name = "jobId", namespace = "") diff --git a/webservices/compbio/data/msa/jaxws/CancelJobResponse.java b/webservices/compbio/data/msa/jaxws/CancelJobResponse.java index 7ccc190..00a92e2 100644 --- a/webservices/compbio/data/msa/jaxws/CancelJobResponse.java +++ b/webservices/compbio/data/msa/jaxws/CancelJobResponse.java @@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlType; -@XmlRootElement(name = "cancelJobResponse", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlRootElement(name = "cancelJobResponse", namespace = "http://msa.data.compbio/01/12/2010/") @XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "cancelJobResponse", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlType(name = "cancelJobResponse", namespace = "http://msa.data.compbio/01/12/2010/") public class CancelJobResponse { @XmlElement(name = "return", namespace = "") diff --git a/webservices/compbio/data/msa/jaxws/GetJobStatus.java b/webservices/compbio/data/msa/jaxws/GetJobStatus.java index 5fd70f5..438b3a0 100644 --- a/webservices/compbio/data/msa/jaxws/GetJobStatus.java +++ b/webservices/compbio/data/msa/jaxws/GetJobStatus.java @@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlType; -@XmlRootElement(name = "getJobStatus", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlRootElement(name = "getJobStatus", namespace = "http://msa.data.compbio/01/12/2010/") @XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "getJobStatus", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlType(name = "getJobStatus", namespace = "http://msa.data.compbio/01/12/2010/") public class GetJobStatus { @XmlElement(name = "jobId", namespace = "") diff --git a/webservices/compbio/data/msa/jaxws/GetJobStatusResponse.java b/webservices/compbio/data/msa/jaxws/GetJobStatusResponse.java index 0f8ba68..0f81c39 100644 --- a/webservices/compbio/data/msa/jaxws/GetJobStatusResponse.java +++ b/webservices/compbio/data/msa/jaxws/GetJobStatusResponse.java @@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlType; -@XmlRootElement(name = "getJobStatusResponse", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlRootElement(name = "getJobStatusResponse", namespace = "http://msa.data.compbio/01/12/2010/") @XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "getJobStatusResponse", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlType(name = "getJobStatusResponse", namespace = "http://msa.data.compbio/01/12/2010/") public class GetJobStatusResponse { @XmlElement(name = "return", namespace = "") diff --git a/webservices/compbio/data/msa/jaxws/GetLimit.java b/webservices/compbio/data/msa/jaxws/GetLimit.java index 6b04bc0..64514ba 100644 --- a/webservices/compbio/data/msa/jaxws/GetLimit.java +++ b/webservices/compbio/data/msa/jaxws/GetLimit.java @@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlType; -@XmlRootElement(name = "getLimit", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlRootElement(name = "getLimit", namespace = "http://msa.data.compbio/01/12/2010/") @XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "getLimit", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlType(name = "getLimit", namespace = "http://msa.data.compbio/01/12/2010/") public class GetLimit { @XmlElement(name = "presetName", namespace = "") diff --git a/webservices/compbio/data/msa/jaxws/GetLimitResponse.java b/webservices/compbio/data/msa/jaxws/GetLimitResponse.java index 249e7e4..8147fa6 100644 --- a/webservices/compbio/data/msa/jaxws/GetLimitResponse.java +++ b/webservices/compbio/data/msa/jaxws/GetLimitResponse.java @@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlType; -@XmlRootElement(name = "getLimitResponse", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlRootElement(name = "getLimitResponse", namespace = "http://msa.data.compbio/01/12/2010/") @XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "getLimitResponse", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlType(name = "getLimitResponse", namespace = "http://msa.data.compbio/01/12/2010/") public class GetLimitResponse { @XmlElement(name = "return", namespace = "") diff --git a/webservices/compbio/data/msa/jaxws/GetLimits.java b/webservices/compbio/data/msa/jaxws/GetLimits.java index b8668d9..152f72e 100644 --- a/webservices/compbio/data/msa/jaxws/GetLimits.java +++ b/webservices/compbio/data/msa/jaxws/GetLimits.java @@ -6,9 +6,9 @@ import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlType; -@XmlRootElement(name = "getLimits", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlRootElement(name = "getLimits", namespace = "http://msa.data.compbio/01/12/2010/") @XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "getLimits", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlType(name = "getLimits", namespace = "http://msa.data.compbio/01/12/2010/") public class GetLimits { diff --git a/webservices/compbio/data/msa/jaxws/GetLimitsResponse.java b/webservices/compbio/data/msa/jaxws/GetLimitsResponse.java index f503c23..8bb6cc9 100644 --- a/webservices/compbio/data/msa/jaxws/GetLimitsResponse.java +++ b/webservices/compbio/data/msa/jaxws/GetLimitsResponse.java @@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlType; -@XmlRootElement(name = "getLimitsResponse", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlRootElement(name = "getLimitsResponse", namespace = "http://msa.data.compbio/01/12/2010/") @XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "getLimitsResponse", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlType(name = "getLimitsResponse", namespace = "http://msa.data.compbio/01/12/2010/") public class GetLimitsResponse { @XmlElement(name = "return", namespace = "") diff --git a/webservices/compbio/data/msa/jaxws/GetPresets.java b/webservices/compbio/data/msa/jaxws/GetPresets.java index 2e57fb8..04d5d12 100644 --- a/webservices/compbio/data/msa/jaxws/GetPresets.java +++ b/webservices/compbio/data/msa/jaxws/GetPresets.java @@ -6,9 +6,9 @@ import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlType; -@XmlRootElement(name = "getPresets", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlRootElement(name = "getPresets", namespace = "http://msa.data.compbio/01/12/2010/") @XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "getPresets", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlType(name = "getPresets", namespace = "http://msa.data.compbio/01/12/2010/") public class GetPresets { diff --git a/webservices/compbio/data/msa/jaxws/GetPresetsResponse.java b/webservices/compbio/data/msa/jaxws/GetPresetsResponse.java index ad2942b..7755793 100644 --- a/webservices/compbio/data/msa/jaxws/GetPresetsResponse.java +++ b/webservices/compbio/data/msa/jaxws/GetPresetsResponse.java @@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlType; -@XmlRootElement(name = "getPresetsResponse", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlRootElement(name = "getPresetsResponse", namespace = "http://msa.data.compbio/01/12/2010/") @XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "getPresetsResponse", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlType(name = "getPresetsResponse", namespace = "http://msa.data.compbio/01/12/2010/") public class GetPresetsResponse { @XmlElement(name = "return", namespace = "") diff --git a/webservices/compbio/data/msa/jaxws/GetRunnerOptions.java b/webservices/compbio/data/msa/jaxws/GetRunnerOptions.java index 9128b3f..9d59cd3 100644 --- a/webservices/compbio/data/msa/jaxws/GetRunnerOptions.java +++ b/webservices/compbio/data/msa/jaxws/GetRunnerOptions.java @@ -6,9 +6,9 @@ import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlType; -@XmlRootElement(name = "getRunnerOptions", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlRootElement(name = "getRunnerOptions", namespace = "http://msa.data.compbio/01/12/2010/") @XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "getRunnerOptions", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlType(name = "getRunnerOptions", namespace = "http://msa.data.compbio/01/12/2010/") public class GetRunnerOptions { diff --git a/webservices/compbio/data/msa/jaxws/GetRunnerOptionsResponse.java b/webservices/compbio/data/msa/jaxws/GetRunnerOptionsResponse.java index fb467ca..2278aa2 100644 --- a/webservices/compbio/data/msa/jaxws/GetRunnerOptionsResponse.java +++ b/webservices/compbio/data/msa/jaxws/GetRunnerOptionsResponse.java @@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlType; -@XmlRootElement(name = "getRunnerOptionsResponse", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlRootElement(name = "getRunnerOptionsResponse", namespace = "http://msa.data.compbio/01/12/2010/") @XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "getRunnerOptionsResponse", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlType(name = "getRunnerOptionsResponse", namespace = "http://msa.data.compbio/01/12/2010/") public class GetRunnerOptionsResponse { @XmlElement(name = "return", namespace = "") diff --git a/webservices/compbio/data/msa/jaxws/JobSubmissionExceptionBean.java b/webservices/compbio/data/msa/jaxws/JobSubmissionExceptionBean.java index 2d75977..30950b4 100644 --- a/webservices/compbio/data/msa/jaxws/JobSubmissionExceptionBean.java +++ b/webservices/compbio/data/msa/jaxws/JobSubmissionExceptionBean.java @@ -13,9 +13,9 @@ import javax.xml.bind.annotation.XmlType; * Generated source version: 2.2.1 * */ -@XmlRootElement(name = "JobSubmissionException", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlRootElement(name = "JobSubmissionException", namespace = "http://msa.data.compbio/01/12/2010/") @XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "JobSubmissionException", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlType(name = "JobSubmissionException", namespace = "http://msa.data.compbio/01/12/2010/") public class JobSubmissionExceptionBean { private String message; diff --git a/webservices/compbio/data/msa/jaxws/LimitExceededExceptionBean.java b/webservices/compbio/data/msa/jaxws/LimitExceededExceptionBean.java index c7a78e0..c9c3a4e 100644 --- a/webservices/compbio/data/msa/jaxws/LimitExceededExceptionBean.java +++ b/webservices/compbio/data/msa/jaxws/LimitExceededExceptionBean.java @@ -13,9 +13,9 @@ import javax.xml.bind.annotation.XmlType; * Generated source version: 2.2.1 * */ -@XmlRootElement(name = "LimitExceededException", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlRootElement(name = "LimitExceededException", namespace = "http://msa.data.compbio/01/12/2010/") @XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "LimitExceededException", namespace = "http://msa.data.compbio/01/01/2010/", propOrder = { +@XmlType(name = "LimitExceededException", namespace = "http://msa.data.compbio/01/12/2010/", propOrder = { "actualNumberofSequences", "message", "numberOfSequencesAllowed", diff --git a/webservices/compbio/data/msa/jaxws/PullExecStatistics.java b/webservices/compbio/data/msa/jaxws/PullExecStatistics.java index db1be6e..7ab918b 100644 --- a/webservices/compbio/data/msa/jaxws/PullExecStatistics.java +++ b/webservices/compbio/data/msa/jaxws/PullExecStatistics.java @@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlType; -@XmlRootElement(name = "pullExecStatistics", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlRootElement(name = "pullExecStatistics", namespace = "http://msa.data.compbio/01/12/2010/") @XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "pullExecStatistics", namespace = "http://msa.data.compbio/01/01/2010/", propOrder = { +@XmlType(name = "pullExecStatistics", namespace = "http://msa.data.compbio/01/12/2010/", propOrder = { "jobId", "position" }) diff --git a/webservices/compbio/data/msa/jaxws/PullExecStatisticsResponse.java b/webservices/compbio/data/msa/jaxws/PullExecStatisticsResponse.java