diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/RefNtSequenceModel.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/RefNtSequenceModel.java index 71d236c70..3ae8eab22 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/RefNtSequenceModel.java +++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/RefNtSequenceModel.java @@ -418,7 +418,7 @@ public byte[] getSequenceBases() public void createFileForSequence(User u, String sequence, @Nullable File outDir) throws IOException { - File output = getExpectedSequenceFile(); + File output = getExpectedSequenceFile(outDir); if (output.exists()) { output.delete(); @@ -443,9 +443,9 @@ public void createFileForSequence(User u, String sequence, @Nullable File outDir Table.update(u, ti, this, _rowid); } - public File getExpectedSequenceFile() throws IllegalArgumentException + public File getExpectedSequenceFile(@Nullable File outDir) throws IllegalArgumentException { - return FileUtil.appendName(getHashedDir(true), _rowid + ".txt.gz"); + return FileUtil.appendName(getSequenceFileBaseDir(outDir, true), _rowid + ".txt.gz"); } private Container getLabKeyContainer() @@ -553,23 +553,15 @@ public File getOffsetsFile() return FileUtil.appendName(d.getFile().getParentFile(), getRowid() + "_offsets.txt"); } - private File getHashedDir(boolean create) + private File getSequenceFileBaseDir(@Nullable File outDir, boolean create) { - File baseDir = getBaseSequenceDir(); - String digest = Crypt.MD5.digest(String.valueOf(getRowid())); + outDir = outDir == null ? getBaseSequenceDir() : outDir; - baseDir = FileUtil.appendName(baseDir, digest.substring(0,4)); - baseDir = FileUtil.appendName(baseDir, digest.substring(4,8)); - baseDir = FileUtil.appendName(baseDir, digest.substring(8,12)); - baseDir = FileUtil.appendName(baseDir, digest.substring(12,20)); - baseDir = FileUtil.appendName(baseDir, digest.substring(20,28)); - baseDir = FileUtil.appendName(baseDir, digest.substring(28,32)); - - if (create) + if (create && !outDir.exists()) { - baseDir.mkdirs(); + outDir.mkdirs(); } - return baseDir; + return outDir; } } diff --git a/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage.query.xml b/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage.query.xml index f4f2e91b2..d78f3a033 100644 --- a/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage.query.xml +++ b/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage.query.xml @@ -9,6 +9,14 @@ true true + + Analysis Id + + sequenceanalysis + sequence_analyses + rowid + + 150 diff --git a/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage.sql b/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage.sql index 7ab8394a5..544b2d361 100644 --- a/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage.sql +++ b/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage.sql @@ -1,51 +1,45 @@ -PARAMETERS(AnalysisId INTEGER) - -select - (CAST(AnalysisId as varchar) || '<>' || a.lineages) as key, - a.analysis_id, - a.lineages, - max(a.totalLineages) as totalLineages, - a.loci, - - sum(a.total) as total, - max(a.total_reads) as total_reads, - round(100 * (cast(sum(a.total) as float) / cast(max(a.total_reads) as float)), 2) as percent, - group_concat(distinct a.haplotypesWithAllele) as haplotypesWithAllele, - - CAST((select sum(s.total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = AnalysisId AND s.rowid IN ( - SELECT distinct asj.alignment_id from sequenceanalysis.alignment_summary_junction asj WHERE asj.analysis_id = AnalysisId AND asj.ref_nt_id.locus = a.loci and asj.status = true - ) - ) as integer) as total_reads_from_locus, - - round(100 * (cast(sum(a.total) as float) / cast((select sum(s.total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = AnalysisId AND s.rowid IN ( - SELECT distinct asj.alignment_id from sequenceanalysis.alignment_summary_junction asj WHERE asj.analysis_id = AnalysisId AND asj.ref_nt_id.locus = a.loci and asj.status = true - ) - ) as float)), 2) as percent_from_locus, - group_concat(distinct a.rowid, ',') as rowids +SELECT + t.*, + CASE WHEN t.total_reads_from_locus = 0 THEN 0 ELSE round(100 * (cast(t.total_reads as float) / cast(t.total_reads_from_locus as float)), 2) END as percent_from_locus, FROM ( - - select - a.analysis_id, - a.rowid, - - group_concat(distinct coalesce(j.ref_nt_id.lineage, j.ref_nt_id.name), chr(10)) as lineages, - count(distinct j.ref_nt_id.lineage) as totalLineages, - group_concat(distinct coalesce(j.ref_nt_id.locus, j.ref_nt_id.name), chr(10)) as loci, - - total, - cast((select sum(total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = AnalysisId) as integer) as total_reads, - group_concat(distinct hs.haplotype, chr(10)) as haplotypesWithAllele - - from sequenceanalysis.alignment_summary a - join sequenceanalysis.alignment_summary_junction j ON (j.analysis_id = AnalysisId AND j.alignment_id = a.rowid and j.status = true) - left join sequenceanalysis.haplotype_sequences hs ON (( - (hs.name = j.ref_nt_id.lineage AND hs.type = 'Lineage') OR - (hs.name = j.ref_nt_id.name AND hs.type = 'Allele') - ) AND hs.haplotype.datedisabled IS NULL) - WHERE a.analysis_id = AnalysisId - group by a.analysis_id, a.rowid, a.total - -) a - -GROUP BY a.analysis_id, a.lineages, a.loci + SELECT + (CAST(a.analysis_id as varchar) || '<>' || a.lineages) as key, + a.analysis_id, + max(a.lineages) as lineages, + coalesce(max(a.totalLineages), 0) as totalLineages, + a.loci, + + sum(a.total) as total_reads, + max(a.total_reads_in_analysis) as total_reads_in_analysis, + CASE WHEN max(a.total_reads_in_analysis) = 0 THEN 0 ELSE round(100 * (cast(sum(a.total) as float) / cast(max(a.total_reads_in_analysis) as float)), 2) END as percent, + + group_concat(a.rowid, ',') as rowids, + group_concat(distinct a.haplotypesWithAllele) as haplotypesWithAllele, + + max(a.total_reads_from_locus) as total_reads_from_locus, + max(a.lastModified) as lastModified, + count(distinct a.rowid) as nAlignments + + FROM ( + + select + ac.analysis_id, + ac.rowid, + + group_concat(distinct coalesce(ac.lineage, ac.ntName), chr(10)) as lineages, + count(distinct ac.lineage) as totalLineages, + group_concat(distinct coalesce(ac.locus, ac.ntName), chr(10)) as loci, + + group_concat(distinct haplotypesWithAllele, chr(10)) as haplotypesWithAllele, + + max(ac.total) as total, + max(ac.total_reads_in_analysis) as total_reads_in_analysis, + max(ac.total_reads_from_locus) as total_reads_from_locus, + max(ac.modified) as lastModified + from sequenceanalysis.alignment_summary_combined ac + group by ac.analysis_id, ac.rowid, ac.total + ) a + + GROUP BY a.analysis_id, a.lineages, a.loci +) t \ No newline at end of file diff --git a/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage/.qview.xml b/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage/.qview.xml index 7b6dac64b..9c03eeb42 100644 --- a/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage/.qview.xml +++ b/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage/.qview.xml @@ -19,8 +19,8 @@ - + diff --git a/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage/With Haplotype Matches.qview.xml b/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage/With Haplotype Matches.qview.xml index 1b4726c31..185a76068 100644 --- a/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage/With Haplotype Matches.qview.xml +++ b/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage/With Haplotype Matches.qview.xml @@ -19,8 +19,8 @@ - + diff --git a/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage_orig.sql b/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage_orig.sql new file mode 100644 index 000000000..7ab8394a5 --- /dev/null +++ b/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage_orig.sql @@ -0,0 +1,51 @@ +PARAMETERS(AnalysisId INTEGER) + +select + (CAST(AnalysisId as varchar) || '<>' || a.lineages) as key, + a.analysis_id, + a.lineages, + max(a.totalLineages) as totalLineages, + a.loci, + + sum(a.total) as total, + max(a.total_reads) as total_reads, + round(100 * (cast(sum(a.total) as float) / cast(max(a.total_reads) as float)), 2) as percent, + group_concat(distinct a.haplotypesWithAllele) as haplotypesWithAllele, + + CAST((select sum(s.total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = AnalysisId AND s.rowid IN ( + SELECT distinct asj.alignment_id from sequenceanalysis.alignment_summary_junction asj WHERE asj.analysis_id = AnalysisId AND asj.ref_nt_id.locus = a.loci and asj.status = true + ) + ) as integer) as total_reads_from_locus, + + round(100 * (cast(sum(a.total) as float) / cast((select sum(s.total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = AnalysisId AND s.rowid IN ( + SELECT distinct asj.alignment_id from sequenceanalysis.alignment_summary_junction asj WHERE asj.analysis_id = AnalysisId AND asj.ref_nt_id.locus = a.loci and asj.status = true + ) + ) as float)), 2) as percent_from_locus, + group_concat(distinct a.rowid, ',') as rowids + +FROM ( + + select + a.analysis_id, + a.rowid, + + group_concat(distinct coalesce(j.ref_nt_id.lineage, j.ref_nt_id.name), chr(10)) as lineages, + count(distinct j.ref_nt_id.lineage) as totalLineages, + group_concat(distinct coalesce(j.ref_nt_id.locus, j.ref_nt_id.name), chr(10)) as loci, + + total, + cast((select sum(total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = AnalysisId) as integer) as total_reads, + group_concat(distinct hs.haplotype, chr(10)) as haplotypesWithAllele + + from sequenceanalysis.alignment_summary a + join sequenceanalysis.alignment_summary_junction j ON (j.analysis_id = AnalysisId AND j.alignment_id = a.rowid and j.status = true) + left join sequenceanalysis.haplotype_sequences hs ON (( + (hs.name = j.ref_nt_id.lineage AND hs.type = 'Lineage') OR + (hs.name = j.ref_nt_id.name AND hs.type = 'Allele') + ) AND hs.haplotype.datedisabled IS NULL) + WHERE a.analysis_id = AnalysisId + group by a.analysis_id, a.rowid, a.total + +) a + +GROUP BY a.analysis_id, a.lineages, a.loci diff --git a/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_combined.query.xml b/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_combined.query.xml new file mode 100644 index 000000000..b96e6d860 --- /dev/null +++ b/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_combined.query.xml @@ -0,0 +1,23 @@ + + + + + Alignment Summary, Combined + + + Total First-Mate Reads + The column shows the number of alignments that contain a first-mate or singleton read + + + Total Second-Mate Reads + The column shows the number of alignments that contain a second-mate read + + + Total Valid Pairs + The column shows the number of alignments that contain valid paired reads (both forward and reverse) + + +
