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bbimberbbimber
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Merge pull request #400 from LabKey/fb_merge_25.7_to_develop
Merge 25.7 to develop
2 parents dbdca95 + f668cfb commit 4e69601

12 files changed

Lines changed: 159 additions & 19 deletions

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‎SequenceAnalysis/pipeline_code/extra_tools_install.sh‎

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@@ -333,3 +333,20 @@ then
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else
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echo "Already installed"
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fi
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if [[ ! -e ${LKTOOLS_DIR}/primer3_core || ! -z $FORCE_REINSTALL ]];
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then
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echo "Cleaning up previous installs"
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rm -Rf $LKTOOLS_DIR/primer3_core*
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rm -Rf primer3*
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rm -Rf v2.6.1.tar.gz
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wget https://github.com/primer3-org/primer3/archive/refs/tags/v2.6.1.tar.gz
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tar -xf v2.6.1.tar.gz
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cd primer3-2.6.1/src
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make
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install primer3_core $LKTOOLS_DIR/
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else
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echo "Already installed"
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fi

‎SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/TagPcrSummaryStep.java‎

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@@ -72,7 +72,7 @@ public Provider()
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put("checked", true);
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}}, true),
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ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("--insert-name"), "insertType", "Insert Type", "The type of insert to detect.", "ldk-simplecombo", new JSONObject(){{
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put("storeValues", "PiggyBac;Lentivirus;PREDICT");
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put("storeValues", "PiggyBac;Lentivirus;PREDICT;BxBI_attP");
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put("allowBlank", false);
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}}, null),
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ToolParameterDescriptor.create(DESIGN_PRIMERS, "Design Primers", "If selected, Primer3 will be used to design primers to flank integration sites", "checkbox", new JSONObject(){{

‎Studies/resources/queries/studies/studyCohorts/.qview.xml‎

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@@ -0,0 +1,22 @@
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<customView xmlns="http://labkey.org/data/xml/queryCustomView" hidden="false" canOverride="false">
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<columns>
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<column name="rowId"/>
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<column name="studyId"/>
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<column name="studyId/description">
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<properties>
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<property name="columnTitle" value="Study Description"/>
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</properties>
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</column>
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<column name="cohortName"/>
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<column name="label"/>
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<column name="category"/>
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<column name="description"/>
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<column name="isControlGroup"/>
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<column name="sortOrder"/>
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</columns>
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<sorts>
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<sort column="studyId/studyName" descending="false"/>
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<sort column="sortOrder" descending="false"/>
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<sort column="cohortName" descending="false"/>
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</sorts>
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</customView>

‎Studies/resources/schemas/dbscripts/postgresql/studies-23.005-23.006.sql‎

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ALTER TABLE studies.subjectAnchorDates ADD COLUMN sourceRecord varchar(1000);

‎Studies/resources/schemas/dbscripts/sqlserver/studies-23.005-23.006.sql‎

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ALTER TABLE studies.subjectAnchorDates ADD sourceRecord varchar(1000);

‎Studies/resources/schemas/studies.xml‎

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@@ -526,6 +526,10 @@
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<fkDisplayColumnName>label</fkDisplayColumnName>
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</fk>
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</column>
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<column columnName="sourceRecord">
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<columnTitle>Source Record</columnTitle>
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<isHidden>true</isHidden>
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</column>
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<column columnName="dataSource">
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<columnTitle>Data Source</columnTitle>
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</column>

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

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@@ -34,7 +34,7 @@ public String getName()
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@Override
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public @Nullable Double getSchemaVersion()
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{
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return 23.005;
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return 23.006;
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}
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@Override

‎Studies/src/org/labkey/studies/query/StudiesTriggerFactory.java‎

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@@ -93,6 +93,11 @@ private void possiblyResolveStudyOrCohort(String tableToQuery, @Nullable Map<Str
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return;
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}
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if (row.get(sourceProperty) instanceof Integer)
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{
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return;
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}
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if (row.get(sourceProperty) != null & row.get(sourceProperty) instanceof String & !String.valueOf(row.get(sourceProperty)).isEmpty())
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{
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if (!NumberUtils.isCreatable(row.get(sourceProperty).toString()))

