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bbimberbbimber
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Finalize implementation of fields/groups provider (#209)
* Use JBrowse fields API to drive details popup and restore VariantTable
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-822
lines changed

‎Studies/api-src/org/labkey/api/studies/StudiesService.java‎

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@@ -0,0 +1,28 @@
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package org.labkey.api.studies;
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import org.labkey.api.data.Container;
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import org.labkey.api.module.Module;
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import org.labkey.api.security.User;
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import org.labkey.api.util.Path;
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import java.io.IOException;
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/**
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* Created by bimber on 11/3/2016.
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*/
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abstract public class StudiesService
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{
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static StudiesService _instance;
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public static StudiesService get()
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{
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return _instance;
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}
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static public void setInstance(StudiesService instance)
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{
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_instance = instance;
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}
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abstract public void importFolderDefinition(Container container, User user, Module m, Path sourceFolderDirPath) throws IOException;
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}

‎Studies/src/org/labkey/studies/StudiesModule.java‎

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Original file line numberDiff line numberDiff line change
@@ -5,6 +5,7 @@
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import org.labkey.api.data.Container;
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import org.labkey.api.module.DefaultModule;
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import org.labkey.api.module.ModuleContext;
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import org.labkey.api.studies.StudiesService;
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import org.labkey.api.view.WebPartFactory;
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import java.util.Collection;
@@ -44,6 +45,8 @@ protected Collection<WebPartFactory> createWebPartFactories()
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protected void init()
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{
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addController(StudiesController.NAME, StudiesController.class);
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StudiesService.setInstance(StudiesServiceImpl.get());
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}
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@Override

‎Studies/src/org/labkey/studies/StudiesServiceImpl.java‎

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package org.labkey.studies;
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import org.apache.logging.log4j.Logger;
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import org.labkey.api.admin.ImportOptions;
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import org.labkey.api.data.Container;
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import org.labkey.api.module.Module;
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import org.labkey.api.pipeline.PipeRoot;
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import org.labkey.api.pipeline.PipelineService;
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import org.labkey.api.resource.DirectoryResource;
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import org.labkey.api.resource.Resource;
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import org.labkey.api.security.User;
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import org.labkey.api.studies.StudiesService;
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import org.labkey.api.util.FileUtil;
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import org.labkey.api.util.Path;
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import org.labkey.api.util.logging.LogHelper;
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import java.io.FileNotFoundException;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.OutputStream;
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import java.nio.file.Files;
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public class StudiesServiceImpl extends StudiesService
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{
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private static final StudiesServiceImpl _instance = new StudiesServiceImpl();
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private static final Logger _log = LogHelper.getLogger(StudiesServiceImpl.class, "StudiesService messages");
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public static StudiesServiceImpl get()
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{
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return _instance;
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}
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private StudiesServiceImpl()
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{
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}
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@Override
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public void importFolderDefinition(Container container, User user, Module m, Path sourceFolderDirPath) throws IOException
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{
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Resource root = m.getModuleResource(sourceFolderDirPath);
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PipeRoot pipeRoot = PipelineService.get().findPipelineRoot(container);
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java.nio.file.Path pipeRootPath = pipeRoot.getRootNioPath();
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java.nio.file.Path folderXmlPath;
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if (root instanceof DirectoryResource && ((DirectoryResource)root).getDir().equals(pipeRootPath.toFile()))
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{
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// The pipeline root is already pointed at the folder definition, like it might be on a dev machine.
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// No need to copy, especially since copying can cause infinite recursion when the paths are nested
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folderXmlPath = pipeRootPath.resolve("folder.xml");
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}
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else
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{
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java.nio.file.Path folderPath = pipeRootPath.resolve("moduleFolderImport");
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folderXmlPath = folderPath.resolve("folder.xml");
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if (Files.exists(folderPath))
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{
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FileUtil.deleteDir(folderPath);
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}
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copyResourceToPath(root, folderPath);
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}
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if (!Files.exists(folderXmlPath))
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{
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throw new FileNotFoundException("Couldn't find an extracted " + folderXmlPath);
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}
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ImportOptions options = new ImportOptions(container.getId(), user.getUserId());
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options.setSkipQueryValidation(true);
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PipelineService.get().runFolderImportJob(container, user, null, folderXmlPath, "folder.xml", pipeRoot, options);
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}
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private void copyResourceToPath(Resource resource, java.nio.file.Path target) throws IOException
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{
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if (resource.isCollection())
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{
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Files.createDirectory(target);
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for (Resource child : resource.list())
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{
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java.nio.file.Path childTarget = target.resolve(child.getName());
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copyResourceToPath(child, childTarget);
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}
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}
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else
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{
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try (InputStream in = resource.getInputStream();
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OutputStream out = Files.newOutputStream(target))
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{
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FileUtil.copyData(in, out);
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}
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}
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}
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}

‎jbrowse/api-src/org/labkey/api/jbrowse/GroupsProvider.java‎

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Original file line numberDiff line numberDiff line change
@@ -4,11 +4,10 @@
44
import org.labkey.api.data.Container;
55
import org.labkey.api.security.User;
66

7-
import java.util.Set;
7+
import java.util.List;
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99
public interface GroupsProvider
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{
11-
@Nullable Set<String> getGroupMembers(String groupName, Container c, User u);
12-
boolean hasGroup(String groupName, Container c, User u);
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@Nullable List<String> getGroupMembers(String trackId, String groupName, Container c, User u);
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boolean isAvailable(Container c, User u);
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}

