- Assigning significance to genetics variants is often a challenge, and this is particularly problematic for model organisms like macaques,
- which has far less developed annotation resources than human.
- To overcome this, we developed a multi-part process to annotate our data.
-
-
+
+
+
+
+ Assigning significance to genetics variants is often a challenge, and this is particularly problematic for model organisms like macaques,
+ which have few sources of genomic annotations, relative to human or mouse.
+ To overcome this, we developed a multipart process to annotate our data.
NHP data are aligned to the latest NCBI genomic build for the species.
+ We use liftOver tools to lift variants to the human genome (GRCh37), with ~65% of variants typically being successfully lifted. These variants are annotated using a variety of human data sources, described below.
+ These annotated variants are translated back to genomic coordinates of the NHP species, and all data sources merged. In addition to human annotations, SnpEff is used to annotate predicted impact on protein coding (run using the Ensembl gene build).
+
+
+ Our annotation sources are drawn from a number of databases and tools. A complete field-by-field list is shown in the table at the bottom of the page. Please note that in most cases the 'Data Source' column is a link to the primary data, which may have more information on that annotation.
+
+
+
+
+
+
+
+
+
+
+
diff --git a/mGAP/resources/views/externalData.html b/mGAP/resources/views/externalData.html
index d8fdf6127..0494b3090 100644
--- a/mGAP/resources/views/externalData.html
+++ b/mGAP/resources/views/externalData.html
@@ -33,15 +33,15 @@
- Principal Investigator Grant # BioProject
+ Principal Investigator Grant # BioProject Species
- Betsy Ferguson, Ph.D. NIH R24OD021324 PRJNA382404
+ Betsy Ferguson, Ph.D. NIH R24OD021324 PRJNA382404 Rhesus macaque
- Jeffrey Rogers, Ph.D. R24-OD11173 PRJNA251548
+ Jeffrey Rogers, Ph.D. R24-OD11173 PRJNA251548 Rhesus macaque
- Robert Norgren, Ph.D. R24-3R24RR017444-07S1 PRJNA255522
+ Robert Norgren, Ph.D. R24-3R24RR017444-07S1 PRJNA255522 Rhesus macaque
diff --git a/mGAP/resources/views/quickLinks.html b/mGAP/resources/views/quickLinks.html
index 78258be0d..72eff359a 100644
--- a/mGAP/resources/views/quickLinks.html
+++ b/mGAP/resources/views/quickLinks.html
@@ -28,9 +28,9 @@
Other Links:
diff --git a/mGAP/resources/web/mGAP/images/annotation.png b/mGAP/resources/web/mGAP/images/annotation.png
index 817cf0dd2..58897d975 100644
Binary files a/mGAP/resources/web/mGAP/images/annotation.png and b/mGAP/resources/web/mGAP/images/annotation.png differ
diff --git a/mGAP/src/org/labkey/mgap/buttons/PopulateAnnotationsButton.java b/mGAP/src/org/labkey/mgap/buttons/PopulateAnnotationsButton.java
new file mode 100644
index 000000000..ffbe68de8
--- /dev/null
+++ b/mGAP/src/org/labkey/mgap/buttons/PopulateAnnotationsButton.java
@@ -0,0 +1,15 @@
+package org.labkey.mgap.buttons;
+
+import org.labkey.api.ldk.table.SimpleButtonConfigFactory;
+import org.labkey.api.module.Module;
+import org.labkey.api.query.DetailsURL;
+import org.labkey.api.security.permissions.AdminPermission;
+
+public class PopulateAnnotationsButton extends SimpleButtonConfigFactory
+{
+ public PopulateAnnotationsButton(Module owner)
+ {
+ super(owner, "Reload Annotations from GitHub", DetailsURL.fromString("/mgap/updateAnnotations.view"));
+ setPermission(AdminPermission.class);
+ }
+}
diff --git a/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java b/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java
index df504b29f..437ab92e3 100644
--- a/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java
+++ b/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java
@@ -1,5 +1,6 @@
package org.labkey.mgap.columnTransforms;
+import org.apache.commons.lang3.StringUtils;
import org.json.JSONObject;
import org.labkey.api.collections.CaseInsensitiveHashMap;
import org.labkey.api.data.ColumnInfo;
@@ -23,6 +24,7 @@
import org.labkey.mgap.mGAPSchema;
import java.sql.SQLException;
+import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
import java.util.HashMap;
@@ -307,6 +309,7 @@ protected String getDatabaseName()
protected String getTrackJson()
{
- return "{\"category\":\"mGAP Variant Catalog\",\"visibleByDefault\": true,\"ensemblId\":\"Macaca_mulatta\",\"additionalFeatureMsg\":\"
**The annotations below are primarily derived from human data sources (not macaque), and must be viewed in that context. \"}";
+ ArrayList
infoFields = new TableSelector(QueryService.get().getUserSchema(getContainerUser().getUser(), getContainerUser().getContainer(), mGAPSchema.NAME).getTable(mGAPSchema.TABLE_VARIANT_ANNOTATIONS), PageFlowUtil.set("infoKey"), new SimpleFilter(FieldKey.fromString("isIndexed"), true), null).getArrayList(String.class);
+ return "{\"category\":\"mGAP Variant Catalog\",\"visibleByDefault\": true,\"ensemblId\":\"Macaca_mulatta\",\"additionalFeatureMsg\":\"**The annotations below are primarily derived from human data sources (not macaque), and must be viewed in that context. \", \"createFullTextIndex\": true,\"infoFieldsForFullTextSearch\":\"" + (infoFields.isEmpty() ? "null" : StringUtils.join(infoFields, ",")) + "\"}";
}
}
diff --git a/mGAP/src/org/labkey/mgap/jbrowse/AnnotationModel.java b/mGAP/src/org/labkey/mgap/jbrowse/AnnotationModel.java
new file mode 100644
index 000000000..395c9486e
--- /dev/null
+++ b/mGAP/src/org/labkey/mgap/jbrowse/AnnotationModel.java
@@ -0,0 +1,186 @@
+package org.labkey.mgap.jbrowse;
+
+public class AnnotationModel
+{
+ private Integer _rowid;
+ private String _category;
+ private String _label;
+ private String _dataSource;
+ private String _infoKey;
+ private String _sourceField;
+ private String _dataType;
+ private String _dataNumber;
+ private String _url;
+ private String _dataUrl;
+ private String _description;
+ private String _toolName;
+ private String _formatString;
+ private Boolean _hidden = false;
+ private Boolean _isIndexed = false;
+ private String _allowableValues;
+
+ public AnnotationModel()
+ {
+
+ }
+
+ public int getRowid()
+ {
+ return _rowid;
+ }
+
+ public void setRowid(int rowid)
+ {
+ _rowid = rowid;
+ }
+
+ public String getCategory()
+ {
+ return _category;
+ }
+
+ public void setCategory(String category)
+ {
+ _category = category;
+ }
+
+ public String getLabel()
+ {
+ return _label;
+ }
+
+ public void setLabel(String label)
+ {
+ _label = label;
+ }
+
+ public String getDataSource()
+ {
+ return _dataSource;
+ }
+
+ public void setDataSource(String dataSource)
+ {
+ _dataSource = dataSource;
+ }
+
+ public String getInfoKey()
+ {
+ return _infoKey;
+ }
+
+ public void setInfoKey(String infoKey)
+ {
+ _infoKey = infoKey;
+ }
+
+ public String getSourceField()
+ {
+ return _sourceField;
+ }
+
+ public void setSourceField(String sourceField)
+ {
+ _sourceField = sourceField;
+ }
+
+ public String getDataType()
+ {
+ return _dataType;
+ }
+
+ public void setDataType(String dataType)
+ {
+ _dataType = dataType;
+ }
+
+ public String getDataNumber()
+ {
+ return _dataNumber;
+ }
+
+ public void setDataNumber(String dataNumber)
+ {
+ _dataNumber = dataNumber;
+ }
+
+ public String getUrl()
+ {
+ return _url;
+ }
+
+ public void setUrl(String url)
+ {
+ _url = url;
+ }
+
+ public String getDataUrl()
+ {
+ return _dataUrl;
+ }
+
+ public void setDataUrl(String dataUrl)
+ {
+ _dataUrl = dataUrl;
+ }
+
+ public String getDescription()
+ {
+ return _description;
+ }
+
+ public void setDescription(String description)
+ {
+ _description = description;
+ }
+
+ public String getToolName()
+ {
+ return _toolName;
+ }
+
+ public void setToolName(String toolName)
+ {
+ _toolName = toolName;
+ }
+
+ public String getFormatString()
+ {
+ return _formatString;
+ }
+
+ public void setFormatString(String formatString)
+ {
+ _formatString = formatString;
+ }
+
+ public boolean isHidden()
+ {
+ return _hidden != null && _hidden;
+ }
+
+ public void setHidden(Boolean hidden)
+ {
+ _hidden = hidden;
+ }
+
+ public boolean isIndexed()
+ {
+ return _isIndexed == null || _isIndexed;
+ }
+
+ public void setIndexed(Boolean indexed)
+ {
+ _isIndexed = indexed;
+ }
+
+ public String getAllowableValues()
+ {
+ return _allowableValues;
+ }
+
+ public void setAllowableValues(String allowableValues)
+ {
+ _allowableValues = allowableValues;
+ }
+}
diff --git a/mGAP/src/org/labkey/mgap/jbrowse/mGAPFieldCustomizer.java b/mGAP/src/org/labkey/mgap/jbrowse/mGAPFieldCustomizer.java
new file mode 100644
index 000000000..b70428a91
--- /dev/null
+++ b/mGAP/src/org/labkey/mgap/jbrowse/mGAPFieldCustomizer.java
@@ -0,0 +1,106 @@
+package org.labkey.mgap.jbrowse;
+
+import org.apache.commons.lang3.StringUtils;
+import org.apache.logging.log4j.Logger;
+import org.labkey.api.data.Container;
+import org.labkey.api.data.SimpleFilter;
+import org.labkey.api.data.TableSelector;
+import org.labkey.api.jbrowse.JBrowseFieldCustomizer;
+import org.labkey.api.jbrowse.JBrowseFieldDescriptor;
+import org.labkey.api.module.ModuleLoader;
+import org.labkey.api.query.FieldKey;
+import org.labkey.api.query.QueryService;
+import org.labkey.api.security.User;
+import org.labkey.api.util.logging.LogHelper;
+import org.labkey.mgap.mGAPModule;
+import org.labkey.mgap.mGAPSchema;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.List;
+
+public class mGAPFieldCustomizer implements JBrowseFieldCustomizer
+{
+ private static final Logger _log = LogHelper.getLogger(mGAPFieldCustomizer.class, "Messages from mGAP Field Customizer");
+
+ @Override
+ public void customizeField(JBrowseFieldDescriptor field, Container c, User u)
+ {
+ Container target = c.isWorkbook() ? c.getParent() : c;
+ List ams = new TableSelector(QueryService.get().getUserSchema(u, target, mGAPSchema.NAME).getTable(mGAPSchema.TABLE_VARIANT_ANNOTATIONS), new SimpleFilter(FieldKey.fromString("infoKey"), field.getFieldName()), null).getArrayList(AnnotationModel.class);
+ if (ams.isEmpty())
+ {
+ return;
+ }
+ else if (ams.size() > 1)
+ {
+ _log.error("Multiple annotation records found for the field: " + field.getFieldName());
+ }
+
+ AnnotationModel am = ams.get(0);
+ if (am.isHidden())
+ {
+ field.setHidden(true);
+ field.setInDefaultColumns(false);
+ }
+
+ if (am.isIndexed())
+ {
+ field.setIndexed(true);
+ }
+
+ if (StringUtils.trimToNull(am.getDescription()) != null)
+ {
+ field.setDescription(am.getDescription());
+ }
+
+ if (StringUtils.trimToNull(am.getLabel()) != null)
+ {
+ field.setLabel(am.getLabel());
+ }
+
+ if (StringUtils.trimToNull(am.getFormatString()) != null)
+ {
+ field.setFormatString(am.getFormatString());
+ }
+
+ if (StringUtils.trimToNull(am.getCategory()) != null)
+ {
+ field.setCategory(am.getCategory());
+ }
+
+ if (StringUtils.trimToNull(am.getAllowableValues()) != null)
+ {
+ field.setAllowableValues(Arrays.stream(am.getAllowableValues().split(",")).toList());
+ }
+
+ if (StringUtils.trimToNull(am.getUrl()) != null)
+ {
+ field.setUrl(am.getUrl());
+ }
+ }
+
+ @Override
+ public List getPromotedFilters(Collection indexedFields, Container c, User u)
+ {
+ List ret = new ArrayList<>();
+ if (indexedFields.contains("IMPACT"))
+ {
+ ret.add("Protein Coding Variants|IMPACT,does not equal,MODIFIER");
+ }
+
+ if (indexedFields.contains("OG"))
+ {
+ ret.add("Overlapping a Gene|OG,is not empty,");
+ }
+
+ return ret;
+ }
+
+ @Override
+ public boolean isAvailable(Container c, User u)
+ {
+ return c.getActiveModules().contains(ModuleLoader.getInstance().getModule(mGAPModule.class));
+ }
+}
diff --git a/mGAP/src/org/labkey/mgap/jbrowse/mGAPGroupsProvider.java b/mGAP/src/org/labkey/mgap/jbrowse/mGAPGroupsProvider.java
new file mode 100644
index 000000000..e7cb9f5d6
--- /dev/null
+++ b/mGAP/src/org/labkey/mgap/jbrowse/mGAPGroupsProvider.java
@@ -0,0 +1,49 @@
+package org.labkey.mgap.jbrowse;
+
+import org.jetbrains.annotations.Nullable;
+import org.labkey.api.data.Container;
+import org.labkey.api.data.DbScope;
+import org.labkey.api.data.SQLFragment;
+import org.labkey.api.data.SimpleFilter;
+import org.labkey.api.data.SqlSelector;
+import org.labkey.api.data.TableInfo;
+import org.labkey.api.data.TableSelector;
+import org.labkey.api.jbrowse.GroupsProvider;
+import org.labkey.api.module.ModuleLoader;
+import org.labkey.api.query.FieldKey;
+import org.labkey.api.query.QueryService;
+import org.labkey.api.security.User;
+import org.labkey.api.util.PageFlowUtil;
+import org.labkey.mgap.mGAPModule;
+import org.labkey.mgap.mGAPSchema;
+
+import java.util.Collections;
+import java.util.List;
+
+public class mGAPGroupsProvider implements GroupsProvider
+{
+ @Override
+ public @Nullable List getGroupMembers(String trackId, String groupName, Container c, User u)
+ {
+ Container target = c.isWorkbook() ? c.getParent() : c;
+ TableInfo ti = QueryService.get().getUserSchema(u, target, mGAPSchema.NAME).getTable(mGAPSchema.TABLE_RELEASE_TRACK_SUBSETS);
+
+ return new TableSelector(ti, PageFlowUtil.set("subjectId"), new SimpleFilter(FieldKey.fromString("trackName"), groupName).addCondition(FieldKey.fromString("trackId"), trackId), null).getArrayList(String.class);
+ }
+
+ @Override
+ public @Nullable List getGroupNames(Container c, User u)
+ {
+ Container target = c.isWorkbook() ? c.getParent() : c;
+ TableInfo ti = QueryService.get().getUserSchema(u, target, mGAPSchema.NAME).getTable(mGAPSchema.TABLE_RELEASE_TRACK_SUBSETS);
+ SqlSelector ss = new SqlSelector(DbScope.getLabKeyScope(), new SQLFragment("SELECT distinct trackName FROM ").append(ti.getFromSQL("x", Collections.singleton(FieldKey.fromString("trackName")))));
+
+ return ss.getArrayList(String.class);
+ }
+
+ @Override
+ public boolean isAvailable(Container c, User u)
+ {
+ return c.getActiveModules().contains(ModuleLoader.getInstance().getModule(mGAPModule.class));
+ }
+}
diff --git a/mGAP/src/org/labkey/mgap/mGAPController.java b/mGAP/src/org/labkey/mgap/mGAPController.java
index 5dfed9fe2..61d528b47 100644
--- a/mGAP/src/org/labkey/mgap/mGAPController.java
+++ b/mGAP/src/org/labkey/mgap/mGAPController.java
@@ -49,6 +49,7 @@
import org.labkey.api.exp.api.ExpData;
import org.labkey.api.module.AllowedDuringUpgrade;
import org.labkey.api.module.ModuleLoader;
+import org.labkey.api.pipeline.PipelineUrls;
import org.labkey.api.query.BatchValidationException;
import org.labkey.api.query.DetailsURL;
import org.labkey.api.query.FieldKey;
@@ -77,12 +78,15 @@
import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome;
import org.labkey.api.settings.AppProps;
import org.labkey.api.settings.LookAndFeelProperties;
+import org.labkey.api.studies.StudiesService;
import org.labkey.api.util.ConfigurationException;
import org.labkey.api.util.ExceptionUtil;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.GUID;
+import org.labkey.api.util.HtmlString;
import org.labkey.api.util.MailHelper;
import org.labkey.api.util.PageFlowUtil;
+import org.labkey.api.util.Path;
import org.labkey.api.util.URLHelper;
import org.labkey.api.view.ActionURL;
import org.labkey.api.view.HtmlView;
@@ -736,8 +740,7 @@ public ModelAndView getConfirmView(Object o, BindException errors) throws Except
{
setTitle("Update Update SnpEff Annotation");
- HtmlView view = new HtmlView("Do you want to continue?");
- return view;
+ return new HtmlView("Do you want to continue?");
}
@Override
@@ -746,7 +749,7 @@ public boolean handlePost(Object o, BindException errors) throws Exception
UserSchema us = QueryService.get().getUserSchema(getUser(), getContainer(), mGAPSchema.NAME);
TableSelector ts = new TableSelector(us.getTable(mGAPSchema.TABLE_VARIANT_CATALOG_RELEASES), PageFlowUtil.set("rowId", "objectId", "container"), null, new Sort("-releaseDate"));
ts.setMaxRows(1);
- Integer releaseRowId;
+ int releaseRowId;
String releaseObjectId;
String releaseContainerId;
try (Results rs = ts.getResults())
@@ -871,6 +874,7 @@ public static class GenomeBrowserForm
private String _databaseId;
private String _species;
private String _trackName;
+ private String _target = "browser";
public String getDatabaseId()
{
@@ -901,6 +905,16 @@ public void setTrackName(String trackName)
{
_trackName = trackName;
}
+
+ public String getTarget()
+ {
+ return _target;
+ }
+
+ public void setTarget(String target)
+ {
+ _target = target;
+ }
}
@RequiresPermission(ReadPermission.class)
@@ -921,6 +935,10 @@ public URLHelper getRedirectURL(GenomeBrowserForm form)
}
JSONObject ctx = ModuleLoader.getInstance().getModule(mGAPModule.class).getPageContextJson(getViewContext());
+ if (ctx.isNull("mgapJBrowse"))
+ {
+ throw new NotFoundException("There is no mGAP release on this server");
+ }
String jbrowseDatabaseId = StringUtils.trimToNull(form.getDatabaseId());
String species = StringUtils.trimToNull(form.getSpecies());
@@ -934,13 +952,37 @@ public URLHelper getRedirectURL(GenomeBrowserForm form)
throw new NotFoundException("No databaseId provided");
}
+ String actionName = form.getTarget() == null ? "browser" : form.getTarget();
+ if (!"browser".equals(actionName) && !"variantSearch".equals(actionName))
+ {
+ throw new IllegalArgumentException("Unknown target: " + actionName);
+ }
+
Map params = new HashMap<>(getViewContext().getRequest().getParameterMap());
params.put("session", new String[]{jbrowseDatabaseId});
+ // This requires trackId
+ if ("variantSearch".equals(actionName))
+ {
+ Collection trackIDs = getTracks(target, jbrowseDatabaseId, ctx.getString("mgapReleaseGUID"), Collections.singletonList("mGAP Release"));
+ if (!trackIDs.isEmpty())
+ {
+ if (trackIDs.size() > 1)
+ {
+ _log.error("More than one track found matching 'mGAP Release' for release: " + ctx.getString("mgapReleaseGUID"));
+ }
+
+ params.put("trackId", new String[]{trackIDs.iterator().next()});
+ }
+ else
+ {
+ throw new IllegalArgumentException("Unable to find primary track for release: " + ctx.getString("mgapReleaseGUID"));
+ }
+ }
+
String trackName = StringUtils.trimToNull(form.getTrackName());
if (trackName != null)
{
-
List trackNames = Arrays.asList(trackName.split(","));
Collection trackIDs = getTracks(target, jbrowseDatabaseId, ctx.getString("mgapReleaseGUID"), trackNames);
if (!trackIDs.isEmpty())
@@ -949,7 +991,7 @@ public URLHelper getRedirectURL(GenomeBrowserForm form)
}
}
- ActionURL ret = DetailsURL.fromString("/jbrowse/browser.view", target).getActionURL();
+ ActionURL ret = DetailsURL.fromString("/jbrowse/" + actionName + ".view", target).getActionURL();
params.forEach((key, value) -> {
Arrays.stream(value).forEach(v -> {
// This is a convenience to allow shorter URLs for active sample filters:
@@ -1067,33 +1109,49 @@ public boolean handlePost(Object o, BindException errors) throws Exception
{
List> toAdd = new ArrayList<>();
- final URL url = new URL("https://raw.githubusercontent.com/bimberlabinternal/VariantAnnotation/master/fieldConfig.txt");
- try (CSVReader reader = new CSVReader(Readers.getReader(url.openStream()), '\t'))
+ final List urls = Arrays.asList(
+ "https://raw.githubusercontent.com/bimberlabinternal/VariantAnnotation/master/fieldConfig.txt",
+ "https://raw.githubusercontent.com/bimberlabinternal/VariantAnnotation/master/otherFieldConfig.txt"
+ );
+
+ for (String urlStr : urls)
{
- String[] line;
- List header = null;
- int idx = 0;
- while ((line = reader.readNext()) != null)
+ final URL url = new URL(urlStr);
+ try (CSVReader reader = new CSVReader(Readers.getReader(url.openStream()), '\t'))
{
- idx++;
- if (idx == 1)
+ String[] line;
+ List header = null;
+ int idx = 0;
+ while ((line = reader.readNext()) != null)
{
- header = Arrays.asList(line);
- continue;
- }
-
- Map row = new CaseInsensitiveHashMap<>();
+ idx++;
+ if (idx == 1)
+ {
+ header = Arrays.asList(line);
+ continue;
+ }
- row.put("category", line[header.indexOf("Category")]);
- row.put("label", line[header.indexOf("Label")]);
- row.put("dataSource", line[header.indexOf("DataSource")]);
- row.put("infoKey", line[header.indexOf("ID")]);
- row.put("dataType", line[header.indexOf("Type")]);
- row.put("dataNumber", line[header.indexOf("Number")]);
- row.put("description", line[header.indexOf("Description")]);
- row.put("url", line[header.indexOf("URL")]);
+ Map row = new CaseInsensitiveHashMap<>();
- toAdd.add(row);
+ row.put("category", line[header.indexOf("Category")]);
+ row.put("label", line[header.indexOf("Label")]);
+ row.put("dataSource", line[header.indexOf("DataSource")]);
+ row.put("infoKey", line[header.indexOf("ID")]);
+ row.put("sourceField", line[header.indexOf("SourceField")]);
+ row.put("dataType", line[header.indexOf("Type")]);
+ row.put("dataNumber", line[header.indexOf("Number")]);
+ row.put("description", line[header.indexOf("Description")]);
+ row.put("url", line[header.indexOf("URL")]);
+ row.put("toolName", line[header.indexOf("ToolName")]);
+
+ getOptionalField(line, header, "DataURL", row, "dataurl");