+ + + diff --git a/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_grouped.query.xml b/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_grouped.query.xml index 4f755a30e..9eb153f0d 100644 --- a/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_grouped.query.xml +++ b/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_grouped.query.xml @@ -6,6 +6,14 @@ Alignment Summary rowids + + Analysis Id + + sequenceanalysis + sequence_analyses + rowid + + RowIds true diff --git a/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_grouped.sql b/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_grouped.sql index ee61c695e..62f16b6e4 100644 --- a/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_grouped.sql +++ b/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_grouped.sql @@ -1,70 +1,55 @@ -PARAMETERS(AnalysisId INTEGER) - -select - a.analysis_id, - a.alleles, - a.alleleIds, - max(a.lineages) as lineages, - coalesce(max(a.totalLineages), 0) as totalLineages, - a.loci, - - sum(a.total) as total_reads, - sum(a.total_forward) as total_forward, - sum(a.total_reverse) as total_reverse, - sum(a.valid_pairs) as valid_pairs, - max(cast(a.total_reads as integer)) as total_reads_in_analysis, - --max(a.loci_total_reads) as total_reads_in_analysis_from_locus, - CASE WHEN max(a.total_reads) = 0 THEN 0 ELSE round(100 * (cast(sum(a.total) as float) / cast(max(a.total_reads) as float)), 2) END as percent, --- case --- when (cast(sum(a.total) as float) / cast(max(a.total_reads) as float)) >= .04 THEN 'Major' --- else 'Minor' --- end as category, - - group_concat(a.rowid, ',') as rowids, - group_concat(distinct a.haplotypesWithAllele) as haplotypesWithAllele, - - CAST((select sum(s.total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = AnalysisId AND s.rowid IN ( - SELECT distinct asj.alignment_id from sequenceanalysis.alignment_summary_junction asj WHERE asj.analysis_id = AnalysisId AND asj.ref_nt_id.locus = a.loci and asj.status = true - ) - ) as INTEGER) as total_reads_from_locus, - - round(100 * (cast(sum(a.total) as float) / CASE WHEN count(a.lineages) = 0 THEN max(a.total_reads) ELSE cast((select sum(s.total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = AnalysisId AND s.rowid IN ( - SELECT distinct asj.alignment_id from sequenceanalysis.alignment_summary_junction asj WHERE asj.analysis_id = AnalysisId AND asj.ref_nt_id.locus = a.loci and asj.status = true - ) - ) as float) END), 2) as percent_from_locus, - max(lastModified) as lastModified, - count(distinct a.rowid) as nAlignments, - max(a.nloci) as nLoci +SELECT + t.*, + CASE WHEN t.total_reads_from_locus = 0 THEN 0 ELSE round(100 * (cast(t.total_reads as float) / cast(t.total_reads_from_locus as float)), 2) END as percent_from_locus, FROM ( - - select - a.analysis_id, - a.rowid, - - group_concat(distinct j.ref_nt_id) as alleleIds, - group_concat(distinct j.ref_nt_id.name, chr(10)) as alleles, - group_concat(distinct j.ref_nt_id.lineage, chr(10)) as lineages, - count(distinct j.ref_nt_id.lineage) as totalLineages, - group_concat(distinct j.ref_nt_id.locus, chr(10)) as loci, - count(distinct j.ref_nt_id.locus) as nloci, - group_concat(distinct hs.haplotype, chr(10)) as haplotypesWithAllele, - - total, - total_forward, - total_reverse, - valid_pairs, - (select sum(total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = AnalysisId) as total_reads, - max(j.modified) as lastModified - from sequenceanalysis.alignment_summary a - left join sequenceanalysis.alignment_summary_junction j ON (j.analysis_id = AnalysisId AND j.alignment_id = a.rowid and j.status = true) - left join sequenceanalysis.haplotype_sequences hs ON (( - (hs.name = j.ref_nt_id.lineage AND hs.type = 'Lineage') OR - (hs.name = j.ref_nt_id.name AND hs.type = 'Allele') - ) AND hs.haplotype.datedisabled IS NULL) - WHERE a.analysis_id = AnalysisId - group by a.analysis_id, a.rowid, a.total, total_forward, total_reverse, valid_pairs - -) a - -GROUP BY a.analysis_id, a.alleles, a.alleleIds, a.loci + SELECT + a.analysis_id, + a.alleles, + a.alleleIds, + max(a.lineages) as lineages, + coalesce(max(a.totalLineages), 0) as totalLineages, + a.loci, + + sum(a.total) as total_reads, + sum(a.total_forward) as total_forward, + sum(a.total_reverse) as total_reverse, + sum(a.valid_pairs) as valid_pairs, + max(a.total_reads_in_analysis) as total_reads_in_analysis, + CASE WHEN max(a.total_reads_in_analysis) = 0 THEN 0 ELSE round(100 * (cast(sum(a.total) as float) / cast(max(a.total_reads_in_analysis) as float)), 2) END as percent, + + group_concat(a.rowid, ',') as rowids, + group_concat(distinct a.haplotypesWithAllele) as haplotypesWithAllele, + + max(a.total_reads_from_locus) as total_reads_from_locus, + max(a.lastModified) as lastModified, + count(distinct a.rowid) as nAlignments, + max(a.nloci) as nLoci + + FROM ( + + select + ac.analysis_id, + ac.rowid, + + group_concat(distinct ac.ref_nt_id) as alleleIds, + group_concat(distinct ac.ntName, chr(10)) as alleles, + group_concat(distinct ac.lineage, chr(10)) as lineages, + count(distinct ac.lineage) as totalLineages, + group_concat(distinct ac.locus, chr(10)) as loci, + count(distinct ac.locus) as nloci, + group_concat(distinct haplotypesWithAllele, chr(10)) as haplotypesWithAllele, + + max(ac.total) as total, + max(ac.total_forward) as total_forward, + max(ac.total_reverse) as total_reverse, + max(ac.valid_pairs) as valid_pairs, + max(ac.total_reads_in_analysis) as total_reads_in_analysis, + max(ac.total_reads_from_locus) as total_reads_from_locus, + max(ac.modified) as lastModified + from sequenceanalysis.alignment_summary_combined ac + group by ac.analysis_id, ac.rowid + ) a + + GROUP BY a.analysis_id, a.alleles, a.alleleIds, a.loci +) t \ No newline at end of file diff --git a/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_grouped_orig.sql b/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_grouped_orig.sql new file mode 100644 index 000000000..ee61c695e --- /dev/null +++ b/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_grouped_orig.sql @@ -0,0 +1,70 @@ +PARAMETERS(AnalysisId INTEGER) + +select + a.analysis_id, + a.alleles, + a.alleleIds, + max(a.lineages) as lineages, + coalesce(max(a.totalLineages), 0) as totalLineages, + a.loci, + + sum(a.total) as total_reads, + sum(a.total_forward) as total_forward, + sum(a.total_reverse) as total_reverse, + sum(a.valid_pairs) as valid_pairs, + max(cast(a.total_reads as integer)) as total_reads_in_analysis, + --max(a.loci_total_reads) as total_reads_in_analysis_from_locus, + CASE WHEN max(a.total_reads) = 0 THEN 0 ELSE round(100 * (cast(sum(a.total) as float) / cast(max(a.total_reads) as float)), 2) END as percent, +-- case +-- when (cast(sum(a.total) as float) / cast(max(a.total_reads) as float)) >= .04 THEN 'Major' +-- else 'Minor' +-- end as category, + + group_concat(a.rowid, ',') as rowids, + group_concat(distinct a.haplotypesWithAllele) as haplotypesWithAllele, + + CAST((select sum(s.total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = AnalysisId AND s.rowid IN ( + SELECT distinct asj.alignment_id from sequenceanalysis.alignment_summary_junction asj WHERE asj.analysis_id = AnalysisId AND asj.ref_nt_id.locus = a.loci and asj.status = true + ) + ) as INTEGER) as total_reads_from_locus, + + round(100 * (cast(sum(a.total) as float) / CASE WHEN count(a.lineages) = 0 THEN max(a.total_reads) ELSE cast((select sum(s.total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = AnalysisId AND s.rowid IN ( + SELECT distinct asj.alignment_id from sequenceanalysis.alignment_summary_junction asj WHERE asj.analysis_id = AnalysisId AND asj.ref_nt_id.locus = a.loci and asj.status = true + ) + ) as float) END), 2) as percent_from_locus, + max(lastModified) as lastModified, + count(distinct a.rowid) as nAlignments, + max(a.nloci) as nLoci + +FROM ( + + select + a.analysis_id, + a.rowid, + + group_concat(distinct j.ref_nt_id) as alleleIds, + group_concat(distinct j.ref_nt_id.name, chr(10)) as alleles, + group_concat(distinct j.ref_nt_id.lineage, chr(10)) as lineages, + count(distinct j.ref_nt_id.lineage) as totalLineages, + group_concat(distinct j.ref_nt_id.locus, chr(10)) as loci, + count(distinct j.ref_nt_id.locus) as nloci, + group_concat(distinct hs.haplotype, chr(10)) as haplotypesWithAllele, + + total, + total_forward, + total_reverse, + valid_pairs, + (select sum(total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = AnalysisId) as total_reads, + max(j.modified) as lastModified + from sequenceanalysis.alignment_summary a + left join sequenceanalysis.alignment_summary_junction j ON (j.analysis_id = AnalysisId AND j.alignment_id = a.rowid and j.status = true) + left join sequenceanalysis.haplotype_sequences hs ON (( + (hs.name = j.ref_nt_id.lineage AND hs.type = 'Lineage') OR + (hs.name = j.ref_nt_id.name AND hs.type = 'Allele') + ) AND hs.haplotype.datedisabled IS NULL) + WHERE a.analysis_id = AnalysisId + group by a.analysis_id, a.rowid, a.total, total_forward, total_reverse, valid_pairs + +) a + +GROUP BY a.analysis_id, a.alleles, a.alleleIds, a.loci diff --git a/SequenceAnalysis/resources/queries/sequenceanalysis/ref_nt_sequences.js b/SequenceAnalysis/resources/queries/sequenceanalysis/ref_nt_sequences.js index 8da0548d5..3bd8bd62d 100644 --- a/SequenceAnalysis/resources/queries/sequenceanalysis/ref_nt_sequences.js +++ b/SequenceAnalysis/resources/queries/sequenceanalysis/ref_nt_sequences.js @@ -61,4 +61,21 @@ function beforeDelete(row, errors){ if (!this.extraContext.deleteFromServer) { errors._form = 'You cannot directly delete reference sequences. To delete these records, use the delete button above the sequences grid.'; } + else { + const errorMessage = triggerHelper.canDeleteNtRecord(row.rowid); + if (errorMessage) { + errors._form = 'The sequence ' + row.rowid + ' cannot be deleted: ' + errorMessage; + } + } +} + +function afterDelete(row, errors){ + if (this.extraContext.deleteFromServer) { + // Ensure no genomes use this, and then delete the sequence file: + triggerHelper.safeDeleteNtRecord(row.rowid) + } + else { + // This should be blocked in beforeDelete + errors._form = 'You cannot directly delete reference sequences. To delete these records, use the delete button above the sequences grid.'; + } } diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java index 63ce77d1b..25a8b5268 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java @@ -157,6 +157,7 @@ import org.labkey.sequenceanalysis.pipeline.SequenceAlignmentJob; import org.labkey.sequenceanalysis.pipeline.SequenceConcatPipelineJob; import org.labkey.sequenceanalysis.pipeline.SequenceJob; +import org.labkey.sequenceanalysis.pipeline.SequenceMigrationPipelineJob; import org.labkey.sequenceanalysis.pipeline.SequenceOutputHandlerJob; import org.labkey.sequenceanalysis.pipeline.SequenceReadsetHandlerJob; import org.labkey.sequenceanalysis.pipeline.SequenceTaskHelper; @@ -5251,4 +5252,39 @@ public void setDataFileUrl(String dataFileUrl) _dataFileUrl = dataFileUrl; } } + + @UtilityAction(label = "Migrate Sequence Files", description = "This will start a background process to migrate sequence files from the flat .sequences folder into a hashed multi-folder scheme") + @RequiresSiteAdmin + public static class MigrateSequenceFilesAction extends ConfirmAction + { + @Override + public ModelAndView getConfirmView(Object o, BindException errors) throws Exception + { + setTitle("Migrate Sequence Files"); + + return(HtmlView.of("This will start a background process to migrate sequence files from the flat .sequences folder into a hashed multi-folder scheme. Do you want to continue?")); + } + + @Override + public boolean handlePost(Object o, BindException errors) throws Exception + { + PipeRoot pr = PipelineService.get().findPipelineRoot(getContainer()); + PipelineService.get().queueJob(new SequenceMigrationPipelineJob(getContainer(), getUser(), getViewContext().getActionURL(), pr)); + + return true; + } + + @Override + public void validateCommand(Object o, Errors errors) + { + + } + + @NotNull + @Override + public URLHelper getSuccessURL(Object o) + { + return getContainer().getStartURL(getUser()); + } + } } diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java index a87859e5e..a7ab7b1c9 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java @@ -37,6 +37,7 @@ import java.io.File; import java.io.IOException; +import java.nio.file.DirectoryStream; import java.nio.file.Files; import java.nio.file.Path; import java.util.ArrayList; @@ -322,8 +323,13 @@ private void processContainer(Container c, Logger log) throws IOException, Pipel if (d.getFile().getAbsolutePath().toLowerCase().startsWith(sequenceDir.getAbsolutePath().toLowerCase())) { + // File existence will be verified below: expectedSequences.add(d.getFile()); } + else if (!d.getFile().exists()) + { + log.error("Missing sequence file {}", d.getFile().getPath()); + } }); if (sequenceDir.exists()) @@ -335,8 +341,14 @@ private void processContainer(Container c, Logger log) throws IOException, Pipel { for (File missing : expectedSequences) { - log.error("expected sequence file does not exist: " + missing.getPath()); - return; + if (missing.exists()) + { + log.error("File exists, but wasnt removed from expectedSequences for folder {}, file: {}", sequenceDir.getPath(), missing.getPath()); + } + else + { + log.error("expected sequence file does not exist: {}", missing.getPath()); + } } } @@ -580,6 +592,15 @@ private void inspectSequenceDir(File sequenceDir, Set expectedSequences, L { if (child.isDirectory()) { + try (DirectoryStream stream = Files.newDirectoryStream(child.toPath())) + { + if (!stream.iterator().hasNext()) + { + FileUtils.deleteDirectory(child); + continue; + } + } + inspectSequenceDir(child, expectedSequences, log); } else diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java index 60186f5ee..eb76eeda3 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java @@ -83,6 +83,7 @@ import org.labkey.sequenceanalysis.pipeline.SequenceAlignmentTask; import org.labkey.sequenceanalysis.pipeline.SequenceJob; import org.labkey.sequenceanalysis.pipeline.SequenceJobSupportImpl; +import org.labkey.sequenceanalysis.pipeline.SequenceMigrationPipelineJob; import org.labkey.sequenceanalysis.pipeline.SequenceOutputHandlerPipelineProvider; import org.labkey.sequenceanalysis.pipeline.SequencePipelineProvider; import org.labkey.sequenceanalysis.pipeline.SequenceReadsetHandlerPipelineProvider; @@ -484,6 +485,7 @@ public Set getExperimentRunTypes(@Nullable Container containe PipelineService.get().registerPipelineProvider(new OrphanFilePipelineProvider(this)); PipelineService.get().registerPipelineProvider(new SequencePipelineProvider(this)); PipelineService.get().registerPipelineProvider(new CacheGenomePipelineJob.Provider(this)); + PipelineService.get().registerPipelineProvider(new SequenceMigrationPipelineJob.Provider(this)); LDKService.get().registerQueryButton(new ReprocessLibraryButton(), SequenceAnalysisSchema.SCHEMA_NAME, SequenceAnalysisSchema.TABLE_REF_LIBRARIES); diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisSchema.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisSchema.java index 452be9a16..3f1c4421f 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisSchema.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisSchema.java @@ -53,6 +53,7 @@ public class SequenceAnalysisSchema public static final String TABLE_ANALYSIS_SETS = "analysisSets"; public static final String TABLE_ANALYSIS_SET_MEMBERS = "analysisSetMembers"; public static final String TABLE_READ_DATA = "readData"; + public static final String TABLE_ALIGNMENT_SUMMARY_COMBINED = "alignment_summary_combined"; public static SequenceAnalysisSchema getInstance() { diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisUpgradeCode.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisUpgradeCode.java index 40b221c70..879ea12a4 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisUpgradeCode.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisUpgradeCode.java @@ -6,6 +6,7 @@ import org.apache.logging.log4j.Logger; import org.biojava.nbio.core.exceptions.CompoundNotFoundException; import org.biojava.nbio.core.sequence.DNASequence; +import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.data.CompareType; import org.labkey.api.data.Container; @@ -19,8 +20,12 @@ import org.labkey.api.exp.api.ExpData; import org.labkey.api.exp.api.ExperimentService; import org.labkey.api.module.ModuleContext; +import org.labkey.api.pipeline.CancelledException; +import org.labkey.api.pipeline.PipelineJob; import org.labkey.api.query.FieldKey; +import org.labkey.api.security.User; import org.labkey.api.sequenceanalysis.RefNtSequenceModel; +import org.labkey.api.util.FileUtil; import org.labkey.api.util.PageFlowUtil; import java.io.File; @@ -234,64 +239,102 @@ public void updateBarcodeRC(final ModuleContext moduleContext) @SuppressWarnings({"UnusedDeclaration"}) @DeferredUpgrade public void migrateSequenceDirs(final ModuleContext moduleContext) + { + doSequenceMigration(moduleContext.getUpgradeUser(), _log, 100000, null); + } + + public static void doSequenceMigration(User u, Logger log, int maxSequences, @Nullable PipelineJob job) { try { TableInfo ti = SequenceAnalysisSchema.getTable(SequenceAnalysisSchema.TABLE_REF_NT_SEQUENCES); TableSelector ts = new TableSelector(ti); List nts = ts.getArrayList(RefNtSequenceModel.class); - _log.info(nts.size() + " total sequences to migrate"); + if (maxSequences > 0 && nts.size() > maxSequences) + { + log.info("There are too many sequences to migrate on startup. Please run MigrateSequenceFilesAction"); + return; + } + + log.info(nts.size() + " total sequences to migrate"); int processed = 0; + int totalMigrated = 0; for (RefNtSequenceModel nt : nts) { processed++; - if (processed % 1000 == 0) { - _log.info("{} of {} sequence files migrated", processed, nts.size()); + log.info("{} of {} sequence files migrated", processed, nts.size()); + if (job != null) + { + job.updateStatusForTask(); + if (job.isCancelled()) + { + throw new CancelledException(); + } + + job.setStatus(PipelineJob.TaskStatus.running, "Processed " + processed + " of " + nts.size()); + } } ExpData legacyExpData = ExperimentService.get().getExpData(nt.getSequenceFile()); if (legacyExpData == null) { - _log.error("Missing ExpData for NT sequence: {}", nt.getSequenceFile()); + log.error("Missing ExpData for NT sequence: {}", nt.getSequenceFile()); continue; } File legacyFile = legacyExpData.getFile(); - if (!legacyFile.exists()) + if (RefNtSequenceModel.BASE_DIRNAME.equals(legacyFile.getParentFile().getName())) + { + continue; + } + + if (!legacyFile.getPath().contains(RefNtSequenceModel.BASE_DIRNAME)) + { + // Includes