index 068b404..ef36b8d 100644 --- a/webservices/compbio/data/msa/jaxws/PullExecStatisticsResponse.java +++ b/webservices/compbio/data/msa/jaxws/PullExecStatisticsResponse.java @@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlType; -@XmlRootElement(name = "pullExecStatisticsResponse", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlRootElement(name = "pullExecStatisticsResponse", namespace = "http://msa.data.compbio/01/12/2010/") @XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "pullExecStatisticsResponse", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlType(name = "pullExecStatisticsResponse", namespace = "http://msa.data.compbio/01/12/2010/") public class PullExecStatisticsResponse { @XmlElement(name = "return", namespace = "") diff --git a/webservices/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.java b/webservices/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.java index d25d496..be8a26d 100644 --- a/webservices/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.java +++ b/webservices/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.java @@ -13,9 +13,9 @@ import javax.xml.bind.annotation.XmlType; * Generated source version: 2.2.1 * */ -@XmlRootElement(name = "ResultNotAvailableException", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlRootElement(name = "ResultNotAvailableException", namespace = "http://msa.data.compbio/01/12/2010/") @XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "ResultNotAvailableException", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlType(name = "ResultNotAvailableException", namespace = "http://msa.data.compbio/01/12/2010/") public class ResultNotAvailableExceptionBean { private String message; diff --git a/webservices/compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.java b/webservices/compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.java index c10959d..5e1268a 100644 --- a/webservices/compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.java +++ b/webservices/compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.java @@ -13,9 +13,9 @@ import javax.xml.bind.annotation.XmlType; * Generated source version: 2.2.1 * */ -@XmlRootElement(name = "UnsupportedRuntimeException", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlRootElement(name = "UnsupportedRuntimeException", namespace = "http://msa.data.compbio/01/12/2010/") @XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "UnsupportedRuntimeException", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlType(name = "UnsupportedRuntimeException", namespace = "http://msa.data.compbio/01/12/2010/") public class UnsupportedRuntimeExceptionBean { private String message; diff --git a/webservices/compbio/data/msa/jaxws/WrongParameterExceptionBean.java b/webservices/compbio/data/msa/jaxws/WrongParameterExceptionBean.java index d110c2c..62be910 100644 --- a/webservices/compbio/data/msa/jaxws/WrongParameterExceptionBean.java +++ b/webservices/compbio/data/msa/jaxws/WrongParameterExceptionBean.java @@ -13,9 +13,9 @@ import javax.xml.bind.annotation.XmlType; * Generated source version: 2.2.1 * */ -@XmlRootElement(name = "WrongParameterException", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlRootElement(name = "WrongParameterException", namespace = "http://msa.data.compbio/01/12/2010/") @XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "WrongParameterException", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlType(name = "WrongParameterException", namespace = "http://msa.data.compbio/01/12/2010/") public class WrongParameterExceptionBean { private String message; diff --git a/webservices/compbio/ws/client/Jws2Client.java b/webservices/compbio/ws/client/Jws2Client.java index 1fc2a68..ec3cf65 100644 --- a/webservices/compbio/ws/client/Jws2Client.java +++ b/webservices/compbio/ws/client/Jws2Client.java @@ -164,7 +164,7 @@ public class