+ getOptionalField(line, header, "Hidden", row, "hidden");
+ getOptionalField(line, header, "FormatString", row, "formatString");
+ getOptionalField(line, header, "AllowableValues", row, "allowableValues");
+ getOptionalField(line, header, "IsIndexed", row, "isIndexed");
+
+ toAdd.add(row);
+ }
}
}
@@ -1111,6 +1169,14 @@ public boolean handlePost(Object o, BindException errors) throws Exception
return true;
}
+ private void getOptionalField(String[] line, List header, String name, Map row, String rowKey)
+ {
+ if (header.contains(name) && line.length > header.indexOf(name))
+ {
+ row.put(rowKey, line[header.indexOf(name)]);
+ }
+ }
+
@Override
public void validateCommand(Object o, Errors errors)
{
@@ -1123,4 +1189,37 @@ public void validateCommand(Object o, Errors errors)
return QueryService.get().urlFor(getUser(), getContainer(), QueryAction.executeQuery, mGAPSchema.NAME, mGAPSchema.TABLE_VARIANT_ANNOTATIONS);
}
}
+
+ @RequiresPermission(AdminPermission.class)
+ public class ImportStudyAction extends ConfirmAction
+ {
+ @Override
+ public ModelAndView getConfirmView(Object o, BindException errors) throws Exception
+ {
+ setTitle("Import mGAP Study");
+
+ return new HtmlView(HtmlString.unsafe("This will import the default mGAP study in this folder and set the EHRStudyContainer property to point to this container. Do you want to continue?"));
+ }
+
+ @Override
+ public boolean handlePost(Object o, BindException errors) throws Exception
+ {
+ StudiesService.get().importFolderDefinition(getContainer(), getUser(), ModuleLoader.getInstance().getModule(mGAPModule.NAME), new Path("referenceStudy"));
+
+ return true;
+ }
+
+ @Override
+ public void validateCommand(Object o, Errors errors)
+ {
+
+ }
+
+ @NotNull
+ @Override
+ public URLHelper getSuccessURL(Object o)
+ {
+ return PageFlowUtil.urlProvider(PipelineUrls.class).urlBegin(getContainer());
+ }
+ }
}
\ No newline at end of file
diff --git a/mGAP/src/org/labkey/mgap/mGAPModule.java b/mGAP/src/org/labkey/mgap/mGAPModule.java
index 0022c73cf..50078dbbf 100644
--- a/mGAP/src/org/labkey/mgap/mGAPModule.java
+++ b/mGAP/src/org/labkey/mgap/mGAPModule.java
@@ -39,9 +39,13 @@
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.util.SystemMaintenance;
import org.labkey.api.writer.ContainerUser;
+import org.labkey.mgap.buttons.PopulateAnnotationsButton;
import org.labkey.mgap.buttons.ReleaseButton;
+import org.labkey.mgap.jbrowse.mGAPFieldCustomizer;
+import org.labkey.mgap.jbrowse.mGAPGroupsProvider;
import org.labkey.mgap.pipeline.AnnotationStep;
import org.labkey.mgap.pipeline.GenerateMgapTracksStep;
+import org.labkey.mgap.pipeline.GroupCompareStep;
import org.labkey.mgap.pipeline.RemoveAnnotationsForMgapStep;
import org.labkey.mgap.pipeline.RenameSamplesForMgapStep;
import org.labkey.mgap.pipeline.SampleSpecificGenotypeFiltrationStep;
@@ -66,7 +70,7 @@ public String getName()
@Override
public Double getSchemaVersion()
{
- return 16.65;
+ return 16.67;
}
@Override
@@ -84,10 +88,13 @@ public void doStartupAfterSpringConfig(ModuleContext moduleContext)
LDKService.get().registerQueryButton(new ShowBulkEditButton(this, mGAPSchema.NAME, mGAPSchema.TABLE_ANIMAL_MAPPING), mGAPSchema.NAME, mGAPSchema.TABLE_ANIMAL_MAPPING);
LDKService.get().registerQueryButton(new ShowBulkEditButton(this, mGAPSchema.NAME, mGAPSchema.TABLE_TRACKS_PER_RELEASE), mGAPSchema.NAME, mGAPSchema.TABLE_TRACKS_PER_RELEASE);
LDKService.get().registerQueryButton(new ReleaseButton(this), mGAPSchema.NAME, mGAPSchema.TABLE_RELEASE_TRACKS);
+ LDKService.get().registerQueryButton(new PopulateAnnotationsButton(this), mGAPSchema.NAME, mGAPSchema.TABLE_VARIANT_ANNOTATIONS);
NotificationService.get().registerNotification(new mGAPUserNotification(this));
JBrowseService.get().registerDemographicsSource(new mGAPDemographicsSource());
+ JBrowseService.get().registerFieldCustomizer(new mGAPFieldCustomizer());
+ JBrowseService.get().registerGroupsProvider(new mGAPGroupsProvider());
SystemMaintenance.addTask(new mGapMaintenanceTask());
@@ -115,6 +122,7 @@ public PipelineStartup()
{
SequenceAnalysisService.get().registerFileHandler(new mGapReleaseGenerator());
SequencePipelineService.get().registerPipelineStep(new AnnotationStep.Provider());
+ SequencePipelineService.get().registerPipelineStep(new GroupCompareStep.Provider());
SequencePipelineService.get().registerPipelineStep(new RemoveAnnotationsForMgapStep.Provider());
SequencePipelineService.get().registerPipelineStep(new RenameSamplesForMgapStep.Provider());
SequencePipelineService.get().registerPipelineStep(new VcfComparisonStep.Provider());
diff --git a/mGAP/src/org/labkey/mgap/pipeline/AnnotationStep.java b/mGAP/src/org/labkey/mgap/pipeline/AnnotationStep.java
index 10daf3009..bf2f22f60 100644
--- a/mGAP/src/org/labkey/mgap/pipeline/AnnotationStep.java
+++ b/mGAP/src/org/labkey/mgap/pipeline/AnnotationStep.java
@@ -7,6 +7,7 @@
import org.jetbrains.annotations.Nullable;
import org.json.JSONObject;
import org.labkey.api.data.CompareType;
+import org.labkey.api.data.Container;
import org.labkey.api.data.DbSchema;
import org.labkey.api.data.DbSchemaType;
import org.labkey.api.data.SimpleFilter;
@@ -18,6 +19,7 @@
import org.labkey.api.pipeline.PipelineJobException;
import org.labkey.api.pipeline.PipelineJobService;
import org.labkey.api.query.FieldKey;
+import org.labkey.api.query.QueryService;
import org.labkey.api.sequenceanalysis.SequenceAnalysisService;
import org.labkey.api.sequenceanalysis.SequenceOutputFile;
import org.labkey.api.sequenceanalysis.pipeline.AbstractVariantProcessingStepProvider;
@@ -35,14 +37,19 @@
import org.labkey.api.sequenceanalysis.run.SimpleScriptWrapper;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.PageFlowUtil;
+import org.labkey.api.writer.PrintWriters;
+import org.labkey.mgap.mGAPSchema;
import java.io.File;
import java.io.IOException;
+import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashSet;
import java.util.List;
+import java.util.Map;
import java.util.Set;
/**
@@ -51,7 +58,6 @@
public class AnnotationStep extends AbstractCommandPipelineStep implements VariantProcessingStep
{
public static final String GRCH37 = "genome37";
- private static final String CLINVAR_VCF = "clinvar37";
private static final String DBNSFP_FILE = "dbnsfpFile";
public static final String CHAIN_FILE = "CHAIN_FILE";
@@ -65,11 +71,7 @@ public static class Provider extends AbstractVariantProcessingStepProvider> sourceFieldMap = new HashMap<>();
+ final HashMap> targetFieldMap = new HashMap<>();
+ new TableSelector(QueryService.get().getUserSchema(getPipelineCtx().getJob().getUser(), targetContainer, mGAPSchema.NAME).getTable(mGAPSchema.TABLE_VARIANT_ANNOTATIONS), PageFlowUtil.set("toolName", "sourceField", "infoKey")).forEachResults(rs -> {
+ if (!sourceFieldMap.containsKey(rs.getString(FieldKey.fromString("toolName"))))
+ {
+ sourceFieldMap.put(rs.getString(FieldKey.fromString("toolName")), new ArrayList<>());
+ targetFieldMap.put(rs.getString(FieldKey.fromString("toolName")), new ArrayList<>());
+ }
+
+ sourceFieldMap.get(rs.getString(FieldKey.fromString("toolName"))).add(rs.getString(FieldKey.fromString("sourceField")));
+ targetFieldMap.get(rs.getString(FieldKey.fromString("toolName"))).add(rs.getString(FieldKey.fromString("infoKey")));
+ });
+
+ getPipelineCtx().getSequenceSupport().cacheObject(SOURCE_FIELDS, sourceFieldMap);
+ getPipelineCtx().getSequenceSupport().cacheObject(TARGET_FIELDS, targetFieldMap);
+ }
+
+ private static final String SOURCE_FIELDS = "sourceFields";
+ private static final String TARGET_FIELDS = "targetFields";
+
+ private List getCachedFields(String key, String toolName) throws PipelineJobException
+ {
+ Map> fieldMap = getPipelineCtx().getSequenceSupport().getCachedObject(key, PipelineJob.createObjectMapper().getTypeFactory().constructParametricType(Map.class, String.class, List.class));
+ return fieldMap.get(toolName).stream().map(String::valueOf).toList();
}
@Override
@@ -140,12 +177,6 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
{
VariantProcessingStepOutputImpl output = new VariantProcessingStepOutputImpl();
- File clinvarVCF = getPipelineCtx().getSequenceSupport().getCachedData(getProvider().getParameterByName(CLINVAR_VCF).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Integer.class));
- if (!clinvarVCF.exists())
- {
- throw new PipelineJobException("Unable to find file: " + clinvarVCF.getPath());
- }
-
ReferenceGenome grch37Genome = getPipelineCtx().getSequenceSupport().getCachedGenome(getProvider().getParameterByName(GRCH37).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Integer.class));
Integer chainFileId = getPipelineCtx().getSequenceSupport().getCachedObject(CHAIN_FILE, Integer.class);
File chainFile = getPipelineCtx().getSequenceSupport().getCachedData(chainFileId);
@@ -311,45 +342,19 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
output.addIntermediateFile(liftedToGRCh37);
output.addIntermediateFile(new File(liftedToGRCh37.getPath() + ".tbi"));
- //annotate with clinvar
- getPipelineCtx().getLogger().info("annotating with ClinVar 2.0");
- File clinvarAnnotated = new File(outputDirectory, SequenceAnalysisService.get().getUnzippedBaseName(liftedToGRCh37.getName()) + ".cv.vcf.gz");
- if (forceRecreate || !indexExists(clinvarAnnotated))
- {
- ClinvarAnnotatorRunner cvRunner = new ClinvarAnnotatorRunner(getPipelineCtx().getLogger());
- cvRunner.execute(liftedToGRCh37, clinvarVCF, clinvarAnnotated);
- }
- else
- {
- getPipelineCtx().getLogger().info("resuming with existing file: " + clinvarAnnotated.getPath());
- }
- output.addOutput(clinvarAnnotated, "VCF Annotated With ClinVar2.0");
- output.addIntermediateFile(clinvarAnnotated);
- output.addIntermediateFile(new File(clinvarAnnotated.getPath() + ".tbi"));
-
- //backport ClinVar
- getPipelineCtx().getLogger().info("backport ClinVar 2.0 to source genome");
- File clinvarAnnotatedBackport = new File(outputDirectory, SequenceAnalysisService.get().getUnzippedBaseName(clinvarAnnotated.getName()) + ".bp.vcf.gz");
- if (forceRecreate || !indexExists(clinvarAnnotatedBackport ))
- {
- BackportLiftedVcfRunner bpRunner = new BackportLiftedVcfRunner(getPipelineCtx().getLogger());
- bpRunner.execute(clinvarAnnotated, originalGenome.getWorkingFastaFile(), grch37Genome.getWorkingFastaFile(), clinvarAnnotatedBackport);
- }
- else
- {
- getPipelineCtx().getLogger().info("resuming with existing file: " + clinvarAnnotatedBackport.getPath());
- }
- output.addOutput(clinvarAnnotatedBackport, "VCF Annotated With Clinvar, Backported");
- output.addIntermediateFile(clinvarAnnotatedBackport);
- output.addIntermediateFile(new File(clinvarAnnotatedBackport.getPath() + ".tbi"));
-
//annotate with SnpSift
getPipelineCtx().getLogger().info("annotating with SnpSift/dbnsfp");
File snpSiftAnnotated = new File(outputDirectory, SequenceAnalysisService.get().getUnzippedBaseName(liftedToGRCh37.getName()) + ".snpSift.vcf.gz");
if (forceRecreate || !indexExists(snpSiftAnnotated))
{
SnpSiftWrapper ssRunner = new SnpSiftWrapper(getPipelineCtx().getLogger());
- ssRunner.runSnpSift(dbnsfpFile, liftedToGRCh37, snpSiftAnnotated);
+ List fieldList = getCachedFields(SOURCE_FIELDS, "SnpSift");
+ if (fieldList.isEmpty())
+ {
+ throw new PipelineJobException("No fields found for SnpSift");
+ }
+
+ ssRunner.runSnpSift(dbnsfpFile, liftedToGRCh37, snpSiftAnnotated, fieldList);
}
else
{
@@ -377,7 +382,8 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
//annotate with cassandra
File cassandraAnnotatedBackport = null;
- if (getProvider().getParameterByName("useCassandra").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Boolean.class, false))
+ boolean useCassandra = getProvider().getParameterByName("useCassandra").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Boolean.class, false);
+ if (useCassandra)
{
getPipelineCtx().getLogger().info("annotating with Cassandra");
String basename = SequenceAnalysisService.get().getUnzippedBaseName(liftedToGRCh37.getName()) + ".cassandra";
@@ -428,7 +434,25 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
{
//we can assume splitting happened upstream, so run over the full VCF
FuncotatorWrapper fr = new FuncotatorWrapper(getPipelineCtx().getLogger());
- fr.runFuncotator(funcotatorSourceDir, liftedToGRCh37, snpSiftAnnotated, genome);
+
+ List extraArgs = new ArrayList<>();
+ String excludedContigs = StringUtils.trimToNull(getProvider().getParameterByName("funcotatorExcludedContigs").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), String.class, null));
+ if (excludedContigs != null)
+ {
+ for (String token : excludedContigs.split(","))
+ {
+ extraArgs.add("-XL");
+ extraArgs.add(token);
+ }
+ }
+
+ boolean printMissingFields = getProvider().getParameterByName("printMissingFields").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Boolean.class, false);
+ if (printMissingFields)
+ {
+ extraArgs.add("-pmf");
+ }
+
+ fr.runFuncotator(funcotatorSourceDir, liftedToGRCh37, funcotatorAnnotated, grch37Genome, extraArgs);
}
else
{
@@ -478,7 +502,14 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
needToSubsetToInterval = false;
}
- maRunner.execute(inputVCF, cassandraAnnotatedBackport, clinvarAnnotatedBackport, liftoverRejects, funcotatorAnnotatedBackport, snpSiftAnnotatedBackport, multiAnnotated, options);
+ if (useFuncotator)
+ {
+ addToolFieldNames("Funcotator", "-ff", options, multiAnnotated.getParentFile(), output);
+ }
+
+ addToolFieldNames("SnpSift", "-ssf", options, multiAnnotated.getParentFile(), output);
+
+ maRunner.execute(inputVCF, cassandraAnnotatedBackport, liftoverRejects, funcotatorAnnotatedBackport, snpSiftAnnotatedBackport, multiAnnotated, options);
}
else
{
@@ -495,6 +526,25 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
return output;
}
+ private void addToolFieldNames(String toolName, String argName, List options, File outDir, VariantProcessingStepOutputImpl output) throws PipelineJobException
+ {
+ List fields = getCachedFields(TARGET_FIELDS, toolName);
+ File fieldFile = new File(outDir, toolName + "Fields.args");
+ try (PrintWriter writer = PrintWriters.getPrintWriter(fieldFile))
+ {
+ fields.forEach(writer::println);
+ }
+ catch (IOException e)
+ {
+ throw new PipelineJobException(e);
+ }
+
+ output.addIntermediateFile(fieldFile);
+
+ options.add(argName);
+ options.add(fieldFile.getPath());
+ }
+
private void runCassandra(File liftedToGRCh37, File finalOutput, VariantProcessingStepOutputImpl output, boolean forceRecreate) throws PipelineJobException
{
List extraArgs = new ArrayList<>();
diff --git a/mGAP/src/org/labkey/mgap/pipeline/FuncotatorWrapper.java b/mGAP/src/org/labkey/mgap/pipeline/FuncotatorWrapper.java
index 5cdde9bf0..88efc0330 100644
--- a/mGAP/src/org/labkey/mgap/pipeline/FuncotatorWrapper.java
+++ b/mGAP/src/org/labkey/mgap/pipeline/FuncotatorWrapper.java
@@ -1,6 +1,7 @@
package org.labkey.mgap.pipeline;
import org.apache.logging.log4j.Logger;
+import org.jetbrains.annotations.Nullable;
import org.labkey.api.pipeline.PipelineJobException;
import org.labkey.api.sequenceanalysis.SequenceAnalysisService;
import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome;
@@ -21,11 +22,11 @@ public FuncotatorWrapper(Logger log)
super(log);
}
- public void runFuncotator(File dataDir, File input, File output, ReferenceGenome genome) throws PipelineJobException
+ public void runFuncotator(File dataDir, File input, File output, ReferenceGenome genome, @Nullable List extraArgs) throws PipelineJobException
{
getLogger().info("Annotating VCF with Funcotator");
- List params = new ArrayList<>(getBaseArgs());
+ List params = new ArrayList<>(getBaseArgs("ExtendedFuncotator"));
params.add("-R");
params.add(genome.getWorkingFastaFile().getPath());
@@ -48,6 +49,11 @@ public void runFuncotator(File dataDir, File input, File output, ReferenceGenome
params.add("-O");
params.add(output.getPath());
+ if (extraArgs != null)
+ {
+ params.addAll(extraArgs);
+ }
+
execute(params);
if (!output.exists())
diff --git a/mGAP/src/org/labkey/mgap/pipeline/GroupCompareStep.java b/mGAP/src/org/labkey/mgap/pipeline/GroupCompareStep.java
new file mode 100644
index 000000000..6e62b3c59
--- /dev/null
+++ b/mGAP/src/org/labkey/mgap/pipeline/GroupCompareStep.java
@@ -0,0 +1,303 @@
+package org.labkey.mgap.pipeline;
+
+import htsjdk.samtools.util.Interval;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.logging.log4j.Logger;
+import org.json.JSONArray;
+import org.json.JSONObject;
+import org.labkey.api.pipeline.PipelineJob;
+import org.labkey.api.pipeline.PipelineJobException;
+import org.labkey.api.reader.Readers;
+import org.labkey.api.sequenceanalysis.SequenceAnalysisService;
+import org.labkey.api.sequenceanalysis.SequenceOutputFile;
+import org.labkey.api.sequenceanalysis.pipeline.AbstractVariantProcessingStepProvider;
+import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
+import org.labkey.api.sequenceanalysis.pipeline.PipelineStepProvider;
+import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome;
+import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler;
+import org.labkey.api.sequenceanalysis.pipeline.TaskFileManager;
+import org.labkey.api.sequenceanalysis.pipeline.ToolParameterDescriptor;
+import org.labkey.api.sequenceanalysis.pipeline.VariantProcessingStep;
+import org.labkey.api.sequenceanalysis.pipeline.VariantProcessingStepOutputImpl;
+import org.labkey.api.sequenceanalysis.run.AbstractCommandPipelineStep;
+import org.labkey.api.sequenceanalysis.run.AbstractDiscvrSeqWrapper;
+import org.labkey.api.writer.PrintWriters;
+
+import javax.annotation.Nullable;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+/**
+ * User: bimber
+ * Date: 6/15/2014
+ * Time: 12:39 PM
+ */
+public class GroupCompareStep extends AbstractCommandPipelineStep implements VariantProcessingStep
+{
+ public static final String REF_VCF = "refVcf";
+ public static String GROUP1 = "group1";
+ public static String GROUP2 = "group2";
+
+
+ public GroupCompareStep(PipelineStepProvider provider, PipelineContext ctx)
+ {
+ super(provider, ctx, new GroupComparison(ctx.getLogger()));
+ }
+
+ public static class Provider extends AbstractVariantProcessingStepProvider implements SupportsScatterGather
+ {
+ public Provider()
+ {
+ super("GroupCompare", "Group Comparison", "DISCVRseq/GroupCompare", "This is designed to help with sifting and prioritizing variants. It will generate a VCF limited to just the samples in group 1 (and group 2 if provided). It will compare the AF, N_HOMVAR, N_HOMREF, and N_HET within each group. If a reference VCF is provided (e.g., population-level data), these values will also be computed on that dataset. The resulting VCF is designed to be the starting point for secondary filtering.", List.of(
+ ToolParameterDescriptor.create(GROUP1, "Group 1 Sample(s)", "Only variants of the selected type(s) will be included", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
+ put("allowBlank", false);
+ }}, null),
+ ToolParameterDescriptor.create(GROUP2, "Group 2 Sample(s)", "Optional. Only variants of the selected type(s) will be included", "sequenceanalysis-trimmingtextarea", null, null),
+ ToolParameterDescriptor.createExpDataParam(REF_VCF, "Reference VCF", "This is the file ID of the VCF to use as the reference.", "ldk-expdatafield", new JSONObject()
+ {{
+
+ }}, null),
+ ToolParameterDescriptor.create("vcfSelects", "VCF Select Expressions", "Filter expressions that can be used to subset variants output in the VCF.", "sequenceanalysis-variantfilterpanel", new JSONObject(){{
+ put("mode", "SELECT");
+ put("showFilterName", false);
+ put("title", "Select Expressions");
+ }}, null),
+ ToolParameterDescriptor.create("tableSelects", "Table Select Expressions", "Filter expressions that can be used to subset variants. Passing variants will be written to a separate TSV file. This does not impact the VCF", "sequenceanalysis-variantfilterpanel", new JSONObject(){{
+ put("mode", "SELECT");
+ put("showFilterName", false);
+ put("title", "Select Expressions");
+ }}, null),
+ ToolParameterDescriptor.create("extraFields", "Additional Fields", "A list of additional fields to include in the table output", "sequenceanalysis-trimmingtextarea", null, null)
+ ), Arrays.asList("/sequenceanalysis/field/TrimmingTextArea.js", "sequenceanalysis/panel/VariantFilterPanel.js"), null);
+ }
+
+ @Override
+ public GroupCompareStep create(PipelineContext ctx)
+ {
+ return new GroupCompareStep(this, ctx);
+ }
+
+ @Override
+ public void performAdditionalMergeTasks(SequenceOutputHandler.JobContext ctx, PipelineJob job, TaskFileManager manager, ReferenceGenome genome, List orderedScatterOutputs) throws PipelineJobException
+ {
+ job.getLogger().info("Merging variant tables");
+ List toConcat = orderedScatterOutputs.stream().map(f -> {
+ f = new File(f.getParentFile(), f.getName().replaceAll("vcf.gz", "txt"));
