Changeset 106 for branches/omero
- Timestamp:
- 06/13/05 15:16:45 (4 years ago)
- Location:
- branches/omero
- Files:
-
- 8 added
- 13 modified
-
components/client/project.xml (modified) (1 diff)
-
components/common/project.xml (modified) (1 diff)
-
components/server/.classpath (modified) (1 diff)
-
components/server/maven.xml (modified) (2 diffs)
-
components/server/project.properties (modified) (1 diff)
-
components/server/project.xml (modified) (3 diffs)
-
components/server/sql (added)
-
components/server/sql/constraints.sql (added)
-
components/server/sql/db-export.xml (added)
-
components/server/sql/tables.sql (added)
-
components/server/src/org/openmicroscopy/omero/logic/ContainerDaoHibernate.java (modified) (1 diff)
-
components/server/src/org/openmicroscopy/omero/logic/queries.hbm.xml (modified) (2 diffs)
-
components/server/test/WEB-INF (added)
-
components/server/test/WEB-INF/test (added)
-
components/server/test/org/openmicroscopy/omero/server/utests/HierarchyBrowsingDbUnitTest.java (added)
-
components/server/web/WEB-INF/config-test.xml (modified) (1 diff)
-
components/shoola-adapter/project.xml (modified) (1 diff)
-
components/test/project.xml (modified) (1 diff)
-
docs/block-diagram.svg (added)
-
maven.xml (modified) (1 diff)
-
project.xml (modified) (1 diff)
Legend:
- Unmodified
- Added
- Removed
-
branches/omero/components/client/project.xml
r103 r106 24 24 <artifactId>spring-mock</artifactId> 25 25 <version>1.2.1</version> 26 </dependency>27 <dependency>28 <groupId>commons-logging</groupId>29 <artifactId>commons-logging</artifactId>30 <version>1.0.4</version>31 26 </dependency> 32 27 <dependency> -
branches/omero/components/common/project.xml
r104 r106 31 31 </dependency> 32 32 <dependency> 33 <groupId>commons-lang</groupId>34 <artifactId>commons-lang</artifactId>35 <version>2.0</version>36 </dependency>37 <dependency>38 <groupId>commons-logging</groupId>39 <artifactId>commons-logging</artifactId>40 <version>1.0.4</version>41 </dependency>42 <dependency>43 33 <groupId>postgresql</groupId> 44 34 <artifactId>postgresql</artifactId> -
branches/omero/components/server/.classpath
r105 r106 11 11 <classpathentry kind="var" path="MAVEN_REPO/acegisecurity/jars/acegi-security-0.8.2.jar"/> 12 12 <classpathentry kind="var" path="MAVEN_REPO/hessian/jars/hessian-2.1.12.jar"/> 13 <classpathentry kind="var" path="MAVEN_REPO/hibernate/jars/hibernate-3.0.5.jar"/>13 <classpathentry sourcepath="HOME/lib/hibernate-3.0.5/src" kind="var" path="MAVEN_REPO/hibernate/jars/hibernate-3.0.5.jar"/> 14 14 <classpathentry kind="var" path="MAVEN_REPO/omero/jars/jta-hibernate.jar"/> 15 15 <classpathentry kind="var" path="MAVEN_REPO/omero/jars/asm-hibernate.jar"/> -
branches/omero/components/server/maven.xml
r102 r106 22 22 </goal> 23 23 24 <goal name="db-load"> 25 <attainGoal name="dbunit"/> 24 <goal name="db-load" prereqs="dbunit"> 26 25 <ant:property name="operation" value="CLEAN_INSERT"/> 27 <ant:property name="file" value=" db-export.xml"/>28 <ant:dbunit driver="${database.driver _class}"26 <ant:property name="file" value="sql/db-export.xml"/> 27 <ant:dbunit driver="${database.driver}" 29 28 supportBatchStatement="false" 30 url="${database.url} "29 url="${database.url}-test" 31 30 userid="${database.username}" 32 31 password="${database.password}"> … … 36 35 </goal> 37 36 38 <goal name="db-export"> 39 <attainGoal name="dbunit"/> 37 <goal name="db-export" prereqs="dbunit"> 40 38 <ant:dbunit driver="${database.driver}" 41 39 url="${database.url}" 42 40 userid="${database.username}" 43 41 password="${database.password}"> 44 <ant:export dest="db-export.xml" format="xml"/> 42 <ant:export dest="sql/db-export.xml" format="xml"> 43 <!