sequences imported as pipeline jobs + continue; + } + + File newLocation = nt.getExpectedSequenceFile(null); + if (legacyFile.equals(newLocation)) { - _log.error("Missing file for NT sequence: {}", legacyFile.getPath()); continue; } - if (!RefNtSequenceModel.BASE_DIRNAME.equals(legacyFile.getParentFile().getName())) + if (!legacyFile.exists()) { - _log.error("Sequence appears to have already been migrated, this might indicate a retry after a failed move: {}", legacyFile.getPath()); + log.error("Missing file for NT sequence: {}", legacyFile.getPath()); continue; } - File newLocation = nt.getExpectedSequenceFile(); if (!newLocation.getParentFile().exists()) { - newLocation.getParentFile().mkdirs(); + FileUtil.mkdirs(newLocation.getParentFile()); } if (newLocation.exists()) { - _log.error("Target location for migrated sequence file exists, this might indicate a retry after a filed move: {}", newLocation.getPath()); - continue; + if (newLocation.length() == legacyFile.length()) + { + continue; + } + + log.error("Target location for migrated sequence file exists, but file size is smaller. this might indicate a retry after a filed move. deleting the target and retrying: {}", newLocation.getPath()); + FileUtils.delete(newLocation); } - FileUtils.copyFile(legacyFile, newLocation); + FileUtils.moveFile(legacyFile, newLocation); legacyExpData.setDataFileURI(newLocation.toURI()); - legacyExpData.save(moduleContext.getUpgradeUser()); - legacyFile.delete(); + legacyExpData.save(u); + totalMigrated++; } + + log.info("Total sequences migrated: {}", totalMigrated); } catch (Exception e) { - _log.error("Error upgrading sequenceanalysis module", e); + log.error("Error migrating sequence files", e); } } } diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportFastaSequencesPipelineJob.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportFastaSequencesPipelineJob.java index 4b840766d..d5b9a29b9 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportFastaSequencesPipelineJob.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportFastaSequencesPipelineJob.java @@ -12,7 +12,6 @@ import org.labkey.api.query.DetailsURL; import org.labkey.api.security.User; import org.labkey.api.security.permissions.InsertPermission; -import org.labkey.api.assay.AssayFileWriter; import org.labkey.api.util.FileType; import org.labkey.api.util.FileUtil; import org.labkey.api.view.ActionURL; @@ -56,23 +55,22 @@ public ImportFastaSequencesPipelineJob(Container c, User user, ActionURL url, Pi _libraryParams = libraryParams; _outDir = createLocalDirectory(pipeRoot); - setLogFile(new File(_outDir, FileUtil.makeFileNameWithTimestamp("fastaImport", "log"))); + setLogFile(FileUtil.appendName(_outDir, FileUtil.makeFileNameWithTimestamp("fastaImport", "log"))); } public static File createLocalDirectory(PipeRoot pipeRoot) throws IOException { - File webserverOutDir = new File(pipeRoot.getRootPath(), _folderPrefix); + File webserverOutDir = FileUtil.appendName(pipeRoot.getRootPath(), _folderPrefix); if (!webserverOutDir.exists()) { - webserverOutDir.mkdir(); + FileUtil.mkdir(webserverOutDir); } - AssayFileWriter writer = new AssayFileWriter(); String folderName = "SequenceImport_" + FileUtil.getTimestamp(); webserverOutDir = FileUtil.findUniqueFileName(folderName, webserverOutDir); if (!webserverOutDir.exists()) { - webserverOutDir.mkdirs(); + FileUtil.mkdirs(webserverOutDir); } return webserverOutDir; @@ -85,7 +83,7 @@ public String getDescription() } @Override - public TaskPipeline getTaskPipeline() + public TaskPipeline getTaskPipeline() { return PipelineJobService.get().getTaskPipeline(new TaskId(ImportFastaSequencesPipelineJob.class)); } diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportFastaSequencesTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportFastaSequencesTask.java index 1bf2b9362..876d32faa 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportFastaSequencesTask.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportFastaSequencesTask.java @@ -72,7 +72,7 @@ public List getProtocolActionNames() } @Override - public PipelineJob.Task createTask(PipelineJob job) + public PipelineJob.Task createTask(PipelineJob job) { return new ImportFastaSequencesTask(this, job); } diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceMigrationPipelineJob.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceMigrationPipelineJob.java new file mode 100644 index 000000000..87baae823 --- /dev/null +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceMigrationPipelineJob.java @@ -0,0 +1,144 @@ +package org.labkey.sequenceanalysis.pipeline; + +import org.jetbrains.annotations.NotNull; +import org.labkey.api.data.Container; +import org.labkey.api.files.FileUrls; +import org.labkey.api.module.Module; +import org.labkey.api.pipeline.AbstractTaskFactory; +import org.labkey.api.pipeline.AbstractTaskFactorySettings; +import org.labkey.api.pipeline.PipeRoot; +import org.labkey.api.pipeline.PipelineDirectory; +import org.labkey.api.pipeline.PipelineJob; +import org.labkey.api.pipeline.PipelineJobException; +import org.labkey.api.pipeline.PipelineJobService; +import org.labkey.api.pipeline.PipelineProvider; +import org.labkey.api.pipeline.RecordedActionSet; +import org.labkey.api.pipeline.TaskId; +import org.labkey.api.pipeline.TaskPipeline; +import org.labkey.api.security.User; +import org.labkey.api.util.FileType; +import org.labkey.api.util.FileUtil; +import org.labkey.api.util.PageFlowUtil; +import org.labkey.api.view.ActionURL; +import org.labkey.api.view.ViewBackgroundInfo; +import org.labkey.api.view.ViewContext; +import org.labkey.sequenceanalysis.SequenceAnalysisUpgradeCode; + +import java.io.File; +import java.util.Collections; +import java.util.List; + +public class SequenceMigrationPipelineJob extends PipelineJob +{ + public static class Provider extends PipelineProvider + { + public static final String NAME = "sequenceMigrationPipeline"; + + public Provider(Module owningModule) + { + super(NAME, owningModule); + } + + @Override + public void updateFileProperties(ViewContext context, PipeRoot pr, PipelineDirectory directory, boolean includeAll) + { + + } + } + + // Default constructor for serialization + protected SequenceMigrationPipelineJob() + { + } + + public SequenceMigrationPipelineJob(Container c, User u, ActionURL url, PipeRoot pipeRoot) + { + super(Provider.NAME, new ViewBackgroundInfo(c, u, url), pipeRoot); + + File subdir = FileUtil.appendName(pipeRoot.getRootPath(), Provider.NAME); + if (!subdir.exists()) + { + subdir.mkdirs(); + } + + setLogFile(FileUtil.appendName(subdir, FileUtil.makeFileNameWithTimestamp("sequenceMigration", "log"))); + + } + + @Override + public ActionURL getStatusHref() + { + return PageFlowUtil.urlProvider(FileUrls.class).urlBegin(getContainer()); + } + + @Override + public String getDescription() + { + return "Migrate Sequence Files"; + } + + @Override + public TaskPipeline getTaskPipeline() + { + return PipelineJobService.get().getTaskPipeline(new TaskId(SequenceMigrationPipelineJob.class)); + } + + public static class Task extends PipelineJob.Task + { + protected Task(Factory factory, PipelineJob job) + { + super(factory, job); + } + + public static class Factory extends AbstractTaskFactory + { + public Factory() + { + super(Task.class); + } + + @Override + public List getInputTypes() + { + return Collections.emptyList(); + } + + @Override + public String getStatusName() + { + return PipelineJob.TaskStatus.running.toString(); + } + + @Override + public List getProtocolActionNames() + { + return List.of("Migrate Sequence Files"); + } + + @Override + public PipelineJob.Task createTask(PipelineJob job) + { + return new Task(this, job); + } + + @Override + public boolean isJobComplete(PipelineJob job) + { + return false; + } + } + + private SequenceMigrationPipelineJob getPipelineJob() + { + return (SequenceMigrationPipelineJob)getJob(); + } + + @Override + public @NotNull RecordedActionSet run() throws PipelineJobException + { + SequenceAnalysisUpgradeCode.doSequenceMigration(getPipelineJob().getUser(), getPipelineJob().getLogger(), -1, getPipelineJob()); + + return new RecordedActionSet(); + } + } +} diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/AlignmentSummaryGroupedTableInfo.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/AlignmentSummaryGroupedTableInfo.java new file mode 100644 index 000000000..7fdd87800 --- /dev/null +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/AlignmentSummaryGroupedTableInfo.java @@ -0,0 +1,163 @@ +package org.labkey.sequenceanalysis.query; + +import org.jetbrains.annotations.NotNull; +import org.labkey.api.data.AbstractTableInfo; +import org.labkey.api.data.BaseColumnInfo; +import org.labkey.api.data.JdbcType; +import org.labkey.api.data.MutableColumnInfo; +import org.labkey.api.data.SQLFragment; +import org.labkey.api.data.dialect.SqlDialect; +import org.labkey.api.query.ExprColumn; +import org.labkey.api.query.QueryForeignKey; +import org.labkey.api.query.UserSchema; +import org.labkey.sequenceanalysis.SequenceAnalysisSchema; + +/** + * The purpose of this table is to perform several important joins without the LK overhead of containers, providing a simpler pre-joined view of the data. + */ +public class AlignmentSummaryGroupedTableInfo extends AbstractTableInfo +{ + private final UserSchema _userSchema; + + public AlignmentSummaryGroupedTableInfo(UserSchema schema) + { + super(schema.getDbSchema(), SequenceAnalysisSchema.TABLE_ALIGNMENT_SUMMARY_COMBINED); + _userSchema = schema; + + setTitle("Alignment Summary Data Combined"); + setupColumns(); + } + + private void setupColumns() + { + MutableColumnInfo analysisIdCol = new BaseColumnInfo("analysis_id", this, JdbcType.BIGINT); + analysisIdCol.setLabel("Analysis