+ if (!f.exists())
+ {
+ throw new IllegalStateException("Missing file: " + f.getPath());
+ }
+
+ ctx.getFileManager().addIntermediateFile(f);
+
+ return f;
+ }).toList();
+
+ String basename = SequenceAnalysisService.get().getUnzippedBaseName(toConcat.get(0).getName());
+ File combined = new File(ctx.getSourceDirectory(), basename + ".txt");
+ try (PrintWriter writer = PrintWriters.getPrintWriter(combined))
+ {
+ boolean hasWrittenHeader = false;
+ for (File f : toConcat)
+ {
+ try (BufferedReader reader = Readers.getReader(f))
+ {
+ String line;
+ int idx = 0;
+ while ((line = reader.readLine()) != null)
+ {
+ idx++;
+ if (idx == 1)
+ {
+ if (!hasWrittenHeader) {
+ writer.println(line);
+ hasWrittenHeader = true;
+ }
+ }
+ else
+ {
+ writer.println(line);
+ }
+ }
+ }
+ }
+ }
+ catch (IOException e)
+ {
+ throw new PipelineJobException(e);
+ }
+
+ SequenceOutputFile so = new SequenceOutputFile();
+ so.setName(basename + ": Selected Variants");
+ so.setFile(combined);
+ so.setCategory("Variant List");
+ so.setLibrary_id(genome.getGenomeId());
+ manager.addSequenceOutput(so);
+ }
+ }
+
+ @Override
+ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGenome genome, @Nullable List intervals) throws PipelineJobException
+ {
+ VariantProcessingStepOutputImpl output = new VariantProcessingStepOutputImpl();
+ getPipelineCtx().getLogger().info("Running GroupCompare");
+
+ List extraArgs = new ArrayList<>();
+ if (intervals != null)
+ {
+ intervals.forEach(interval -> {
+ extraArgs.add("-L");
+ extraArgs.add(interval.getContig() + ":" + interval.getStart() + "-" + interval.getEnd());
+ });
+ }
+
+ Integer refFileId = getProvider().getParameterByName(REF_VCF).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Integer.class);
+ if (refFileId != null)
+ {
+ File refVcf = getPipelineCtx().getSequenceSupport().getCachedData(refFileId);
+ if (!refVcf.exists())
+ {
+ throw new PipelineJobException("Unable to find file: " + refVcf.getPath());
+ }
+
+ extraArgs.add("-RV");
+ extraArgs.add(refVcf.getPath());
+ }
+
+ //JEXL
+ addSelects("vcfSelects", "-select", extraArgs);
+ addSelects("tableSelects", "-table-select", extraArgs);
+
+ String fieldsText = StringUtils.trimToNull(getProvider().getParameterByName("extraFields").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), String.class, null));
+ if (fieldsText != null)
+ {
+ String[] names = fieldsText.split(";");
+ for (String name : names)
+ {
+ extraArgs.add("-F");
+ extraArgs.add(name);
+ }
+ }
+
+ String group1Raw = StringUtils.trimToNull(getProvider().getParameterByName(GROUP1).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), String.class, null));
+ List group1 = Arrays.asList(group1Raw.split(";"));
+ getPipelineCtx().getLogger().info("Total group 1 samples: " + group1.size());
+
+ String group2Raw = StringUtils.trimToNull(getProvider().getParameterByName(GROUP2).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), String.class, null));
+ List group2 = null;
+ if (group2Raw != null)
+ {
+ group2 = Arrays.asList(group2Raw.split(";"));
+ getPipelineCtx().getLogger().info("Total group 2 samples: " + group2.size());
+ }
+
+ File outputVcf = new File(outputDirectory, SequenceAnalysisService.get().getUnzippedBaseName(inputVCF.getName()) + ".gc.vcf.gz");
+ File outputTable = new File(outputDirectory, SequenceAnalysisService.get().getUnzippedBaseName(inputVCF.getName()) + ".gc.txt");
+
+ getWrapper().runTool(inputVCF, outputVcf, outputTable, genome.getWorkingFastaFile(), group1, group2, extraArgs);
+ if (!outputTable.exists())
+ {
+ throw new PipelineJobException("Unable to find output: " + outputTable.getPath());
+ }
+
+ output.addInput(inputVCF, "Input VCF");
+ output.addInput(genome.getWorkingFastaFile(), "Reference Genome");
+ output.addOutput(outputTable, "GroupCompare Table");
+ output.setVcf(outputVcf);
+
+ return output;
+ }
+
+ private void addSelects(String param, String arg, List extraArgs) throws PipelineJobException
+ {
+ String selectText = getProvider().getParameterByName(param).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), String.class, null);
+ if (selectText != null)
+ {
+ JSONArray filterArr = new JSONArray(selectText);
+ for (int i = 0; i < filterArr.length(); i++)
+ {
+ JSONArray arr = filterArr.getJSONArray(i);
+ if (arr.length() < 2)
+ {
+ throw new PipelineJobException("Improper select expression: " + filterArr.getString(i));
+ }
+
+ extraArgs.add(arg);
+ extraArgs.add(arr.getString(1));
+ }
+ }
+ }
+
+ public static class GroupComparison extends AbstractDiscvrSeqWrapper
+ {
+ public GroupComparison(Logger log)
+ {
+ super(log);
+ }
+
+ public void runTool(File inputVCF, File outputVcf, File outputTable, File genomeFasta, List group1, @Nullable List group2, List extraArgs) throws PipelineJobException
+ {
+ List args = new ArrayList<>(getBaseArgs());
+ args.add("GroupCompare");
+ args.add("-R");
+ args.add(genomeFasta.getPath());
+
+ args.add("-V");
+ args.add(inputVCF.getPath());
+
+ args.add("-O");
+ args.add(outputVcf.getPath());
+
+ args.add("-OT");
+ args.add(outputTable.getPath());
+
+ args.add("--ignore-variants-starting-outside-interval");
+
+ File group1File = new File(outputVcf.getParentFile(), "group1.args");
+ File group2File = new File(outputVcf.getParentFile(), "group2.args");
+ try (PrintWriter writer = PrintWriters.getPrintWriter(group1File))
+ {
+ group1.forEach(writer::println);
+ }
+ catch (IOException e)
+ {
+ throw new PipelineJobException(e);
+ }
+ args.add("-G1");
+ args.add(group1File.getPath());
+
+ if (group2 != null)
+ {
+ try (PrintWriter writer = PrintWriters.getPrintWriter(group2File))
+ {
+ group2.forEach(writer::println);
+ }
+ catch (IOException e)
+ {
+ throw new PipelineJobException(e);
+ }
+
+ args.add("-G2");
+ args.add(group2File.getPath());
+ }
+
+ if (extraArgs != null)
+ {
+ args.addAll(extraArgs);
+ }
+
+ execute(args);
+
+ group1File.delete();
+ if (group2File != null)
+ {
+ group2File.delete();
+ }
+ }
+ }
+}
diff --git a/mGAP/src/org/labkey/mgap/pipeline/MultiSourceAnnotatorRunner.java b/mGAP/src/org/labkey/mgap/pipeline/MultiSourceAnnotatorRunner.java
index ab0a30f36..03ee5e2dc 100644
--- a/mGAP/src/org/labkey/mgap/pipeline/MultiSourceAnnotatorRunner.java
+++ b/mGAP/src/org/labkey/mgap/pipeline/MultiSourceAnnotatorRunner.java
@@ -15,16 +15,13 @@ public MultiSourceAnnotatorRunner(Logger log)
super(log);
}
- public File execute(File inputVcf, @Nullable File cassandraVcf, File clinvarVcf, File liftoverRejects, @Nullable File funcotator, @Nullable File snpSift, File outputVcf, @Nullable List options) throws PipelineJobException
+ public File execute(File inputVcf, @Nullable File cassandraVcf, File liftoverRejects, @Nullable File funcotator, @Nullable File snpSift, File outputVcf, @Nullable List options) throws PipelineJobException
{
List args = getBaseArgs("MultiSourceAnnotator");
args.add("-V");
args.add(inputVcf.getPath());
- args.add("-cv");
- args.add(clinvarVcf.getPath());
-
if (cassandraVcf != null)
{
args.add("-c");
diff --git a/mGAP/src/org/labkey/mgap/pipeline/RemoveAnnotationsForMgapStep.java b/mGAP/src/org/labkey/mgap/pipeline/RemoveAnnotationsForMgapStep.java
index 0e9b9d901..b4f5d2874 100644
--- a/mGAP/src/org/labkey/mgap/pipeline/RemoveAnnotationsForMgapStep.java
+++ b/mGAP/src/org/labkey/mgap/pipeline/RemoveAnnotationsForMgapStep.java
@@ -3,17 +3,25 @@
import htsjdk.samtools.util.Interval;
import org.apache.logging.log4j.Logger;
import org.jetbrains.annotations.Nullable;
+import org.labkey.api.data.Container;
+import org.labkey.api.data.TableSelector;
+import org.labkey.api.pipeline.PipelineJob;
import org.labkey.api.pipeline.PipelineJobException;
+import org.labkey.api.query.QueryService;
import org.labkey.api.sequenceanalysis.SequenceAnalysisService;
+import org.labkey.api.sequenceanalysis.SequenceOutputFile;
import org.labkey.api.sequenceanalysis.pipeline.AbstractVariantProcessingStepProvider;
import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
import org.labkey.api.sequenceanalysis.pipeline.PipelineStep;
import org.labkey.api.sequenceanalysis.pipeline.PipelineStepProvider;
import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome;
+import org.labkey.api.sequenceanalysis.pipeline.SequenceAnalysisJobSupport;
import org.labkey.api.sequenceanalysis.pipeline.VariantProcessingStep;
import org.labkey.api.sequenceanalysis.pipeline.VariantProcessingStepOutputImpl;
import org.labkey.api.sequenceanalysis.run.AbstractCommandPipelineStep;
import org.labkey.api.sequenceanalysis.run.AbstractDiscvrSeqWrapper;
+import org.labkey.api.util.PageFlowUtil;
+import org.labkey.mgap.mGAPSchema;
import java.io.File;
import java.util.ArrayList;
@@ -23,9 +31,10 @@
public class RemoveAnnotationsForMgapStep extends AbstractCommandPipelineStep implements VariantProcessingStep
{
+ // TODO: base this on annotation table
public static List ALLOWABLE_ANNOTATIONS = Collections.unmodifiableList(Arrays.asList("AF", "AC", "END", "ANN", "LOF", "MAF", "CADD_PH", "CADD_RS", "CCDS", "ENC", "ENCDNA_CT", "ENCDNA_SC", "ENCSEG_CT", "ENCSEG_NM", "ENCTFBS_CL", "ENCTFBS_SC", "ENCTFBS_TF", "ENN", "ERBCTA_CT", "ERBCTA_NM", "ERBCTA_SC", "ERBSEG_CT", "ERBSEG_NM", "ERBSEG_SC", "ERBSUM_NM", "ERBSUM_SC", "ERBTFBS_PB", "ERBTFBS_TF", "FC", "FE", "FS_EN", "FS_NS", "FS_SC", "FS_SN", "FS_TG", "FS_US", "FS_WS", "GRASP_AN", "GRASP_P", "GRASP_PH", "GRASP_PL", "GRASP_PMID", "GRASP_RS", "LOF", "NC", "NE", "NF", "NG", "NH", "NJ", "NK", "NL", "NM", "NMD", "OMIMC", "OMIMD", "OMIMM", "OMIMMUS", "OMIMN", "OMIMS", "OMIMT", "OREGANNO_PMID", "OREGANNO_TYPE", "PC_PL", "PC_PR", "PC_VB", "PP_PL", "PP_PR", "PP_VB", "RDB_MF", "RDB_WS", "RFG", "RSID", "SCSNV_ADA", "SCSNV_RS", "SD", "SF", "SM", "SP_SC", "SX", "TMAF", "LF", "CLN_ALLELE", "CLN_ALLELEID", "CLN_DN", "CLN_DNINCL", "CLN_DISDB", "CLN_DISDBINCL", "CLN_HGVS", "CLN_REVSTAT", "CLN_SIG", "CLN_SIGINCL", "CLN_VC", "CLN_VCSO", "CLN_VI", "CLN_DBVARID", "CLN_GENEINFO", "CLN_MC", "CLN_ORIGIN", "CLN_RS", "CLN_SSR", "ReverseComplementedAlleles", "LiftedContig", "LiftedStart", "LiftedStop"));
- public RemoveAnnotationsForMgapStep(PipelineStepProvider provider, PipelineContext ctx)
+ public RemoveAnnotationsForMgapStep(PipelineStepProvider provider, PipelineContext ctx)
{
super(provider, ctx, new RemoveAnnotationsWrapper(ctx.getLogger()));
}
@@ -44,6 +53,24 @@ public PipelineStep create(PipelineContext context)
}
}
+ private static final String INFO_FIELDS = "infoFields";
+
+ @Override
+ public void init(PipelineJob job, SequenceAnalysisJobSupport support, List inputFiles) throws PipelineJobException
+ {
+ // find/cache annotations:
+ Container targetContainer = getPipelineCtx().getJob().getContainer().isWorkbook() ? getPipelineCtx().getJob().getContainer().getParent() : getPipelineCtx().getJob().getContainer();
+ ArrayList infoFields = new TableSelector(QueryService.get().getUserSchema(getPipelineCtx().getJob().getUser(), targetContainer, mGAPSchema.NAME).getTable(mGAPSchema.TABLE_VARIANT_ANNOTATIONS), PageFlowUtil.set("infoKey")).getArrayList(String.class);
+
+ getPipelineCtx().getSequenceSupport().cacheObject(INFO_FIELDS, infoFields);
+
+ }
+
+ private List getInfoFields() throws PipelineJobException
+ {
+ return getPipelineCtx().getSequenceSupport().getCachedObject(INFO_FIELDS, PipelineJob.createObjectMapper().getTypeFactory().constructParametricType(List.class, String.class));
+ }
+
@Override
public Output processVariants(File inputVCF, File outputDirectory, ReferenceGenome genome, @Nullable List intervals) throws PipelineJobException
{
@@ -56,7 +83,7 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
}
else
{
- getWrapper().execute(inputVCF, outputFile, genome.getWorkingFastaFile(), intervals);
+ getWrapper().execute(inputVCF, outputFile, genome.getWorkingFastaFile(), getInfoFields(), intervals);
}
output.setVcf(outputFile);
@@ -78,7 +105,7 @@ public RemoveAnnotationsWrapper(Logger log)
super(log);
}
- public void execute(File input, File outputFile, File referenceFasta, @Nullable List intervals) throws PipelineJobException
+ public void execute(File input, File outputFile, File referenceFasta, List allowableFields, @Nullable List intervals) throws PipelineJobException
{
List args = new ArrayList<>(getBaseArgs());
args.add("RemoveAnnotations");
@@ -97,7 +124,7 @@ public void execute(File input, File outputFile, File referenceFasta, @Nullable
});
}
- for (String key : ALLOWABLE_ANNOTATIONS)
+ for (String key : allowableFields)
{
args.add("-A");
args.add(key);
diff --git a/mGAP/src/org/labkey/mgap/pipeline/SnpSiftWrapper.java b/mGAP/src/org/labkey/mgap/pipeline/SnpSiftWrapper.java
index 1057086d1..706f91bb3 100644
--- a/mGAP/src/org/labkey/mgap/pipeline/SnpSiftWrapper.java
+++ b/mGAP/src/org/labkey/mgap/pipeline/SnpSiftWrapper.java
@@ -1,6 +1,7 @@
package org.labkey.mgap.pipeline;
import org.apache.commons.io.FileUtils;
+import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.labkey.api.pipeline.PipelineJobException;
import org.labkey.api.pipeline.PipelineJobService;
@@ -23,7 +24,7 @@ public SnpSiftWrapper(Logger log)
super(log);
}
- public void runSnpSift(File dbnsfpFile, File input, File output) throws PipelineJobException
+ public void runSnpSift(File dbnsfpFile, File input, File output, List fieldList) throws PipelineJobException
{
getLogger().info("Annotating VCF with SnpSift");
@@ -38,6 +39,9 @@ public void runSnpSift(File dbnsfpFile, File input, File output) throws Pipeline
params.add("-noDownload");
+ params.add("-f");
+ params.add(StringUtils.join(fieldList, ","));
+
params.add(input.getPath());
File unzippedVcf = new File(getOutputDir(output), "snpSift.vcf");
diff --git a/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java b/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java
index e9462a65a..893f01984 100644
--- a/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java
+++ b/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java
@@ -16,7 +16,6 @@
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.jetbrains.annotations.Nullable;
-import org.json.JSONArray;
import org.json.JSONObject;
import org.junit.Assert;
import org.junit.Test;
@@ -933,7 +932,7 @@ private void checkVcfAnnotationsAndSamples(File vcfInput, boolean skipAnnotation
if (!skipAnnotationChecks)
{
- for (String info : Arrays.asList("CADD_PH", "OMIMN", "CLN_ALLELE", "AF", "mGAPV"))
+ for (String info : Arrays.asList("CADD_PH", "OMIM_PHENO", "CLN_ALLELE", "AF", "mGAPV"))
{
if (!header.hasInfoLine(info))
{
@@ -1080,16 +1079,16 @@ private void inspectAndSummarizeVcf(JobContext ctx, File vcfInput, GeneToNameTra
}
}
- Set omims = new LinkedHashSet<>();
- Set omimds = new LinkedHashSet<>();
- if (vc.getAttribute("OMIMN") != null)
+ Set omimIds = new LinkedHashSet<>();
+ Set omimPhenotypes = new LinkedHashSet<>();
+ if (vc.getAttribute("MIMNUMBER") != null)
{
- omims.add(vc.getAttributeAsString("OMIMN", null));
+ omimIds.add(vc.getAttributeAsString("MIMNUMBER", null));
}
- if (vc.getAttribute("OMIMD") != null)
+ if (vc.getAttribute("OMIM_PHENO") != null)
{
- omimds.addAll(parseRawOmimd(vc, ctx.getLogger()));
+ omimPhenotypes.addAll(parseRawOmimPheno(vc, ctx.getLogger()));
}
Set overlappingGenes = new TreeSet<>();
@@ -1131,6 +1130,11 @@ private void inspectAndSummarizeVcf(JobContext ctx, File vcfInput, GeneToNameTra
geneName = translator.getGeneMap().get(geneName).get("gene_name");
}
+ if (tokens.length > 7 && !"protein_coding".equals(tokens[7])) {
+ ctx.getLogger().info("skipping non protein_coding ANN: " + ann);
+ continue;
+ }
+
overlappingGenes.add(geneName);
}
}
@@ -1162,7 +1166,7 @@ private void inspectAndSummarizeVcf(JobContext ctx, File vcfInput, GeneToNameTra
String overlappingGenesJoin = StringUtils.join(overlappingGenes, ",");
if (!overlappingGenesReported.contains(overlappingGenesJoin))
{
- maybeWriteVariantLine(queuedLines, vc, tokens[0], "SNPEff", "Predicted High Impact", description, overlappingGenes, omims, omimds, ctx.getLogger(), null);
+ maybeWriteVariantLine(queuedLines, vc, tokens[0], "SNPEff", "Predicted High Impact", description, overlappingGenes, omimIds, omimPhenotypes, ctx.getLogger(), null);
// NOTE: a given site could have multiple overlapping ORFs (usually different isoforms), so if we hit one allow this to tag that site and skip the remaining.
overlappingGenesReported.add(overlappingGenesJoin);
@@ -1173,14 +1177,24 @@ private void inspectAndSummarizeVcf(JobContext ctx, File vcfInput, GeneToNameTra
if (vc.getAttribute("CLN_SIG") != null)
{
- List clnAlleles = vc.getAttributeAsStringList("CLN_ALLELE", "");
List clnSigs = vc.getAttributeAsStringList("CLN_SIG", "");
+ if (clnSigs.size() != vc.getAlternateAlleles().size())
+ {
+ throw new IllegalStateException("CLN_SIG and alt alleles were not the same length: " + vc.toStringWithoutGenotypes());
+ }
+
List clnDisease = vc.getAttributeAsStringList("CLN_DN", "");
List clnAlleleIds = vc.getAttributeAsStringList("CLN_ALLELEID", "");
int i = -1;
for (String sigList : clnSigs)
{
i++;
+ if (sigList.isEmpty())
+ {
+ continue;
+ }
+
+ Allele altAllele = vc.getAlternateAllele(i);
String[] sigSplit = sigList.split("\\|");
List diseaseSplit = Arrays.asList(clnDisease.get(i).split("\\|"));
@@ -1196,8 +1210,7 @@ private void inspectAndSummarizeVcf(JobContext ctx, File vcfInput, GeneToNameTra
try
{
- String allele = clnAlleles.get(i);
- maybeWriteVariantLine(queuedLines, vc, allele, "ClinVar", diseaseSplit.get(j), description, overlappingGenes, omims, omimds, ctx.getLogger(), "ClinVar:" + clnAlleleIds.get(i));
+ maybeWriteVariantLine(queuedLines, vc, altAllele.getBaseString(), "ClinVar", diseaseSplit.get(j), description, overlappingGenes, omimIds, omimPhenotypes, ctx.getLogger(), "ClinVar:" + clnAlleleIds.get(i));
}
catch (IndexOutOfBoundsException e)
@@ -1214,36 +1227,57 @@ private void inspectAndSummarizeVcf(JobContext ctx, File vcfInput, GeneToNameTra
}
}
- //NE: nsdb Polyphen2_HVAR_score: Polyphen2 score based on HumVar, i.e. hvar_prob. The score ranges from 0 to 1, and the corresponding prediction is 'probably damaging' if it is in [0.909,1], 'possibly damaging' if it is in [0.447,0.908], 'benign' if it is in [0,0.446]. Score cutoff for binary classification is 0.5, i.e. the prediction is 'neutral' if the score is smaller than 0.5 and 'deleterious' if the score is larger than 0.5. Multiple entries separated by
- //NF: nsdb Polyphen2_HVAR_pred: Polyphen2 prediction based on HumVar, 'D' ('probably damaging'),'P' ('possibly damaging') and 'B' ('benign'). Multiple entries separated by
- if (vc.getAttribute("NF") != null && !".".equals(vc.getAttribute("NF")))
+ //Polyphen2_HVAR_S: Polyphen2 score based on HumVar, i.e. hvar_prob. The score ranges from 0 to 1, and the corresponding prediction is 'probably damaging' if it is in [0.909,1], 'possibly damaging' if it is in [0.447,0.908], 'benign' if it is in [0,0.446]. Score cutoff for binary classification is 0.5, i.e. the prediction is 'neutral' if the score is smaller than 0.5 and 'deleterious' if the score is larger than 0.5. Multiple entries separated by
+ //Polyphen2_HVAR_pred: Polyphen2 prediction based on HumVar, 'D' ('probably damaging'),'P' ('possibly damaging') and 'B' ('benign'). Multiple entries separated by
+ if (vc.getAttribute("Polyphen2_HVAR_pred") != null && !".".equals(vc.getAttribute("Polyphen2_HVAR_pred")))
{
- Set polyphenPredictions = new HashSet<>(vc.getAttributeAsStringList("NF", null));
- polyphenPredictions.remove("B");
- polyphenPredictions.remove("P");
+ List polyphenPredictions = vc.getAttributeAsStringList("Polyphen2_HVAR_pred", null);
+ List polyphenScores = vc.getAttributeAsDoubleList("Polyphen2_HVAR_S", 0.0);
+
+ if (polyphenPredictions.size() != vc.getAlternateAlleles().size())
+ {
+ throw new IllegalStateException("Polyphen2_HVAR_pred and alt alleles were not the same length: " + vc.toStringWithoutGenotypes());
+ }
+
+ if (polyphenScores.size() != vc.getAlternateAlleles().size())
+ {
+ throw new IllegalStateException("Polyphen2_HVAR_S and alt alleles were not the same length: " + vc.toStringWithoutGenotypes());
+ }
- String description = null;
- if (!polyphenPredictions.isEmpty())
+ int alleleIdx = -1;
+ for (Allele alt : vc.getAlternateAlleles())
{
+ alleleIdx++;
+
+ String prediction = polyphenPredictions.get(alleleIdx);
+ if (StringUtils.isEmpty(prediction) || "B".equals(prediction) || "P".equals(prediction) || ".".equals(prediction))
+ {
+ continue;
+ }
+
+ String description = null;
try
{
- Double maxScore = Collections.max(vc.getAttributeAsDoubleList("NE", 0.0));
- description = StringUtils.join(new String[]{
- "Score: " + maxScore
- }, ",");
+ Double maxScore = polyphenScores.get(alleleIdx);
+ if (maxScore == 0.0)
+ {
+ ctx.getLogger().error("Suspicious values for Polyphen2_HVAR_S: " + maxScore + ", at position: " + vc.toStringWithoutGenotypes());
+ }
+