‎singlecell/resources/chunks/StudyMetadata.R‎

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@@ -32,7 +32,7 @@ for (datasetId in names(seuratObjects)) {
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seuratObj <- Rdiscvr::ApplyEC_Metadata(seuratObj, errorIfUnknownIdsFound = errorIfUnknownIdsFound)
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} else if (studyName == 'PPG_Stims') {
3434
seuratObj <- Rdiscvr::ApplyPPG_Stim_Metadata(seuratObj, errorIfUnknownIdsFound = errorIfUnknownIdsFound)
35-
] else if (studyName == 'IMPAC_TB_Human') {
35+
} else if (studyName == 'IMPAC_TB_Human') {
3636
seuratObj <- Rdiscvr::ApplyIMPAC_TB_Human_Metadata(seuratObj, errorIfUnknownIdsFound = errorIfUnknownIdsFound)
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} else {
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stop(paste0('Unknown study: ', studyName))

‎singlecell/src/org/labkey/singlecell/run/CellRangerGexCountStep.java‎

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@@ -5,6 +5,7 @@
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import org.apache.commons.io.FileUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.lang3.tuple.Pair;
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import org.apache.logging.log4j.Logger;
89
import org.jetbrains.annotations.Nullable;
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import org.json.JSONObject;
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import org.labkey.api.collections.CaseInsensitiveHashMap;
@@ -47,15 +48,19 @@
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import org.labkey.api.writer.PrintWriters;
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import org.labkey.singlecell.SingleCellSchema;
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51+
import java.io.BufferedReader;
5052
import java.io.File;
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import java.io.IOException;
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import java.nio.file.Files;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collection;
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import java.util.Date;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
62+
import java.util.regex.Matcher;
63+
import java.util.regex.Pattern;
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6065
public class CellRangerGexCountStep extends AbstractAlignmentPipelineStep<CellRangerWrapper> implements AlignmentStep
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{
@@ -613,4 +618,88 @@ public void complete(SequenceAnalysisJobSupport support, AnalysisModel model, Co
613618
}
614619
}
615620
}
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public enum Chemistry
623+
{
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// See: https://kb.10xgenomics.com/s/article/115004506263-What-is-a-barcode-inclusion-list-formerly-barcode-whitelist
625+
// cellranger-x.y.z/lib/python/cellranger/barcodes/
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FivePE_V3("Single Cell 5' PE v3", "3M-5pgex-jan-2023.txt.gz"),
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FivePE_V2("Single Cell 5' PE v2", "737k-august-2016.txt");
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final String _label;
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final String _inclusionListFile;
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Chemistry(String label, String inclusionListFile)
633+
{
634+
_label = label;
635+
_inclusionListFile = inclusionListFile;
636+
}
637+
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public File getInclusionListFile(Logger logger) throws PipelineJobException
639+
{
640+
File exe = new CellRangerWrapper(logger).getExe();
641+
if (Files.isSymbolicLink(exe.toPath()))
642+
{
643+
try
644+
{
645+
exe = Files.readSymbolicLink(exe.toPath()).toFile();
646+
}
647+
catch (IOException e)
648+
{
649+
throw new PipelineJobException(e);
650+
}
651+
}
652+
653+
File il = new File(exe.getParentFile(), "lib/python/cellranger/barcodes/" + _inclusionListFile);
654+
if (!il.exists())
655+
{
656+
throw new PipelineJobException("Unable to find file: " + il.getPath());
657+
}
658+
659+
return il;
660+
}
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public static Chemistry getByLabel(String label)
663+
{
664+
for (Chemistry c : Chemistry.values())
665+
{
666+
if (c._label.equals(label))
667+
{
668+
return c;
669+
}
670+
}
671+
672+
throw new IllegalArgumentException("Unknown chemistry: " + label);
673+
}
674+
}
675+
676+
public static Chemistry inferChemistry(File cloupeFile) throws PipelineJobException
677+
{
678+
File html = new File(cloupeFile.getPath().replaceAll("_cloupe.cloupe$", "_web_summary.html"));
679+
if (!html.exists())
680+
{
681+
throw new IllegalArgumentException("Missing file: " + html.getPath());
682+
}
683+
684+
final Pattern pattern = Pattern.compile("\\[\"Chemistry\",\"(.*?)\"],");
685+
try (BufferedReader reader = Readers.getReader(html))
686+
{
687+
String line;
688+
while ((line = reader.readLine()) != null)
689+
{
690+
Matcher m = pattern.matcher(line);
691+
if (m.find())
692+
{
693+
String chem = m.group(1);
694+
return Chemistry.getByLabel(chem);
695+
}
696+
}
697+
}
698+
catch (IOException e)
699+
{
700+
throw new PipelineJobException(e);
701+
}
702+
703+
throw new IllegalArgumentException("Unable to infer chemistry for file: " + html.getPath());
704+
}
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}

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