Id"); + //analysisIdCol.setFk(new QueryForeignKey.Builder(getUserSchema(), getContainerFilter()).schema(SequenceAnalysisSchema.SCHEMA_NAME).table(SequenceAnalysisSchema.TABLE_ANALYSES).key("rowid").display("rowid")); + addColumn(analysisIdCol); + + MutableColumnInfo rowIdCol = new BaseColumnInfo("rowid", this, JdbcType.BIGINT); + rowIdCol.setLabel("Alignment Id"); + //analysisIdCol.setFk(new QueryForeignKey.Builder(getUserSchema(), getContainerFilter()).schema(SequenceAnalysisSchema.SCHEMA_NAME).table(SequenceAnalysisSchema.TABLE_ANALYSES).key("rowid").display("rowid")); + addColumn(rowIdCol); + + MutableColumnInfo readsetCol = new BaseColumnInfo("readset", this, JdbcType.BIGINT); + readsetCol.setLabel("Readset"); + //readsetCol.setFk(new QueryForeignKey.Builder(getUserSchema(), getContainerFilter()).schema(SequenceAnalysisSchema.SCHEMA_NAME).table(SequenceAnalysisSchema.TABLE_READSETS).key("rowid").display("name")); + addColumn(readsetCol); + + MutableColumnInfo ntId = new BaseColumnInfo("ref_nt_id", this, JdbcType.BIGINT); + ntId.setLabel("NT Sequence"); + //ntId.setFk(new QueryForeignKey.Builder(getUserSchema(), getContainerFilter()).schema(SequenceAnalysisSchema.SCHEMA_NAME).table(SequenceAnalysisSchema.TABLE_REF_NT_SEQUENCES).key("rowid").display("name")); + addColumn(ntId); + + MutableColumnInfo ntName = new BaseColumnInfo("ntName", this, JdbcType.VARCHAR); + ntName.setLabel("NT Sequence Name"); + addColumn(ntName); + + MutableColumnInfo ntLineage = new BaseColumnInfo("lineage", this, JdbcType.VARCHAR); + ntLineage.setLabel("NT Lineage"); + addColumn(ntLineage); + + MutableColumnInfo ntLocus = new BaseColumnInfo("locus", this, JdbcType.VARCHAR); + ntLocus.setLabel("NT Locus"); + addColumn(ntLocus); + + MutableColumnInfo totalCol = new BaseColumnInfo("total", this, JdbcType.BIGINT); + totalCol.setLabel("Total Reads"); + addColumn(totalCol); + + MutableColumnInfo totalForwardCol = new BaseColumnInfo("total_forward", this, JdbcType.BIGINT); + totalForwardCol.setLabel("Total Forward Reads"); + addColumn(totalForwardCol); + + MutableColumnInfo totalReverseCol = new BaseColumnInfo("total_reverse", this, JdbcType.BIGINT); + totalReverseCol.setLabel("Total Reverse Reads"); + addColumn(totalReverseCol); + + MutableColumnInfo validPairsCol = new BaseColumnInfo("valid_pairs", this, JdbcType.BIGINT); + validPairsCol.setLabel("Total Valid Pairs"); + addColumn(validPairsCol); + + MutableColumnInfo totalReadsInAnalysis = new BaseColumnInfo("total_reads_in_analysis", this, JdbcType.BIGINT); + totalReadsInAnalysis.setLabel("Total Reads In Analysis"); + addColumn(totalReadsInAnalysis); + + SQLFragment sql = new SQLFragment("(SELECT sum(xs.total) as expr FROM (SELECT xs.total \n" + + "FROM sequenceanalysis.sequence_analyses xa\n" + + "JOIN sequenceanalysis.alignment_summary xs ON (xa.rowid = xs.analysis_id) \n" + + "JOIN sequenceanalysis.alignment_summary_junction xasj ON (xasj.status = " + getSqlDialect().getBooleanTRUE() + " AND xs.rowid = xasj.alignment_id)\n" + + "JOIN sequenceanalysis.ref_nt_sequences xnt ON (xnt.rowid = xasj.ref_nt_id)\n" + + "WHERE xa.rowid = " + ExprColumn.STR_TABLE_ALIAS + ".analysis_id AND xnt.locus = " + ExprColumn.STR_TABLE_ALIAS + ".locus\n" + + "GROUP BY xs.rowid, xs.total) xs)"); + + ExprColumn totalReadsFromLocus = new ExprColumn(this, "total_reads_from_locus", sql, JdbcType.BIGINT, getColumn("analysis_id"), getColumn("locus")); + totalReadsFromLocus.setLabel("Total Reads From Locus"); + addColumn(totalReadsFromLocus); + + MutableColumnInfo haplotypesWithAlleleCol = new BaseColumnInfo("haplotypesWithAllele", this, JdbcType.VARCHAR); + haplotypesWithAlleleCol.setLabel("Haplotypes With Allele"); + addColumn(haplotypesWithAlleleCol); + + MutableColumnInfo containerCol = new BaseColumnInfo("container", this, JdbcType.GUID); + containerCol.setLabel("Folder"); + containerCol.setFk(new QueryForeignKey.Builder(getUserSchema(), getContainerFilter()).schema("core").table("containers")); + addColumn(containerCol); + + MutableColumnInfo createdCol = new BaseColumnInfo("created", this, JdbcType.TIMESTAMP); + createdCol.setLabel("Created"); + addColumn(createdCol); + + MutableColumnInfo createdByCol = new BaseColumnInfo("createdby", this, JdbcType.BIGINT); + createdByCol.setLabel("Created By"); + createdByCol.setFk(new QueryForeignKey.Builder(getUserSchema(), getContainerFilter()).schema("core").table("users").key("rowid")); + addColumn(createdByCol); + + MutableColumnInfo modifiedCol = new BaseColumnInfo("modified", this, JdbcType.TIMESTAMP); + modifiedCol.setLabel("Modified"); + addColumn(modifiedCol); + + MutableColumnInfo modifiedByCol = new BaseColumnInfo("modifiedby", this, JdbcType.BIGINT); + modifiedByCol.setLabel("Modified By"); + modifiedByCol.setFk(new QueryForeignKey.Builder(getUserSchema(), getContainerFilter()).schema("core").table("users").key("rowid")); + addColumn(modifiedByCol); + } + + @Override + protected SQLFragment getFromSQL() + { + final SqlDialect sd = getUserSchema().getDbSchema().getSqlDialect(); + final String chr = sd.isPostgreSQL() ? "chr" : "char"; + + return new SQLFragment("SELECT\n" + + "a.rowid as analysis_id,\n" + + "al.rowid,\n" + + "a.readset,\n" + + "nt.rowid as ref_nt_id,\n" + + "nt.name as ntName,\n" + + "nt.lineage as lineage,\n" + + "nt.locus as locus,\n" + + "a.container,\n" + + "a.created,\n" + + "a.createdBy,\n" + + "a.modified,\n" + + "a.modifiedBy,\n" + + "al.total,\n" + + "al.total_forward,\n" + + "al.total_reverse,\n" + + "al.valid_pairs,\n" + + "(SELECT sum(s.total) as expr FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_ALIGNMENT_SUMMARY + " s WHERE s.analysis_id = a.rowId) as total_reads_in_analysis,\n" + + "(SELECT ").append(sd.getGroupConcat(new SQLFragment("hs.haplotype"), true, true, new SQLFragment(chr + "(10)"))). + append(" as expr FROM sequenceanalysis.haplotype_sequences hs JOIN sequenceanalysis.haplotypes ht ON (hs.haplotype = ht.name) WHERE ht.datedisabled IS NULL AND ((hs.type = 'Lineage' AND hs.name = nt.lineage) OR (hs.type = 'Allele' AND hs.name = nt.name))) as haplotypesWithAllele\n" + "\n" + + "FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_ANALYSES + " a\n" + + "JOIN " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_ALIGNMENT_SUMMARY + " al ON (a.RowId = al.analysis_id)\n" + + "LEFT JOIN " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_ALIGNMENT_SUMMARY_JUNCTION + " asj ON (al.rowid = asj.alignment_id)\n" + + "LEFT JOIN " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_REF_NT_SEQUENCES + " nt ON (nt.rowid = asj.ref_nt_id)\n" + + "WHERE asj.status = ").append(sd.getBooleanTRUE()); + } + + @Override + public @NotNull UserSchema getUserSchema() + { + return _userSchema; + } +} diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceAnalysisUserSchema.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceAnalysisUserSchema.java index 9757cfc34..162a93f6e 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceAnalysisUserSchema.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceAnalysisUserSchema.java @@ -1,8 +1,10 @@ package org.labkey.sequenceanalysis.query; import org.apache.commons.lang3.StringUtils; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; +import org.labkey.api.collections.CaseInsensitiveTreeSet; import org.labkey.api.data.AbstractTableInfo; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.CompareType; @@ -15,6 +17,7 @@ import org.labkey.api.data.JdbcType; import org.labkey.api.data.RenderContext; import org.labkey.api.data.SQLFragment; +import org.labkey.api.data.SchemaTableInfo; import org.labkey.api.data.TableInfo; import org.labkey.api.data.WrappedColumn; import org.labkey.api.ldk.LDKService; @@ -25,6 +28,7 @@ import org.labkey.api.query.DetailsURL; import org.labkey.api.query.ExprColumn; import org.labkey.api.query.FieldKey; +import org.labkey.api.query.FilteredTable; import org.labkey.api.query.QueryAction; import org.labkey.api.query.QuerySchema; import org.labkey.api.query.QueryService; @@ -34,13 +38,17 @@ import org.labkey.api.util.HtmlString; import org.labkey.api.util.LinkBuilder; import org.labkey.api.util.PageFlowUtil; +import org.labkey.api.util.logging.LogHelper; import org.labkey.api.view.ActionURL; import org.labkey.api.writer.HtmlWriter; import org.labkey.sequenceanalysis.SequenceAnalysisSchema; import org.labkey.sequenceanalysis.SequenceAnalysisServiceImpl; import java.util.Arrays; +import java.util.Collections; +import java.util.HashSet; import java.util.LinkedHashSet; +import java.util.Set; /** * User: bimber @@ -49,25 +57,48 @@ */ public class SequenceAnalysisUserSchema extends SimpleUserSchema { - private SequenceAnalysisUserSchema(User user, Container container, DbSchema schema) + private static final Logger _log = LogHelper.getLogger(SequenceAnalysisUserSchema.class, "Messages related to SequenceAnalysisUserSchema"); + + private SequenceAnalysisUserSchema(User user, Container container, DbSchema schema, Set available) { - super(SequenceAnalysisSchema.SCHEMA_NAME, null, user, container, schema); + super(SequenceAnalysisSchema.SCHEMA_NAME, null, user, container, schema, null, available, null); } public static void register(final Module m) { final DbSchema dbSchema = SequenceAnalysisSchema.getInstance().getSchema(); + final Set available = new CaseInsensitiveTreeSet(); + for (String tableName : dbSchema.getTableNames()) + { + SchemaTableInfo table = dbSchema.getTable(tableName); + if (null != table) + available.add(table.getName()); + else + _log.error("Schema '" + dbSchema.getName() + "' provided tableName '" + tableName + "', but not actual table."); + } + available.add(SequenceAnalysisSchema.TABLE_ALIGNMENT_SUMMARY_COMBINED); DefaultSchema.registerProvider(SequenceAnalysisSchema.SCHEMA_NAME, new