+ description = "Score: " + maxScore;
}
catch (NumberFormatException e)
{
- ctx.getLogger().warn("Unable to parse NE attribute decimal (" + vc.getAttribute("NE") + ") for variant at position: " + vc.toStringWithoutGenotypes());
+ ctx.getLogger().error("Unable to parse Polyphen2_HVAR_S attribute decimal (" + vc.getAttribute("Polyphen2_HVAR_S") + ") for variant at position: " + vc.toStringWithoutGenotypes());
}
- maybeWriteVariantLine(queuedLines, vc, null, "Polyphen2", "Prediction: " + StringUtils.join(polyphenPredictions, ","), description, overlappingGenes, omims, omimds, ctx.getLogger(), null);
+ maybeWriteVariantLine(queuedLines, vc, alt.getBaseString(), "Polyphen2", "Prediction: " + prediction, description, overlappingGenes, omimIds, omimPhenotypes, ctx.getLogger(), null);
}
}
for (List line : queuedLines)
{
- writer.writeNext(line.toArray(new String[line.size()]));
+ writer.writeNext(line.toArray(new String[0]));
}
}
}
@@ -1264,17 +1298,17 @@ private void inspectAndSummarizeVcf(JobContext ctx, File vcfInput, GeneToNameTra
}
}
- public Collection parseRawOmimd(VariantContext vc, Logger log)
+ public Collection parseRawOmimPheno(VariantContext vc, Logger log)
{
//NOTE: because this field can have internal commas, this can be parsed incorrectly, so ignore this and re-join
String rawVal;
- if (vc.getAttribute("OMIMD") instanceof Collection)
+ if (vc.getAttribute("OMIM_PHENO") instanceof Collection)
{
- rawVal = StringUtils.join(vc.getAttributeAsStringList("OMIMD", null), ",");
+ rawVal = StringUtils.join(vc.getAttributeAsStringList("OMIM_PHENO", null), ",");
}
else
{
- rawVal = vc.getAttributeAsString("OMIMD", null);
+ rawVal = vc.getAttributeAsString("OMIM_PHENO", null);
}
if (!StringUtils.isEmpty(rawVal) && ! ".".equals(rawVal))
@@ -1331,7 +1365,7 @@ private void generateSummaries(JobContext ctx, File vcf, ReferenceGenome genome,
generateSummary(ctx, variantsToTable, summaryTable, summaryTableByField, totalVariants, totalPrivateVariants, totalSubjects, typeCounts);
}
- private static final List allowedFields = Arrays.asList("CHROM", "ANN", "CLN_SIG", "GRASP_PH", "ENCTFBS_TF", "FE", "NF", "ENCSEG_NM");
+ private static final List allowedFields = Arrays.asList("CHROM", "ANN", "CLN_SIG", "FANTOM5_TFBS", "FANTOM_ENHANCER", "Polyphen2_HVAR_pred");
private class FieldTracker
{
@@ -1413,30 +1447,18 @@ else if ("CLN_SIG".equals(fieldName))
addForValue("AnnotationSummary", "ClinVar Overlap");
}
}
- else if ("GRASP_PH".equals(fieldName))
- {
- addForValue("AnnotationSummary", "GWAS Associations (GRASP)");
- }
- else if ("FE".equals(fieldName) && "Y".equals(val))
+ else if ("FANTOM_ENHANCER".equals(fieldName) && "Y".equals(val))
{
addForValue("AnnotationSummary", "Enhancer Region (FANTOM5)");
}
- else if ("ENCTFBS_TF".equals(fieldName))
+ else if ("FANTOM5_TFBS".equals(fieldName))
{
- addForValue("AnnotationSummary", "Transcription Factor Binding (ENCODE)");
+ addForValue("AnnotationSummary", "Transcription Factor Binding (FANTOM5)");
}
- else if ("NF".equals(fieldName) && val.contains("D"))
+ else if ("Polyphen2_HVAR_pred".equals(fieldName) && val.contains("D"))
{
addForValue("AnnotationSummary", "Damaging (Polyphen2)");
}
- else if ("ENCSEG_NM".equals(fieldName))
- {
- List values = Arrays.asList(val.split(","));
- if (values.contains("E"))
- {
- addForValue("AnnotationSummary", "Predicted Enhancer (ENCODE)");
- }
- }
else if ("CHROM".equals(fieldName))
{
addForValue("PerChromosome", val);
@@ -1586,7 +1608,7 @@ private void generateSummary(JobContext ctx, File variantsToTable, File output,
}
}
- private void maybeWriteVariantLine(Set> queuedLines, VariantContext vc, @Nullable String allele, String source, String reason, String description, Collection overlappingGenes, Collection omims, Collection omimds, Logger log, String identifier)
+ private void maybeWriteVariantLine(Set> queuedLines, VariantContext vc, @Nullable String allele, String source, String reason, String description, Collection overlappingGenes, Collection omimIds, Collection omimPhenotypes, Logger log, String identifier)
{
if (allele == null)
{
@@ -1635,7 +1657,7 @@ else if (af != null)
Object cadd = vc.getAttribute("CADD_PH");
- queuedLines.add(Arrays.asList(vc.getContig(), String.valueOf(vc.getStart()), vc.getReference().getDisplayString(), allele, source, reason, (description == null ? "" : description), StringUtils.join(overlappingGenes, ";"), StringUtils.join(omims, ";"), StringUtils.join(omimds, ";"), af == null ? "" : af.toString(), identifier == null ? "" : identifier, cadd == null ? "" : cadd.toString()));
+ queuedLines.add(Arrays.asList(vc.getContig(), String.valueOf(vc.getStart()), vc.getReference().getDisplayString(), allele, source, reason, (description == null ? "" : description), StringUtils.join(overlappingGenes, ";"), StringUtils.join(omimIds, ";"), StringUtils.join(omimPhenotypes, ";"), af == null ? "" : af.toString(), identifier == null ? "" : identifier, cadd == null ? "" : cadd.toString()));
}
private boolean indexExists(File vcf)
@@ -1658,7 +1680,7 @@ public Set parseOmim(String input, Logger log)
{
if (StringUtils.isEmpty(token))
{
- log.warn("OMIMD was empty: " + input + ", " + StringUtils.join(tokens, ";"));
+ log.warn("OMIM_PHENO was empty: " + input + ", " + StringUtils.join(tokens, ";"));
continue;
}
@@ -1830,13 +1852,6 @@ public void testOMIMParse() throws Exception
{
Set ret = pr.parseOmim(pair.getLeft(), _log);
Assert.assertEquals(pair.getRight(), ret);
-
- //NOTE: since this requires an API key and queries OMIM not suitable to general testing, but this can be uncommented for local dev
- //for (String term : ret)
- //{
- // String updated = pr.updateOmimD(term, ContainerManager.getRoot(), _log);
- // Assert.assertNotNull(updated);
- //}
}
}
}
diff --git a/mGAP/test/src/org/labkey/test/tests/mgap/MgapTest.java b/mGAP/test/src/org/labkey/test/tests/mgap/MgapTest.java
new file mode 100644
index 000000000..b51dcd161
--- /dev/null
+++ b/mGAP/test/src/org/labkey/test/tests/mgap/MgapTest.java
@@ -0,0 +1,148 @@
+/*
+ * Copyright (c) 2020 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.labkey.test.tests.mgap;
+
+import org.apache.commons.lang3.tuple.Pair;
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.experimental.categories.Category;
+import org.labkey.test.BaseWebDriverTest;
+import org.labkey.test.Locator;
+import org.labkey.test.TestTimeoutException;
+import org.labkey.test.WebTestHelper;
+import org.labkey.test.categories.External;
+import org.labkey.test.categories.LabModule;
+import org.labkey.test.tests.external.labModules.JBrowseTest;
+import org.labkey.test.tests.external.labModules.JBrowseTestHelper;
+import org.labkey.test.tests.external.labModules.SequenceTest;
+import org.labkey.test.util.external.labModules.LabModuleHelper;
+import org.openqa.selenium.WebElement;
+import org.openqa.selenium.interactions.Actions;
+
+import java.util.List;
+
+@Category({External.class, LabModule.class})
+public class MgapTest extends BaseWebDriverTest
+{
+ protected LabModuleHelper _helper = new LabModuleHelper(this);
+
+ @Test
+ public void testMgapModule() throws Exception
+ {
+ setupTest();
+
+ testSessionCardDisplay();
+ testmGapSessionCardDisplay();
+ testFullTextSearch();
+ }
+
+ @Override
+ protected void doCleanup(boolean afterTest) throws TestTimeoutException
+ {
+ super.doCleanup(afterTest);
+ }
+
+ private void setupTest() throws Exception
+ {
+ _containerHelper.createProject(getProjectName(), "mGAP");
+
+ goToProjectHome();
+
+ beginAt("/mgap/" + getProjectName() + "/updateAnnotations.view");
+ clickButton("OK");
+
+ beginAt(WebTestHelper.getBaseURL() + "/mgap/" + getProjectName() + "/importStudy.view");
+ clickButton("OK");
+ waitForPipelineJobsToComplete(1, "Study import", false, MAX_WAIT_SECONDS * 2500);
+
+ if (!SequenceTest.isExternalPipelineEnabled(getProjectName()))
+ {
+ log("JBrowseTest.testFullTextSearch() requires external tools, including DISCVRSeq.jar, skipping");
+ return;
+ }
+
+ String seq = SequenceTest.readSeqFromFile(JBrowseTestHelper.GRCH37_GENOME);
+ SequenceTest.ensureRefSeqExists(this, "1", seq);
+ SequenceTest.createReferenceGenome(this, 1, JBrowseTest.JB_GENOME_NAME, "1");
+
+ SequenceTest.addOutputFile(this, JBrowseTestHelper.MGAP_TEST_VCF, JBrowseTest.JB_GENOME_NAME, "TestVCF", "VCF File", "This is an output file to test VCF full-text search", false);
+ }
+
+ private void testSessionCardDisplay()
+ {
+ beginAt("/" + getProjectName() + "/jbrowse-jbrowse.view?session=mgap&location=1:8328..8842");
+ JBrowseTestHelper.waitForJBrowseToLoad(this);
+
+ Actions actions = new Actions(getDriver());
+ WebElement toClick = getDriver().findElements(JBrowseTestHelper.getVariantWithinTrack(this, "mgap_hg38", "SNV A -> G")).stream().filter(WebElement::isDisplayed).collect(JBrowseTestHelper.toSingleton());
+ actions.click(toClick).perform();
+ waitForElement(Locator.tagWithText("span", "Section 1"));
+
+ waitForElement(Locator.tagWithText("td", "Allele Count"));
+ }
+
+ private void testmGapSessionCardDisplay()
+ {
+ beginAt("/" + getProjectName() + "/jbrowse-jbrowse.view?session=mgapF&location=1:8328..8842");
+ JBrowseTestHelper.waitForJBrowseToLoad(this);
+ sleep(200); // The session can refresh after filter applied
+
+ Actions actions = new Actions(getDriver());
+ Assert.assertEquals("Incorrect number of variants", 1, JBrowseTestHelper.getTotalVariantFeatures(this));
+
+ WebElement toClick = getDriver().findElements(JBrowseTestHelper.getVariantWithinTrack(this, "mgap_hg38", "SNV A -> T")).stream().filter(WebElement::isDisplayed).collect(JBrowseTestHelper.toSingleton());
+ actions.click(toClick).perform();
+ waitForElement(Locator.tagWithText("span", "Genes and Gene Predictions"));
+
+ waitForElement(Locator.tagWithText("td", "Unable to Lift to Human"));
+ }
+
+ private void testFullTextSearch() throws Exception
+ {
+ if (!SequenceTest.isExternalPipelineEnabled(getProjectName()))
+ {
+ log("JBrowseTest.testFullTextSearch() requires external tools, including DISCVRSeq.jar, skipping");
+ return;
+ }
+
+ JBrowseTestHelper.prepareSearchSession(this, getProjectName());
+ Pair info = JBrowseTestHelper.configureSearchSession(this, getProjectName());
+ String sessionId = info.getKey();
+ String trackId = info.getValue();
+
+
+ }
+
+ @Before
+ public void preTest()
+ {
+ goToProjectHome();
+ }
+
+ @Override
+ protected String getProjectName()
+ {
+ return "MgapTestProject";
+ }
+
+ @Override
+ public List getAssociatedModules()
+ {
+ return List.of("jbrowse", "mGAP");
+ }
+}
\ No newline at end of file
diff --git a/mGAP/tools/images/AnnotationStrategy.pdf b/mGAP/tools/images/AnnotationStrategy.pdf
new file mode 100644
index 000000000..9cdb0e008
Binary files /dev/null and b/mGAP/tools/images/AnnotationStrategy.pdf differ
diff --git a/mcc/build.gradle b/mcc/build.gradle
index ada581be9..f96ede315 100644
--- a/mcc/build.gradle
+++ b/mcc/build.gradle
@@ -9,6 +9,7 @@ configurations.all {
}
dependencies {
+ BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:Studies", depProjectConfig: "apiJarFile")
BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:jbrowse", depProjectConfig: "apiJarFile")
BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:SequenceAnalysis", depProjectConfig: "apiJarFile")
BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:laboratory", depProjectConfig: "apiJarFile")
diff --git a/mcc/package-lock.json b/mcc/package-lock.json
index dfa8d782d..655fad19e 100644
--- a/mcc/package-lock.json
+++ b/mcc/package-lock.json
@@ -8,7 +8,7 @@
"name": "mcc",
"version": "0.0.0",
"dependencies": {
- "@labkey/api": "^1.16.0",
+ "@labkey/api": "^1.23.0",
"@labkey/components": "~2.217.0",
"@material-ui/core": "^4.12.4",
"@material-ui/styles": "^4.11.5",
@@ -20,30 +20,32 @@
"react-hot-loader": "^4.13.0",
"react-tooltip": "^4.2.21",
"tsv": "^0.2.0",
- "uuid": "^8.3.2"
+ "uuid": "^9.0.0"
},
"devDependencies": {
- "@labkey/build": "~6.1.0",
+ "@labkey/build": "^6.14.0",
"@types/chart.js": "^2.9.37",
- "@types/enzyme": "3.10.9",
- "@types/enzyme-adapter-react-16": "1.0.6",
- "@types/jest": "^27.5.2",
- "@types/react-dom": "^17.0.2",
+ "@types/jest": "^29.0.0",
+ "@types/jexl": "^2.3.1",
+ "@types/jquery": "^3.0.0",
+ "@types/node": "^18.17.1",
"@types/tsv": "^0.2.1",
- "@types/uuid": "^8.3.4",
+ "@wojtekmaj/enzyme-adapter-react-17": "^0.8.0",
"enzyme": "^3.11.0",
- "enzyme-adapter-react-16": "1.15.6",
- "jest": "^27.4.7",
- "jest-cli": "^27.5.1",
- "ts-jest": "^27.1.5"
+ "jest": "^29.0.0",
+ "jest-cli": "^29.0.0",
+ "jest-mock": "^29.0.0",
+ "jsdom-global": "^3.0.2",
+ "rimraf": "^3.0.2",
+ "ts-jest": "^29.0.0"
}
},
"node_modules/@ampproject/remapping": {
- "version": "2.2.0",
- "resolved": "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.2.0.tgz",
- "integrity": "sha512-qRmjj8nj9qmLTQXXmaR1cck3UXSRMPrbsLJAasZpF+t3riI71BXed5ebIOYwQntykeZuhjsdweEc9BxH5Jc26w==",
+ "version": "2.2.1",
+ "resolved": "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.2.1.tgz",
+ "integrity": "sha512-lFMjJTrFL3j7L9yBxwYfCq2k6qqwHyzuUl/XBnif78PWTJYyL/dfowQHWE3sp6U6ZzqWiiIZnpTMO96zhkjwtg==",
"dependencies": {
- "@jridgewell/gen-mapping": "^0.1.0",
+ "@jridgewell/gen-mapping": "^0.3.0",
"@jridgewell/trace-mapping": "^0.3.9"
},
"engines": {
@@ -51,43 +53,43 @@
}
},
"node_modules/@babel/code-frame": {
- "version": "7.16.7",
- "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.16.7.tgz",
- "integrity": "sha512-iAXqUn8IIeBTNd72xsFlgaXHkMBMt6y4HJp1tIaK465CWLT/fG1aqB7ykr95gHHmlBdGbFeWWfyB4NJJ0nmeIg==",
+ "version": "7.22.5",
+ "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.22.5.tgz",
+ "integrity": "sha512-Xmwn266vad+6DAqEB2A6V/CcZVp62BbwVmcOJc2RPuwih1kw02TjQvWVWlcKGbBPd+8/0V5DEkOcizRGYsspYQ==",
"dependencies": {
- "@babel/highlight": "^7.16.7"
+ "@babel/highlight": "^7.22.5"
},
"engines": {
"node": ">=6.9.0"
}
},
"node_modules/@babel/compat-data": {
- "version": "7.17.10",
- "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.17.10.tgz",
- "integrity": "sha512-GZt/TCsG70Ms19gfZO1tM4CVnXsPgEPBCpJu+Qz3L0LUDsY5nZqFZglIoPC1kIYOtNBZlrnFT+klg12vFGZXrw==",
+ "version": "7.22.9",
+ "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.22.9.tgz",
+ "integrity": "sha512-5UamI7xkUcJ3i9qVDS+KFDEK8/7oJ55/sJMB1Ge7IEapr7KfdfV/HErR+koZwOfd+SgtFKOKRhRakdg++DcJpQ==",
"engines": {
"node": ">=6.9.0"
}
},
"node_modules/@babel/core": {
- "version": "7.17.8",
- "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.17.8.tgz",
- "integrity": "sha512-OdQDV/7cRBtJHLSOBqqbYNkOcydOgnX59TZx4puf41fzcVtN3e/4yqY8lMQsK+5X2lJtAdmA+6OHqsj1hBJ4IQ==",
+ "version": "7.20.12",
+ "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.20.12.tgz",
+ "integrity": "sha512-XsMfHovsUYHFMdrIHkZphTN/2Hzzi78R08NuHfDBehym2VsPDL6Zn/JAD/JQdnRvbSsbQc4mVaU1m6JgtTEElg==",
"dependencies": {
"@ampproject/remapping": "^2.1.0",
- "@babel/code-frame": "^7.16.7",
- "@babel/generator": "^7.17.7",
- "@babel/helper-compilation-targets": "^7.17.7",
- "@babel/helper-module-transforms": "^7.17.7",
- "@babel/helpers": "^7.17.8",
- "@babel/parser": "^7.17.8",
- "@babel/template": "^7.16.7",
- "@babel/traverse": "^7.17.3",
- "@babel/types": "^7.17.0",
+ "@babel/code-frame": "^7.18.6",
+ "@babel/generator": "^7.20.7",
+ "@babel/helper-compilation-targets": "^7.20.7",
+ "@babel/helper-module-transforms": "^7.20.11",
+ "@babel/helpers": "^7.20.7",
+ "@babel/parser": "^7.20.7",
+ "@babel/template": "^7.20.7",
+ "@babel/traverse": "^7.20.12",
+ "@babel/types": "^7.20.7",
"convert-source-map": "^1.7.0",
"debug": "^4.1.0",
"gensync": "^1.0.0-beta.2",
- "json5": "^2.1.2",
+ "json5": "^2.2.2",
"semver": "^6.3.0"
},
"engines": {
@@ -98,74 +100,54 @@
"url": "https://opencollective.com/babel"
}
},
- "node_modules/@babel/core/node_modules/semver": {
- "version": "6.3.0",
- "resolved": "https://registry.npmjs.org/semver/-/semver-6.3.0.tgz",
- "integrity": "sha512-b39TBaTSfV6yBrapU89p5fKekE2m/NwnDocOVruQFS1/veMgdzuPcnOM34M6CwxW8jH/lxEa5rBoDeUwu5HHTw==",
- "bin": {
- "semver": "bin/semver.js"
- }
- },
"node_modules/@babel/generator": {
- "version": "7.18.0",
- "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.18.0.tgz",
- "integrity": "sha512-81YO9gGx6voPXlvYdZBliFXAZU8vZ9AZ6z+CjlmcnaeOcYSFbMTpdeDUO9xD9dh/68Vq03I8ZspfUTPfitcDHg==",
+ "version": "7.22.9",
+ "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.22.9.tgz",
+ "integrity": "sha512-KtLMbmicyuK2Ak/FTCJVbDnkN1SlT8/kceFTiuDiiRUUSMnHMidxSCdG4ndkTOHHpoomWe/4xkvHkEOncwjYIw==",
"dependencies": {
- "@babel/types": "^7.18.0",
- "@jridgewell/gen-mapping": "^0.3.0",
+ "@babel/types": "^7.22.5",
+ "@jridgewell/gen-mapping": "^0.3.2",
+ "@jridgewell/trace-mapping": "^0.3.17",
"jsesc": "^2.5.1"
},
"engines": {
"node": ">=6.9.0"
}
},
- "node_modules/@babel/generator/node_modules/@jridgewell/gen-mapping": {
- "version": "0.3.1",
- "resolved": "https://registry.npmjs.org/@jridgewell/gen-mapping/-/gen-mapping-0.3.1.tgz",
- "integrity": "sha512-GcHwniMlA2z+WFPWuY8lp3fsza0I8xPFMWL5+n8LYyP6PSvPrXf4+n8stDHZY2DM0zy9sVkRDy1jDI4XGzYVqg==",
- "dependencies": {
- "@jridgewell/set-array": "^1.0.0",
- "@jridgewell/sourcemap-codec": "^1.4.10",
- "@jridgewell/trace-mapping": "^0.3.9"
- },
- "engines": {
- "node": ">=6.0.0"
- }
- },
"node_modules/@babel/helper-annotate-as-pure": {
- "version": "7.16.7",
- "resolved": "https://registry.npmjs.org/@babel/helper-annotate-as-pure/-/helper-annotate-as-pure-7.16.7.tgz",
- "integrity": "sha512-s6t2w/IPQVTAET1HitoowRGXooX8mCgtuP5195wD/QJPV6wYjpujCGF7JuMODVX2ZAJOf1GT6DT9MHEZvLOFSw==",
+ "version": "7.22.5",
+ "resolved": "https://registry.npmjs.org/@babel/helper-annotate-as-pure/-/helper-annotate-as-pure-7.22.5.tgz",
+ "integrity": "sha512-LvBTxu8bQSQkcyKOU+a1btnNFQ1dMAd0R6PyW3arXes06F6QLWLIrd681bxRPIXlrMGR3XYnW9JyML7dP3qgxg==",
"dev": true,
"dependencies": {
- "@babel/types": "^7.16.7"
+ "@babel/types": "^7.22.5"
},
"engines": {
"node": ">=6.9.0"
}
},
"node_modules/@babel/helper-builder-binary-assignment-operator-visitor": {
- "version": "7.16.7",
- "resolved": "https://registry.npmjs.org/@babel/helper-builder-binary-assignment-operator-visitor/-/helper-builder-binary-assignment-operator-visitor-7.16.7.tgz",
- "integrity": "sha512-C6FdbRaxYjwVu/geKW4ZeQ0Q31AftgRcdSnZ5/jsH6BzCJbtvXvhpfkbkThYSuutZA7nCXpPR6AD9zd1dprMkA==",
+ "version": "7.22.5",
+ "resolved": "https://registry.npmjs.org/@babel/helper-builder-binary-assignment-operator-visitor/-/helper-builder-binary-assignment-operator-visitor-7.22.5.tgz",
+ "integrity": "sha512-m1EP3lVOPptR+2DwD125gziZNcmoNSHGmJROKoy87loWUQyJaVXDgpmruWqDARZSmtYQ+Dl25okU8+qhVzuykw==",
"dev": true,
"dependencies": {
- "@babel/helper-explode-assignable-expression": "^7.16.7",
- "@babel/types": "^7.16.7"
+ "@babel/types": "^7.22.5"
},
"engines": {
"node": ">=6.9.0"
}
},
"node_modules/@babel/helper-compilation-targets": {
- "version": "7.17.10",
- "resolved": "https://registry.npmjs.org/@babel/helper-compilation-targets/-/helper-compilation-targets-7.17.10.tgz",
- "integrity": "sha512-gh3RxjWbauw/dFiU/7whjd0qN9K6nPJMqe6+Er7rOavFh0CQUSwhAE3IcTho2rywPJFxej6TUUHDkWcYI6gGqQ==",
+ "version": "7.22.9",
+ "resolved": "https://registry.npmjs.org/@babel/helper-compilation-targets/-/helper-compilation-targets-7.22.9.tgz",
+ "integrity": "sha512-7qYrNM6HjpnPHJbopxmb8hSPoZ0gsX8IvUS32JGVoy+pU9e5N0nLr1VjJoR6kA4d9dmGLxNYOjeB8sUDal2WMw==",
"dependencies": {
- "@babel/compat-data": "^7.17.10",
- "@babel/helper-validator-option": "^7.16.7",
- "browserslist": "^4.20.2",
- "semver": "^6.3.0"
+ "@babel/compat-data": "^7.22.9",
+ "@babel/helper-validator-option": "^7.22.5",
+ "browserslist": "^4.21.9",
+ "lru-cache": "^5.1.1",
+ "semver": "^6.3.1"
},
"engines": {
"node": ">=6.9.0"
@@ -174,27 +156,21 @@
"@babel/core": "^7.0.0"
}
},
- "node_modules/@babel/helper-compilation-targets/node_modules/semver": {
- "version": "6.3.0",
- "resolved": "https://registry.npmjs.org/semver/-/semver-6.3.0.tgz",
- "integrity": "sha512-b39TBaTSfV6yBrapU89p5fKekE2m/NwnDocOVruQFS1/veMgdzuPcnOM34M6CwxW8jH/lxEa5rBoDeUwu5HHTw==",
- "bin": {
- "semver": "bin/semver.js"
- }
- },
"node_modules/@babel/helper-create-class-features-plugin": {
- "version": "7.18.0",
- "resolved": "https://registry.npmjs.org/@babel/helper-create-class-features-plugin/-/helper-create-class-features-plugin-7.18.0.tgz",
- "integrity": "sha512-Kh8zTGR9de3J63e5nS0rQUdRs/kbtwoeQQ0sriS0lItjC96u8XXZN6lKpuyWd2coKSU13py/y+LTmThLuVX0Pg==",
+ "version": "7.22.9",
+ "resolved": "https://registry.npmjs.org/@babel/helper-create-class-features-plugin/-/helper-create-class-features-plugin-7.22.9.tgz",
+ "integrity": "sha512-Pwyi89uO4YrGKxL/eNJ8lfEH55DnRloGPOseaA8NFNL6jAUnn+KccaISiFazCj5IolPPDjGSdzQzXVzODVRqUQ==",
"dev": true,
"dependencies": {
- "@babel/helper-annotate-as-pure": "^7.16.7",
- "@babel/helper-environment-visitor": "^7.16.7",
- "@babel/helper-function-name": "^7.17.9",
- "@babel/helper-member-expression-to-functions": "^7.17.7",
