Changeset 3151

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Timestamp:
03/05/10 13:42:58 (5 months ago)
Author:
thomas
Message:

fixed build path errors due to API and jar name changes
increased version number of superpathways plugin (for release with new gpml schema)

Location:
trunk/tools
Files:
10 modified

Legend:

Unmodified
Added
Removed

  • trunk/tools/AtlasMapper/build.xml

    r2642 r3151  
    3030                <include name="lib/resources.jar" /> 
    3131                <include name="lib/jdom.jar" /> 
    32                 <include name="lib/bridgedb.jar" /> 
    33                 <include name="lib/bridgedb-bio.jar" /> 
     32                <include name="lib/org.bridgedb.jar" /> 
     33                <include name="lib/org.bridgedb.bio.jar" /> 
     34                <include name="lib/org.bridgedb.rdb.jar" /> 
     35                <include name="lib/org.bridgedb.rdb.construct.jar" /> 
    3436        </fileset> 
    3537 

  • trunk/tools/AtlasMapper/src/atlas/util/AtlasStatistics.java

    r2979 r3151  
    1717 
    1818import org.bridgedb.DataSource; 
     19import org.bridgedb.IDMapper; 
    1920import org.bridgedb.IDMapperException; 
    2021import org.bridgedb.Xref; 
    21 import org.bridgedb.bio.GdbProvider; 
    2222import org.bridgedb.bio.Organism; 
    23 import org.bridgedb.rdb.IDMapperRdb; 
     23import org.bridgedb.rdb.GdbProvider; 
    2424import org.pathvisio.debug.Logger; 
    2525import org.pathvisio.model.ConverterException; 
    2626import org.pathvisio.model.Pathway; 
    27 import org.pathvisio.util.Utils; 
    2827import org.pathvisio.wikipathways.WikiPathwaysClient; 
    2928import org.pathvisio.wikipathways.server.AtlasMapperServiceImpl; 
    … …  
    5251        PathwayCache pwCache; 
    5352 
    54         public AtlasStatistics(File cachePath, File gdbConfig) throws IDMapperException, IOException, ServiceException { 
     53        public AtlasStatistics(File cachePath, File gdbConfig) throws IDMapperException, IOException, ServiceException, ClassNotFoundException { 
    5554                this.cachePath = cachePath; 
    5655                gdbProv = GdbProvider.fromConfigFile(gdbConfig); 
    … …  
    7473                                        for(Xref x : p.getDataNodeXrefs()) { 
    7574                                                if(x.getId() == null || x.getDataSource() == null) continue; 
    76                                                 for(IDMapperRdb gdb : gdbProv.getGdbs(Organism.fromLatinName(wpi.getSpecies()))) { 
     75                                                for(IDMapper gdb : gdbProv.getGdbs(Organism.fromLatinName(wpi.getSpecies()))) { 
    7776                                                        for(Xref ens : gdb.mapID(x, orgEns)) { 
    7877                                                                ensIds.add(ens.getId()); 

  • trunk/tools/AtlasMapper/src/org/pathvisio/wikipathways/server/AtlasCache.java

    r2979 r3151  
    3232 
    3333import org.bridgedb.DataSource; 
     34import org.bridgedb.IDMapper; 
    3435import org.bridgedb.IDMapperException; 
    3536import org.bridgedb.Xref; 
    3637import org.bridgedb.bio.BioDataSource; 
    37 import org.bridgedb.bio.GdbProvider; 
    3838import org.bridgedb.bio.Organism; 
    39 import org.bridgedb.rdb.IDMapperRdb; 
     39import org.bridgedb.rdb.GdbProvider; 
    4040import org.pathvisio.debug.Logger; 
    4141import org.pathvisio.model.ConverterException; 
    4242import org.pathvisio.model.Pathway; 
    4343import org.pathvisio.preferences.PreferenceManager; 
    44 import org.pathvisio.util.Utils; 
    4544import org.pathvisio.wikipathways.WikiPathwaysClient; 
    4645import org.pathvisio.wikipathways.webservice.WSPathwayInfo; 
    … …  
    103102                        Logger.log.warn("No organism found in pahtway " + p.getId() + ", assuming human"); 
    104103                } 
    105                 List<IDMapperRdb> gdbList = gdbs.getGdbs(org); 
     104                List<IDMapper> gdbList = gdbs.getGdbs(org); 
    106105 
    107106                //Get all ensembl genes on the pathway 
    … …  
    109108                for(Xref x : pathway.getDataNodeXrefs()) { 
    110109                        if(x.getId() == null || x.getDataSource() == null) continue; 
    111                         for(IDMapperRdb gdb : gdbList) { 
     110                        for(IDMapper gdb : gdbList) { 
    112111                                for(Xref c : gdb.mapID(x, ensDs)) { 
    113112                                        ensIds.add(c.getId()); 

