Removed (c) Univ of Manchester LGPL license header These were part of Software Grant to ASF filed 2015-02-23 and can thus be relicensed to Apache license 2.0
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/repo Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/commit/33e003af Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/tree/33e003af Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/diff/33e003af Branch: refs/heads/master Commit: 33e003af24b7bf088692ef0578a650b7b6066f52 Parents: 39d65ba Author: Stian Soiland-Reyes <[email protected]> Authored: Wed Sep 7 13:13:37 2016 +0100 Committer: Stian Soiland-Reyes <[email protected]> Committed: Wed Sep 7 13:13:37 2016 +0100 ---------------------------------------------------------------------- .../BiomartActivityConfigurationAction.java | 18 --- .../actions/BiomartConfigurationPanel.java | 18 --- .../BiomartActivityIcon.java | 18 --- .../BiomartServiceDescription.java | 18 --- .../views/BiomartActivityContextualView.java | 18 --- .../views/BiomartActivityViewFactory.java | 18 --- .../TestBiomartActivityContextualView.java | 18 --- .../t2/activities/biomart/BiomartActivity.java | 18 --- .../BiomartActivityConfigurationBean.java | 18 --- .../biomart/BiomartActivityFactory.java | 18 --- .../biomart/BiomartActivityHealthChecker.java | 18 --- .../biomart/BiomartActivityFactoryTest.java | 18 --- .../org/biomart/martservice/DatasetLink.java | 33 ------ .../org/biomart/martservice/MartDataset.java | 33 ------ .../java/org/biomart/martservice/MartQuery.java | 65 +++-------- .../org/biomart/martservice/MartRegistry.java | 39 +------ .../org/biomart/martservice/MartService.java | 83 +++++--------- .../martservice/MartServiceException.java | 43 +------- .../biomart/martservice/MartServiceUtils.java | 59 +++------- .../martservice/MartServiceXMLHandler.java | 53 ++------- .../biomart/martservice/MartURLLocation.java | 71 ++++-------- .../org/biomart/martservice/ResultReceiver.java | 47 ++------ .../martservice/ResultReceiverException.java | 43 +------- .../config/QueryConfigController.java | 69 +++--------- .../martservice/config/QueryConfigUtils.java | 77 ++++--------- .../config/event/QueryComponentAdapter.java | 51 ++------- .../config/event/QueryComponentEvent.java | 45 +------- .../config/event/QueryComponentListener.java | 51 ++------- .../config/ui/ConfigDisplayObject.java | 49 ++------- .../martservice/config/ui/ExpandableBox.java | 37 +------ .../martservice/config/ui/MartServiceIcons.java | 35 +----- .../ui/MartServiceQueryConfigUIFactory.java | 33 ------ .../martservice/config/ui/MinimalLayout.java | 45 +------- .../martservice/config/ui/QueryComponent.java | 75 ++++--------- .../config/ui/QueryConfigUIFactory.java | 73 ++++--------- .../biomart/martservice/query/Attribute.java | 33 ------ .../org/biomart/martservice/query/Dataset.java | 77 ++++--------- .../org/biomart/martservice/query/Filter.java | 67 +++--------- .../org/biomart/martservice/query/Link.java | 57 ++-------- .../org/biomart/martservice/query/Query.java | 109 +++++++------------ .../martservice/query/QueryListener.java | 51 ++------- .../martservice/query/QueryXMLHandler.java | 69 +++--------- .../biomart/martservice/MartDatasetTest.java | 31 ------ .../biomart/martservice/MartRegistryTest.java | 31 ------ .../martservice/MartServiceUtilsTest.java | 31 ------ .../martservice/MartServiceXMLHandlerTest.java | 31 ------ .../martservice/MartURLLocationTest.java | 31 ------ .../config/event/QueryComponentEventTest.java | 31 ------ .../config/ui/MartServiceIconsTest.java | 31 ------ .../martservice/query/AttributeTest.java | 31 ------ .../biomart/martservice/query/DatasetTest.java | 31 ------ .../biomart/martservice/query/FilterTest.java | 31 ------ .../biomart/martservice/query/QueryTest.java | 31 ------ .../actions/MobyObjectDetailsAction.java | 19 ---- .../biomoby/actions/MobyParserAction.java | 19 ---- .../edits/AddBiomobyCollectionDataTypeEdit.java | 19 ---- .../edits/AddBiomobyConsumingServiceEdit.java | 22 ---- .../biomoby/edits/AddMobyParseDatatypeEdit.java | 19 ---- .../biomoby/edits/AddUpstreamObjectEdit.java | 22 ---- .../BiomobyServiceProvider.java | 18 --- .../BiomobyObjectActivityContextualView.java | 19 ---- ...mobyObjectActivityContextualViewFactory.java | 19 ---- .../view/MobyParseDatatypeContextualView.java | 19 ---- .../MobyParseDatatypeContextualViewFactory.java | 19 ---- .../SoaplabActivityConfigurationAction.java | 18 --- .../actions/SoaplabConfigurationPanel.java | 18 --- .../MissingSoaplabException.java | 49 --------- .../SoaplabActivityIcon.java | 18 --- .../servicedescriptions/SoaplabCategory.java | 49 --------- .../SoaplabScavengerAgent.java | 49 --------- .../views/SoaplabActivityContextualView.java | 18 --- .../views/SoaplabActivityViewFactory.java | 18 --- .../TestSoaplabActivityContextualView.java | 18 --- .../sf/taverna/t2/activities/soaplab/Soap.java | 18 --- .../t2/activities/soaplab/SoaplabActivity.java | 18 --- .../SoaplabActivityConfigurationBean.java | 18 --- .../soaplab/SoaplabActivityFactory.java | 18 --- .../soaplab/SoaplabActivityHealthChecker.java | 18 --- .../SoaplabActivityConfigurationBeanTest.java | 18 --- .../activities/soaplab/SoaplabActivityTest.java | 18 --- 80 files changed, 341 insertions(+), 2483 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartActivityConfigurationAction.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartActivityConfigurationAction.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartActivityConfigurationAction.java index ad290f0..6df1af9 100644 --- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartActivityConfigurationAction.java +++ b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartActivityConfigurationAction.java @@ -1,22 +1,4 @@ /******************************************************************************* - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 ******************************************************************************/ package net.sf.taverna.t2.activities.biomart.actions; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartConfigurationPanel.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartConfigurationPanel.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartConfigurationPanel.java index 4d0a118..06d1a6a 100644 --- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartConfigurationPanel.java +++ b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartConfigurationPanel.java @@ -1,22 +1,4 @@ /******************************************************************************* - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 ******************************************************************************/ package net.sf.taverna.t2.activities.biomart.actions; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartActivityIcon.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartActivityIcon.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartActivityIcon.java index 845665e..4affb62 100644 --- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartActivityIcon.java +++ b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartActivityIcon.java @@ -1,22 +1,4 @@ /******************************************************************************* - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 ******************************************************************************/ package net.sf.taverna.t2.activities.biomart.servicedescriptions; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceDescription.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceDescription.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceDescription.java index 7508b4d..0114053 100644 --- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceDescription.java +++ b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceDescription.java @@ -1,21 +1,3 @@ -/* Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 ******************************************************************************/ package net.sf.taverna.t2.activities.biomart.servicedescriptions; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityContextualView.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityContextualView.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityContextualView.java index eacf193..c6c2bd9 100644 --- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityContextualView.java +++ b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityContextualView.java @@ -1,22 +1,4 @@ /******************************************************************************* - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 ******************************************************************************/ package net.sf.taverna.t2.activities.biomart.views; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityViewFactory.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityViewFactory.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityViewFactory.java index 4a866bc..1836dfc 100644 --- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityViewFactory.java +++ b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityViewFactory.java @@ -1,22 +1,4 @@ /******************************************************************************* - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 ******************************************************************************/ package net.sf.taverna.t2.activities.biomart.views; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-activity-ui/src/test/java/net/sf/taverna/t2/biomart/views/TestBiomartActivityContextualView.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-activity-ui/src/test/java/net/sf/taverna/t2/biomart/views/TestBiomartActivityContextualView.java b/taverna-biomart-activity-ui/src/test/java/net/sf/taverna/t2/biomart/views/TestBiomartActivityContextualView.java index 8ad6242..f8d5c9b 100644 --- a/taverna-biomart-activity-ui/src/test/java/net/sf/taverna/t2/biomart/views/TestBiomartActivityContextualView.java +++ b/taverna-biomart-activity-ui/src/test/java/net/sf/taverna/t2/biomart/views/TestBiomartActivityContextualView.java @@ -1,22 +1,4 @@ /******************************************************************************* - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 ******************************************************************************/ package net.sf.taverna.t2.biomart.views; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivity.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivity.java b/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivity.java index 7e87939..13fc4f2 100644 --- a/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivity.java +++ b/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivity.java @@ -1,22 +1,4 @@ /******************************************************************************* - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 ******************************************************************************/ package net.sf.taverna.t2.activities.biomart; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityConfigurationBean.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityConfigurationBean.java b/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityConfigurationBean.java index 91cc323..da71551 100644 --- a/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityConfigurationBean.java +++ b/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityConfigurationBean.java @@ -1,22 +1,4 @@ /******************************************************************************* - * Copyright (C) 2011 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 ******************************************************************************/ package net.sf.taverna.t2.activities.biomart; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityFactory.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityFactory.java b/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityFactory.java index 4aaf043..a4b8877 100644 --- a/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityFactory.java +++ b/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityFactory.java @@ -1,22 +1,4 @@ /******************************************************************************* - * Copyright (C) 2011 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 ******************************************************************************/ package net.sf.taverna.t2.activities.biomart; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityHealthChecker.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityHealthChecker.java b/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityHealthChecker.java index 8e48635..7fb67a6 100644 --- a/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityHealthChecker.java +++ b/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityHealthChecker.java @@ -1,22 +1,4 @@ /******************************************************************************* - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 ******************************************************************************/ package net.sf.taverna.t2.activities.biomart; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-activity/src/test/java/net/sf/taverna/t2/activities/biomart/BiomartActivityFactoryTest.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-activity/src/test/java/net/sf/taverna/t2/activities/biomart/BiomartActivityFactoryTest.java b/taverna-biomart-activity/src/test/java/net/sf/taverna/t2/activities/biomart/BiomartActivityFactoryTest.java index 78ed2f6..eec2c46 100644 --- a/taverna-biomart-activity/src/test/java/net/sf/taverna/t2/activities/biomart/BiomartActivityFactoryTest.java +++ b/taverna-biomart-activity/src/test/java/net/sf/taverna/t2/activities/biomart/BiomartActivityFactoryTest.java @@ -1,22 +1,4 @@ /******************************************************************************* - * Copyright (C) 2011 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 ******************************************************************************/ package net.sf.taverna.t2.activities.biomart; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/DatasetLink.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/DatasetLink.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/DatasetLink.java index e5dccd4..65330cf 100644 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/DatasetLink.java +++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/DatasetLink.java @@ -1,36 +1,3 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: DatasetLink.java,v $ - * Revision $Revision: 1.2 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/12/13 11:38:55 $ - * by $Author: davidwithers $ - * Created on 12-Apr-2006 - *****************************************************************/ package org.biomart.martservice; import java.util.Comparator; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartDataset.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartDataset.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartDataset.java index 8c0f584..6090dcf 100644 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartDataset.java +++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartDataset.java @@ -1,36 +1,3 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: MartDataset.java,v $ - * Revision $Revision: 1.2 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/10/04 14:17:19 $ - * by $Author: davidwithers $ - * Created on 17-Mar-2006 - *****************************************************************/ package org.biomart.martservice; import java.util.Comparator; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartQuery.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartQuery.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartQuery.java index 9f75566..fe4be71 100644 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartQuery.java +++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartQuery.java @@ -1,36 +1,3 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: MartQuery.java,v $ - * Revision $Revision: 1.2 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/12/13 11:38:55 $ - * by $Author: davidwithers $ - * Created on 08-May-2006 - *****************************************************************/ package org.biomart.martservice; import java.util.ArrayList; @@ -50,7 +17,7 @@ import org.ensembl.mart.lib.config.DatasetConfig; /** * Class for creating queries to send to a BioMart web service. - * + * * @author David Withers */ public class MartQuery { @@ -98,7 +65,7 @@ public class MartQuery { /** * Returns the martDataset. - * + * * @return the martDataset. */ public MartDataset getMartDataset() { @@ -107,7 +74,7 @@ public class MartQuery { /** * Sets the martDataset. - * + * * @param martDataset * the martDataset to set. */ @@ -117,7 +84,7 @@ public class MartQuery { /** * Returns the martService. - * + * * @return the martService. */ public MartService getMartService() { @@ -126,7 +93,7 @@ public class MartQuery { /** * Sets the martService. - * + * * @param martService * the martService to set. */ @@ -136,7 +103,7 @@ public class MartQuery { /** * Returns the query. - * + * * @return the query. */ public Query getQuery() { @@ -145,7 +112,7 @@ public class MartQuery { /** * Sets the query. - * + * * @param query * the query to set. */ @@ -156,7 +123,7 @@ public class MartQuery { /** * Adds the ID that links the specified dataset to the initial dataset. - * + * * @param datasetName * the dataset * @param linkId @@ -168,7 +135,7 @@ public class MartQuery { /** * Removes a dataset and any