- "@babel/helper-optimise-call-expression": "^7.16.7",
- "@babel/helper-replace-supers": "^7.16.7",
- "@babel/helper-split-export-declaration": "^7.16.7"
+ "@babel/helper-annotate-as-pure": "^7.22.5",
+ "@babel/helper-environment-visitor": "^7.22.5",
+ "@babel/helper-function-name": "^7.22.5",
+ "@babel/helper-member-expression-to-functions": "^7.22.5",
+ "@babel/helper-optimise-call-expression": "^7.22.5",
+ "@babel/helper-replace-supers": "^7.22.9",
+ "@babel/helper-skip-transparent-expression-wrappers": "^7.22.5",
+ "@babel/helper-split-export-declaration": "^7.22.6",
+ "semver": "^6.3.1"
},
"engines": {
"node": ">=6.9.0"
@@ -204,13 +180,14 @@
}
},
"node_modules/@babel/helper-create-regexp-features-plugin": {
- "version": "7.17.12",
- "resolved": "https://registry.npmjs.org/@babel/helper-create-regexp-features-plugin/-/helper-create-regexp-features-plugin-7.17.12.tgz",
- "integrity": "sha512-b2aZrV4zvutr9AIa6/gA3wsZKRwTKYoDxYiFKcESS3Ug2GTXzwBEvMuuFLhCQpEnRXs1zng4ISAXSUxxKBIcxw==",
+ "version": "7.22.9",
+ "resolved": "https://registry.npmjs.org/@babel/helper-create-regexp-features-plugin/-/helper-create-regexp-features-plugin-7.22.9.tgz",
+ "integrity": "sha512-+svjVa/tFwsNSG4NEy1h85+HQ5imbT92Q5/bgtS7P0GTQlP8WuFdqsiABmQouhiFGyV66oGxZFpeYHza1rNsKw==",
"dev": true,
"dependencies": {
- "@babel/helper-annotate-as-pure": "^7.16.7",
- "regexpu-core": "^5.0.1"
+ "@babel/helper-annotate-as-pure": "^7.22.5",
+ "regexpu-core": "^5.3.1",
+ "semver": "^6.3.1"
},
"engines": {
"node": ">=6.9.0"
@@ -220,15 +197,13 @@
}
},
"node_modules/@babel/helper-define-polyfill-provider": {
- "version": "0.3.1",
- "resolved": "https://registry.npmjs.org/@babel/helper-define-polyfill-provider/-/helper-define-polyfill-provider-0.3.1.tgz",
- "integrity": "sha512-J9hGMpJQmtWmj46B3kBHmL38UhJGhYX7eqkcq+2gsstyYt341HmPeWspihX43yVRA0mS+8GGk2Gckc7bY/HCmA==",
+ "version": "0.3.3",
+ "resolved": "https://registry.npmjs.org/@babel/helper-define-polyfill-provider/-/helper-define-polyfill-provider-0.3.3.tgz",
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- "babel-plugin-polyfill-corejs3": "^0.5.0",
- "babel-plugin-polyfill-regenerator": "^0.3.0",
- "core-js-compat": "^3.20.2",
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+ "babel-plugin-polyfill-corejs3": "^0.6.0",
+ "babel-plugin-polyfill-regenerator": "^0.4.1",
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},
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@@ -1661,19 +1658,10 @@
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}
},
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- "dev": true,
- "bin": {
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- }
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+ "resolved": "https://registry.npmjs.org/@babel/preset-modules/-/preset-modules-0.1.6.tgz",
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@@ -1683,21 +1671,21 @@
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},
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- "@babel/core": "^7.0.0-0"
+ "@babel/core": "^7.0.0-0 || ^8.0.0-0 <8.0.0"
}
},
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+ "resolved": "https://registry.npmjs.org/@babel/preset-react/-/preset-react-7.18.6.tgz",
+ "integrity": "sha512-zXr6atUmyYdiWRVLOZahakYmOBHtWc2WGCkP8PYTgZi0iJXDY2CN180TdrIW4OGOAdLc7TifzDIvtx6izaRIzg==",
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@@ -1707,14 +1695,14 @@
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+ "resolved": "https://registry.npmjs.org/@babel/preset-typescript/-/preset-typescript-7.18.6.tgz",
+ "integrity": "sha512-s9ik86kXBAnD760aybBucdpnLsAt0jK1xqJn2juOn9lkOvSHV60os5hxoVJsPzMQxvnUJFAlkont2DvvaYEBtQ==",
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+ "@babel/helper-validator-option": "^7.18.6",
+ "@babel/plugin-transform-typescript": "^7.18.6"
},
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@@ -1723,55 +1711,61 @@
"@babel/core": "^7.0.0-0"
}
},
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+ "resolved": "https://registry.npmjs.org/@babel/regjsgen/-/regjsgen-0.8.0.tgz",
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- "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.17.9.tgz",
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+ "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.22.6.tgz",
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+ "regenerator-runtime": "^0.13.11"
},
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}
},
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+ "core-js": "^2.6.12",
+ "regenerator-runtime": "^0.13.11"
},
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}
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+ "resolved": "https://registry.npmjs.org/@babel/template/-/template-7.22.5.tgz",
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},
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+ "version": "7.22.8",
+ "resolved": "https://registry.npmjs.org/@babel/traverse/-/traverse-7.22.8.tgz",
+ "integrity": "sha512-y6LPR+wpM2I3qJrsheCTwhIinzkETbplIgPBbwvqPKc+uljeA5gP+3nP8irdYt1mjQaDnlIcG+dw8OjAco4GXw==",
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@@ -1780,11 +1774,12 @@
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+ "version": "7.22.5",
+ "resolved": "https://registry.npmjs.org/@babel/types/-/types-7.22.5.tgz",
+ "integrity": "sha512-zo3MIHGOkPOfoRXitsgHLjEXmlDaD/5KU1Uzuc9GNiZPhSqVxVRtxuPaSBZDsYZ9qV88AjtMtWW7ww98loJ9KA==",
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+ "@babel/helper-string-parser": "^7.22.5",
+ "@babel/helper-validator-identifier": "^7.22.5",
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},
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@@ -1806,27 +1801,28 @@
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+ "resolved": "https://registry.npmjs.org/@emotion/babel-plugin/-/babel-plugin-11.11.0.tgz",
+ "integrity": "sha512-m4HEDZleaaCH+XgDDsPF15Ht6wTLsgDTeR3WYj9Q/k76JtWhrJjcP4+/XlG8LGT/Rol9qUfOIztXeA84ATpqPQ==",
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- "@emotion/memoize": "^0.7.5",
- "@emotion/serialize": "^1.0.2",
- "babel-plugin-macros": "^2.6.1",
+ "@babel/helper-module-imports": "^7.16.7",
+ "@babel/runtime": "^7.18.3",
+ "@emotion/hash": "^0.9.1",
+ "@emotion/memoize": "^0.8.1",
+ "@emotion/serialize": "^1.1.2",
+ "babel-plugin-macros": "^3.1.0",
"convert-source-map": "^1.5.0",
"escape-string-regexp": "^4.0.0",
"find-root": "^1.1.0",
"source-map": "^0.5.7",
- "stylis": "4.0.13"
- },
- "peerDependencies": {
- "@babel/core": "^7.0.0"
+ "stylis": "4.2.0"
}
},
+ "node_modules/@emotion/babel-plugin/node_modules/@emotion/hash": {
+ "version": "0.9.1",
+ "resolved": "https://registry.npmjs.org/@emotion/hash/-/hash-0.9.1.tgz",
+ "integrity": "sha512-gJB6HLm5rYwSLI6PQa+X1t5CFGrv1J1TWG+sOyMCeKz2ojaj6Fnl/rZEspogG+cvqbt4AE/2eIyD2QfLKTBNlQ=="
+ },
"node_modules/@emotion/babel-plugin/node_modules/escape-string-regexp": {
"version": "4.0.0",
"resolved": "https://registry.npmjs.org/escape-string-regexp/-/escape-string-regexp-4.0.0.tgz",
@@ -1838,16 +1834,24 @@
"url": "https://github.com/sponsors/sindresorhus"
}
},
+ "node_modules/@emotion/babel-plugin/node_modules/source-map": {
+ "version": "0.5.7",
+ "resolved": "https://registry.npmjs.org/source-map/-/source-map-0.5.7.tgz",
+ "integrity": "sha512-LbrmJOMUSdEVxIKvdcJzQC+nQhe8FUZQTXQy6+I75skNgn3OoQ0DZA8YnFa7gp8tqtL3KPf1kmo0R5DoApeSGQ==",
+ "engines": {
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+ "version": "11.11.0",
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},
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+ "resolved": "https://registry.npmjs.org/@emotion/weak-memoize/-/weak-memoize-0.2.5.tgz",
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},
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@@ -1936,16 +1945,16 @@
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+ "resolved": "https://registry.npmjs.org/@emotion/unitless/-/unitless-0.7.5.tgz",
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},
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"version": "10.3.0",
@@ -2057,35 +2073,43 @@
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}
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+ "resolved": "https://registry.npmjs.org/@emotion/unitless/-/unitless-0.7.5.tgz",
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+ },
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+ "resolved": "https://registry.npmjs.org/@emotion/unitless/-/unitless-0.8.1.tgz",
+ "integrity": "sha512-KOEGMu6dmJZtpadb476IsZBclKvILjopjUii3V+7MnXIQCYh8W3NgNcgwo21n9LXZX6EDIKvqfjYxXebDwxKmQ=="
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+ "resolved": "https://registry.npmjs.org/@emotion/use-insertion-effect-with-fallbacks/-/use-insertion-effect-with-fallbacks-1.0.1.tgz",
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+ "version": "0.3.1",
+ "resolved": "https://registry.npmjs.org/@emotion/weak-memoize/-/weak-memoize-0.3.1.tgz",
+ "integrity": "sha512-EsBwpc7hBUJWAsNPBmJy4hxWx12v6bshQsldrVmjxJoc3isbxhOrF2IcCpaXxfvq03NwkI7sbsOLXbYuqF/8Ww=="
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@@ -2142,14 +2166,14 @@
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+ "resolved": "https://registry.npmjs.org/@fortawesome/react-fontawesome/-/react-fontawesome-0.1.19.tgz",
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+ "prop-types": "^15.8.1"
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+ "@fortawesome/fontawesome-svg-core": "~1 || ~6",
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}
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@@ -2193,20 +2217,20 @@
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+ "version": "29.6.2",
+ "resolved": "https://registry.npmjs.org/@jest/console/-/console-29.6.2.tgz",
+ "integrity": "sha512-0N0yZof5hi44HAR2pPS+ikJ3nzKNoZdVu8FffRf3wy47I7Dm7etk/3KetMdRUqzVd16V4O2m2ISpNTbnIuqy1w==",
"dev": true,
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}
},
"node_modules/@jest/console/node_modules/ansi-styles": {
@@ -2267,6 +2291,15 @@
"node": ">=8"
}
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+ "version": "3.0.0",
+ "resolved": "https://registry.npmjs.org/slash/-/slash-3.0.0.tgz",
+ "integrity": "sha512-g9Q1haeby36OSStwb4ntCGGGaKsaVSjQ68fBxoQcutl5fS1vuY18H3wSt3jFyFtrkx+Kz0V1G85A4MyAdDMi2Q==",
+ "dev": true,
+ "engines": {
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+ }
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@@ -2280,42 +2313,42 @@
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+ "resolved": "https://registry.npmjs.org/@jest/core/-/core-29.6.2.tgz",
+ "integrity": "sha512-Oj+5B+sDMiMWLhPFF+4/DvHOf+U10rgvCLGPHP8Xlsy/7QxS51aU/eBngudHlJXnaWD5EohAgJ4js+T6pa+zOg==",
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@@ -2384,6 +2417,15 @@
"node": ">=8"
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+ "resolved": "https://registry.npmjs.org/slash/-/slash-3.0.0.tgz",
+ "integrity": "sha512-g9Q1haeby36OSStwb4ntCGGGaKsaVSjQ68fBxoQcutl5fS1vuY18H3wSt3jFyFtrkx+Kz0V1G85A4MyAdDMi2Q==",
+ "dev": true,
+ "engines": {
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@@ -2397,104 +2439,125 @@
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"dependencies": {
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@@ -4402,18 +4020,15 @@
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@@ -4441,11 +4056,6 @@
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"resolved": "https://registry.npmjs.org/react/-/react-16.14.0.tgz",
@@ -4473,13 +4083,18 @@
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@@ -4491,6 +4106,11 @@
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@@ -4512,7 +4132,7 @@
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- "integrity": "sha1-/O3M6PEpdTcVRdc1RhAzV5ptrpw=",
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@@ -4520,6 +4140,19 @@
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"dev": true,
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@@ -6426,6 +6030,10 @@
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@@ -8622,6 +8152,17 @@
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+ "funding": [
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+ "url": "https://github.com/sponsors/mdevils"
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@@ -9446,6 +9028,45 @@
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@@ -10739,6 +10260,15 @@
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@@ -10855,10 +10370,22 @@
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@@ -10882,13 +10409,19 @@
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}
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+ "resolved": "https://registry.npmjs.org/yallist/-/yallist-4.0.0.tgz",
+ "integrity": "sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A==",
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@@ -10970,20 +10503,20 @@
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+ "integrity": "sha512-GZitlqkMkhkefjfN/p3SJjrDaxPflqxEAv3/ik10OirZqJGYH5rPiIsgVcfof0Tdqg3shQGdEIxDBx+B4tuLzA==",
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+ "version": "29.6.2",
+ "resolved": "https://registry.npmjs.org/jest-worker/-/jest-worker-29.6.2.tgz",
+ "integrity": "sha512-l3ccBOabTdkng8I/ORCkADz4eSMKejTYv1vB/Z83UiubqhC1oQ5Li6dWCyqOIvSifGjUBxuvxvlm6KGK2DtuAQ==",
"devOptional": true,
"dependencies": {
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+ "jest-util": "^29.6.2",
"merge-stream": "^2.0.0",
"supports-color": "^8.0.0"
},
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- "node": ">= 10.13.0"
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@@ -11212,41 +10747,38 @@
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+ "version": "22.1.0",
+ "resolved": "https://registry.npmjs.org/jsdom/-/jsdom-22.1.0.tgz",
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@@ -11257,41 +10789,35 @@
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+ "node_modules/jsdom-global": {
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+ "integrity": "sha512-t1KMcBkz/pT5JrvcJbpUR2u/w1kO9jXctaaGJ0vZDzwFnIvGWw9IDSRciT83kIs8Bnw4qpOl8bQK08V01YgMPg==",
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- "punycode": "^2.1.1",
- "universalify": "^0.1.2"
- },
- "engines": {
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+ "peerDependencies": {
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+ "node_modules/jsdom/node_modules/ws": {
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+ "resolved": "https://registry.npmjs.org/ws/-/ws-8.13.0.tgz",
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"dev": true,
+ "peer": true,
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+ "node": ">=10.0.0"
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@@ -11340,9 +10866,9 @@
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+ "resolved": "https://registry.npmjs.org/jss/-/jss-10.10.0.tgz",
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@@ -11355,72 +10881,77 @@
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+ "version": "10.10.0",
+ "resolved": "https://registry.npmjs.org/jss-plugin-camel-case/-/jss-plugin-camel-case-10.10.0.tgz",
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- "jss": "10.9.0"
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+ "version": "10.10.0",
+ "resolved": "https://registry.npmjs.org/jss-plugin-default-unit/-/jss-plugin-default-unit-10.10.0.tgz",
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+ "resolved": "https://registry.npmjs.org/jss-plugin-global/-/jss-plugin-global-10.10.0.tgz",
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+ "version": "10.10.0",
+ "resolved": "https://registry.npmjs.org/jss-plugin-vendor-prefixer/-/jss-plugin-vendor-prefixer-10.10.0.tgz",
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+ "resolved": "https://registry.npmjs.org/csstype/-/csstype-3.1.2.tgz",
+ "integrity": "sha512-I7K1Uu0MBPzaFKg4nI5Q7Vs2t+3gWWW648spaF+Rg7pI9ds18Ugn+lvg4SHczUdKlHI5LWBXyqfS8+DufyBsgQ=="
+ },
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@@ -11450,9 +10981,9 @@
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+ "resolved": "https://registry.npmjs.org/klona/-/klona-2.0.6.tgz",
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@@ -11466,55 +10997,31 @@
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}
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"define-properties": "^1.1.4",
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"supports-color": "^7.0.0"
@@ -14272,11 +13973,23 @@
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+ "engines": {
+ "node": ">= 0.4"
+ },
+ "funding": {
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+ }
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"resolved": "https://registry.npmjs.org/symbol-tree/-/symbol-tree-3.2.4.tgz",
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+ "resolved": "https://registry.npmjs.org/terser/-/terser-5.19.2.tgz",
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"dependencies": {
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+ "@jridgewell/source-map": "^0.3.3",
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+ "resolved": "https://registry.npmjs.org/terser-webpack-plugin/-/terser-webpack-plugin-5.3.9.tgz",
+ "integrity": "sha512-ZuXsqE07EcggTWQjXUj+Aot/OMcD0bMKGgF63f7UxYcu5/AJF53aIpK1YoP5xR9l6s/Hy2b+t1AM0bLNPRuhwA==",
"dev": true,
"dependencies": {
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- "source-map": "^0.6.1",
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@@ -14354,10 +14067,33 @@
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+ "resolved": "https://registry.npmjs.org/has-flag/-/has-flag-4.0.0.tgz",
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+ "dev": true,
+ "engines": {
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+ "node_modules/terser-webpack-plugin/node_modules/jest-worker": {
+ "version": "27.5.1",
+ "resolved": "https://registry.npmjs.org/jest-worker/-/jest-worker-27.5.1.tgz",
+ "integrity": "sha512-7vuh85V5cdDofPyxn58nrPjBktZo0u9x1g8WtjQol+jZDaE+fhN+cIvTj11GndBnMnyfrUOG1sZQxCdjKh+DKg==",
+ "dev": true,
+ "dependencies": {
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+ "version": "3.3.0",
+ "resolved": "https://registry.npmjs.org/schema-utils/-/schema-utils-3.3.0.tgz",
+ "integrity": "sha512-pN/yOAvcC+5rQ5nERGuwrjLlYvLTbCibnZ1I7B1LaiAz9BRBlE9GMgE/eqV30P7aJQUf7Ddimy/RsbYO/GrVGg==",
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+ "node_modules/terser-webpack-plugin/node_modules/supports-color": {
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+ "resolved": "https://registry.npmjs.org/supports-color/-/supports-color-8.1.1.tgz",
+ "integrity": "sha512-MpUEN2OodtUzxvKQl72cUF7RQ5EiHsGvSsVG0ia9c5RbWGL2CI4C7EpPS8UTBIplnlzZiNuV56w+FuNxy3ty2Q==",
"dev": true,
+ "dependencies": {
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+ },
"engines": {
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+ "node": ">=10"
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+ "funding": {
+ "url": "https://github.com/chalk/supports-color?sponsor=1"
}
},
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"dev": true
},
+ "node_modules/terser/node_modules/source-map-support": {
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+ "resolved": "https://registry.npmjs.org/source-map-support/-/source-map-support-0.5.21.tgz",
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+ "dev": true,
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"resolved": "https://registry.npmjs.org/test-exclude/-/test-exclude-6.0.0.tgz",
@@ -14400,12 +14152,6 @@
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@@ -14413,9 +14159,9 @@
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+ "version": "1.3.1",
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- "engines": {
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+ "version": "1.6.0",
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},
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@@ -14438,7 +14181,7 @@
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"engines": {
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@@ -14454,60 +14197,96 @@
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+ "node_modules/toidentifier": {
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+ "dev": true,
+ "engines": {
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+ "resolved": "https://registry.npmjs.org/totalist/-/totalist-1.1.0.tgz",
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+ "dev": true,
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+ "node_modules/tough-cookie": {
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+ "engines": {
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+ "node_modules/tough-cookie/node_modules/universalify": {