  • trunk/tools/AtlasMapper/src/org/pathvisio/wikipathways/server/AtlasMapperServiceImpl.java

    r2979 r3151  
    2828 
    2929import org.bridgedb.DataSource; 
     30import org.bridgedb.IDMapper; 
    3031import org.bridgedb.Xref; 
    3132import org.bridgedb.bio.BioDataSource; 
    3233import org.bridgedb.bio.Organism; 
    33 import org.bridgedb.rdb.IDMapperRdb; 
    3434import org.pathvisio.debug.Logger; 
    3535import org.pathvisio.model.ObjectType; 
    … …  
    3737import org.pathvisio.model.PathwayElement; 
    3838import org.pathvisio.preferences.PreferenceManager; 
    39 import org.pathvisio.util.Utils; 
    4039import org.pathvisio.view.VPathway; 
    4140import org.pathvisio.view.VPathwayWrapperBase; 
    … …  
    186185                        DataSource orgEns = AtlasMapperServiceImpl.getEnsemblDataSource(org); 
    187186 
    188                         List<IDMapperRdb> gdbs = getCacheManager().getGdbProvider().getGdbs(org); 
     187                        List<IDMapper> gdbs = getCacheManager().getGdbProvider().getGdbs(org); 
    189188 
    190189                        List<GeneInfo> genes = new ArrayList<GeneInfo>(); 
    … …  
    199198 
    200199                                        Set<Xref> xrefs = new HashSet<Xref>(); 
    201                                         for(IDMapperRdb gdb : gdbs) { 
     200                                        for(IDMapper gdb : gdbs) { 
    202201                                                Xref x = pwe.getXref(); 
    203202                                                if(x.getId() == null || x.getDataSource() == null) continue; 

  • trunk/tools/AtlasMapper/src/org/pathvisio/wikipathways/server/AtlasVisualizer.java

    r2979 r3151  
    2828 
    2929import org.bridgedb.DataSource; 
     30import org.bridgedb.IDMapper; 
    3031import org.bridgedb.IDMapperException; 
    3132import org.bridgedb.Xref; 
    3233import org.bridgedb.bio.Organism; 
    33 import org.bridgedb.rdb.IDMapperRdb; 
    3434import org.pathvisio.model.BatikImageExporter; 
    3535import org.pathvisio.model.ConverterException; 
    … …  
    3939import org.pathvisio.preferences.PreferenceManager; 
    4040import org.pathvisio.util.ColorExporter; 
    41 import org.pathvisio.util.Utils; 
    4241 
    4342import atlas.model.Factor; 
    … …  
    5453        GeneSet atlasGenes; 
    5554        List<Factor> factors; 
    56         List<IDMapperRdb> gdbs; 
     55        List<IDMapper> gdbs; 
    5756        Organism organism; 
    5857 
    59         public AtlasVisualizer(Pathway pathway, GeneSet atlasGenes, List<Factor> factors, List<IDMapperRdb> gdbs) { 
     58        public AtlasVisualizer(Pathway pathway, GeneSet atlasGenes, List<Factor> factors, List<IDMapper> list) { 
    6059                this.pathway = pathway; 
    6160                this.atlasGenes = atlasGenes; 
    6261                this.factors = factors; 
    63                 this.gdbs = gdbs; 
     62                this.gdbs = list; 
    6463                this.organism = Organism.fromLatinName(pathway.getMappInfo().getOrganism()); 
    6564                PreferenceManager.init(); 