datasets linked to it. - * + * * @param datasetName * the dataset to remove */ @@ -192,7 +159,7 @@ public class MartQuery { /** * Changes the ID that links a dataset. This method performs no function, * nor does it throw an exception, if the specified dataset does not exist. - * + * * @param datasetName * the dataset * @param linkId @@ -218,7 +185,7 @@ public class MartQuery { /** * Returns the Datasets that this Query contains in the order specified by * the links. - * + * * @return the Datasets that this Query contains in the order specified by * the links */ @@ -257,7 +224,7 @@ public class MartQuery { /** * Returns all the Attributes from all the Datasets in this Query in the * order specified by the links. - * + * * @return all the Attributes from all the Datasets in this Query in the * order specified by the links */ @@ -278,7 +245,7 @@ public class MartQuery { /** * Adds an Attribute to the Dataset with the given datasetName. If the Query * has no Dataset with the given datasetName then a new Dataset is created. - * + * * @param datasetName * the name of the Dataset to add the Attribute to * @param attribute @@ -300,7 +267,7 @@ public class MartQuery { /** * Removes an Attribute from its containing Dataset. - * + * * @param attribute */ public void removeAttribute(Attribute attribute) { @@ -320,7 +287,7 @@ public class MartQuery { /** * Adds a Filter to the Dataset with the given datasetName. If the Query has * no Dataset with the given datasetName then a new Dataset is created. - * + * * @param datasetName * the name of the Dataset to add the Filter to * @param filter @@ -342,7 +309,7 @@ public class MartQuery { /** * Removes a Filter from its containing Dataset. - * + * * @param filter */ public void removeFilter(Filter filter) { http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartRegistry.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartRegistry.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartRegistry.java index 93bf04d..85df4ae 100644 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartRegistry.java +++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartRegistry.java @@ -1,36 +1,3 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: MartRegistry.java,v $ - * Revision $Revision: 1.2 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/12/13 11:38:55 $ - * by $Author: davidwithers $ - * Created on 17-Mar-2006 - *****************************************************************/ package org.biomart.martservice; import java.util.ArrayList; @@ -38,7 +5,7 @@ import java.util.List; /** * The MartRegistry returned by a BioMart web service. - * + * * @author David Withers */ public class MartRegistry { @@ -46,7 +13,7 @@ public class MartRegistry { /** * Returns the martURLLocations. - * + * * @return the martURLLocations. */ public MartURLLocation[] getMartURLLocations() { @@ -56,7 +23,7 @@ public class MartRegistry { /** * Adds a martURLLocation to the registry. - * + * * @param martURLLocations * the martURLLocations to add. */ http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartService.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartService.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartService.java index c02bbb5..c6f4de1 100644 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartService.java +++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartService.java @@ -1,36 +1,3 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: MartService.java,v $errors/failure.html - * Revision $Revision: 1.7 $ - * Release status $State: Exp $ - * Last modified on $Date: 2008/08/11 12:48:29 $ - * by $Author: davidwithers $ - * Created on 17-Mar-2006 - *****************************************************************/ package org.biomart.martservice; import java.io.File; @@ -63,7 +30,7 @@ import org.xml.sax.InputSource; /** * A class for interacting with a BioMart web service. - * + * * @author David Withers */ public class MartService { @@ -102,10 +69,10 @@ public class MartService { /** * Constructs an instance of a <code>MartService</code> with the specified * location. - * + * * The location must be the URL of a valid BioMart MartService, e.g. * http://www.biomart.org/biomart/martservice - * + * * @param location * the URL of the MartService */ @@ -117,10 +84,10 @@ public class MartService { * Returns a <code>MartService</code> for the specified location. If a * <code>MartService</code> does not exist for the location a new one is * constructed. - * + * * The location must be the URL of a valid BioMart MartService, e.g. * http://www.biomart.org/biomart/martservice - * + * * @param location * the URL of the MartService */ @@ -133,7 +100,7 @@ public class MartService { /** * Returns the requestId. - * + * * @return the requestId */ public String getRequestId() { @@ -142,7 +109,7 @@ public class MartService { /** * Sets the requestId. - * + * * @param requestId * the new requestId */ @@ -152,7 +119,7 @@ public class MartService { /** * Returns the cacheDirectory. - * + * * @return the cacheDirectory */ public File getCacheDirectory() { @@ -161,7 +128,7 @@ public class MartService { /** * Sets the cacheDirectory. - * + * * @param cacheDirectory * the new cacheDirectory */ @@ -171,7 +138,7 @@ public class MartService { /** * Returns the URL of the MartService. - * + * * @return the URL of the MartService */ public String getLocation() { @@ -191,7 +158,7 @@ public class MartService { /** * Returns the MartRegistry for this MartService. - * + * * @return the MartRegistry for this MartService * @throws MartServiceException * if the MartService returns an error or is unavailable @@ -214,7 +181,7 @@ public class MartService { /** * Returns all the datasets available from this MartService. - * + * * @return all the datasets available from this MartService. * @throws MartServiceException * if the