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"dev": true,
+ "peer": true,
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+ "version": "4.1.1",
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"dev": true,
+ "peer": true,
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},
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"dependencies": {
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"fast-json-stable-stringify": "2.x",
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"lodash.memoize": "4.x",
"make-error": "1.x",
- "semver": "7.x",
- "yargs-parser": "20.x"
+ "semver": "^7.5.3",
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},
"bin": {
"ts-jest": "cli.js"
},
"engines": {
- "node": "^10.13.0 || ^12.13.0 || ^14.15.0 || >=15.0.0"
+ "node": "^14.15.0 || ^16.10.0 || >=18.0.0"
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},
"peerDependenciesMeta": {
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},
- "@types/jest": {
+ "@jest/types": {
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},
"babel-jest": {
@@ -14518,10 +14297,22 @@
}
}
},
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+ "resolved": "https://registry.npmjs.org/lru-cache/-/lru-cache-6.0.0.tgz",
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+ "dev": true,
+ "dependencies": {
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+ },
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@@ -14927,7 +14763,7 @@
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"terser-webpack-plugin": "^5.1.3",
- "watchpack": "^2.3.1",
+ "watchpack": "^2.4.0",
"webpack-sources": "^3.2.3"
},
"bin": {
@@ -14946,45 +14782,145 @@
}
}
},
+ "node_modules/webpack-bundle-analyzer": {
+ "version": "4.7.0",
+ "resolved": "https://registry.npmjs.org/webpack-bundle-analyzer/-/webpack-bundle-analyzer-4.7.0.tgz",
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+ "acorn-walk": "^8.0.0",
+ "chalk": "^4.1.0",
+ "commander": "^7.2.0",
+ "gzip-size": "^6.0.0",
+ "lodash": "^4.17.20",
+ "opener": "^1.5.2",
+ "sirv": "^1.0.7",
+ "ws": "^7.3.1"
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+ "bin": {
+ "webpack-bundle-analyzer": "lib/bin/analyzer.js"
+ },
+ "engines": {
+ "node": ">= 10.13.0"
+ }
+ },
+ "node_modules/webpack-bundle-analyzer/node_modules/ansi-styles": {
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+ "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-4.3.0.tgz",
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+ "dependencies": {
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+ "engines": {
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+ },
+ "funding": {
+ "url": "https://github.com/chalk/ansi-styles?sponsor=1"
+ }
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+ "node_modules/webpack-bundle-analyzer/node_modules/chalk": {
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+ "resolved": "https://registry.npmjs.org/chalk/-/chalk-4.1.2.tgz",
+ "integrity": "sha512-oKnbhFyRIXpUuez8iBMmyEa4nbj4IOQyuhc/wy9kY7/WVPcwIO9VA668Pu8RkO7+0G76SLROeyw9CpQ061i4mA==",
+ "dev": true,
+ "dependencies": {
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+ "supports-color": "^7.1.0"
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+ "engines": {
+ "node": ">=10"
+ },
+ "funding": {
+ "url": "https://github.com/chalk/chalk?sponsor=1"
+ }
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+ "node_modules/webpack-bundle-analyzer/node_modules/color-convert": {
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+ "resolved": "https://registry.npmjs.org/color-convert/-/color-convert-2.0.1.tgz",
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+ "engines": {
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+ "node_modules/webpack-bundle-analyzer/node_modules/color-name": {
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+ "resolved": "https://registry.npmjs.org/color-name/-/color-name-1.1.4.tgz",
+ "integrity": "sha512-dOy+3AuW3a2wNbZHIuMZpTcgjGuLU/uBL/ubcZF9OXbDo8ff4O8yVp5Bf0efS8uEoYo5q4Fx7dY9OgQGXgAsQA==",
+ "dev": true
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+ "node_modules/webpack-bundle-analyzer/node_modules/commander": {
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+ "resolved": "https://registry.npmjs.org/commander/-/commander-7.2.0.tgz",
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+ "dev": true,
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+ "resolved": "https://registry.npmjs.org/has-flag/-/has-flag-4.0.0.tgz",
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+ "dev": true,
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+ "node_modules/webpack-bundle-analyzer/node_modules/supports-color": {
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+ "resolved": "https://registry.npmjs.org/supports-color/-/supports-color-7.2.0.tgz",
+ "integrity": "sha512-qpCAvRl9stuOHveKsn7HncJRvv501qIacKzQlO/+Lwxc9+0q2wLyv4Dfvt80/DPn2pqOBsJdDiogXGR9+OvwRw==",
+ "dev": true,
+ "dependencies": {
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+ },
+ "engines": {
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- "resolved": "https://registry.npmjs.org/webpack-cli/-/webpack-cli-4.10.0.tgz",
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+ "version": "5.0.2",
+ "resolved": "https://registry.npmjs.org/webpack-cli/-/webpack-cli-5.0.2.tgz",
+ "integrity": "sha512-4y3W5Dawri5+8dXm3+diW6Mn1Ya+Dei6eEVAdIduAmYNLzv1koKVAqsfgrrc9P2mhrYHQphx5htnGkcNwtubyQ==",
"dev": true,
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- "@webpack-cli/configtest": "^1.2.0",
- "@webpack-cli/info": "^1.5.0",
- "@webpack-cli/serve": "^1.7.0",
+ "@webpack-cli/configtest": "^2.0.1",
+ "@webpack-cli/info": "^2.0.1",
+ "@webpack-cli/serve": "^2.0.2",
"colorette": "^2.0.14",
- "commander": "^7.0.0",
+ "commander": "^10.0.1",
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+ "envinfo": "^7.7.3",
"fastest-levenshtein": "^1.0.12",
"import-local": "^3.0.2",
- "interpret": "^2.2.0",
- "rechoir": "^0.7.0",
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+ "rechoir": "^0.8.0",
"webpack-merge": "^5.7.3"
},
"bin": {
"webpack-cli": "bin/cli.js"
},
"engines": {
- "node": ">=10.13.0"
+ "node": ">=14.15.0"
},
"funding": {
"type": "opencollective",
"url": "https://opencollective.com/webpack"
},
"peerDependencies": {
- "webpack": "4.x.x || 5.x.x"
+ "webpack": "5.x.x"
},
"peerDependenciesMeta": {
"@webpack-cli/generators": {
"optional": true
},
- "@webpack-cli/migrate": {
- "optional": true
- },
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},
@@ -14994,12 +14930,12 @@
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- "integrity": "sha512-QrWXB+ZQSVPmIWIhtEO9H+gwHaMGYiF5ChvoJ+K9ZGHG/sVsa6yiesAD1GC/x46sET00Xlwo1u49RVVVzvcSkw==",
+ "version": "10.0.1",
+ "resolved": "https://registry.npmjs.org/commander/-/commander-10.0.1.tgz",
+ "integrity": "sha512-y4Mg2tXshplEbSGzx7amzPwKKOCGuoSRP/CjEdwwk0FOGlUbq6lKuoyDZTNZkmxHdJtp54hdfY/JUrdL7Xfdug==",
"dev": true,
"engines": {
- "node": ">= 10"
+ "node": ">=14"
}
},
"node_modules/webpack-dev-middleware": {
@@ -15026,9 +14962,9 @@
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- "resolved": "https://registry.npmjs.org/ajv/-/ajv-8.11.0.tgz",
- "integrity": "sha512-wGgprdCvMalC0BztXvitD2hC04YffAvtsUn93JbGXYLAtCUO4xd17mCCZQxUOItiBwZvJScWo8NIvQMQ71rdpg==",
+ "version": "8.12.0",
+ "resolved": "https://registry.npmjs.org/ajv/-/ajv-8.12.0.tgz",
+ "integrity": "sha512-sRu1kpcO9yLtYxBKvqfTeh9KzZEwO3STyX1HT+4CaDzC6HpTGYhIhPIzj9XuKU7KYDwnaeh5hcOwjy1QuJzBPA==",
"dev": true,
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@@ -15060,15 +14996,15 @@
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+ "version": "4.2.0",
+ "resolved": "https://registry.npmjs.org/schema-utils/-/schema-utils-4.2.0.tgz",
+ "integrity": "sha512-L0jRsrPpjdckP3oPug3/VxNKt2trR8TcabrM6FOAAlvC/9Phcmm+cuAgTlxBqdBR1WJx7Naj9WHw+aOmheSVbw==",
"dev": true,
"dependencies": {
"@types/json-schema": "^7.0.9",
- "ajv": "^8.8.0",
+ "ajv": "^8.9.0",
"ajv-formats": "^2.1.1",
- "ajv-keywords": "^5.0.0"
+ "ajv-keywords": "^5.1.0"
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@@ -15079,9 +15015,9 @@
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- "resolved": "https://registry.npmjs.org/webpack-dev-server/-/webpack-dev-server-4.9.3.tgz",
- "integrity": "sha512-3qp/eoboZG5/6QgiZ3llN8TUzkSpYg1Ko9khWX1h40MIEUNS2mDoIa8aXsPfskER+GbTvs/IJZ1QTBBhhuetSw==",
+ "version": "4.11.1",
+ "resolved": "https://registry.npmjs.org/webpack-dev-server/-/webpack-dev-server-4.11.1.tgz",
+ "integrity": "sha512-lILVz9tAUy1zGFwieuaQtYiadImb5M3d+H+L1zDYalYoDl0cksAB1UNyuE5MMWJrG6zR1tXkCP2fitl7yoUJiw==",
"dev": true,
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@@ -15107,7 +15043,7 @@
"p-retry": "^4.5.0",
"rimraf": "^3.0.2",
"schema-utils": "^4.0.0",
- "selfsigned": "^2.0.1",
+ "selfsigned": "^2.1.1",
"serve-index": "^1.9.1",
"sockjs": "^0.3.24",
"spdy": "^4.0.2",
@@ -15134,9 +15070,9 @@
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- "resolved": "https://registry.npmjs.org/ajv/-/ajv-8.11.0.tgz",
- "integrity": "sha512-wGgprdCvMalC0BztXvitD2hC04YffAvtsUn93JbGXYLAtCUO4xd17mCCZQxUOItiBwZvJScWo8NIvQMQ71rdpg==",
+ "version": "8.12.0",
+ "resolved": "https://registry.npmjs.org/ajv/-/ajv-8.12.0.tgz",
+ "integrity": "sha512-sRu1kpcO9yLtYxBKvqfTeh9KzZEwO3STyX1HT+4CaDzC6HpTGYhIhPIzj9XuKU7KYDwnaeh5hcOwjy1QuJzBPA==",
"dev": true,
"dependencies": {
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@@ -15168,15 +15104,15 @@
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- "resolved": "https://registry.npmjs.org/schema-utils/-/schema-utils-4.0.0.tgz",
- "integrity": "sha512-1edyXKgh6XnJsJSQ8mKWXnN/BVaIbFMLpouRUrXgVq7WYne5kw3MW7UPhO44uRXQSIpTSXoJbmrR2X0w9kUTyg==",
+ "version": "4.2.0",
+ "resolved": "https://registry.npmjs.org/schema-utils/-/schema-utils-4.2.0.tgz",
+ "integrity": "sha512-L0jRsrPpjdckP3oPug3/VxNKt2trR8TcabrM6FOAAlvC/9Phcmm+cuAgTlxBqdBR1WJx7Naj9WHw+aOmheSVbw==",
"dev": true,
"dependencies": {
"@types/json-schema": "^7.0.9",
- "ajv": "^8.8.0",
+ "ajv": "^8.9.0",
"ajv-formats": "^2.1.1",
- "ajv-keywords": "^5.0.0"
+ "ajv-keywords": "^5.1.0"
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"engines": {
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@@ -15187,16 +15123,16 @@
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"node_modules/webpack-dev-server/node_modules/ws": {
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- "resolved": "https://registry.npmjs.org/ws/-/ws-8.8.1.tgz",
- "integrity": "sha512-bGy2JzvzkPowEJV++hF07hAD6niYSr0JzBNo/J29WsB57A2r7Wlc1UFcTR9IzrPvuNVO4B8LGqF8qcpsVOhJCA==",
+ "version": "8.13.0",
+ "resolved": "https://registry.npmjs.org/ws/-/ws-8.13.0.tgz",
+ "integrity": "sha512-x9vcZYTrFPC7aSIbj7sRCYo7L/Xb8Iy+pW0ng0wt2vCJv7M9HOMy0UoN3rr+IFC7hb7vXoqS+P9ktyLLLhO+LA==",
"dev": true,
"engines": {
"node": ">=10.0.0"
},
"peerDependencies": {
"bufferutil": "^4.0.1",
- "utf-8-validate": "^5.0.2"
+ "utf-8-validate": ">=5.0.2"
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@@ -15208,9 +15144,9 @@
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- "resolved": "https://registry.npmjs.org/webpack-merge/-/webpack-merge-5.8.0.tgz",
- "integrity": "sha512-/SaI7xY0831XwP6kzuwhKWVKDP9t1QY1h65lAFLbZqMPIuYcD9QAW4u9STIbU9kaJbPBB/geU/gLr1wDjOhQ+Q==",
+ "version": "5.9.0",
+ "resolved": "https://registry.npmjs.org/webpack-merge/-/webpack-merge-5.9.0.tgz",
+ "integrity": "sha512-6NbRQw4+Sy50vYNTw7EyOn41OZItPiXB8GNv3INSoe3PSFaHJEz3SHTrYVaRm2LilNGnFUzh0FAwqPEmU/CwDg==",
"dev": true,
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@@ -15230,9 +15166,9 @@
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- "resolved": "https://registry.npmjs.org/schema-utils/-/schema-utils-3.1.1.tgz",
- "integrity": "sha512-Y5PQxS4ITlC+EahLuXaY86TXfR7Dc5lw294alXOq86JAHCihAIZfqv8nNCWvaEJvaC51uN9hbLGeV0cFBdH+Fw==",
+ "version": "3.3.0",
+ "resolved": "https://registry.npmjs.org/schema-utils/-/schema-utils-3.3.0.tgz",
+ "integrity": "sha512-pN/yOAvcC+5rQ5nERGuwrjLlYvLTbCibnZ1I7B1LaiAz9BRBlE9GMgE/eqV30P7aJQUf7Ddimy/RsbYO/GrVGg==",
"dev": true,
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@@ -15271,32 +15207,53 @@
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+ "version": "2.0.0",
+ "resolved": "https://registry.npmjs.org/whatwg-encoding/-/whatwg-encoding-2.0.0.tgz",
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+ "dev": true,
+ "peer": true,
+ "dependencies": {
+ "iconv-lite": "0.6.3"
+ },
+ "engines": {
+ "node": ">=12"
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+ "node_modules/whatwg-encoding/node_modules/iconv-lite": {
+ "version": "0.6.3",
+ "resolved": "https://registry.npmjs.org/iconv-lite/-/iconv-lite-0.6.3.tgz",
+ "integrity": "sha512-4fCk79wshMdzMp2rH06qWrJE4iolqLhCUH+OiuIgU++RB0+94NlDL81atO7GX55uUKueo0txHNtvEyI6D7WdMw==",
"dev": true,
+ "peer": true,
"dependencies": {
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+ "safer-buffer": ">= 2.1.2 < 3.0.0"
+ },
+ "engines": {
+ "node": ">=0.10.0"
}
},
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- "resolved": "https://registry.npmjs.org/whatwg-mimetype/-/whatwg-mimetype-2.3.0.tgz",
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+ "version": "3.0.0",
+ "resolved": "https://registry.npmjs.org/whatwg-mimetype/-/whatwg-mimetype-3.0.0.tgz",
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+ "dev": true,
+ "peer": true,
+ "engines": {
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},
"node_modules/whatwg-url": {
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- "resolved": "https://registry.npmjs.org/whatwg-url/-/whatwg-url-8.7.0.tgz",
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+ "version": "12.0.1",
+ "resolved": "https://registry.npmjs.org/whatwg-url/-/whatwg-url-12.0.1.tgz",
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"dev": true,
+ "peer": true,
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@@ -15328,21 +15285,30 @@
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- "dev": true,
+ "node_modules/which-typed-array": {
+ "version": "1.1.11",
+ "resolved": "https://registry.npmjs.org/which-typed-array/-/which-typed-array-1.1.11.tgz",
+ "integrity": "sha512-qe9UWWpkeG5yzZ0tNYxDmd7vo58HDBc39mZ0xWWpolAGADdFOzkfamWLDxkOWcvHQKVmdTyQdLD4NOfjLWTKew==",
+ "dependencies": {
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+ "call-bind": "^1.0.2",
+ "for-each": "^0.3.3",
+ "gopd": "^1.0.1",
+ "has-tostringtag": "^1.0.0"
+ },
"engines": {
- "node": ">=0.10.0"
+ "node": ">= 0.4"
+ },
+ "funding": {
+ "url": "https://github.com/sponsors/ljharb"
}
},
+ "node_modules/wildcard": {
+ "version": "2.0.1",
+ "resolved": "https://registry.npmjs.org/wildcard/-/wildcard-2.0.1.tgz",
+ "integrity": "sha512-CC1bOL87PIWSBhDcTrdeLo6eGT7mCFtrg0uIJtqJUFyK+eJnzl8A1niH56uu7KMa5XFrtiV+AQuHO3n7DsHnLQ==",
+ "dev": true
+ },
"node_modules/wrap-ansi": {
"version": "7.0.0",
"resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-7.0.0.tgz",
@@ -15392,18 +15358,18 @@
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@@ -16956,15 +16922,15 @@
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@@ -18815,18 +18471,30 @@
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"dev": true,
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@@ -22127,6 +21712,12 @@
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"dev": true,
+ "peer": true,
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"dev": true,
+ "peer": true,
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@@ -23720,16 +23256,22 @@
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"@webassemblyjs/wasm-parser": "1.11.1",
- "acorn": "^8.4.1",
+ "acorn": "^8.7.1",
"acorn-import-assertions": "^1.7.6",
"browserslist": "^4.14.5",
"chrome-trace-event": "^1.0.2",
- "enhanced-resolve": "^5.9.3",
+ "enhanced-resolve": "^5.10.0",
"es-module-lexer": "^0.9.0",
"eslint-scope": "5.1.1",
"events": "^3.2.0",
@@ -26786,14 +26506,14 @@
"schema-utils": "^3.1.0",
"tapable": "^2.1.1",
"terser-webpack-plugin": "^5.1.3",
- "watchpack": "^2.3.1",
+ "watchpack": "^2.4.0",
"webpack-sources": "^3.2.3"
},
"dependencies": {
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- "version": "3.1.1",
- "resolved": "https://registry.npmjs.org/schema-utils/-/schema-utils-3.1.1.tgz",
- "integrity": "sha512-Y5PQxS4ITlC+EahLuXaY86TXfR7Dc5lw294alXOq86JAHCihAIZfqv8nNCWvaEJvaC51uN9hbLGeV0cFBdH+Fw==",
+ "version": "3.3.0",
+ "resolved": "https://registry.npmjs.org/schema-utils/-/schema-utils-3.3.0.tgz",
+ "integrity": "sha512-pN/yOAvcC+5rQ5nERGuwrjLlYvLTbCibnZ1I7B1LaiAz9BRBlE9GMgE/eqV30P7aJQUf7Ddimy/RsbYO/GrVGg==",
"dev": true,
"requires": {
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@@ -26803,30 +26523,105 @@
}
}
},
+ "webpack-bundle-analyzer": {
+ "version": "4.7.0",
+ "resolved": "https://registry.npmjs.org/webpack-bundle-analyzer/-/webpack-bundle-analyzer-4.7.0.tgz",
+ "integrity": "sha512-j9b8ynpJS4K+zfO5GGwsAcQX4ZHpWV+yRiHDiL+bE0XHJ8NiPYLTNVQdlFYWxtpg9lfAQNlwJg16J9AJtFSXRg==",
+ "dev": true,
+ "requires": {
+ "acorn": "^8.0.4",
+ "acorn-walk": "^8.0.0",
+ "chalk": "^4.1.0",
+ "commander": "^7.2.0",
+ "gzip-size": "^6.0.0",
+ "lodash": "^4.17.20",
+ "opener": "^1.5.2",
+ "sirv": "^1.0.7",
+ "ws": "^7.3.1"
+ },
+ "dependencies": {
+ "ansi-styles": {
+ "version": "4.3.0",
+ "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-4.3.0.tgz",
+ "integrity": "sha512-zbB9rCJAT1rbjiVDb2hqKFHNYLxgtk8NURxZ3IZwD3F6NtxbXZQCnnSi1Lkx+IDohdPlFp222wVALIheZJQSEg==",
+ "dev": true,
+ "requires": {
+ "color-convert": "^2.0.1"
+ }
+ },
+ "chalk": {
+ "version": "4.1.2",
+ "resolved": "https://registry.npmjs.org/chalk/-/chalk-4.1.2.tgz",
+ "integrity": "sha512-oKnbhFyRIXpUuez8iBMmyEa4nbj4IOQyuhc/wy9kY7/WVPcwIO9VA668Pu8RkO7+0G76SLROeyw9CpQ061i4mA==",
+ "dev": true,
+ "requires": {
+ "ansi-styles": "^4.1.0",
+ "supports-color": "^7.1.0"
+ }
+ },
+ "color-convert": {
+ "version": "2.0.1",
+ "resolved": "https://registry.npmjs.org/color-convert/-/color-convert-2.0.1.tgz",
+ "integrity": "sha512-RRECPsj7iu/xb5oKYcsFHSppFNnsj/52OVTRKb4zP5onXwVF3zVmmToNcOfGC+CRDpfK/U584fMg38ZHCaElKQ==",
+ "dev": true,
+ "requires": {
+ "color-name": "~1.1.4"
+ }
+ },
+ "color-name": {
+ "version": "1.1.4",
+ "resolved": "https://registry.npmjs.org/color-name/-/color-name-1.1.4.tgz",
+ "integrity": "sha512-dOy+3AuW3a2wNbZHIuMZpTcgjGuLU/uBL/ubcZF9OXbDo8ff4O8yVp5Bf0efS8uEoYo5q4Fx7dY9OgQGXgAsQA==",
+ "dev": true
+ },
+ "commander": {
+ "version": "7.2.0",
+ "resolved": "https://registry.npmjs.org/commander/-/commander-7.2.0.tgz",
+ "integrity": "sha512-QrWXB+ZQSVPmIWIhtEO9H+gwHaMGYiF5ChvoJ+K9ZGHG/sVsa6yiesAD1GC/x46sET00Xlwo1u49RVVVzvcSkw==",
+ "dev": true
+ },
+ "has-flag": {
+ "version": "4.0.0",
+ "resolved": "https://registry.npmjs.org/has-flag/-/has-flag-4.0.0.tgz",
+ "integrity": "sha512-EykJT/Q1KjTWctppgIAgfSO0tKVuZUjhgMr17kqTumMl6Afv3EISleU7qZUzoXDFTAHTDC4NOoG/ZxU3EvlMPQ==",
+ "dev": true
+ },
+ "supports-color": {
+ "version": "7.2.0",
+ "resolved": "https://registry.npmjs.org/supports-color/-/supports-color-7.2.0.tgz",
+ "integrity": "sha512-qpCAvRl9stuOHveKsn7HncJRvv501qIacKzQlO/+Lwxc9+0q2wLyv4Dfvt80/DPn2pqOBsJdDiogXGR9+OvwRw==",
+ "dev": true,
+ "requires": {
+ "has-flag": "^4.0.0"
+ }
+ }
+ }
+ },
"webpack-cli": {
- "version": "4.10.0",
- "resolved": "https://registry.npmjs.org/webpack-cli/-/webpack-cli-4.10.0.tgz",
- "integrity": "sha512-NLhDfH/h4O6UOy+0LSso42xvYypClINuMNBVVzX4vX98TmTaTUxwRbXdhucbFMd2qLaCTcLq/PdYrvi8onw90w==",
+ "version": "5.0.2",
+ "resolved": "https://registry.npmjs.org/webpack-cli/-/webpack-cli-5.0.2.tgz",
+ "integrity": "sha512-4y3W5Dawri5+8dXm3+diW6Mn1Ya+Dei6eEVAdIduAmYNLzv1koKVAqsfgrrc9P2mhrYHQphx5htnGkcNwtubyQ==",
"dev": true,
"requires": {
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- "@webpack-cli/configtest": "^1.2.0",
- "@webpack-cli/info": "^1.5.0",
- "@webpack-cli/serve": "^1.7.0",
+ "@webpack-cli/configtest": "^2.0.1",
+ "@webpack-cli/info": "^2.0.1",
+ "@webpack-cli/serve": "^2.0.2",
"colorette": "^2.0.14",
- "commander": "^7.0.0",
+ "commander": "^10.0.1",
"cross-spawn": "^7.0.3",
+ "envinfo": "^7.7.3",
"fastest-levenshtein": "^1.0.12",
"import-local": "^3.0.2",
- "interpret": "^2.2.0",
- "rechoir": "^0.7.0",
+ "interpret": "^3.1.1",
+ "rechoir": "^0.8.0",
"webpack-merge": "^5.7.3"
},
"dependencies": {
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- "version": "7.2.0",
- "resolved": "https://registry.npmjs.org/commander/-/commander-7.2.0.tgz",
- "integrity": "sha512-QrWXB+ZQSVPmIWIhtEO9H+gwHaMGYiF5ChvoJ+K9ZGHG/sVsa6yiesAD1GC/x46sET00Xlwo1u49RVVVzvcSkw==",
+ "version": "10.0.1",
+ "resolved": "https://registry.npmjs.org/commander/-/commander-10.0.1.tgz",
+ "integrity": "sha512-y4Mg2tXshplEbSGzx7amzPwKKOCGuoSRP/CjEdwwk0FOGlUbq6lKuoyDZTNZkmxHdJtp54hdfY/JUrdL7Xfdug==",