--remove elements for all--> 44 <!-- <ant:query name="images" 45 sql="select * from images where image_id < 46 10"/>--> 47 <!-- This list comes from the middlegen-build.xml file --> 48 <ant:query name="module_executions" 49 sql="select * from module_executions where module_execution_id in 50 ${mex} ;"/> 51 <ant:query name="projects" 52 sql="select * from projects where project_id in ${prj};"/> 53 <ant:query name="datasets" 54 sql="select * from datasets where dataset_id in ${ds};"/> 55 <ant:query name="project_dataset_map" 56 sql="select * from project_dataset_map where project_id in ${prj} or 57 dataset_id in ${ds}"/> 58 <ant:query name="image_dataset_map" 59 sql="select * from image_dataset_map where image_id in ${img} or 60 dataset_id in ${ds}"/> 61 <ant:table name="image_dataset_map"/> 62 <ant:query name="images" 63 sql="select * from images where image_id in ${img} ;"/> 64 <ant:table name="experimenters"/> 65 <ant:table name="experimenter_group_map"/> 66 <ant:table name="groups"/> 67 <ant:table name="classification"/> 68 <ant:table name="categories"/> 69 <ant:table name="category_groups"/> 70 <ant:table name="dataset_annotations"/> 71 <ant:table name="image_annotations"/> 72 <ant:query name="image_dimensions" 73 sql="select * from image_dimensions where image_id in ${img} ;"/> 74 <ant:query name="image_pixels" 75 sql="select * from image_pixels where image_id in ${img} ;"/> 76 <ant:table name="image_info"/> 77 <ant:table name="image_plates"/> 78 <ant:table name="thumbnails"/> 79 <ant:table name="repositories"/> 80 <ant:table name="display_roi"/> 81 <!-- 82 <ant:table name="channel_components"/> 83 <ant:table name="features"/> 84 <ant:table name="display_options"/> 85 --> 86 </ant:export> 45 87 </ant:dbunit> 46 88 </goal> -
branches/omero/components/server/project.properties
r100 r106 21 21 #maven.jam.master.ignoreFailures=false 22 22 23 24 mex=(1192, 1431, 1485, 1490, 1491, 1496, 1498, 1612, 1613, 1617, 1711, 1712, 1713, 1971, 1985, 1988, 1996, 2004, 2005, 2006, 2027, 2029, 2030, 2033, 2044, 2050, 2257, 2258, 2259, 2302, 2567, 2583, 3217, 3316, 3322, 3323, 3338, 3623, 17696, 18055, 18056, 18057, 18058, 18059, 18060, 18061, 18062, 18063, 18162, 18249, 18250, 18251, 18252, 18253, 18581, 18582, 18596, 18605, 19070, 19071, 19072, 19073, 19382, 19383, 19844, 22060, 22061, 22062, 22063, 22064, 22065, 22066, 22067, 23205, 23206, 23207, 23209, 23210, 23212, 23217, 23218, 23220) 25 prj=(63,64,59) 26 ds=(115,120,124,125) 27 img=(296, 313, 340, 357, 485, 558, 4391, 4446, 4507, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 51, 54, 56, 60, 73, 363, 369, 370, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480, 481, 482, 483, 484, 485, 486, 487, 488, 489, 490, 491, 492, 493, 494, 495, 496, 746, 747, 748, 749, 750, 751, 752, 753, 754, 755, 756, 757, 758, 759, 760, 761, 762, 763, 764, 765, 766, 767, 768, 769, 770, 771, 772, 773, 774, 775, 776, 777, 778, 779, 780, 781, 782, 4373, 4374, 4375, 4376, 4377, 4378, 4379, 4380, 4381, 4382, 4383, 4384, 4385, 4386, 4387, 4388, 4389, 4390, 4409, 4415, 4431, 4434, 4446, 4447, 4458, 4459, 4462, 4463, 4470, 4479, 4485, 4486, 4487, 4489, 4490, 4492, 4493, 4494, 4495, 4496, 4497, 4498, 4499, 4500, 4503, 4505, 4506, 4507, 4508, 4509, 4510, 4511, 4512, 4516, 4517, 4518, 4521, 4522, 4523, 4524, 4526, 4527, 4528, 4529, 5210, 5212, 5213, 5214, 5218, 5219) -