MartService returns an error or is unavailable @@ -230,7 +197,7 @@ public class MartService { /** * Returns the datasets belonging to the virtualSchema. - * + * * @param virtualSchema * the virtual schema to include datasets from. * @return the datasets belonging to the virtualSchema. @@ -252,7 +219,7 @@ public class MartService { /** * Returns the datasets specified by martURLLocation. - * + * * @param martURLLocation * where to find the datasets. * @return the datasets specified by martURLLocation. @@ -271,7 +238,7 @@ public class MartService { /** * Returns the dataset specified by a virtualSchema and a dataset name. - * + * * @param virtualSchema * the virtualSchema containing the dataset * @param datasetName @@ -295,7 +262,7 @@ public class MartService { /** * Returns the configuration for a dataset. - * + * * @param dataset * the dataset to get the configuration for * @return the configuration for a dataset @@ -398,7 +365,7 @@ public class MartService { /** * Returns the importables for a dataset. - * + * * @param dataset * @return the importables for a dataset * @throws MartServiceException @@ -420,7 +387,7 @@ public class MartService { /** * Returns the exportables for a dataset. - * + * * @param dataset * @return the exportables for a dataset * @throws MartServiceException @@ -443,10 +410,10 @@ public class MartService { /** * Sends a <code>Query</code> to the MartService and returns the results * of executing the query. - * + * * The results are returned as an array of lists; one list for each * attribute specified in the query. - * + * * @param query * the query to execute * @return the results of executing the query @@ -462,12 +429,12 @@ public class MartService { * Sends a <code>Query</code> to the MartService and writes the results to * the <code>ResultReceiver</code> as each line of the result stream is * read. - * + * * @param query * @param resultReceiver * @throws MartServiceException * if the MartService returns an error or is unavailable - * @throws ResultReceiverException + * @throws ResultReceiverException * if the ResultReceiver cannot receive the result * @see ResultReceiver */ @@ -478,7 +445,7 @@ public class MartService { /** * Returns a list of datasets that can be linked to the specified dataset. - * + * * @param martDataset * @return datasets that can be linked to the specified dataset * @throws MartServiceException @@ -520,7 +487,7 @@ public class MartService { /* * (non-Javadoc) - * + * * @see java.lang.Object#equals(java.lang.Object) */ public boolean equals(Object obj) { @@ -538,7 +505,7 @@ public class MartService { /* * (non-Javadoc) - * + * * @see java.lang.Object#hashCode() */ public int hashCode() { http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceException.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceException.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceException.java index f1f0639..a6adb3b 100644 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceException.java +++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceException.java @@ -1,41 +1,8 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: MartServiceException.java,v $ - * Revision $Revision: 1.1 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/01/31 14:12:05 $ - * by $Author: davidwithers $ - * Created on 05-May-2006 - *****************************************************************/ package org.biomart.martservice; /** * Thrown when a MartService is inaccessable or returns an error. - * + * * @author David Withers */ public class MartServiceException extends Exception { @@ -43,7 +10,7 @@ public class MartServiceException extends Exception { /** * Constructs a new exception with no detail message. - * + * */ public MartServiceException() { super(); @@ -51,7 +18,7 @@ public class MartServiceException extends Exception { /** * Constructs a new exception with the specified detail message. - * + * * @param message * the detail message * @param cause @@ -64,7 +31,7 @@ public class MartServiceException extends Exception { /** * Constructs a new exception with the specified detail message and cause. - * + * * @param message * the detail message */ @@ -74,7 +41,7 @@ public class MartServiceException extends Exception { /** * Constructs a new exception with the specified cause. - * + * * @param cause * the cause (a null value is permitted, and indicates that the * cause is nonexistent or unknown) http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceUtils.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceUtils.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceUtils.java index cdcb400..9319cee 100644 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceUtils.java +++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceUtils.java @@ -1,36 +1,3 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: MartServiceUtils.java,v $ - * Revision $Revision: 1.12 $ - * Release status $State: Exp $ - * Last modified on $Date: 2008/07/31 15:06:49 $ - * by $Author: davidwithers $ - * Created on 17-Mar-2006 - *****************************************************************/ package org.biomart.martservice; import java.io.BufferedReader; @@ -73,7 +40,7 @@ import org.xml.sax.InputSource; /** * Utility class for interacting with a BioMart web service. - * + * * @author David Withers */ public class MartServiceUtils { @@ -110,7 +77,7 @@ public class MartServiceUtils { /** * Sends a registry request to the Biomart webservice and constructs a * MartRegistry from the XML returned by the webservice. - * + * * @param martServiceLocation * the URL of the Biomart webservice * @return a MartRegistry @@ -197,7 +164,7 @@ public class MartServiceUtils { * Sends a datasets request to the Biomart webservice and constructs an * array of MartDataset from the tab separated rows of data returned by the * webservice. - * + * * @param