"dev": true
}
}
@@ -26845,9 +26640,9 @@
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- "resolved": "https://registry.npmjs.org/ajv/-/ajv-8.11.0.tgz",
- "integrity": "sha512-wGgprdCvMalC0BztXvitD2hC04YffAvtsUn93JbGXYLAtCUO4xd17mCCZQxUOItiBwZvJScWo8NIvQMQ71rdpg==",
+ "version": "8.12.0",
+ "resolved": "https://registry.npmjs.org/ajv/-/ajv-8.12.0.tgz",
+ "integrity": "sha512-sRu1kpcO9yLtYxBKvqfTeh9KzZEwO3STyX1HT+4CaDzC6HpTGYhIhPIzj9XuKU7KYDwnaeh5hcOwjy1QuJzBPA==",
"dev": true,
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@@ -26872,23 +26667,23 @@
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- "resolved": "https://registry.npmjs.org/schema-utils/-/schema-utils-4.0.0.tgz",
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+ "version": "4.2.0",
+ "resolved": "https://registry.npmjs.org/schema-utils/-/schema-utils-4.2.0.tgz",
+ "integrity": "sha512-L0jRsrPpjdckP3oPug3/VxNKt2trR8TcabrM6FOAAlvC/9Phcmm+cuAgTlxBqdBR1WJx7Naj9WHw+aOmheSVbw==",
"dev": true,
"requires": {
"@types/json-schema": "^7.0.9",
- "ajv": "^8.8.0",
+ "ajv": "^8.9.0",
"ajv-formats": "^2.1.1",
- "ajv-keywords": "^5.0.0"
+ "ajv-keywords": "^5.1.0"
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"webpack-dev-server": {
- "version": "4.9.3",
- "resolved": "https://registry.npmjs.org/webpack-dev-server/-/webpack-dev-server-4.9.3.tgz",
- "integrity": "sha512-3qp/eoboZG5/6QgiZ3llN8TUzkSpYg1Ko9khWX1h40MIEUNS2mDoIa8aXsPfskER+GbTvs/IJZ1QTBBhhuetSw==",
+ "version": "4.11.1",
+ "resolved": "https://registry.npmjs.org/webpack-dev-server/-/webpack-dev-server-4.11.1.tgz",
+ "integrity": "sha512-lILVz9tAUy1zGFwieuaQtYiadImb5M3d+H+L1zDYalYoDl0cksAB1UNyuE5MMWJrG6zR1tXkCP2fitl7yoUJiw==",
"dev": true,
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@@ -26914,7 +26709,7 @@
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"rimraf": "^3.0.2",
"schema-utils": "^4.0.0",
- "selfsigned": "^2.0.1",
+ "selfsigned": "^2.1.1",
"serve-index": "^1.9.1",
"sockjs": "^0.3.24",
"spdy": "^4.0.2",
@@ -26923,9 +26718,9 @@
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- "resolved": "https://registry.npmjs.org/ajv/-/ajv-8.11.0.tgz",
- "integrity": "sha512-wGgprdCvMalC0BztXvitD2hC04YffAvtsUn93JbGXYLAtCUO4xd17mCCZQxUOItiBwZvJScWo8NIvQMQ71rdpg==",
+ "version": "8.12.0",
+ "resolved": "https://registry.npmjs.org/ajv/-/ajv-8.12.0.tgz",
+ "integrity": "sha512-sRu1kpcO9yLtYxBKvqfTeh9KzZEwO3STyX1HT+4CaDzC6HpTGYhIhPIzj9XuKU7KYDwnaeh5hcOwjy1QuJzBPA==",
"dev": true,
"requires": {
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@@ -26950,30 +26745,30 @@
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- "resolved": "https://registry.npmjs.org/schema-utils/-/schema-utils-4.0.0.tgz",
- "integrity": "sha512-1edyXKgh6XnJsJSQ8mKWXnN/BVaIbFMLpouRUrXgVq7WYne5kw3MW7UPhO44uRXQSIpTSXoJbmrR2X0w9kUTyg==",
+ "version": "4.2.0",
+ "resolved": "https://registry.npmjs.org/schema-utils/-/schema-utils-4.2.0.tgz",
+ "integrity": "sha512-L0jRsrPpjdckP3oPug3/VxNKt2trR8TcabrM6FOAAlvC/9Phcmm+cuAgTlxBqdBR1WJx7Naj9WHw+aOmheSVbw==",
"dev": true,
"requires": {
"@types/json-schema": "^7.0.9",
- "ajv": "^8.8.0",
+ "ajv": "^8.9.0",
"ajv-formats": "^2.1.1",
- "ajv-keywords": "^5.0.0"
+ "ajv-keywords": "^5.1.0"
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"ws": {
- "version": "8.8.1",
- "resolved": "https://registry.npmjs.org/ws/-/ws-8.8.1.tgz",
- "integrity": "sha512-bGy2JzvzkPowEJV++hF07hAD6niYSr0JzBNo/J29WsB57A2r7Wlc1UFcTR9IzrPvuNVO4B8LGqF8qcpsVOhJCA==",
+ "version": "8.13.0",
+ "resolved": "https://registry.npmjs.org/ws/-/ws-8.13.0.tgz",
+ "integrity": "sha512-x9vcZYTrFPC7aSIbj7sRCYo7L/Xb8Iy+pW0ng0wt2vCJv7M9HOMy0UoN3rr+IFC7hb7vXoqS+P9ktyLLLhO+LA==",
"dev": true,
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"webpack-merge": {
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- "resolved": "https://registry.npmjs.org/webpack-merge/-/webpack-merge-5.8.0.tgz",
- "integrity": "sha512-/SaI7xY0831XwP6kzuwhKWVKDP9t1QY1h65lAFLbZqMPIuYcD9QAW4u9STIbU9kaJbPBB/geU/gLr1wDjOhQ+Q==",
+ "version": "5.9.0",
+ "resolved": "https://registry.npmjs.org/webpack-merge/-/webpack-merge-5.9.0.tgz",
+ "integrity": "sha512-6NbRQw4+Sy50vYNTw7EyOn41OZItPiXB8GNv3INSoe3PSFaHJEz3SHTrYVaRm2LilNGnFUzh0FAwqPEmU/CwDg==",
"dev": true,
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@@ -27004,29 +26799,43 @@
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- "resolved": "https://registry.npmjs.org/whatwg-encoding/-/whatwg-encoding-1.0.5.tgz",
- "integrity": "sha512-b5lim54JOPN9HtzvK9HFXvBma/rnfFeqsic0hSpjtDbVxR3dJKLc+KB4V6GgiGOvl7CY/KNh8rxSo9DKQrnUEw==",
+ "version": "2.0.0",
+ "resolved": "https://registry.npmjs.org/whatwg-encoding/-/whatwg-encoding-2.0.0.tgz",
+ "integrity": "sha512-p41ogyeMUrw3jWclHWTQg1k05DSVXPLcVxRTYsXUk+ZooOCZLcoYgPZ/HL/D/N+uQPOtcp1me1WhBEaX02mhWg==",
"dev": true,
+ "peer": true,
"requires": {
- "iconv-lite": "0.4.24"
+ "iconv-lite": "0.6.3"
+ },
+ "dependencies": {
+ "iconv-lite": {
+ "version": "0.6.3",
+ "resolved": "https://registry.npmjs.org/iconv-lite/-/iconv-lite-0.6.3.tgz",
+ "integrity": "sha512-4fCk79wshMdzMp2rH06qWrJE4iolqLhCUH+OiuIgU++RB0+94NlDL81atO7GX55uUKueo0txHNtvEyI6D7WdMw==",
+ "dev": true,
+ "peer": true,
+ "requires": {
+ "safer-buffer": ">= 2.1.2 < 3.0.0"
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}
},
"whatwg-mimetype": {
- "version": "2.3.0",
- "resolved": "https://registry.npmjs.org/whatwg-mimetype/-/whatwg-mimetype-2.3.0.tgz",
- "integrity": "sha512-M4yMwr6mAnQz76TbJm914+gPpB/nCwvZbJU28cUD6dR004SAxDLOOSUaB1JDRqLtaOV/vi0IC5lEAGFgrjGv/g==",
- "dev": true
+ "version": "3.0.0",
+ "resolved": "https://registry.npmjs.org/whatwg-mimetype/-/whatwg-mimetype-3.0.0.tgz",
+ "integrity": "sha512-nt+N2dzIutVRxARx1nghPKGv1xHikU7HKdfafKkLNLindmPU/ch3U31NOCGGA/dmPcmb1VlofO0vnKAcsm0o/Q==",
+ "dev": true,
+ "peer": true
},
"whatwg-url": {
- "version": "8.7.0",
- "resolved": "https://registry.npmjs.org/whatwg-url/-/whatwg-url-8.7.0.tgz",
- "integrity": "sha512-gAojqb/m9Q8a5IV96E3fHJM70AzCkgt4uXYX2O7EmuyOnLrViCQlsEBmF9UQIu3/aeAIp2U17rtbpZWNntQqdg==",
+ "version": "12.0.1",
+ "resolved": "https://registry.npmjs.org/whatwg-url/-/whatwg-url-12.0.1.tgz",
+ "integrity": "sha512-Ed/LrqB8EPlGxjS+TrsXcpUond1mhccS3pchLhzSgPCnTimUCKj3IZE75pAs5m6heB2U2TMerKFUXheyHY+VDQ==",
"dev": true,
+ "peer": true,
"requires": {
- "lodash": "^4.7.0",
- "tr46": "^2.1.0",
- "webidl-conversions": "^6.1.0"
+ "tr46": "^4.1.1",
+ "webidl-conversions": "^7.0.0"
}
},
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@@ -27049,16 +26858,22 @@
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- "integrity": "sha512-JcKqAHLPxcdb9KM49dufGXn2x3ssnfjbcaQdLlfZsL9rH9wgDQjUtDxbo8NE0F6SFvydeu1VhZe7hZuHsB2/pw==",
- "dev": true
+ "which-typed-array": {
+ "version": "1.1.11",
+ "resolved": "https://registry.npmjs.org/which-typed-array/-/which-typed-array-1.1.11.tgz",
+ "integrity": "sha512-qe9UWWpkeG5yzZ0tNYxDmd7vo58HDBc39mZ0xWWpolAGADdFOzkfamWLDxkOWcvHQKVmdTyQdLD4NOfjLWTKew==",
+ "requires": {
+ "available-typed-arrays": "^1.0.5",
+ "call-bind": "^1.0.2",
+ "for-each": "^0.3.3",
+ "gopd": "^1.0.1",
+ "has-tostringtag": "^1.0.0"
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- "word-wrap": {
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- "resolved": "https://registry.npmjs.org/word-wrap/-/word-wrap-1.2.3.tgz",
- "integrity": "sha512-Hz/mrNwitNRh/HUAtM/VT/5VH+ygD6DV7mYKZAtHOrbs8U7lvPS6xf7EJKMF0uW1KJCl0H701g3ZGus+muE5vQ==",
+ "wildcard": {
+ "version": "2.0.1",
+ "resolved": "https://registry.npmjs.org/wildcard/-/wildcard-2.0.1.tgz",
+ "integrity": "sha512-CC1bOL87PIWSBhDcTrdeLo6eGT7mCFtrg0uIJtqJUFyK+eJnzl8A1niH56uu7KMa5XFrtiV+AQuHO3n7DsHnLQ==",
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@@ -27097,18 +26912,15 @@
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- "integrity": "sha1-tSQ9jz7BqjXxNkYFvA0QNuMKtp8="
+ "integrity": "sha512-l4Sp/DRseor9wL6EvV2+TuQn63dMkPjZ/sp9XkghTEbV9KlPS1xUsZ3u7/IQO4wxtcFB4bgpQPRcR3QCvezPcQ=="
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- "resolved": "https://registry.npmjs.org/write-file-atomic/-/write-file-atomic-3.0.3.tgz",
- "integrity": "sha512-AvHcyZ5JnSfq3ioSyjrBkH9yW4m7Ayk8/9My/DD9onKeu/94fwrMocemO2QAJFAlnnDN+ZDS+ZjAR5ua1/PV/Q==",
- "dev": true,
+ "version": "4.0.2",
+ "resolved": "https://registry.npmjs.org/write-file-atomic/-/write-file-atomic-4.0.2.tgz",
+ "integrity": "sha512-7KxauUdBmSdWnmpaGFg+ppNjKF8uNLry8LyzjauQDOVONfFLNKrKvQOxZ/VuTIcS/gge/YNahf5RIIQWTSarlg==",
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- "is-typedarray": "^1.0.0",
- "signal-exit": "^3.0.2",
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+ "signal-exit": "^3.0.7"
}
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@@ -27119,16 +26931,18 @@
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- "dev": true
+ "version": "4.0.0",
+ "resolved": "https://registry.npmjs.org/xml-name-validator/-/xml-name-validator-4.0.0.tgz",
+ "integrity": "sha512-ICP2e+jsHvAj2E2lIHxa5tjXRlKDJo4IdvPvCXbXQGdzSfmSpNVyIKMvoZHjDY9DP0zV17iI85o90vRFXNccRw==",
+ "dev": true,
+ "peer": true
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"xmlchars": {
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"integrity": "sha512-JZnDKK8B0RCDw84FNdDAIpZK+JuJw+s7Lz8nksI7SIuU3UXJJslUthsi+uWBUYOwPFwW7W7PRLRfUKpxjtjFCw==",
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+ "dev": true,
+ "peer": true
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@@ -27136,9 +26950,9 @@
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},
"yallist": {
- "version": "4.0.0",
- "resolved": "https://registry.npmjs.org/yallist/-/yallist-4.0.0.tgz",
- "integrity": "sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A=="
+ "version": "3.1.1",
+ "resolved": "https://registry.npmjs.org/yallist/-/yallist-3.1.1.tgz",
+ "integrity": "sha512-a4UGQaWPH59mOXUYnAG2ewncQS4i4F43Tv3JoAM+s2VDAmS9NsK8GpDMLrCHPksFT7h3K6TOoUNn2pb7RoXx4g=="
},
"yaml": {
"version": "1.10.2",
@@ -27146,31 +26960,23 @@
"integrity": "sha512-r3vXyErRCYJ7wg28yvBY5VSoAF8ZvlcW9/BwUzEtUsjvX/DKs24dIkuwjtuprwJJHsbyUbLApepYTR1BN4uHrg=="
},
"yargs": {
- "version": "17.5.1",
- "resolved": "https://registry.npmjs.org/yargs/-/yargs-17.5.1.tgz",
- "integrity": "sha512-t6YAJcxDkNX7NFYiVtKvWUz8l+PaKTLiL63mJYWR2GnHq2gjEWISzsLp9wg3aY36dY1j+gfIEL3pIF+XlJJfbA==",
+ "version": "17.7.2",
+ "resolved": "https://registry.npmjs.org/yargs/-/yargs-17.7.2.tgz",
+ "integrity": "sha512-7dSzzRQ++CKnNI/krKnYRV7JKKPUXMEh61soaHKg9mrWEhzFWhFnxPxGl+69cD1Ou63C13NUPCnmIcrvqCuM6w==",
"requires": {
- "cliui": "^7.0.2",
+ "cliui": "^8.0.1",
"escalade": "^3.1.1",
"get-caller-file": "^2.0.5",
"require-directory": "^2.1.1",
"string-width": "^4.2.3",
"y18n": "^5.0.5",
- "yargs-parser": "^21.0.0"
- },
- "dependencies": {
- "yargs-parser": {
- "version": "21.1.1",
- "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-21.1.1.tgz",
- "integrity": "sha512-tVpsJW7DdjecAiFpbIB1e3qxIQsE6NoPc5/eTdrbbIC4h0LVsWhnoa3g+m2HclBIujHzsxZ4VJVA+GUuc2/LBw=="
- }
+ "yargs-parser": "^21.1.1"
}
},
"yargs-parser": {
- "version": "20.2.9",
- "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-20.2.9.tgz",
- "integrity": "sha512-y11nGElTIV+CT3Zv9t7VKl+Q3hTQoT9a1Qzezhhl6Rp21gJ/IVTW7Z3y9EWXhuUBC2Shnf+DX0antecpAwSP8w==",
- "dev": true
+ "version": "21.1.1",
+ "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-21.1.1.tgz",
+ "integrity": "sha512-tVpsJW7DdjecAiFpbIB1e3qxIQsE6NoPc5/eTdrbbIC4h0LVsWhnoa3g+m2HclBIujHzsxZ4VJVA+GUuc2/LBw=="
},
"yocto-queue": {
"version": "0.1.0",
@@ -27178,4 +26984,4 @@
"integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q=="
}
}
-}
\ No newline at end of file
+}
diff --git a/mcc/package.json b/mcc/package.json
index ae19069df..1ad23823c 100644
--- a/mcc/package.json
+++ b/mcc/package.json
@@ -11,11 +11,11 @@
"test": "cross-env NODE_ENV=test jest"
},
"dependencies": {
- "@labkey/api": "^1.16.0",
+ "@labkey/api": "^1.23.0",
"@labkey/components": "~2.217.0",
"chart.js": "^3.7.0",
"react-chartjs-2": "^4.3.1",
- "uuid": "^8.3.2",
+ "uuid": "^9.0.0",
"react": "^17.0.2",
"react-dom": "^17.0.2",
"react-hot-loader": "^4.13.0",
@@ -26,19 +26,21 @@
"tsv": "^0.2.0"
},
"devDependencies": {
- "@labkey/build": "~6.1.0",
- "@types/jest": "^27.5.2",
- "@types/uuid": "^8.3.4",
+ "@labkey/build": "^6.14.0",
+ "@types/jest": "^29.0.0",
+ "@types/jquery": "^3.0.0",
"@types/tsv": "^0.2.1",
- "@types/react-dom": "^17.0.2",
"@types/chart.js": "^2.9.37",
+ "@types/jexl": "^2.3.1",
+ "@types/node": "^18.17.1",
"enzyme": "^3.11.0",
- "enzyme-adapter-react-16": "1.15.6",
- "@types/enzyme": "3.10.9",
- "@types/enzyme-adapter-react-16": "1.0.6",
- "jest": "^27.4.7",
- "jest-cli": "^27.5.1",
- "ts-jest": "^27.1.5"
+ "jest": "^29.0.0",
+ "jest-cli": "^29.0.0",
+ "jest-mock": "^29.0.0",
+ "ts-jest": "^29.0.0",
+ "rimraf": "^3.0.2",
+ "@wojtekmaj/enzyme-adapter-react-17": "^0.8.0",
+ "jsdom-global": "^3.0.2"
},
"jest": {
"globals": {
diff --git a/mcc/resources/queries/mcc/duplicatedAggregatedDemographics.sql b/mcc/resources/queries/mcc/duplicatedAggregatedDemographics.sql
new file mode 100644
index 000000000..93d33162c
--- /dev/null
+++ b/mcc/resources/queries/mcc/duplicatedAggregatedDemographics.sql
@@ -0,0 +1,9 @@
+SELECT
+
+ m.Id,
+ GROUP_CONCAT(distinct m.originalId, ',') as originalIds
+
+FROM mcc.aggregatedDemographics m
+
+GROUP BY m.Id
+HAVING COUNT(*) > 1
\ No newline at end of file
diff --git a/mcc/resources/web/mcc/panel/MccImportPanel.js b/mcc/resources/web/mcc/panel/MccImportPanel.js
index f2a385072..5b4fa157c 100644
--- a/mcc/resources/web/mcc/panel/MccImportPanel.js
+++ b/mcc/resources/web/mcc/panel/MccImportPanel.js
@@ -806,7 +806,7 @@ Ext4.define('MCC.panel.MccImportPanel', {
if (departureInserts.length) {
commands.push({
- type: 'insert',
+ command: 'insert',
schemaName: 'study',
queryName: 'departure',
rows: departureInserts
diff --git a/mcc/src/client/Dashboard/BarChart.spec.tsx b/mcc/src/client/Dashboard/BarChart.spec.tsx
index 1bbe3555a..8750d0979 100644
--- a/mcc/src/client/Dashboard/BarChart.spec.tsx
+++ b/mcc/src/client/Dashboard/BarChart.spec.tsx
@@ -1,27 +1,28 @@
+import 'jsdom-global/register'
import React from 'react';
import { mount, shallow } from 'enzyme';
-import { mocked } from 'ts-jest/utils';
+import { mocked } from 'jest-mock';
import { jest, describe, expect, test, beforeEach } from '@jest/globals';
import { Chart } from 'chart.js';
import BarChart from './BarChart';
-jest.mock('chart.js');
-const MockChart = mocked(Chart, true);
+describe('BarChart', () => {
+ jest.mock('chart.js');
+ const MockChart = mocked(Chart);
-const mockData = [
- {
- gender: 'M'
- },
- {
- gender: 'F'
- },
- {
- gender: 'F'
- }
-];
+ const mockData = [
+ {
+ gender: 'M'
+ },
+ {
+ gender: 'F'
+ },
+ {
+ gender: 'F'
+ }
+ ];
-describe('BarChart', () => {
test('it has a canvas element', () => {
const wrapper = shallow( getSection(String path)
}
@RequiresSiteAdmin
- public class EnsureModuleActiveAction extends ConfirmAction
+ public static class EnsureModuleActiveAction extends ConfirmAction
{
@Override
public ModelAndView getConfirmView(Object o, BindException errors) throws Exception
@@ -618,4 +621,66 @@ public Collection getJobRowIds()
return ret;
}
}
+
+ @RequiresPermission(UpdatePermission.class)
+ public static class PerformMhcCleanupAction extends ConfirmAction
+ {
+ @Override
+ public ModelAndView getConfirmView(PerformMhcCleanupForm o, BindException errors) throws Exception
+ {
+ setTitle("Run MHC Maintenance");
+
+ return new HtmlView(HtmlString.unsafe(HtmlString.of("This will run a pipeline job to delete low-frequency MHC results to save space. Do you want to continue?") +
+ "
+ {
+ protected Task(Factory factory, PipelineJob job)
+ {
+ super(factory, job);
+ }
+
+ public static class Factory extends AbstractTaskFactory
+ {
+ public Factory()
+ {
+ super(Task.class);
+ setLocation("webserver-high-priority");
+ }
+
+ @Override
+ public List getInputTypes()
+ {
+ return Collections.emptyList();
+ }
+
+ @Override
+ public String getStatusName()
+ {
+ return TaskStatus.running.toString();
+ }
+
+ @Override
+ public List getProtocolActionNames()
+ {
+ return List.of("Cleanup MHC Data");
+ }
+
+ @Override
+ public PipelineJob.Task createTask(PipelineJob job)
+ {
+ return new Task(this, job);
+ }
+
+ @Override
+ public boolean isJobComplete(PipelineJob job)
+ {
+ return false;
+ }
+ }
+
+ private MhcCleanupPipelineJob getPipelineJob()
+ {
+ return (MhcCleanupPipelineJob) getJob();
+ }
+
+ private Map alignmentSummaryDeleted = new HashMap<>();
+ private Map alignmentSummaryJunctionDeleted = new HashMap<>();
+ @Override
+ public RecordedActionSet run() throws PipelineJobException
+ {
+ UserSchema sequenceAnalysisSchema = QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis");
+ TableInfo alignmentSummary = sequenceAnalysisSchema.getTable("alignment_summary");
+ TableInfo alignmentSummaryJunction = sequenceAnalysisSchema.getTable("alignment_summary_junction");
+
+ long startingRowsAlignmentSummary = new TableSelector(alignmentSummary).getRowCount();
+ getJob().getLogger().info("Starting rows in alignment_summary: " + startingRowsAlignmentSummary);
+
+ long startingRowsAlignmentSummaryJ = new TableSelector(alignmentSummaryJunction).getRowCount();
+ getJob().getLogger().info("Starting rows in alignment_summary_junction: " + startingRowsAlignmentSummaryJ);
+ getJob().getLogger().info(getPipelineJob().doPerformDeletes() ? "**This is a production run, records will be deleted" : "**This is a test run, records will not be deleted");
+
+ // Iterate each analysis:
+ AtomicInteger ai = new AtomicInteger(0);
+ SimpleFilter filter = new SimpleFilter();
+ if (getPipelineJob().getMinAnalysisId() > 0)
+ {
+ filter.addCondition(FieldKey.fromString("rowid"), getPipelineJob().getMinAnalysisId(), CompareType.GT);
+ }
+
+ TableInfo sequenceAnalyses = sequenceAnalysisSchema.getTable("sequence_analyses");
+ final long totalAnalyses = new TableSelector(sequenceAnalyses).getRowCount();
+
+ new TableSelector(sequenceAnalyses, PageFlowUtil.set("rowId"), filter, new Sort("-rowid")).forEachResults(rs -> {
+ ai.getAndIncrement();
+ if (ai.get() % 50 == 0)
+ {
+ getJob().getLogger().info("Processed " + ai.get() + " analysis records of " + totalAnalyses);
+ }
+
+ if (getJob().isCancelled())
+ {
+ throw new CancelledException();
+ }
+
+ int rowId = rs.getInt(FieldKey.fromString("rowId"));
+ getJob().setStatus(TaskStatus.running, "Processing: " + ai.get() + " of " + totalAnalyses);
+ processAnalysis(rowId);
+ });
+
+ getJob().getLogger().info("Deleted rows in alignment_summary:");
+ alignmentSummaryDeleted.keySet().forEach(x -> getJob().getLogger().info(x + ": " + alignmentSummaryDeleted.get(x)));
+
+ getJob().getLogger().info("Deleted rows in alignment_summary_junction: ");
+ alignmentSummaryJunctionDeleted.keySet().forEach(x -> getJob().getLogger().info(x + ": " + alignmentSummaryJunctionDeleted.get(x)));
+
+ getJob().getLogger().info("Ending rows in alignment_summary: " + new TableSelector(alignmentSummary).getRowCount() + " (from " + startingRowsAlignmentSummary + ")");
+ getJob().getLogger().info("Ending rows in alignment_summary_junction: " + new TableSelector(alignmentSummaryJunction).getRowCount() + " (from " + startingRowsAlignmentSummaryJ + ")");
+
+ return new RecordedActionSet();
+ }
+
+ private void processAnalysis(int analysisId)
+ {
+ getJob().getLogger().info("Processing: " + analysisId);
+
+ try (DbScope.Transaction transaction = DbScope.getLabKeyScope().ensureTransaction())
+ {
+ TableInfo alignmentSummary = DbSchema.get("sequenceanalysis", DbSchemaType.Module).getTable("alignment_summary");
+ TableInfo alignmentSummaryJunction = DbSchema.get("sequenceanalysis", DbSchemaType.Module).getTable("alignment_summary_junction");
+
+ // snapshot data:
+ final Map existingData = new HashMap<>();
+ SimpleFilter dataFilter = new SimpleFilter(FieldKey.fromString("analysis_id"), analysisId, CompareType.EQUAL);
+ dataFilter.addCondition(FieldKey.fromString("percent_from_locus"), getPipelineJob().getLineageThreshold(), CompareType.GT);
+ new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_by_lineage"), PageFlowUtil.set("lineages", "percent_from_locus"), dataFilter, null).forEachResults(rs -> {
+ existingData.put(rs.getString(FieldKey.fromString("lineages")), rs.getDouble(FieldKey.fromString("percent_from_locus")));
+ });
+
+ // This is important to run first, since it will adjust percentages for many:
+ AlignmentGroupCompare agc = new AlignmentGroupCompare(analysisId, getJob().getContainer(), getJob().getUser());
+ Pair collapsed = agc.collapseGroups(getJob().getLogger(), getJob().getUser());
+ if (collapsed != null)
+ {
+ if (!alignmentSummaryDeleted.containsKey("collapsed groups"))
+ {
+ alignmentSummaryDeleted.put("collapsed groups", 0);
+ }
+ alignmentSummaryDeleted.put("collapsed groups", alignmentSummaryDeleted.get("collapsed groups") + collapsed.first);