branches/omero/components/server/project.xml
r102 r106 179 179 </dependency> 180 180 <dependency> 181 <groupId>commons-lang</groupId>182 <artifactId>commons-lang</artifactId>183 <version>2.0</version>184 </dependency>185 <dependency>186 181 <groupId>commons-pool</groupId> 187 182 <artifactId>commons-pool</artifactId> … … 196 191 <artifactId>commons-dbcp</artifactId> 197 192 <version>1.2.1</version> 198 <type>jar</type>199 <properties>200 <war.bundle>true</war.bundle>201 </properties>202 </dependency>203 <dependency>204 <groupId>commons-logging</groupId>205 <artifactId>commons-logging</artifactId>206 <version>1.0.4</version>207 193 <type>jar</type> 208 194 <properties> … … 276 262 </includes> 277 263 </resource> 264 <resource> 265 <directory>test</directory> 266 <includes> 267 <include>**/*.xml</include> 268 </includes> 269 </resource> 278 270 </resources> 279 271 </build> -
branches/omero/components/server/src/org/openmicroscopy/omero/logic/ContainerDaoHibernate.java
r104 r106 68 68 arg0.getPackage().getName().length() + 1); 69 69 70 Query q = session.getNamedQuery("loadHierarchy_by_" + klass); 70 Query q = session.getNamedQuery("loadHierarchy_by_" + klass); 71 71 q.setLong("id", arg1); 72 72 return q.uniqueResult(); -
branches/omero/components/server/src/org/openmicroscopy/omero/logic/queries.hbm.xml
r105 r106 3 3 "-//Hibernate/Hibernate Mapping DTD 3.0//EN" 4 4 "http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd" > 5 5 6 6 <hibernate-mapping> 7 7 <!-- load*Hierarchy 8 8 TODO if all ids where called *.getId() then we could merge these 9 9 --> 10 10 <!--TODO need to add default_pixel once FK from Ilya --> 11 <!--TODO some way to DRY here would be great --> 11 12 <query name="loadHierarchy_by_Project"><![CDATA[ 12 from Project as p join fetch p.experimenter 13 where p.projectId = :id 13 from Project as p 14 left outer join fetch p.experimenter as p_e 15 left outer join fetch p.group as p_g 16 left outer join fetch p.datasets as d 17 left outer join fetch d.experimenter as d_e 18 left outer join fetch d.group as d_g 19 left outer join fetch d.images as i 20 left outer join fetch i.group as i_g 21 left outer join fetch i.experimenter as i_e 22 where p.projectId = :id 14 23 ]]></query> 15 24 16 25 <query name="loadHierarchy_by_Dataset"><![CDATA[ 17 from Dataset as d join fetch d.experimenter join fetch d.images as img 18 where d.datasetId = :id 26 from Dataset as d 27 left outer join fetch d.experimenter as d_e 28 left outer join fetch d.group as d_g 29 left outer join fetch d.images as i 30 left outer join fetch i.group as i_g 31 left outer join fetch i.experimenter as i_e 32 where d.datasetId = :id 19 33 ]]></query> 20 34 21 35 <query name="loadHierarchy_by_CategoryGroup"><![CDATA[ 22 from CategoryGroup cg join fetch cg.moduleExecution as mex join fetch mex.experimenter as exp 23 where cg.attributeId = :id 36 from CategoryGroup cg 37 left outer join fetch cg.moduleExecution as cg_mex 38 left outer join fetch cg_mex.experimenter as cg_exp 39 left outer join fetch cg_mex.categories as c 40 left outer join fetch c.moduleExecution as c_mex 41 left outer join fetch c_mex.experimenter as c_exp 42 left outer join fetch c_mex.classifications as cla 43 left outer join fetch cla.moduleExecution as cla_mex 44 left outer join fetch cla_mex.experimenter as cla_exp 45 left outer join fetch cla.image as i 46 where cg.attributeId = :id 24 47 ]]></query> 25 48 26 49 <query name="loadHierarchy_by_Category"><![CDATA[ 27 from Category c join fetch c.moduleExecution as mex join fetch mex.experimenter as exp 28 where c.attributeId = :id 50 from Category c 51 left outer join fetch c.moduleExecution as c_mex 52 left outer join fetch c_mex.experimenter as c_exp 53 left outer join fetch c_mex.classifications as cla 54 left outer join fetch cla.moduleExecution as cla_mex 55 left outer join fetch cla_mex.experimenter as cla_exp 56 left outer join fetch cla.image as i 57 where c.attributeId = :id 29 58 ]]></query> 30 59 … … 32 61 <query name="findPDI"><![CDATA[ 33 62 from Image as i 34 left outer join fetch i.datasets as ds 35 left outer join fetch ds.projects as prj 36 where i in (:img_list) 63 left outer join fetch i.datasets as d 64 left outer join fetch d.experimenter as d_exp 65 left outer join fetch d.group as d_g 66 left outer join fetch d.projects as p 67 left outer join fetch p.experimenter as p_exp 68 left outer join fetch p.group as p_g 69 where i in (:img_list) 37 70 ]]></query> 38 71 72 <!-- this is standard style temporarily using theta style 39 73 <query name="findCGCI"><![CDATA[ 40 from Image as i join fetch i.classifications as cla 41 where i in (:img_list) 42 and cla.valid = true 74 from Image as i 75 left outer join fetch i.classifications as cla 76 left outer join fetch cla.category as c 77 left outer join fetch c.moduleExecution as c_mex 78 left outer join fetch c_mex.experimenter as c_exp 79 left outer join fetch c.categoryGroup as cg 80 left outer join fetch cg.moduleExecution as cg_mex 81 left outer join fetch cg_mex.experimenter as cg_exp 82 where i in (:img_list) 83 and cla.valid = true 43 84 ]]></query> 44 85 --> 86 <query name="findCGCI"><![CDATA[ 87 from Image as i 88 left outer join fetch i.classifications as cla 89 where i in (:img_list) 90 and cla.valid = true 91 ]]></query> 92 45 93 <!-- findAnnotations --> 46 94 <query name="findImageAnn"><![CDATA[ 47 from ImageAnnotation as ann join fetch ann.image as i 48 where ann.image in (:img_list) 49 and ann.valid = true 95 from ImageAnnotation as ann 96 left outer join fetch ann.image as i 97 left outer join fetch ann.moduleExecution as ann_mex 98 left outer join fetch ann_mex.experimenter as ann_exp 99 where ann.image in (:img_list) 100 and ann.valid = true 50 101 ]]></query> 51 102 52 103 <query name="findImageAnnWithID"><![CDATA[ 53 from ImageAnnotation as ann join fetch ann.image as i 54 where ann.image in (:img_list) 55 and ann.valid = true 56 and ann.moduleExecution.experimenter = :expId 104 from ImageAnnotation as ann 105 left outer join fetch ann.image as i 106 left outer join fetch ann.moduleExecution as ann_mex 107 left outer join fetch ann_mex.experimenter as ann_exp 108 where ann.image in (:img_list) 109 and ann.valid = true 110 and ann_exp = :expId 57 111 ]]></query> 58 112 59 113 <query name="findDatasetAnn"><![CDATA[ 60 from DatasetAnnotation as ann join fetch ann.dataset as d 61 where ann.dataset in (:ds_list) 62 and ann.valid = true 114 from DatasetAnnotation as ann 115 left outer join fetch ann.dataset as d 116 left outer join fetch ann.moduleExecution as ann_mex 117 left outer join fetch ann_mex.experimenter as ann_exp 118 where ann.dataset in (:ds_list) 119 and ann.valid = true 63 120 ]]></query> 64 121 65 122 <query name="findDatasetAnnWithID"><![CDATA[ 66 from DatasetAnnotation as ann join fetch ann.dataset as d 67 where ann.dataset in (:ds_list) 68 and ann.valid = true 69 and ann.moduleExecution.experimenter = :expId 123 from DatasetAnnotation as ann 124 left outer join fetch ann.dataset as d 125 left outer join fetch ann.moduleExecution as ann_mex 126 left outer join fetch ann_mex.experimenter as ann_exp 127 where d in (:ds_list) 128 and ann.valid = true 129 and ann_exp = :expId 70 130 ]]></query> 71 131 72 <!