martServiceLocation * the URL of the Biomart webservice * @param mart @@ -245,7 +212,7 @@ public class MartServiceUtils { /** * Sends a configuration request to the Biomart webservice and constructs a * DatasetConfig from the XML returned by the webservice. - * + * * @param martServiceLocation * the URL of the Biomart webservice * @param dataset @@ -320,7 +287,7 @@ public class MartServiceUtils { * Sends a query to the Biomart webservice and constructs an array of List * of String results from the tab separated rows of data returned by the * webservice. - * + * * @param martServiceLocation * the URL of the Biomart webservice * @param query @@ -435,7 +402,7 @@ public class MartServiceUtils { } } - + // private static String getLocation(MartURLLocation martUrlLocation) { // StringBuffer location = new StringBuffer("http://";); // location.append(martUrlLocation.getHost()); @@ -443,7 +410,7 @@ public class MartServiceUtils { // location.append(martUrlLocation.getPath()); // return location.toString(); // } - + private static int getAttributeCount(List<Attribute> attributeList) { int result = 0; for (Attribute attribute : attributeList) { @@ -526,10 +493,10 @@ public class MartServiceUtils { } else if ("XLS".equals(formatter)) { mimeType = "'application/excel'"; } - + return mimeType; } - + private static List<String>[] tabSeparatedReaderToResults(Reader reader, int resultsCount) throws IOException { List<String>[] results = new List[resultsCount]; @@ -550,7 +517,7 @@ public class MartServiceUtils { private static Object[] readResult(InputStream inputStream, String formatter) throws IOException { Object[] result = new Object[1]; - + if (getMimeTypeForFormatter(formatter).contains("application/")) { result[0] = IOUtils.toByteArray(inputStream); } else { @@ -558,7 +525,7 @@ public class MartServiceUtils { } return result; } - + private static MartDataset[] tabSeparatedReaderToDatasets(Reader reader, MartURLLocation martURLLocation) throws IOException { List<MartDataset> datasetList = new ArrayList<MartDataset>(); @@ -606,7 +573,7 @@ public class MartServiceUtils { /** * Creates an XML string from a query - * + * * @param query * @return an XML string */ @@ -644,7 +611,7 @@ public class MartServiceUtils { } /** - * + * * @param client */ public static void setProxy(HttpClient client) { http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceXMLHandler.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceXMLHandler.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceXMLHandler.java index e8a5189..c4d3982 100644 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceXMLHandler.java +++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceXMLHandler.java @@ -1,36 +1,3 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: MartServiceXMLHandler.java,v $ - * Revision $Revision: 1.4 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/12/13 11:38:55 $ - * by $Author: davidwithers $ - * Created on 28-Apr-2006 - *****************************************************************/ package org.biomart.martservice; import java.util.Iterator; @@ -43,7 +10,7 @@ import org.jdom.Namespace; /** * Utility class for serializing mart service classes to XML. - * + * * @author David Withers */ public class MartServiceXMLHandler { @@ -105,7 +72,7 @@ public class MartServiceXMLHandler { /** * Converts a <code>MartService</code> to an XML element. - * + * * @param martService * the <code>MartService</code> to serialize * @param namespace @@ -122,7 +89,7 @@ public class MartServiceXMLHandler { /** * Creates a <code>MartService</code> from an XML element. - * + * * @param element * the <code>Element</code> to deserialize * @return a deserialized <code>MartService</code> @@ -134,7 +101,7 @@ public class MartServiceXMLHandler { /** * Converts a <code>MartDataset</code> to an XML element. - * + * * @param dataset * the <code>MartDataset</code> to serialize * @param namespace @@ -167,7 +134,7 @@ public class MartServiceXMLHandler { /** * Creates a <code>MartDataset</code> from an XML element. - * + * * @param element * the <code>Element</code> to deserialize * @param namespace @@ -197,7 +164,7 @@ public class MartServiceXMLHandler { /** * Creates a <code>MartRegistry</code> from an XML element. - * + * * @param element * the <code>Element</code> to deserialize * @param namespace @@ -236,7 +203,7 @@ public class MartServiceXMLHandler { /** * Converts a <code>MartURLLocation</code> to an XML element. - * + * * @param location * the <code>MartURLLocation</code> to serialize * @param namespace @@ -283,7 +250,7 @@ public class MartServiceXMLHandler { /** * Creates a <code>MartURLLocation</code> from an XML element. - * + * * @param element * the <code>Element</code> to deserialize * @return a deserialized <code>MartURLLocation</code> @@ -320,7 +287,7 @@ public class MartServiceXMLHandler { /** * Creates a <code>MartQuery</code> from an XML element. - * + * * @param element * the <code>Element</code> to deserialize * @param namespace @@ -354,7 +321,7 @@ public class MartServiceXMLHandler { /** * Converts a <code>MartQuery</code> to an XML element. - * + * * @param martQuery * the <code>MartQuery</code> to serialize * @param namespace http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartURLLocation.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartURLLocation.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartURLLocation.java index 476956d..6a15aa1 100644 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartURLLocation.java +++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartURLLocation.java @@ -1,36 +1,3 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: MartURLLocation.java,v $ - * Revision $Revision: 1.2 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/10/04 14:15:59 $ - * by $Author: davidwithers $ - * Created on 17-Mar-2006 - *****************************************************************/ package org.biomart.martservice; import org.ensembl.mart.lib.config.MartLocation; @@ -38,7 +5,7 @@ import org.ensembl.mart.lib.config.MartLocation; /** * The MartURLLocation contained by the MartRegistry returned by a BioMart web * service. - * + * * @author David Withers */ public class MartURLLocation implements MartLocation { @@ -90,7 +57,7 @@ public class MartURLLocation implements MartLocation { /** * Returns true if the default flag is set. - * + * * @return true if the default flag is set */ public boolean isDefault() { @@ -99,7 +66,7 @@ public class MartURLLocation implements MartLocation { /** * Sets the default flag. - * + * * @param defaultValue * the value of the default flag */ @@ -109,7 +76,7 @@ public class MartURLLocation implements MartLocation { /** * Returns the displayName. - * + * * @return the displayName. */ public String getDisplayName() { @@ -118,7 +85,7 @@ public class MartURLLocation implements MartLocation { /** * Sets the displayName. - * + * * @param displayName * the displayName to set. */ @@ -128,7 +95,7 @@ public class MartURLLocation implements MartLocation { /** * Returns the host. - * + * * @return the host. */ public String getHost() { @@ -137,7 +104,7 @@ public class MartURLLocation implements MartLocation { /** * Sets the host. - * + * * @param host * the host to set. */ @@ -183,7 +150,7 @@ public class MartURLLocation implements MartLocation { /** * Returns the name - * + * * @return the name. */ public String getName() { @@ -192,7 +159,7 @@ public class MartURLLocation implements MartLocation { /** * Sets the name. - * + * * @param name * the name to set. */ @@ -220,7 +187,7 @@ public class MartURLLocation implements MartLocation { /** * Returns the port. - * + * * @return the port. */ public int getPort() { @@ -229,7 +196,7 @@ public class MartURLLocation implements MartLocation { /** * Sets the port. - * + * * @param port * the port to set. */ @@ -239,7 +206,7 @@ public class MartURLLocation implements MartLocation { /** * Returns the serverVirtualSchema. - * + * * @return the serverVirtualSchema. */ public String getServerVirtualSchema() { @@ -248,7 +215,7 @@ public class MartURLLocation implements MartLocation { /** * Sets the serverVirtualSchema. - * + * * @param serverVirtualSchema * the serverVirtualSchema to set. */ @@ -258,7 +225,7 @@ public class MartURLLocation implements MartLocation { /** * Returns the virtualSchema. - * + * * @return the virtualSchema. */ public String getVirtualSchema() { @@ -267,7 +234,7 @@ public class MartURLLocation implements MartLocation { /** * Sets the virtualSchema. - * + * * @param virtualSchema * the virtualSchema to set. */ @@ -277,7 +244,7 @@ public class MartURLLocation implements MartLocation { /** * Returns true if the location is visible. - * + * * @return Returns the visible. */ public boolean isVisible() { @@ -294,7 +261,7 @@ public class MartURLLocation implements MartLocation { /** * Returns true if this location is redirected. - * + * * @return the redirect */ public boolean isRedirect() { @@ -310,7 +277,7 @@ public class MartURLLocation implements MartLocation { /* * (non-Javadoc) - * + * * @see org.ensembl.mart.lib.config.MartLocation#getType() */ public String getType() { @@ -319,7 +286,7 @@ public class MartURLLocation implements MartLocation { /** * Returns the display name. - * + * * @return the display name */ public String toString() { http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiver.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiver.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiver.java index cc1d062..952899c 100644 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiver.java +++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiver.java @@ -1,61 +1,28 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: ResultReceiver.java,v $ - * Revision $Revision: 1.2 $ - * Release status $State: Exp $ - * Last modified on $Date: 2008/07/31 15:06:49 $ - * by $Author: davidwithers $ - * Created on Jan 18, 2008 - *****************************************************************/ package org.biomart.martservice; /** * An interface for receiving results of a Query. - * + * * @author David Withers */ public interface ResultReceiver { /** * Receives a single row from the results of executing a Query. - * + * * This method will be called frequently and should not block. - * + * * @param resultRow */ public void receiveResult(Object[] resultRow, long index) throws ResultReceiverException; - + /** * Receives an error for a single row from the results of executing a Query. - * + * * This method will be called frequently and should not block. - * + * * @param resultRow */ public void receiveError(String errorMessage, long index) throws ResultReceiverException; - + } http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiverException.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiverException.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiverException.java index c3498e6..6386c9b 100644 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiverException.java +++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiverException.java @@ -1,40 +1,7 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: ResultReceiverException.java,v $ - * Revision $Revision: 1.1 $ - * Release status $State: Exp $ - * Last modified on $Date: 2008/03/04 16:47:57 $ - * by $Author: davidwithers $ - * Created on 05-May-2006 - *****************************************************************/ package org.biomart.martservice; /** - * + * * @author David Withers */ public class ResultReceiverException extends Exception { @@ -42,7 +9,7 @@ public class ResultReceiverException extends Exception { /** * Constructs a new exception with no detail message. - * + * */ public ResultReceiverException() { super(); @@ -50,7 +17,7 @@ public class ResultReceiverException extends Exception { /** * Constructs a new exception with the specified detail message. - * + * * @param message * the detail message * @param cause @@ -63,7 +30,7 @@ public class ResultReceiverException extends Exception { /** * Constructs a new exception with the specified detail message and cause. - * + * * @param message * the detail message */ @@ -73,7 +40,7 @@ public class ResultReceiverException extends Exception { /** * Constructs a new exception with the specified cause. - * + * * @param cause * the cause (a null value is permitted, and indicates that the * cause is nonexistent or unknown) http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/QueryConfigController.