‎jbrowse/api-src/org/labkey/api/jbrowse/JBrowseFieldCustomizer.java‎

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@@ -4,7 +4,7 @@
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import org.labkey.api.security.User;
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66
public interface JBrowseFieldCustomizer {
7-
public void customizeField(JBrowseFieldDescriptor field);
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public void customizeField(JBrowseFieldDescriptor field, Container c, User u);
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public boolean isAvailable(Container c, User u);
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}

‎jbrowse/api-src/org/labkey/api/jbrowse/JBrowseFieldDescriptor.java‎

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@@ -11,17 +11,19 @@ public class JBrowseFieldDescriptor {
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private final String _fieldName;
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private final VCFHeaderLineType _type;
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private String _label;
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private final String _description;
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private final boolean _isInDefaultColumns;
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private final boolean _isIndexed;
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private String _description;
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private boolean _isInDefaultColumns;
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private boolean _isIndexed;
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private boolean _isMultiValued = false;
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private List<String> _allowableValues = null;
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private boolean _isHidden = false;
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private String _colWidth = null;
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private Integer _orderKey = null;
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private Integer _orderKey = 8;
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// NOTE: this should support "jexl:xxxxxx" syntax, like other JBrowse formatting
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private String _formatString = null;
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private String _category = null;
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private String _url = null;
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public JBrowseFieldDescriptor(String luceneFieldName, @Nullable String description, boolean isInDefaultColumns, boolean isIndexed, VCFHeaderLineType type, Integer orderKey) {
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_fieldName = luceneFieldName;
@@ -49,7 +51,14 @@ public JBrowseFieldDescriptor formatString(String formatString) {
4951
}
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public JBrowseFieldDescriptor allowableValues(List<String> allowableValues) {
52-
_allowableValues = Collections.unmodifiableList(allowableValues);
54+
_allowableValues = allowableValues == null ? null : Collections.unmodifiableList(allowableValues);
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// Only change the value if we are certain there are multiple values:
57+
if (_allowableValues != null && !_allowableValues.isEmpty())
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{
59+
_isMultiValued = true;
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}
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return this;
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}
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@@ -103,6 +112,21 @@ public void setLabel(String label) {
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_label = label;
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}
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public void setInDefaultColumns(boolean inDefaultColumns)
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{
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_isInDefaultColumns = inDefaultColumns;
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}
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public void setCategory(String category)
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{
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_category = category;
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}
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public void setUrl(String url)
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{
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_url = url;
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}
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106130
public void setMultiValued(boolean multiValued) {
107131
_isMultiValued = multiValued;
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}
@@ -111,6 +135,10 @@ public void setHidden(boolean hidden) {
111135
_isHidden = hidden;
112136
}
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138+
public void setIndexed(boolean indexed) {
139+
_isIndexed = indexed;
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}
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public void setColWidth(String colWidth) {
115143
_colWidth = colWidth;
116144
}
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119147
_orderKey = orderKey;
120148
}
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150+
public void setAllowableValues(List<String> allowableValues)
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{
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_allowableValues = allowableValues;
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}
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public void setFormatString(String formatString)
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{
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_formatString = formatString;
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}
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public void setDescription(String description)
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{
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_description = description;
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}
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public JSONObject toJSON() {
123166
JSONObject fieldDescriptorJSON = new JSONObject();
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fieldDescriptorJSON.put("name", _fieldName);
@@ -133,6 +176,8 @@ public JSONObject toJSON() {
133176
fieldDescriptorJSON.put("formatString", _formatString);
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fieldDescriptorJSON.put("orderKey", _orderKey);
135178
fieldDescriptorJSON.put("allowableValues", _allowableValues);
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fieldDescriptorJSON.put("category", _category);
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fieldDescriptorJSON.put("url", _url);
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137182
return fieldDescriptorJSON;
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}

‎jbrowse/package-lock.json‎

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‎jbrowse/package.json‎

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"@jbrowse/plugin-linear-genome-view": "^1.7.4",
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"@jbrowse/react-linear-genome-view": "^1.7.4",
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"@labkey/api": "^1.21.0",
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"@labkey/components": "^2.345.0",
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"@labkey/components": "^2.351.0",
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"@gmod/vcf": "^5.0.6",
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"react": "^16.14.0",
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"assert": "^2.0.0",

‎jbrowse/resources/external/mGAPSession.json‎

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{
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"type": "ExtendedVariantTrack",
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"trackId": "mgap_hg38",
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"name": "mgap",
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"name": "mGAP",
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"assemblyNames": [
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"hg38"
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],

‎jbrowse/src/client/JBrowse/Browser/Browser.tsx‎

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import JBrowseFooter from './components/JBrowseFooter';
99
import { ErrorBoundary } from '@labkey/components';
1010
import { fetchSession } from '../utils';
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import JBrowseFilterPanel from './components/JBrowseFilterPanel';
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const nativePlugins = [ExtendedVariantPlugin, LogSession]
1314
const refTheme = createTheme()
@@ -39,20 +40,22 @@ function View(){
3940
}, []);
4041

4142
if (session === null){
42-
return(<p>Error - no session provided.</p>)
43+
return (<p>Error - no session provided.</p>)
4344
}
4445
else if (state === null){
4546
return (<p>Loading...</p>)
4647
}
4748
else if (state == "invalid") {
4849
return (<p>Error fetching config. See console for more details</p>)
4950
}
51+
5052
return (
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//TODO: can we make this expand to full page height?
5254
<div style={{height: "100%"}}>
5355
<ErrorBoundary>
5456
<JBrowseLinearGenomeView viewState={state as ViewModel} />
5557
<JBrowseFooter viewState={state} bgColor={bgColor}/>
58+
<JBrowseFilterPanel session={state.session}/>
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</ErrorBoundary>
5760
</div>
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)

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