--73 from A a left join fetch a.bs74 from C c left join fetch c.ds where c.id in (:cids)75 from D d left join fetch d.es where d.id in (:dids)76 77 Or maybe:78 79 from A a80 left join fetch a.bs81 where a.xyz = 'foo'82 83 from A a84 left join a.bs b85 left join b.c c86 left join fetch c.ds87 where a.xyz = 'foo'88 89 from A a90 left join a.bs b91 left join b.c c92 left join c.ds d93 left join fetch d.es94 where a.xyz = 'foo'95 96 from Image i left join fetch i.datasets97 from Image i left join i.datsets as d left join fetch d.projects98 99 -->100 101 102 103 132 </hibernate-mapping> -
branches/omero/components/server/web/WEB-INF/config-test.xml
r104 r106 55 55 <!-- Add this config file to the getConfigLocations() of your tests 56 56 if you want data and interfaces injected --> 57 <!-- TODO this needs to be somewhere else 57 58 <bean id="data" class="org.openmicroscopy.omero.tests.OMEPerformanceData" init-method="init"> 58 59 <property name="dataSource" ref="dataSource"/> 59 60 </bean> 61 --> 60 62 61 63 </beans> -
branches/omero/components/shoola-adapter/project.xml
r103 r106 30 30 <version>2.4.0</version> 31 31 </dependency> 32 <dependency>33 <groupId>commons-logging</groupId>34 <artifactId>commons-logging</artifactId>35 <version>1.0.4</version>36 </dependency>37 <dependency>38 <groupId>commons-lang</groupId>39 <artifactId>commons-lang</artifactId>40 <version>2.0</version>41 </dependency>42 32 43 33 </dependencies> -
branches/omero/components/test/project.xml
r105 r106 34 34 <artifactId>spring-mock</artifactId> 35 35 <version>1.2.1</version> 36 </dependency>37 <dependency>38 <groupId>commons-logging</groupId>39 <artifactId>commons-logging</artifactId>40 <version>1.0.4</version>41 </dependency>42 <dependency>43 <groupId>commons-lang</groupId>44 <artifactId>commons-lang</artifactId>45 <version>2.0</version>46 36 </dependency> 47 37 <dependency> -
branches/omero/maven.xml
r102 r106 43 43 <ant:mkdir dir="${maven.build.dest}"/> 44 44 <ant:propertyfile 45 comment=" Database and Server properties generated from build 46 properties TODO remove from svn" 47 file="${basedir}/src/spring.properties"> 45 comment=" DO NOT EDIT: Generated Database and Server properties from build.properties" 46 file="${basedir}/src/spring.properties"> 48 47 <ant:entry key="database.driver" value="${database.driver}"/> 49 48 <ant:entry key="database.url" value="${database.url}"/> -
branches/omero/project.xml
r98 r106 42 42 <type>plugin</type> 43 43 </depdendency> 44 <depdendency> 45 <groupId>maven-plugins</groupId> 46 <artifactId>maven-dbunit-plugin</artifactId> 47 <version>1.5</version> 48 <type>plugin</type> 49 </depdendency> 50 <dependency> 51 <groupId>commons-lang</groupId> 52 <artifactId>commons-lang</artifactId> 53 <version>2.0</version> 54 <properties> 55 <war.bundle>true</war.bundle> 56 </properties> 57 </dependency> 58 <dependency> 59 <groupId>commons-logging</groupId> 60 <artifactId>commons-logging</artifactId> 61 <version>1.0.4</version> 62 <properties> 63 <war.bundle>true</war.bundle> 64 </properties> 65 </dependency> 44 66 </dependencies> 45 67 <reports>