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/QueryConfigController.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/QueryConfigController.java index 450b2ba..bd44a7f 100644 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/QueryConfigController.java +++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/QueryConfigController.java @@ -1,36 +1,3 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: QueryConfigController.java,v $ - * Revision $Revision: 1.4 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/12/13 11:38:57 $ - * by $Author: davidwithers $ - * Created on 27-Mar-2006 - *****************************************************************/ package org.biomart.martservice.config; import java.util.HashMap; @@ -52,7 +19,7 @@ import org.ensembl.mart.lib.config.FilterDescription; /** * Controls the interaction between graphical <code>QueryComponent</code>s * and <code>Query</code>s. - * + * * @author David Withers */ public class QueryConfigController { @@ -77,7 +44,7 @@ public class QueryConfigController { /** * Constructs an instance of a <code>QueryConfigController</code>. - * + * * @param martQuery */ public QueryConfigController(MartQuery martQuery) { @@ -97,7 +64,7 @@ public class QueryConfigController { /* * (non-Javadoc) - * + * * @see java.lang.Object#finalize() */ protected void finalize() throws Throwable { @@ -107,7 +74,7 @@ public class QueryConfigController { /** * Returns the <code>MartQuery</code> under control. - * + * * @return the <code>MartQuery</code> under control */ public MartQuery getMartQuery() { @@ -116,7 +83,7 @@ public class QueryConfigController { /** * Removes a <code>QueryComponent</code> from the controller. - * + * * @param queryComponent * the <code>QueryComponent</code> to remove */ @@ -126,11 +93,11 @@ public class QueryConfigController { /** * Registers a <code>QueryComponent</code> with the controller. - * + * * If the <code>Query</code> already contains an <code>Attribute</code> * or <code>Filter</code> with the corresponding name the * <code>QueryComponent</code> is set as selected. - * + * * @param queryComponent * the <code>QueryComponent</code> to register */ @@ -182,7 +149,7 @@ public class QueryConfigController { * Returns the <code>Attribute</code> mapped to the * <code>QueryComponent</code>. If no <code>Attribute</code> is mapped * a new <code>Attribute</code> is created and added to the map. - * + * * @param queryComponent * @return */ @@ -205,7 +172,7 @@ public class QueryConfigController { * Returns the <code>Filter</code> mapped to the * <code>QueryComponent</code>. If no <code>Filter</code> is mapped a * new <code>Filter</code> is created and added to the map. - * + * * @param queryComponent * @return */ @@ -250,7 +217,7 @@ public class QueryConfigController { /* * (non-Javadoc) - * + * * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentListener#attributeAdded(org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentEvent) */ public void attributeAdded(QueryComponentEvent event) { @@ -264,7 +231,7 @@ public class QueryConfigController { /* * (non-Javadoc) - * + * * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentListener#attributeRemoved(org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentEvent) */ public void attributeRemoved(QueryComponentEvent event) { @@ -278,7 +245,7 @@ public class QueryConfigController { /* * (non-Javadoc) - * + * * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentListener#filterAdded(org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentEvent) */ public void filterAdded(QueryComponentEvent event) { @@ -292,7 +259,7 @@ public class QueryConfigController { /* * (non-Javadoc) - * + * * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentListener#filterRemoved(org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentEvent) */ public void filterRemoved(QueryComponentEvent event) { @@ -306,7 +273,7 @@ public class QueryConfigController { /* * (non-Javadoc) - * + * * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentListener#filterChanged(org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentEvent) */ public void filterChanged(QueryComponentEvent event) { @@ -320,7 +287,7 @@ public class QueryConfigController { /* * (non-Javadoc) - * + * * @see org.biomart.martservice.config.event.QueryComponentListener#linkAdded(org.biomart.martservice.config.event.QueryComponentEvent) */ public void linkAdded(QueryComponentEvent event) { @@ -329,7 +296,7 @@ public class QueryConfigController { /* * (non-Javadoc) - * + * * @see org.biomart.martservice.config.event.QueryComponentListener#linkRemoved(org.biomart.martservice.config.event.QueryComponentEvent) */ public void linkRemoved(QueryComponentEvent event) { @@ -338,7 +305,7 @@ public class QueryConfigController { /* * (non-Javadoc) - * + * * @see org.biomart.martservice.config.QueryComponentListener#linkChanged(org.biomart.martservice.config.QueryComponentEvent) */ public void linkChanged(QueryComponentEvent event) { @@ -385,4 +352,4 @@ public class QueryConfigController { } -} \ No newline at end of file +}