+
+ if (!alignmentSummaryJunctionDeleted.containsKey("collapsed groups"))
+ {
+ alignmentSummaryJunctionDeleted.put("collapsed groups", 0);
+ }
+ alignmentSummaryJunctionDeleted.put("collapsed groups", alignmentSummaryJunctionDeleted.get("collapsed groups") + collapsed.second);
+ }
+
+ // Delete low-freq lineages:
+ if (getPipelineJob().getLineageThreshold() > 0)
+ {
+ SimpleFilter filter = new SimpleFilter(FieldKey.fromString("analysis_id"), analysisId, CompareType.EQUAL);
+ filter.addCondition(FieldKey.fromString("percent_from_locus"), getPipelineJob().getLineageThreshold(), CompareType.LT);
+
+ List lowFreqRowIdList = new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_by_lineage"), PageFlowUtil.set("rowids"), filter, null).getArrayList(String.class);
+ if (!lowFreqRowIdList.isEmpty())
+ {
+ getJob().getLogger().info("Analysis: " + analysisId + ", low freq lineages: " + lowFreqRowIdList.size());
+ List alignmentIdsToDelete = lowFreqRowIdList.stream().map(x -> Arrays.asList(x.split(","))).flatMap(List::stream).map(Integer::parseInt).toList();
+ if (!alignmentIdsToDelete.isEmpty())
+ {
+ deleteAlignmentSummaryAndJunction(alignmentIdsToDelete, analysisId, alignmentSummary, alignmentSummaryJunction, "below lineage threshold");
+ }
+ }
+ }
+
+ // Delete low-freq allele groups:
+ if (getPipelineJob().getAlleleGroupThreshold() > 0)
+ {
+ SimpleFilter filter = new SimpleFilter(FieldKey.fromString("analysis_id"), analysisId, CompareType.EQUAL);
+ filter.addCondition(FieldKey.fromString("percent_from_locus"), getPipelineJob().getAlleleGroupThreshold(), CompareType.LT);
+
+ List lowFreqRowIdList = new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_grouped"), PageFlowUtil.set("rowids"), filter, null).getArrayList(String.class);
+ if (!lowFreqRowIdList.isEmpty())
+ {
+ getJob().getLogger().info("Analysis: " + analysisId + ", low freq allele groups: " + lowFreqRowIdList.size());
+ List alignmentIdsToDelete = lowFreqRowIdList.stream().map(x -> Arrays.asList(x.split(","))).flatMap(List::stream).map(Integer::parseInt).toList();
+ if (!alignmentIdsToDelete.isEmpty())
+ {
+ deleteAlignmentSummaryAndJunction(alignmentIdsToDelete, analysisId, alignmentSummary, alignmentSummaryJunction, "below allele-group threshold");
+ }
+ }
+ }
+
+ if (getPipelineJob().isDropDisabledResults())
+ {
+ SimpleFilter filter = new SimpleFilter(FieldKey.fromString("analysis_id"), analysisId, CompareType.EQUAL);
+ filter.addCondition(FieldKey.fromString("status"), false, CompareType.EQUAL);
+
+ List junctionRecordsToDelete = new TableSelector(alignmentSummaryJunction, PageFlowUtil.set("rowid"), filter, null).getArrayList(Integer.class);
+ if (!junctionRecordsToDelete.isEmpty())
+ {
+ getJob().getLogger().info("Deleting " + junctionRecordsToDelete.size() + " disabled records from alignment_summary_junction");
+ alignmentSummaryJunctionDeleted.put("disabled records", alignmentSummaryJunctionDeleted.getOrDefault("disabled records", 0) + junctionRecordsToDelete.size());
+ junctionRecordsToDelete.forEach(rowId -> {
+ Table.delete(alignmentSummaryJunction, rowId);
+ });
+ }
+ }
+
+ if (getPipelineJob().isDropMultiLineageMHC())
+ {
+ SimpleFilter filter = new SimpleFilter(FieldKey.fromString("analysis_id"), analysisId, CompareType.EQUAL);
+ filter.addCondition(FieldKey.fromString("totalLineages"), 1, CompareType.GT);
+ filter.addCondition(FieldKey.fromString("loci"), "MHC", CompareType.CONTAINS);
+
+ List rowIdList = new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_grouped"), PageFlowUtil.set("rowids"), filter, null).getArrayList(String.class);
+ if (!rowIdList.isEmpty())
+ {
+ getJob().getLogger().info("Analysis: " + analysisId + ", multi-lineage records: " + rowIdList.size());
+ List alignmentIdsToDelete = rowIdList.stream().map(x -> Arrays.asList(x.split(","))).flatMap(List::stream).map(Integer::parseInt).toList();
+ if (!alignmentIdsToDelete.isEmpty())
+ {
+ deleteAlignmentSummaryAndJunction(alignmentIdsToDelete, analysisId, alignmentSummary, alignmentSummaryJunction, "multi-lineage MHC");
+ }
+ }
+ }
+
+ // Redundant groups:
+ if (getPipelineJob().isCombineRedundantGroups())
+ {
+ SimpleFilter nAlignmentFilter = new SimpleFilter(FieldKey.fromString("analysis_id"), analysisId, CompareType.EQUAL);
+ nAlignmentFilter.addCondition(FieldKey.fromString("nAlignments"), 1, CompareType.GT);
+ List redundantAlignmentSets = new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_grouped"), PageFlowUtil.set("rowids"), nAlignmentFilter, null).getArrayList(String.class);
+ if (!redundantAlignmentSets.isEmpty())
+ {
+ getJob().getLogger().info("Analysis: " + analysisId + ", redundant alignment sets: " + redundantAlignmentSets.size());
+ redundantAlignmentSets.forEach(x -> {
+ List alignmentIds = Arrays.stream(x.split(",")).map(Integer::parseInt).toList();
+ if (!alignmentIds.isEmpty())
+ {
+ final AtomicInteger rowIdToAppend = new AtomicInteger(-1);
+ final AtomicInteger originalTotal = new AtomicInteger(0);
+ final AtomicInteger totalToAppend = new AtomicInteger(0);
+ final AtomicInteger totalF = new AtomicInteger(0);
+ final AtomicInteger totalR = new AtomicInteger(0);
+ final AtomicInteger totalVP = new AtomicInteger(0);
+ final List rowIdsToDelete = new ArrayList<>();
+ new TableSelector(alignmentSummary, PageFlowUtil.set("rowid", "total", "total_forward", "total_reverse", "valid_pairs"), new SimpleFilter(FieldKey.fromString("rowid"), alignmentIds, CompareType.IN), new Sort("-total")).forEachResults(rs -> {
+ if (rowIdToAppend.get() == -1)
+ {
+ rowIdToAppend.set(rs.getInt(FieldKey.fromString("rowid")));
+ originalTotal.set(rs.getInt(FieldKey.fromString("total")));
+ }
+ else
+ {
+ rowIdsToDelete.add(rs.getInt(FieldKey.fromString("rowid")));
+ totalToAppend.getAndAdd(rs.getInt(FieldKey.fromString("total")));
+ }
+
+ // Just keep a running total, rather than separate new/old:
+ totalF.getAndAdd(rs.getInt(FieldKey.fromString("total_forward")));
+ totalR.getAndAdd(rs.getInt(FieldKey.fromString("total_reverse")));
+ totalVP.getAndAdd(rs.getInt(FieldKey.fromString("valid_pairs")));
+ });
+
+ deleteAlignmentSummaryAndJunction(rowIdsToDelete, analysisId, alignmentSummary, alignmentSummaryJunction, "redundant allele sets");
+ getJob().getLogger().info("increasing total by: " + totalToAppend.get() + ", from: " + originalTotal.get());
+ Map toUpdate = new CaseInsensitiveHashMap<>();
+ toUpdate.put("rowid", rowIdToAppend.get());
+ toUpdate.put("total", originalTotal.get() + totalToAppend.get());
+ toUpdate.put("total_forward", totalF.get());
+ toUpdate.put("total_reverse", totalR.get());
+ toUpdate.put("valid_pairs", totalVP.get());
+ Table.update(getJob().getUser(), alignmentSummary, toUpdate, rowIdToAppend.get());
+ }
+ });
+ }
+ }
+
+ // Find alignment_summary records without any remaining results:
+ List alignmentIdsToDelete = new SqlSelector(alignmentSummary.getSchema().getScope(),
+ new SQLFragment("SELECT x.rowId FROM sequenceanalysis.alignment_summary x ")
+ .append(new SQLFragment("WHERE x.analysis_id = ? ", analysisId))
+ .append(new SQLFragment(" AND x.valid_pairs IS NOT NULL"))
+ .append(new SQLFragment(" AND (SELECT count(*) FROM sequenceanalysis.alignment_summary_junction j WHERE j.analysis_id = ? AND j.alignment_id = x.rowid) = 0", analysisId))
+ ).getArrayList(Integer.class);
+
+ if (!alignmentIdsToDelete.isEmpty())
+ {
+ getJob().getLogger().info("Deleting " + alignmentIdsToDelete.size() + " alignment_summary records lacking alignment_summary_junction");
+ alignmentSummaryDeleted.put("lacking alignment_summary_junction records", alignmentSummaryDeleted.getOrDefault("lacking alignment_summary_junction records", 0) + alignmentIdsToDelete.size());
+ alignmentIdsToDelete.forEach(rowId -> {
+ Table.delete(alignmentSummary, rowId);
+ });
+ }
+
+ // verify ending data:
+ final Map endingData = new HashMap<>();
+ new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_by_lineage"), PageFlowUtil.set("lineages", "percent_from_locus"), dataFilter, null).forEachResults(rs -> {
+ endingData.put(rs.getString(FieldKey.fromString("lineages")), rs.getDouble(FieldKey.fromString("percent_from_locus")));
+ });
+
+ Set allLineages = new TreeSet<>(existingData.keySet());
+ allLineages.addAll(endingData.keySet());
+ allLineages.forEach(l -> {
+ if (!existingData.containsKey(l))
+ {
+ getJob().getLogger().warn("New lineage >0.25 for analysis: " + analysisId + ", " + l + ", new value: " + endingData.get(l));
+ }
+ else if (!endingData.containsKey(l))
+ {
+ if (!l.contains("\n"))
+ {
+ getJob().getLogger().warn("Missing lineage >0.25 for analysis: " + analysisId + ", " + l + ", was: " + existingData.get(l));
+ }
+ }
+ else
+ {
+ double pctDiff = Math.abs(existingData.get(l) - endingData.get(l)) / existingData.get(l);
+ if (pctDiff > 0.35)
+ {
+ Level lvl = existingData.get(l) < 2 ? Level.INFO : Level.WARN;
+ getJob().getLogger().log(lvl, "Significant change in freq for lineage: " + l + ", for analysis: " + analysisId + ", change: " + existingData.get(l) + " -> " + endingData.get(l) + ", pct diff: " + pctDiff);
+ }
+ }
+ });
+
+ if (getPipelineJob().doPerformDeletes())
+ {
+ getJob().getLogger().info("committing changes");
+ transaction.commit();
+ }
+ }
+ }
+
+ private void deleteAlignmentSummaryAndJunction(List alignmentIdsToDelete, int analysisId, TableInfo alignmentSummary, TableInfo alignmentSummaryJunction, String reason)
+ {
+ getJob().getLogger().info("Deleting " + alignmentIdsToDelete.size() + " alignment_summary records. reason: " + reason);
+ alignmentSummaryDeleted.put(reason, alignmentSummaryDeleted.getOrDefault(reason, 0) + alignmentIdsToDelete.size());
+ alignmentIdsToDelete.forEach(rowId -> {
+ Table.delete(alignmentSummary, rowId);
+ });
+
+ // also junction records:
+ SimpleFilter alignmentIdFilter = new SimpleFilter(FieldKey.fromString("analysis_id"), analysisId, CompareType.EQUAL);
+ alignmentIdFilter.addCondition(FieldKey.fromString("alignment_id"), alignmentIdsToDelete, CompareType.IN);
+ List junctionRecordsToDelete = new TableSelector(alignmentSummaryJunction, PageFlowUtil.set("rowid"), alignmentIdFilter, null).getArrayList(Integer.class);
+ getJob().getLogger().info("Deleting " + junctionRecordsToDelete.size() + " alignment_summary_junction records");
+ if (!junctionRecordsToDelete.isEmpty())
+ {
+ alignmentSummaryJunctionDeleted.put(reason, alignmentSummaryJunctionDeleted.getOrDefault(reason, 0) + junctionRecordsToDelete.size());
+ junctionRecordsToDelete.forEach(rowId -> {
+ Table.delete(alignmentSummaryJunction, rowId);
+ });
+ }
+ }
+ }
+
+ public static class AlignmentGroupCompare
+ {
+ private final int analysisId;
+ private final List groups = new ArrayList<>();
+
+ public AlignmentGroupCompare(final int analysisId, Container c, User u)
+ {
+ this.analysisId = analysisId;
+
+ new TableSelector(QueryService.get().getUserSchema(u, c, "sequenceanalysis").getTable("alignment_summary_grouped"), PageFlowUtil.set("analysis_id", "alleles", "lineages", "totalLineages", "total_reads", "total_forward", "total_reverse", "valid_pairs", "rowids"), new SimpleFilter(FieldKey.fromString("analysis_id"), analysisId), null).forEachResults(rs -> {
+ if (rs.getString(FieldKey.fromString("alleles")) == null)
+ {
+ return;
+ }
+
+ AlignmentGroup g = new AlignmentGroup();
+ g.analysisId = analysisId;
+ g.alleles.addAll(Arrays.stream(rs.getString(FieldKey.fromString("alleles")).split("\n")).toList());
+ g.lineages = rs.getString(FieldKey.fromString("lineages"));
+ g.totalLineages = rs.getInt(FieldKey.fromString("totalLineages"));
+ g.totalReads = rs.getInt(FieldKey.fromString("total_reads"));
+ g.totalForward = rs.getInt(FieldKey.fromString("total_forward"));
+ g.totalReverse = rs.getInt(FieldKey.fromString("total_reverse"));
+ g.validPairs = rs.getInt(FieldKey.fromString("valid_pairs"));
+ g.rowIds.addAll(Arrays.stream(rs.getString(FieldKey.fromString("rowids")).split(",")).map(Integer::parseInt).toList());
+
+ groups.add(g);
+ });
+
+ sortGroups();
+ }
+
+ private void sortGroups()
+ {
+ groups.sort(Comparator.comparingInt(o -> o.alleles.size()));
+ Collections.reverse(groups);
+ }
+
+ public Pair collapseGroups(Logger log, User user)
+ {
+ final long initialCounts = groups.stream().map(x -> x.totalReads).mapToInt(Integer::intValue).sum();
+
+ if (groups.isEmpty())
+ {
+ return null;
+ }
+
+ Pair ret = Pair.of(0, 0);
+ while (doCollapse(log))
+ {
+ //do work. each time we have any groups collapsed, we will restart. once there are no collapsed allele groups, we finish
+ sortGroups();
+ }
+
+ final int endCounts = groups.stream().map(x -> x.totalReads).mapToInt(Integer::intValue).sum();
+ if (initialCounts != endCounts)
+ {
+ throw new IllegalStateException("Starting/ending counts not equal: " + initialCounts + " / " + endCounts);
+ }
+
+ List alignmentIdsToDelete = groups.stream().map(x -> x.rowIdsToDelete).flatMap(List::stream).toList();
+ List alignmentGroupsToUpdate = groups.stream().filter(g -> !g.rowIdsToDelete.isEmpty()).toList();
+ log.info("Alignment IDs to delete: " + alignmentIdsToDelete.size());
+ log.info("Alignment groups to update counts: " + alignmentGroupsToUpdate.size());
+
+ if (!alignmentGroupsToUpdate.isEmpty())
+ {
+ log.info("Updating counts in " + alignmentGroupsToUpdate.size() + " groups after collapse");
+ TableInfo alignmentSummary = DbSchema.get("sequenceanalysis", DbSchemaType.Module).getTable("alignment_summary");
+
+ alignmentGroupsToUpdate.forEach(ag -> {
+ Map toUpdate = new CaseInsensitiveHashMap<>();
+ toUpdate.put("rowId", ag.rowIds.get(0));
+ toUpdate.put("total", ag.totalReads);
+ toUpdate.put("total_forward", ag.totalForward);
+ toUpdate.put("total_reverse", ag.totalReverse);
+ toUpdate.put("valid_pairs", ag.validPairs);
+ Table.update(user, alignmentSummary, toUpdate, ag.rowIds.get(0));
+
+ if (ag.rowIds.size() > 1) {
+ log.info("The following IDs are redundant and will also be removed: " + ag.rowIds.subList(1, ag.rowIds.size()).stream().map(String::valueOf).collect(Collectors.joining(", ")));
+ alignmentIdsToDelete.addAll(ag.rowIds.subList(1, ag.rowIds.size()));
+ }
+ });
+ }
+
+ if (!alignmentIdsToDelete.isEmpty())
+ {
+ log.info("Deleting " + alignmentIdsToDelete.size() + " alignment_summary records after collapse");
+
+ TableInfo alignmentSummary = DbSchema.get("sequenceanalysis", DbSchemaType.Module).getTable("alignment_summary");
+ TableInfo alignmentSummaryJunction = DbSchema.get("sequenceanalysis", DbSchemaType.Module).getTable("alignment_summary_junction");
+
+ alignmentIdsToDelete.forEach(rowId -> {
+ Table.delete(alignmentSummary, rowId);
+ });
+ ret.first += alignmentIdsToDelete.size();
+
+ // also junction records:
+ SimpleFilter alignmentIdFilter = new SimpleFilter(FieldKey.fromString("analysis_id"), analysisId, CompareType.EQUAL);
+ alignmentIdFilter.addCondition(FieldKey.fromString("alignment_id"), alignmentIdsToDelete, CompareType.IN);
+ List junctionRecordsToDelete = new TableSelector(alignmentSummaryJunction, PageFlowUtil.set("rowid"), alignmentIdFilter, null).getArrayList(Integer.class);
+ log.info("Deleting " + junctionRecordsToDelete.size() + " alignment_summary_junction records");
+ if (!junctionRecordsToDelete.isEmpty())
+ {
+ junctionRecordsToDelete.forEach(rowId -> {
+ Table.delete(alignmentSummaryJunction, rowId);
+ });
+ ret.second += junctionRecordsToDelete.size();
+ }
+ }
+
+ return ret;
+ }
+
+ private boolean doCollapse(Logger log)
+ {
+ ListIterator it = groups.listIterator();
+ AlignmentGroup g1 = it.next();
+ while (it.hasNext())
+ {
+ int orig = g1.alleles.size();
+ if (compareGroupToOthers(g1))
+ {
+ log.info("Collapsed: " + g1.lineages + ", from: " + orig + " to " + g1.alleles.size() + " alleles");
+ return true; // abort and restart the process with a new list iterator
+ }
+
+ g1 = it.next();
+ }
+
+ return false;
+ }
+
+ private boolean compareGroupToOthers(AlignmentGroup g1)
+ {
+ boolean didCollapse = false;
+ int idx = groups.indexOf(g1);
+ if (idx == groups.size() - 1)
+ {
+ return false;
+ }
+
+ List groupsClone = new ArrayList<>(groups.subList(idx + 1, groups.size()));
+ ListIterator it = groupsClone.listIterator();
+ while (it.hasNext())
+ {
+ AlignmentGroup g2 = it.next();
+ if (g2.equals(g1))
+ {
+ throw new IllegalStateException("Should not happen");
+ }
+
+ if (g1.canCombine(g2))
+ {
+ AlignmentGroup combined = g1.combine(g2);
+ groups.remove(g1);
+ groups.add(idx, combined);
+ g1 = combined;
+ groups.remove(g2);
+
+ didCollapse = true;
+ }
+ }
+
+ return didCollapse;
+ }
+
+ public static class AlignmentGroup
+ {
+ int analysisId;
+ Set alleles = new TreeSet<>();
+ String lineages;
+ int totalLineages;
+ int totalReads;
+ int totalForward;
+ int totalReverse;
+ int validPairs;
+ List rowIds = new ArrayList<>();
+
+ List rowIdsToDelete = new ArrayList<>();
+
+ public boolean canCombine(AlignmentGroup g2)
+ {
+ if (this.totalLineages > 1 || g2.totalLineages > 1 || this.alleles.size() < 4 || g2.alleles.size() < 4)
+ {
+ return false;
+ }
+
+ // Allow greater level of collapse with highly ambiguous results:
+ // Require similar sizes, but disjoint allele sets (e.g., A/B/D and A/C/D, but not A/B/C and A/D/E)
+ int setDiffThreshold;
+ int sizeDiffThreshold;
+ if (this.alleles.size() >= 16)
+ {
+ setDiffThreshold = 6;
+ sizeDiffThreshold = 3;
+ }
+ else if (this.alleles.size() >= 8)
+ {
+ setDiffThreshold = 4;
+ sizeDiffThreshold = 2;
+ }
+ else
+ {
+ setDiffThreshold = 2;
+ sizeDiffThreshold = 1;
+ }
+
+ return Math.abs(this.alleles.size() - g2.alleles.size()) <= sizeDiffThreshold && CollectionUtils.disjunction(this.alleles, g2.alleles).size() <= setDiffThreshold;
+ }
+
+ public AlignmentGroup combine(AlignmentGroup g2)
+ {
+ // Take the union of the allele sets:
+ TreeSet allAlleles = Stream.of(this.alleles, g2.alleles).flatMap(Collection::stream).collect(Collectors.toCollection(TreeSet::new));
+ if (g2.alleles.size() > this.alleles.size())
+ {
+ g2.alleles = allAlleles;
+ g2.rowIdsToDelete.addAll(this.rowIds);
+ g2.rowIdsToDelete.addAll(this.rowIdsToDelete);
+ g2.totalReads = g2.totalReads + totalReads;
+ g2.totalForward = g2.totalForward + totalForward;
+ g2.totalReverse = g2.totalReverse + totalReverse;
+ g2.validPairs = g2.validPairs + validPairs;
+
+ return g2;
+ }
+ else
+ {
+ this.alleles = allAlleles;
+ this.rowIdsToDelete.addAll(g2.rowIds);
+ this.rowIdsToDelete.addAll(g2.rowIdsToDelete);
+ this.totalReads = g2.totalReads + totalReads;
+ this.totalForward = g2.totalForward + totalForward;
+ this.totalReverse = g2.totalReverse + totalReverse;
+ this.validPairs = g2.validPairs + validPairs;
+
+ return this;
+ }
+ }
+ }
+ }
+}
diff --git a/primeseq/src/org/labkey/primeseq/pipeline/MhcMigrationPipelineJob.java b/primeseq/src/org/labkey/primeseq/pipeline/MhcMigrationPipelineJob.java
index 15f015b51..339b31543 100644
--- a/primeseq/src/org/labkey/primeseq/pipeline/MhcMigrationPipelineJob.java
+++ b/primeseq/src/org/labkey/primeseq/pipeline/MhcMigrationPipelineJob.java
@@ -449,8 +449,7 @@ private void createAlignmentSummary() throws PipelineJobException
}
map.put("ref_nt_id", localNT);
map.put("status", rs.getValue("status"));
-
- map.put("alignment_id", alignmentSummaryMap.get("alignment_id"));
+ map.put("alignment_id", alignmentSummaryMap.get(rs.getValue("alignment_id")));
Container c = workbookMap.get((int) rs.getValue("analysis_id/workbook/workbookId"));
map.put("container", c.getId());
diff --git a/primeseq/src/org/labkey/primeseq/query/PerformMhcCleanupButton.java b/primeseq/src/org/labkey/primeseq/query/PerformMhcCleanupButton.java
new file mode 100644
index 000000000..944bc2298
--- /dev/null
+++ b/primeseq/src/org/labkey/primeseq/query/PerformMhcCleanupButton.java
@@ -0,0 +1,19 @@
+package org.labkey.primeseq.query;
+
+import org.labkey.api.data.ContainerManager;
+import org.labkey.api.data.TableInfo;
+import org.labkey.api.ldk.table.SimpleButtonConfigFactory;
+import org.labkey.api.module.ModuleLoader;
+import org.labkey.api.query.DetailsURL;
+import org.labkey.api.view.template.ClientDependency;
+import org.labkey.primeseq.PrimeseqModule;
+
+import java.util.Arrays;
+
+public class PerformMhcCleanupButton extends SimpleButtonConfigFactory
+{
+ public PerformMhcCleanupButton()
+ {
+ super(ModuleLoader.getInstance().getModule(PrimeseqModule.class), "Perform MHC Cleanup", DetailsURL.fromString("primeseq/performMhcCleanup.view"));
+ }
+}
\ No newline at end of file
diff --git a/primeseq/webapp/WEB-INF/primeseqContext.xml b/primeseq/webapp/WEB-INF/primeseqContext.xml
index b91d3dfb3..0cb854609 100644
--- a/primeseq/webapp/WEB-INF/primeseqContext.xml
+++ b/primeseq/webapp/WEB-INF/primeseqContext.xml
@@ -6,18 +6,18 @@
-
-
+
-
- org.labkey.primeseq.pipeline.MhcMigrationPipelineJob.Task
+ org.labkey.primeseq.pipeline.MhcCleanupPipelineJob.Task
+
+
+