Jws2Client { if (service.getServiceType() == SequenceAnnotation.class) { Map> result = analize(inputFile, ((SequenceAnnotation) msaws), preset, customOptions); - assert result != null && !result.values().isEmpty() : "No Result reported!"; + assert !result.values().isEmpty() : "No Result reported!"; IOHelper.writeOut(outStream, result); } else { alignment = align(inputFile, (MsaWS) msaws, preset, @@ -212,6 +212,7 @@ public class Jws2Client { HashMap> scores = null; try { fastalist = SequenceUtil.openInputStream(file.getAbsolutePath()); + assert !fastalist.isEmpty() : "Input is empty!"; String jobId = null; if (customOptions != null && preset != null) { @@ -223,11 +224,14 @@ public class Jws2Client { } else if (preset != null) { jobId = wsproxy.presetAnalize(fastalist, preset); } else { + System.out.println("\n\ncalling analise........."); jobId = wsproxy.analize(fastalist); } Thread.sleep(2000); + scores = wsproxy.getAnnotation(jobId); - assert scores != null && !scores.values().isEmpty() : "Scores are NULL"; + assert scores != null && !scores.values().isEmpty() : "Scores are NULL for job: " + + jobId; } catch (IOException e) { System.err @@ -292,11 +296,12 @@ public class Jws2Client { } } if (serv == null) { - System.err.println("Could not connect to " + url); + System.err.println("Could not connect to " + url + + " the server is down?"); // FIXME } JABAService serviceIF = service.getInterface(serv); - log.log(Level.FINE, "Connected successfully!"); + log.log(Level.INFO, "Connected successfully!"); return serviceIF; } diff --git a/webservices/compbio/ws/server/resource/AAConWS.wsdl b/webservices/compbio/ws/server/resource/AAConWS.wsdl index 11401a5..dffcb48 100644 --- a/webservices/compbio/ws/server/resource/AAConWS.wsdl +++ b/webservices/compbio/ws/server/resource/AAConWS.wsdl @@ -6,15 +6,6 @@ - - - - - - - - - @@ -45,6 +36,15 @@ + + + + + + + + + @@ -87,78 +87,66 @@ - - - - - - + - - - - - + + + + + - - - - - - + + + + + + - - - - - - + + + + + + + + + + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - + - - - - - - - - - - - - @@ -219,6 +207,18 @@ + + + + + + + + + + + + diff --git a/webservices/compbio/ws/server/resource/AAConWS_schema1.xsd b/webservices/compbio/ws/server/resource/AAConWS_schema1.xsd index ddd1c72..77fe8df 100644 --- a/webservices/compbio/ws/server/resource/AAConWS_schema1.xsd +++ b/webservices/compbio/ws/server/resource/AAConWS_schema1.xsd @@ -23,9 +23,9 @@ - + - + @@ -47,14 +47,20 @@ + + + + + + @@ -74,7 +80,10 @@ - + + + + @@ -120,25 +129,26 @@ - + - - + + + - - + + - + @@ -147,7 +157,9 @@ - + + + @@ -160,9 +172,15 @@ + - - + + + + + + + @@ -178,6 +196,36 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -189,7 +237,19 @@ - + + + + + + + + + + + + + @@ -204,10 +264,6 @@ - - - - @@ -220,8 +276,8 @@ - - + + @@ -250,31 +306,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - - @@ -289,7 +320,10 @@ - + + + + @@ -312,28 +346,5 @@ - - - - - - - - - - - - - - - - - - - - - - - diff --git a/webservices/compbio/ws/server/resource/ClustalWS_schema1.xsd b/webservices/compbio/ws/server/resource/ClustalWS_schema1.xsd index 8947341..d15007b 100644 --- a/webservices/compbio/ws/server/resource/ClustalWS_schema1.xsd +++ b/webservices/compbio/ws/server/resource/ClustalWS_schema1.xsd @@ -47,14 +47,20 @@ + + + + + + @@ -82,25 +88,26 @@ - + - - + + + - - + + - + @@ -109,7 +116,9 @@ - + + + @@ -126,7 +135,24 @@ - + + + + + + + + + + + + + + + + + + @@ -146,7 +172,19 @@ - + + + + + + + + + + + + + @@ -161,10 +199,6 @@ - - - - @@ -177,16 +211,22 @@ - - + + + - - + + + + + + + @@ -209,10 +249,6 @@ - - - - @@ -261,7 +297,10 @@ - + + + + @@ -309,5 +348,15 @@ + + + + + + + + + + diff --git a/webservices/compbio/ws/server/resource/DisemblWS.wsdl b/webservices/compbio/ws/server/resource/DisemblWS.wsdl new file mode 100644 index 0000000..0682949 --- /dev/null +++ b/webservices/compbio/ws/server/resource/DisemblWS.wsdl @@ -0,0 +1,292 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/webservices/compbio/ws/server/resource/DisemblWS_schema1.xsd b/webservices/compbio/ws/server/resource/DisemblWS_schema1.xsd new file mode 100644 index 0000000..6185886 --- /dev/null +++ b/webservices/compbio/ws/server/resource/DisemblWS_schema1.xsd @@ -0,0 +1,350 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/webservices/compbio/ws/server/resource/GlobPlotWS.wsdl b/webservices/compbio/ws/server/resource/GlobPlotWS.wsdl new file mode 100644 index 0000000..aed2c95 --- /dev/null +++ b/webservices/compbio/ws/server/resource/GlobPlotWS.wsdl @@ -0,0 +1,292 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/webservices/compbio/ws/server/resource/GlobPlotWS_schema1.xsd b/webservices/compbio/ws/server/resource/GlobPlotWS_schema1.xsd new file mode 100644 index 0000000..109e3fb --- /dev/null +++ b/webservices/compbio/ws/server/resource/GlobPlotWS_schema1.xsd @@ -0,0 +1,350 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/webservices/compbio/ws/server/resource/JronnWS.wsdl b/webservices/compbio/ws/server/resource/JronnWS.wsdl new file mode 100644 index 0000000..fc9670e --- /dev/null +++ b/webservices/compbio/ws/server/resource/JronnWS.wsdl @@ -0,0 +1,292 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/webservices/compbio/ws/server/resource/JronnWS_schema1.xsd b/webservices/compbio/ws/server/resource/JronnWS_schema1.xsd new file mode 100644 index 0000000..77fe8df --- /dev/null +++ b/webservices/compbio/ws/server/resource/JronnWS_schema1.xsd @@ -0,0 +1,350 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/webservices/compbio/ws/server/resource/MafftWS_schema1.xsd b/webservices/compbio/ws/server/resource/MafftWS_schema1.xsd index 8947341..d15007b 100644 --- a/webservices/compbio/ws/server/resource/MafftWS_schema1.xsd +++ b/webservices/compbio/ws/server/resource/MafftWS_schema1.xsd @@ -47,14 +47,20 @@ + + + + + + @@ -82,25 +88,26 @@ - + - - + + + - - + + - + @@ -109,7 +116,9 @@ - + + + @@ -126,7 +135,24 @@ - + + + + + + + + + + + + + + + + + + @@ -146,7 +172,19 @@ - + + + + + + + + + + + + + @@ -161,10 +199,6 @@ - - - - @@ -177,16 +211,22 @@ - - + + + - - + + + + + + + @@ -209,10 +249,6 @@ - - - - @@ -261,7 +297,10 @@ - + + + + @@ -309,5 +348,15 @@ + + + + + + + + + + diff --git a/webservices/compbio/ws/server/resource/MuscleWS_schema1.xsd b/webservices/compbio/ws/server/resource/MuscleWS_schema1.xsd index 90e1132..e0440e8 100644 --- a/webservices/compbio/ws/server/resource/MuscleWS_schema1.xsd +++ b/webservices/compbio/ws/server/resource/MuscleWS_schema1.xsd @@ -47,14 +47,20 @@ + + + + + + @@ -69,7 +75,10 @@ - + + + + @@ -79,7 +88,10 @@ - + + + + @@ -119,12 +131,13 @@ - - + + + - - + + @@ -150,7 +163,19 @@ - + + + + + + + + + + + + + @@ -165,10 +190,6 @@ - - - - @@ -181,16 +202,22 @@ - - + + + - - + + + + + + + @@ -234,7 +261,7 @@ - + @@ -242,7 +269,7 @@ - + @@ -251,7 +278,9 @@ - + + + @@ -268,7 +297,17 @@ - + + + + + + + + + + + @@ -296,6 +335,16 @@ + + + + + + + + + + diff --git a/webservices/compbio/ws/server/resource/TcoffeeWS_schema1.xsd b/webservices/compbio/ws/server/resource/TcoffeeWS_schema1.xsd index 3c82a56..bf15fb2 100644 --- a/webservices/compbio/ws/server/resource/TcoffeeWS_schema1.xsd +++ b/webservices/compbio/ws/server/resource/TcoffeeWS_schema1.xsd @@ -47,14 +47,20 @@ + + + + + + @@ -69,7 +75,10 @@ - + + + + @@ -80,17 +89,21 @@ - + + + + - - + + + - - + + @@ -150,7 +163,19 @@ - + + + + + + + + + + + + + @@ -165,10 +190,6 @@ - - - - @@ -181,16 +202,22 @@ - - + + + - - + + + + + + + @@ -234,7 +261,7 @@ - + @@ -242,7 +269,7 @@ - + @@ -251,7 +278,9 @@ - + + + @@ -268,7 +297,17 @@ - + + + + + + + + + + + @@ -296,6 +335,16 @@ + + + + + + + + + + diff --git a/wsbuild.xml b/wsbuild.xml index 8e7cc8b..dad6d25 100644 --- a/wsbuild.xml +++ b/wsbuild.xml @@ -23,6 +23,9 @@ + + + @@ -98,9 +101,41 @@ verbose="true"> - - - + + + + + + + + + + + + + + -- 1.7.10.2