  • trunk/tools/AtlasMapper/src/org/pathvisio/wikipathways/server/CacheManager.java

    r2979 r3151  
    2828 
    2929import org.bridgedb.IDMapperException; 
    30 import org.bridgedb.bio.GdbProvider; 
     30import org.bridgedb.rdb.GdbProvider; 
    3131import org.pathvisio.debug.Logger; 
    3232import org.pathvisio.wikipathways.WikiPathwaysClient; 
    … …  
    8585        } 
    8686 
    87         public ImageCache getImageCache() throws ServiceException, IOException, IDMapperException { 
     87        public ImageCache getImageCache() throws ServiceException, IOException, IDMapperException, ClassNotFoundException { 
    8888                if(imageCache == null) { 
    8989                        imageCache = new ImageCache( 
    … …  
    9898        } 
    9999 
    100         public AtlasCache getAtlasCache() throws ServiceException, IOException, IDMapperException { 
     100        public AtlasCache getAtlasCache() throws ServiceException, IOException, IDMapperException, ClassNotFoundException { 
    101101                if(atlasCache == null) { 
    102102                        atlasCache = new AtlasCache( 
    … …  
    120120        } 
    121121 
    122         public GdbProvider getGdbProvider() throws IOException, IDMapperException { 
     122        public GdbProvider getGdbProvider() throws IOException, IDMapperException, ClassNotFoundException { 
    123123                if(gdbs == null) { 
    124124                        gdbs = GdbProvider.fromConfigFile( 

  • trunk/tools/AtlasMapper/src/org/pathvisio/wikipathways/server/ImageCache.java

    r2979 r3151  
    2727 
    2828import org.bridgedb.IDMapperException; 
    29 import org.bridgedb.bio.GdbProvider; 
    3029import org.bridgedb.bio.Organism; 
     30import org.bridgedb.rdb.GdbProvider; 
    3131import org.pathvisio.model.BatikImageExporter; 
    3232import org.pathvisio.model.ConverterException; 

  • trunk/tools/AtlasMapper/src/org/pathvisio/wikipathways/server/ImageServiceImpl.java

    r2979 r3151  
    5454        } 
    5555 
    56         private ImageCache getImageCache() throws ServiceException, IOException, IDMapperException { 
     56        private ImageCache getImageCache() throws ServiceException, IOException, IDMapperException, ClassNotFoundException { 
    5757                return getCacheManager().getImageCache(); 
    5858        } 

  • trunk/tools/lucene-indexer/build.xml

    r3127 r3151  
    2323                        <include name="lib/org.bridgedb.bio.jar"/> 
    2424                        <include name="lib/org.bridgedb.jar"/> 
     25                        <include name="lib/org.bridgedb.rdb.jar"/> 
     26                        <include name="lib/org.bridgedb.rdb.construct.jar"/> 
    2527                        <include name="lib/derby.jar"/> 
    2628                        <include name="lib/apache/*.jar"/> 
    … …  
    8789                <copy file="${pathvisio.dir}/lib/org.bridgedb.jar" toDir="${dist.dir}/lib"/> 
    8890                <copy file="${pathvisio.dir}/lib/org.bridgedb.bio.jar" toDir="${dist.dir}/lib"/> 
     91                <copy file="${pathvisio.dir}/lib/org.bridgedb.rdb.jar" toDir="${dist.dir}/lib"/> 
     92                <copy file="${pathvisio.dir}/lib/org.bridgedb.rdb.construct.jar" toDir="${dist.dir}/lib"/> 
    8993                <copy file="bridge.config" toDir="${dist.dir}"/> 
    9094                <copy file="indexer.config" toDir="${dist.dir}"/> 

  • trunk/tools/superpathways/plugin.props

    r2788 r3151  
    1414 
    1515# Plugin version number, this must be two numbers separated by a decimlal.  Ex. 0.2, 14.03 
    16 pluginVersion=1.0 
     16pluginVersion=1.1 
    1717 
    1818# Compatible Cytoscape version. If there are more than one version, seperate by ",".