DefaultSchema.SchemaProvider(m) { @Override public QuerySchema createSchema(final DefaultSchema schema, Module module) { - return new SequenceAnalysisUserSchema(schema.getUser(), schema.getContainer(), dbSchema); + return new SequenceAnalysisUserSchema(schema.getUser(), schema.getContainer(), dbSchema, available); } }); } + @Override + public TableInfo createTable(String name, ContainerFilter cf) + { + if (SequenceAnalysisSchema.TABLE_ALIGNMENT_SUMMARY_COMBINED.equalsIgnoreCase(name)) + { + return createAlignmentSummaryCombined(cf); + } + + return super.createTable(name, cf); + } + @Override @Nullable protected TableInfo createWrappedTable(String name, @NotNull TableInfo sourceTable, ContainerFilter cf) @@ -131,7 +162,29 @@ else if (SequenceAnalysisSchema.TABLE_ANALYSES.equalsIgnoreCase(name)) return createAnalysesTable(sourceTable, cf); } else + { return super.createWrappedTable(name, sourceTable, cf); + } + } + + @Override + public Set getTableNames() + { + Set ret = new HashSet<>(super.getTableNames()); + ret.add(SequenceAnalysisSchema.TABLE_ALIGNMENT_SUMMARY_COMBINED); + + return Collections.unmodifiableSet(ret); + } + + @Override + public synchronized Set getVisibleTableNames() + { + return getTableNames(); + } + + private TableInfo createAlignmentSummaryCombined(ContainerFilter cf) + { + return new SimpleTable<>(this, new AlignmentSummaryGroupedTableInfo(this), cf).init(); } private TableInfo createAnalysesTable(TableInfo sourceTable, ContainerFilter cf) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceTriggerHelper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceTriggerHelper.java index 91cf88e07..7f1fde9d9 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceTriggerHelper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceTriggerHelper.java @@ -11,6 +11,7 @@ import org.biojava.nbio.core.sequence.compound.NucleotideCompound; import org.biojava.nbio.core.sequence.template.Sequence; import org.biojava.nbio.core.sequence.transcription.TranscriptionEngine; +import org.jetbrains.annotations.Nullable; import org.junit.Assert; import org.junit.Test; import org.labkey.api.collections.IntHashMap; @@ -29,9 +30,11 @@ import org.labkey.api.query.QueryService; import org.labkey.api.security.User; import org.labkey.api.security.UserManager; +import org.labkey.api.security.permissions.DeletePermission; import org.labkey.api.sequenceanalysis.RefNtSequenceModel; import org.labkey.api.util.FileUtil; import org.labkey.api.util.Path; +import org.labkey.api.view.UnauthorizedException; import org.labkey.sequenceanalysis.ReadDataImpl; import org.labkey.sequenceanalysis.SequenceAnalysisSchema; import org.labkey.sequenceanalysis.SequenceAnalysisServiceImpl; @@ -42,6 +45,7 @@ import java.io.File; import java.io.IOException; import java.io.StringWriter; +import java.nio.file.Files; import java.util.Arrays; import java.util.Date; import java.util.List; @@ -324,4 +328,61 @@ public void createReaddataForSra(int readsetId, String sraAccessions) Table.insert(_user, rd, rd1); } } + + public @Nullable String canDeleteNtRecord(int rowId) + { + RefNtSequenceModel model = RefNtSequenceModel.getForRowId(rowId); + if (model == null) + { + return "Unknown ref nt record: " + rowId; + } + + Container c = ContainerManager.getForId(model.getContainer()); + if (c == null) + { + return "Unable to find container for: " + model.getContainer(); + } + + if (new TableSelector(SequenceAnalysisSchema.getTable(SequenceAnalysisSchema.TABLE_REF_LIBRARY_MEMBERS), new SimpleFilter(FieldKey.fromString("ref_nt_id"), rowId), null).exists()) + { + return "Sequence " + rowId + " is still used by genomes, cannot delete"; + } + + if (!c.hasPermission(_user, DeletePermission.class)) + { + return "The user does not have sufficient permissions to delete record: " + rowId; + } + + return null; + } + + public void safeDeleteNtRecord(int rowId) + { + RefNtSequenceModel model = RefNtSequenceModel.getForRowId(rowId); + if (model == null || model.getSequenceFile() == null) + { + return; + } + + ExpData d = ExperimentService.get().getExpData(model.getSequenceFile()); + if (d == null || d.getFile() == null) + { + return; + } + + // This assumes canDeleteNtRecord() was called earlier + try + { + if (d.getFile().exists()) + { + Files.delete(d.getFile().toPath()); + } + } + catch (IOException e) + { + _log.error(e.getMessage(), e); + } + + d.delete(_user, false); + } } diff --git a/SequenceAnalysis/webapp/WEB-INF/SequenceAnalysis/sequenceanalysisContext.xml b/SequenceAnalysis/webapp/WEB-INF/SequenceAnalysis/sequenceanalysisContext.xml index f0c892ae2..a03756677 100644 --- a/SequenceAnalysis/webapp/WEB-INF/SequenceAnalysis/sequenceanalysisContext.xml +++ b/SequenceAnalysis/webapp/WEB-INF/SequenceAnalysis/sequenceanalysisContext.xml @@ -129,6 +129,9 @@ + + + @@ -234,6 +237,14 @@ + + + + + org.labkey.sequenceanalysis.pipeline.SequenceMigrationPipelineJob.Task + + + diff --git a/Studies/resources/web/studies/panel/StudiesFilterType.js b/Studies/resources/web/studies/panel/StudiesFilterType.js index 85b3f6e28..79b502f42 100644 --- a/Studies/resources/web/studies/panel/StudiesFilterType.js +++ b/Studies/resources/web/studies/panel/StudiesFilterType.js @@ -32,10 +32,14 @@ Ext4.define('Laboratory.panel.StudiesFilterType', { displayField: 'studyName', valueField: 'studyName', multiSelect: false, + forceSelection: true, + triggerAction: 'all', + queryMode: 'local', store: { type: 'labkey-store', schemaName: 'studies', queryName: 'studies', + columns: 'studyName', autoLoad: true }, value: Ext4.isArray(ctx.studies) ? ctx.studies.join(';') : ctx.studies diff --git a/jbrowse/package-lock.json b/jbrowse/package-lock.json index 6539df623..3b06f7e42 100644 --- a/jbrowse/package-lock.json +++ b/jbrowse/package-lock.json @@ -7,16 +7,18 @@ "": { "name": "jbrowse-lk", "version": "1.0.0", + "hasInstallScript": true, "dependencies": { - "@gmod/vcf": "^6.0.9", - "@jbrowse/core": "^3.2.0", - "@jbrowse/plugin-linear-genome-view": "^3.2.0", - "@jbrowse/plugin-svg": "^3.2.0", - "@jbrowse/plugin-variants": "^3.2.0", - "@jbrowse/product-core": "^3.2.0", - "@jbrowse/react-linear-genome-view2": "^3.2.0", + "@gmod/vcf": "^7.0.0", + "@jbrowse/core": "^4.1.13", + "@jbrowse/mobx-state-tree": "^5.5.0", + "@jbrowse/plugin-canvas": "^4.1.13", + "@jbrowse/plugin-linear-genome-view": "^4.1.13", + "@jbrowse/plugin-variants": "^4.1.13", + "@jbrowse/product-core": "^4.1.13", + "@jbrowse/react-linear-genome-view2": "^4.1.13", "@labkey/api": "^1.39.0", - "@labkey/components": "^6.32.2", + "@labkey/components": "^7.16.0", "@mui/x-data-grid": "^7.28.1", "assert": "^2.1.0", "browserify-zlib": "^0.2.0", @@ -40,12 +42,14 @@ "vm-browserify": "^1.1.2" }, "devDependencies": { - "@labkey/build": "^8.4.0", + "@labkey/build": "^8.8.0", "@types/jexl": "^2.3.4", "@types/jquery": "^3.5.32", "@types/node": "^20.14.11", "@types/react": "^18.3.0", "@types/react-dom": "^18.3.0", + "patch-package": "^8.0.1", + "postinstall-postinstall": "^2.1.0", "rimraf": "^6.0.1", "tar": "^7.5.7", "typescript": "^5.1.6", @@ -58,11 +62,12 @@ "integrity": "sha512-Elp+iwUx5rN5+Y8xLt5/GRoG20WGoDCQ/1Fb+1LiGtvwbDavuSk0jhD/eZdckHAuzcDzccnkv+rEjyWfRx18gg==" }, "node_modules/@babel/code-frame": { - "version": "7.27.1", - "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.27.1.tgz", - "integrity": "sha512-cjQ7ZlQ0Mv3b47hABuTevyTuYN4i+loJKGeV9flcCgIK37cCXRh+L1bd3iBHlynerhQ7BhCkn2BPbQUL+rGqFg==", + "version": "7.29.0", + "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.29.0.tgz", + "integrity": "sha512-9NhCeYjq9+3uxgdtp20LSiJXJvN0FeCtNGpJxuMFZ1Kv3cWUNb6DOhJwUvcVCzKGR66cw4njwM6hrJLqgOwbcw==", + "license": "MIT", "dependencies": { - "@babel/helper-validator-identifier": "^7.27.1", + "@babel/helper-validator-identifier": "^7.28.5", "js-tokens": "^4.0.0", "picocolors": 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"node_modules/webpack-dev-middleware/node_modules/mime-types": { + "version": "3.0.2", + "resolved": "https://registry.npmjs.org/mime-types/-/mime-types-3.0.2.tgz", + "integrity": "sha512-Lbgzdk0h4juoQ9fCKXW4by0UJqj+nOOrI9MJ1sSj4nI8aI2eo1qmvQEie4VD1glsS250n15LsWsYtCugiStS5A==", + "dev": true, + "license": "MIT", + "dependencies": { + "mime-db": "^1.54.0" + }, + "engines": { + "node": ">=18" + }, + "funding": { + "type": "opencollective", + "url": "https://opencollective.com/express" } }, "node_modules/webpack-dev-server": { - "version": "5.2.2", - "resolved": "https://registry.npmjs.org/webpack-dev-server/-/webpack-dev-server-5.2.2.tgz", - "integrity": "sha512-QcQ72gh8a+7JO63TAx/6XZf/CWhgMzu5m0QirvPfGvptOusAxG12w2+aua1Jkjr7hzaWDnJ2n6JFeexMHI+Zjg==", + "version": "5.2.3", + "resolved": "https://registry.npmjs.org/webpack-dev-server/-/webpack-dev-server-5.2.3.tgz", + "integrity": "sha512-9Gyu2F7+bg4Vv+pjbovuYDhHX+mqdqITykfzdM9UyKqKHlsE5aAjRhR+oOEfXW5vBeu8tarzlJFIZva4ZjAdrQ==", "dev": true, + "license": "MIT", "dependencies": { "@types/bonjour": "^3.5.13", "@types/connect-history-api-fallback": "^1.5.4", - "@types/express": "^4.17.21", + "@types/express": "^4.17.25", "@types/express-serve-static-core": "^4.17.21", "@types/serve-index": "^1.9.4", "@types/serve-static": "^1.15.5", @@ -11707,9 +12911,9 @@ "bonjour-service": "^1.2.1", "chokidar": "^3.6.0", "colorette": "^2.0.10", - "compression": "^1.7.4", + "compression": "^1.8.1", "connect-history-api-fallback": "^2.0.0", - "express": "^4.21.2", + "express": "^4.22.1", "graceful-fs": "^4.2.6", "http-proxy-middleware": "^2.0.9", "ipaddr.js": "^2.1.0", @@ -11717,7 +12921,7 @@ "open": "^10.0.3", "p-retry": "^6.2.0", "schema-utils": "^4.2.0", - "selfsigned": "^2.4.1", + "selfsigned": "^5.5.0", "serve-index": "^1.9.1", "sockjs": "^0.3.24", "spdy": "^4.0.2", @@ -11751,6 +12955,7 @@ "resolved": "https://registry.npmjs.org/chokidar/-/chokidar-3.6.0.tgz", "integrity": "sha512-7VT13fmjotKpGipCW9JEQAusEPE+Ei8nl6/g4FBAmIm0GOOLMua9NDDo/DWp0ZAxCr3cPq5ZpBqmPAQgDda2Pw==", "dev": true, + "license": "MIT", "dependencies": { "anymatch": "~3.1.2", "braces": "~3.0.2", @@ -11775,6 +12980,7 @@ "resolved": "https://registry.npmjs.org/glob-parent/-/glob-parent-5.1.2.tgz", "integrity": "sha512-AOIgSQCepiJYwP3ARnGx+5VnTu2HBYdzbGP45eLw1vr3zB3vZLeyed1sC9hnbcOc9/SrMyM5RPQrkGz4aS9Zow==", "dev": true, + "license": "ISC", "dependencies": { "is-glob": "^4.0.1" }, @@ -11787,6 +12993,7 @@ "resolved": "https://registry.npmjs.org/readdirp/-/readdirp-3.6.0.tgz", "integrity": "sha512-hOS089on8RduqdbhvQ5Z37A0ESjsqz6qnRcffsMU3495FuTdqSm+7bhJ29JvIOsBDEEnan5DPu9t3To9VRlMzA==", "dev": true, + "license": "MIT", "dependencies": { "picomatch": "^2.2.1" }, @@ -11821,6 +13028,7 @@ "resolved": "https://registry.npmjs.org/websocket-driver/-/websocket-driver-0.7.4.tgz", "integrity": "sha512-b17KeDIQVjvb0ssuSDF2cYXSg2iztliJ4B9WdsuB6J952qCPKmnVq4DyW5motImXHDC1cBT/1UezrJVsKw5zjg==", "dev": true, + "license": "Apache-2.0", "dependencies": { "http-parser-js": ">=0.5.1", "safe-buffer": ">=5.1.0", @@ -11835,6 +13043,7 @@ "resolved": "https://registry.npmjs.org/websocket-extensions/-/websocket-extensions-0.1.4.tgz", "integrity": "sha512-OqedPIGOfsDlo31UNwYbCFMSaO9m9G/0faIHj5/dZFDMFqPTcx6UwqyOy3COEaEOg/9VsGIpdqn62W5KhoKSpg==", "dev": true, + "license": "Apache-2.0", "engines": { "node": ">=0.8.0" } @@ -11880,10 +13089,11 @@ "dev": true }, "node_modules/ws": { - "version": "8.18.3", - "resolved": "https://registry.npmjs.org/ws/-/ws-8.18.3.tgz", - "integrity": "sha512-PEIGCY5tSlUt50cqyMXfCzX+oOPqN0vuGqWzbcJ2xvnkzkq46oOpz7dQaTDBdfICb4N14+GARUDw2XV2N4tvzg==", + "version": "8.19.0", + "resolved": "https://registry.npmjs.org/ws/-/ws-8.19.0.tgz", + "integrity": "sha512-blAT2mjOEIi0ZzruJfIhb3nps74PRWTCz1IjglWEEpQl5XS/UNama6u2/rjFkDDouqr4L67ry+1aGIALViWjDg==", "dev": true, + "license": "MIT", "engines": { "node": ">=10.0.0" }, @@ -11905,6 +13115,7 @@ "resolved": "https://registry.npmjs.org/wsl-utils/-/wsl-utils-0.1.0.tgz", "integrity": "sha512-h3Fbisa2nKGPxCpm89Hk33lBLsnaGBvctQopaBSOW/uIs6FTe1ATyAnKFJrzVs9vpGdsTe73WF3V4lIsk4Gacw==", "dev": true, + "license": "MIT", "dependencies": { "is-wsl": "^3.1.0" }, @@ -11923,19 +13134,12 @@ "node": ">=0.4" } }, - "node_modules/xz-decompress": { - "version": "0.2.2", - "resolved": "https://registry.npmjs.org/xz-decompress/-/xz-decompress-0.2.2.tgz", - "integrity": "sha512-DSOnX+ZLVTrsW+CtjZPwjrMWvuRkzCcEpwLsY2faZyVgLH/ZHpTg3h3+KyN16mGuduMgO+/pc9rSEG735oGN0g==", - "engines": { - "node": ">=16" - } - }, "node_modules/yallist": { "version": "3.1.1", "resolved": "https://registry.npmjs.org/yallist/-/yallist-3.1.1.tgz", "integrity": "sha512-a4UGQaWPH59mOXUYnAG2ewncQS4i4F43Tv3JoAM+s2VDAmS9NsK8GpDMLrCHPksFT7h3K6TOoUNn2pb7RoXx4g==", - "dev": true + "dev": true, + "license": "ISC" }, "node_modules/yaml": { "version": "1.10.2", diff --git a/jbrowse/package.json b/jbrowse/package.json index 7eb561f69..d6240d1f1 100644 --- a/jbrowse/package.json +++ b/jbrowse/package.json @@ -11,18 +11,20 @@ "clean": "rimraf resources/web/gen && rimraf resources/web/jbrowse/gen && rimraf resources/views/gen", "jb-sea:fetch": "node ./resources/external/fetch-jbrowse-bundle.mjs", "jb-sea:build": "node ./resources/external/build-sea.mjs ./resources/external/jbrowse.js", - "jb-sea": "npm run jb-sea:fetch && npm run jb-sea:build" + "jb-sea": "npm run jb-sea:fetch && npm run jb-sea:build", + "postinstall": "patch-package" }, "dependencies": { - "@gmod/vcf": "^6.0.9", - "@jbrowse/core": "^3.2.0", - "@jbrowse/plugin-linear-genome-view": "^3.2.0", - "@jbrowse/plugin-svg": "^3.2.0", - "@jbrowse/plugin-variants": "^3.2.0", - "@jbrowse/product-core": "^3.2.0", - "@jbrowse/react-linear-genome-view2": "^3.2.0", + "@gmod/vcf": "^7.0.0", + "@jbrowse/core": "^4.1.13", + "@jbrowse/mobx-state-tree": "^5.5.0", + "@jbrowse/plugin-canvas": "^4.1.13", + "@jbrowse/plugin-linear-genome-view": "^4.1.13", + "@jbrowse/plugin-variants": "^4.1.13", + "@jbrowse/product-core": "^4.1.13", + "@jbrowse/react-linear-genome-view2": "^4.1.13", "@labkey/api": "^1.39.0", - "@labkey/components": "^6.32.2", + "@labkey/components": "^7.16.0", "@mui/x-data-grid": "^7.28.1", "assert": "^2.1.0", "browserify-zlib": "^0.2.0", @@ -46,12 +48,14 @@ "vm-browserify": "^1.1.2" }, "devDependencies": { - "@labkey/build": "^8.4.0", + "@labkey/build": "^8.8.0", "@types/jexl": "^2.3.4", "@types/jquery": "^3.5.32", "@types/node": "^20.14.11", "@types/react": "^18.3.0", "@types/react-dom": "^18.3.0", + "patch-package": "^8.0.1", + "postinstall-postinstall": "^2.1.0", "rimraf": "^6.0.1", "tar": "^7.5.7", "typescript": "^5.1.6", diff --git a/jbrowse/patches/@gmod+bbi+8.1.1.patch b/jbrowse/patches/@gmod+bbi+8.1.1.patch new file mode 100644 index 000000000..d6fe87faf --- /dev/null +++ b/jbrowse/patches/@gmod+bbi+8.1.1.patch @@ -0,0 +1,25 @@ +diff --git a/node_modules/@gmod/bbi/esm/wasm/inflate-wasm-inlined.js b/node_modules/@gmod/bbi/esm/wasm/inflate-wasm-inlined.js +index b2d8cfa..07f8d05 100644 +--- a/node_modules/@gmod/bbi/esm/wasm/inflate-wasm-inlined.js ++++ b/node_modules/@gmod/bbi/esm/wasm/inflate-wasm-inlined.js +@@ -357,10 +357,17 @@ async function init() { + return wrapper_wasm; + if (!initPromise) { + initPromise = (async () => { +- const response = await fetch(inflate_wasm_bg_namespaceObject); +- const bytes = await response.arrayBuffer(); ++ const b64 = inflate_wasm_bg_namespaceObject.replace( ++ 'data:application/wasm;base64,', ++ '', ++ ); ++ const bin = atob(b64); ++ const bytes = new Uint8Array(bin.length); ++ for (let i = 0; i < bin.length; i++) { ++ bytes[i] = bin.charCodeAt(i); ++ } + const { instance } = await WebAssembly.instantiate(bytes, { +- './inflate_wasm_bg.js': src_wasm_inflate_wasm_bg_namespaceObject, ++ './inflate_wasm_bg.js': src_wasm_inflate_wasm_bg_namespaceObject, + }); + wrapper_wasm = instance.exports; + __wbg_set_wasm(wrapper_wasm); diff --git a/jbrowse/patches/@gmod+bgzf-filehandle+6.0.12.patch b/jbrowse/patches/@gmod+bgzf-filehandle+6.0.12.patch new file mode 100644 index 000000000..2af78e567 --- /dev/null +++ b/jbrowse/patches/@gmod+bgzf-filehandle+6.0.12.patch @@ -0,0 +1,27 @@ +diff --git a/node_modules/@gmod/bgzf-filehandle/esm/wasm/bgzf-wasm-inlined.js b/node_modules/@gmod/bgzf-filehandle/esm/wasm/bgzf-wasm-inlined.js +index b8a4365..5227798 100644 +--- a/node_modules/@gmod/bgzf-filehandle/esm/wasm/bgzf-wasm-inlined.js ++++ b/node_modules/@gmod/bgzf-filehandle/esm/wasm/bgzf-wasm-inlined.js +@@ -350,11 +350,19 @@ async function init() { + if (!initPromise) { + initPromise = (async () => { + // wasmData is a data URL from asset/inline +- const response = await fetch(bgzf_wasm_bg_namespaceObject); +- const bytes = await response.arrayBuffer(); ++ const b64 = bgzf_wasm_bg_namespaceObject.replace( ++ 'data:application/wasm;base64,', ++ '', ++ ); ++ const bin = atob(b64); ++ const bytes = new Uint8Array(bin.length); ++ for (let i = 0; i < bin.length; i++) { ++ bytes[i] = bin.charCodeAt(i); ++ } + const { instance } = await WebAssembly.instantiate(bytes, { +- './bgzf_wasm_bg.js': src_wasm_bgzf_wasm_bg_namespaceObject, ++ './bgzf_wasm_bg.js': src_wasm_bgzf_wasm_bg_namespaceObject, + }); ++ + wrapper_wasm = instance.exports; + __wbg_set_wasm(wrapper_wasm); + return wrapper_wasm; diff --git a/jbrowse/resources/external/mGAPSession.json b/jbrowse/resources/external/mGAPSession.json index f30be70a2..f701f2716 100644 --- a/jbrowse/resources/external/mGAPSession.json +++ b/jbrowse/resources/external/mGAPSession.json @@ -60,9 +60,6 @@ "maxFeatureScreenDensity": 100, "height": 400, "mouseover": "jexl:'Position: ' + formatWithCommas(get(feature,'POS'))", - "renderer": { - "type": "ExtendedVariantRenderer" - }, "detailsConfig": { "sections": [ { diff --git a/jbrowse/resources/external/minimalSession.json b/jbrowse/resources/external/minimalSession.json index c19f79578..2973c97e6 100644 --- a/jbrowse/resources/external/minimalSession.json +++ b/jbrowse/resources/external/minimalSession.json @@ -51,10 +51,7 @@ }, "displays": [{ "type": "ExtendedVariantDisplay", - "displayId": "clinvar_ncbi_hg38-ExtendedVariantDisplay", - "renderer": { - "type": "ExtendedVariantRenderer" - } + "displayId": "clinvar_ncbi_hg38-ExtendedVariantDisplay" }], "metadata": { "extendedVariantDisplayConfig" : [ diff --git a/jbrowse/src/client/JBrowse/Browser/components/JBrowseFilterPanel.tsx b/jbrowse/src/client/JBrowse/Browser/components/JBrowseFilterPanel.tsx index f6d36ecf5..55c2bb6e0 100644 --- a/jbrowse/src/client/JBrowse/Browser/components/JBrowseFilterPanel.tsx +++ b/jbrowse/src/client/JBrowse/Browser/components/JBrowseFilterPanel.tsx @@ -47,7 +47,7 @@ const JBrowseFilterPanel = observer(props => { const filterDisplayItems = [] for (const track of tracks) { // @ts-ignore - const activeSamples = getConf(track, ['displays', '0', 'renderer', 'activeSamples']) + const activeSamples = getConf(track, ['displays', '0', 'activeSamples']) const trackId = getConf(track, ['trackId']) if (activeSamples) { const sampleText = activeSamples.split(',').length > 5 ? '' : activeSamples @@ -56,7 +56,7 @@ const JBrowseFilterPanel = observer(props => { filterDisplayItems.push() } - const infoFilters = getConf(track, ['displays', '0', 'renderer', 'infoFilters']) + const infoFilters = getConf(track, ['displays', '0', 'infoFilters']) if (infoFilters?.length) { const filterText = infoFilters.map(filter => generateUserFriendlyLabel(filter)).join(', ') const label = getConf(track, ['name']) || getConf(track, ['trackId']) diff --git a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ColorWidget/ColorWidget.tsx b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ColorWidget/ColorWidget.tsx index 06508bf27..3b3356129 100644 --- a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ColorWidget/ColorWidget.tsx +++ b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ColorWidget/ColorWidget.tsx @@ -23,7 +23,7 @@ export default jbrowse => { // @ts-ignore const displays = readConfObject(track, ['displays']) || [] - let paletteName = displays[0].renderer.palette + let paletteName = displays[0].palette paletteName = paletteName || 'IMPACT' const [palette, setPalette] = useState(paletteName) @@ -34,7 +34,7 @@ export default jbrowse => { const onApply = (event) => { // NOTE: preProcessSnapshot in the renderer schema should set color1 - track.displays[0].renderer.palette.set(palette) + track.displays[0].palette.set(palette) track.displays[0].renderer.color1.set(generateSchemeJexl(palette)) const m = getSession(model) as SessionWithWidgets diff --git a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/ExtendedVcfFeature.ts b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/ExtendedVcfFeature.ts index 0af562dab..d2641137b 100644 --- a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/ExtendedVcfFeature.ts +++ b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/ExtendedVcfFeature.ts @@ -8,25 +8,36 @@ export default class ExtendedVcfFeature extends VcfFeature { super(args) } + toJSON() { + const ret: any = super.toJSON() + + // Preserve VCF INFO header metadata through JSON/snapshot flows used by + // JBrowse widgets. parser is not guaranteed to survive serialization. + ret.vcfMetadataInfo = (this as any).parser?.metadata?.INFO || {} + + return ret + } + static extractImpact(variant: Variant) { // Only append if not present: if (variant.INFO["IMPACT"]) { return(variant); } - if (!variant.INFO["ANN"]) { + const ann = variant.INFO["ANN"] as string[] | undefined + if (!ann) { return(variant); } let IMPACTs = new Set() - for (let i = 0; i < variant.INFO["ANN"].length; i++){ - if (/HIGH/g.exec(variant.INFO["ANN"][i])){ + for (let i = 0; i < ann.length; i++){ + if (/HIGH/g.exec(ann[i])){ IMPACTs.add("HIGH") } - else if (/MODERATE/g.exec(variant.INFO["ANN"][i])){ + else if (/MODERATE/g.exec(ann[i])){ IMPACTs.add("MODERATE") } - else if (/LOW/g.exec(variant.INFO["ANN"][i])){ + else if (/LOW/g.exec(ann[i])){ IMPACTs.add("LOW") } } diff --git a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/configSchema.ts b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/configSchema.ts index f4e0998b8..c47abdbe2 100644 --- a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/configSchema.ts +++ b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/configSchema.ts @@ -1,4 +1,4 @@ -import { types } from 'mobx-state-tree' +import { types } from '@jbrowse/mobx-state-tree' import { ConfigurationSchema } from '@jbrowse/core/configuration' // TODO: avoid this duplication diff --git a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantDisplay/configSchema.ts b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantDisplay/configSchema.ts index a6660c58b..27048c02a 100644 --- a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantDisplay/configSchema.ts +++ b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantDisplay/configSchema.ts @@ -1,5 +1,6 @@ import { ConfigurationSchema } from '@jbrowse/core/configuration' -import {types} from "mobx-state-tree"; +import {types} from "@jbrowse/mobx-state-tree"; + export const variantDetailsConfig = ConfigurationSchema('VariantDetailsConfig', { sections: types.array(ConfigurationSchema('VariantDetailsSection', { @@ -35,8 +36,30 @@ export default pluginManager => { contextVariable: ['feature'], }, - renderer: pluginManager.pluggableConfigSchemaType('renderer'), - detailsConfig: variantDetailsConfig + renderer: types.optional( + pluginManager.pluggableConfigSchemaType('renderer'), + { type: 'CanvasFeatureRenderer' }, + ), + detailsConfig: variantDetailsConfig, + infoFilters: { + type: 'stringArray', + description: 'the active filter set by the user', + defaultValue: [] + }, + activeSamples: { + type: 'string', + defaultValue: '', + description: 'comma-delineated string of sample IDs to filter' + }, + supportsLuceneIndex: { + type: 'boolean', + defaultValue: false + }, + palette: { + type: 'string', + description: 'The names of the palette to use for coloring features', + defaultValue: 'IMPACT', + } }, { baseConfiguration: baseLinearDisplayConfigSchema, explicitlyTyped: true }, ) diff --git a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantDisplay/model.tsx b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantDisplay/model.tsx index 329c1f4c9..2fb50de6a 100644 --- a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantDisplay/model.tsx +++ b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantDisplay/model.tsx @@ -1,13 +1,19 @@ -import { ConfigurationReference, getConf } from '@jbrowse/core/configuration'; -import { AnyConfigurationModel, } from '@jbrowse/core/configuration/configurationSchema'; +import { ConfigurationReference, getConf, readConfObject } from '@jbrowse/core/configuration'; +import { AnyConfigurationModel } from '@jbrowse/core/configuration'; import { getContainingTrack, getContainingView, getSession } from '@jbrowse/core/util'; import FilterListIcon from '@mui/icons-material/FilterList'; import VisibilityIcon from '@mui/icons-material/Visibility'; import configSchemaF from './configSchema'; -import { getEnv, IAnyStateTreeNode, types } from 'mobx-state-tree'; +import { getEnv, IAnyStateTreeNode, types } from '@jbrowse/mobx-state-tree'; import PaletteIcon from '@mui/icons-material/Palette'; import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'; import { navigateToSearch, navigateToTable } from '../../../../utils'; +import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'; +import { generateSchemeJexl } from '../ColorWidget/colorUtil'; + +function escapeForSingleQuotedJexl(value: string) { + return value.replace(/\\/g, '\\\\').replace(/'/g, "\\'") +} function getContainingTrackWithConfig(node: IAnyStateTreeNode): IAnyStateTreeNode & { configuration: AnyConfigurationModel } { return getContainingTrack(node) as any; @@ -53,7 +59,7 @@ export default jbrowse => { // @ts-ignore const trackId = getConf(track, ['trackId']) - const detailsConfig = getConf(track, ['displays', '0', 'detailsConfig']) + const detailsConfig = readConfObject(self.configuration, 'detailsConfig') const widgetId = 'Variant-' + trackId; const featureWidget = session.addWidget( @@ -73,7 +79,10 @@ export default jbrowse => { })) .views(self => { - const { renderProps: superRenderProps } = self + const { + renderProps: superRenderProps, + renderingProps: superRenderingProps, + } = self const filterMenu = { label: 'Filter By Attributes', icon: FilterListIcon, @@ -127,20 +136,78 @@ export default jbrowse => { return { ...superRenderProps(), config: config, - rendererConfig: config + rendererConfig: config, + filters: new SerializableFilterChain({ + filters: this.activeFilters(), + jexl: jbrowse.jexl, + }), } }, + renderingProps() { + const superProps = superRenderingProps() + return { + ...superProps, + async onFeatureClick(_, featureId) { + const session = getSession(self) + try { + const f = featureId || self.featureIdUnderMouse + if (!f) { + self.clearFeatureSelection() + } + else { + await self.selectFeatureById(f) + } + } catch (e) { + console.error(e) + session.notifyError(`${e}`, e) + } + }, + } + }, + + activeFilters() { + const staticJexlFilters = (getConf(self, 'jexlFilters') || []).map((f: string) => + f?.startsWith('jexl:') ? f : `jexl:${f}`, + ) + + const infoFilters = getConf(self, 'infoFilters') || [] + const activeSamples = getConf(self, 'activeSamples') || '' + const sampleFilters = activeSamples + ? activeSamples + .split(',') + .map((s: string) => s.trim()) + .filter((s: string) => !!s) + : [] + + const dynamicFilters: string[] = [] + + if (infoFilters.length) { + const serialized = escapeForSingleQuotedJexl(JSON.stringify(infoFilters)) + dynamicFilters.push(`jexl:passesInfoFilters(feature,'${serialized}')`) + } + + if (sampleFilters.length) { + const serialized = escapeForSingleQuotedJexl(JSON.stringify(sampleFilters)) + dynamicFilters.push(`jexl:passesSampleFilters(feature,'${serialized}')`) + } + + return [...staticJexlFilters, ...dynamicFilters] + }, + get rendererTypeName() { return self.configuration.renderer.type }, get rendererConfig() { const configBlob = getConf(self, ['renderer']) || {} + const palette = getConf(self, 'palette') || 'IMPACT' + const color1 = configBlob.color1 ?? generateSchemeJexl(palette) return self.rendererType.configSchema.create( { ...configBlob, + color1, showLabels: this.showLabels, displayMode: this.displayMode, maxHeight: this.maxHeight @@ -206,7 +273,7 @@ export default jbrowse => { } }] - const supportsLuceneIndex = getConf(self, ['renderer', 'supportsLuceneIndex']) + const supportsLuceneIndex = getConf(self, ['supportsLuceneIndex']) if (supportsLuceneIndex) { buttons.push({ label: 'Variant Search', diff --git a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantRenderer/components/Diamond.tsx b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantRenderer/components/Diamond.tsx deleted file mode 100644 index 80abbae72..000000000 --- a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantRenderer/components/Diamond.tsx +++ /dev/null @@ -1,69 +0,0 @@ -import { readConfObject } from '@jbrowse/core/configuration'; -import { emphasize } from '@jbrowse/core/util/color'; -import { observer } from 'mobx-react'; -import React from 'react'; -import { Feature } from '@jbrowse/core/util/simpleFeature'; - -const utrHeightFraction = 0.65 - -function isUTR(feature: Feature) { - return /(\bUTR|_UTR|untranslated[_\s]region)\b/.test( - feature.get('type') || '', - ) -} - -function Diamond(props) { - const { - feature, - bpPerPx, - region, - config, - featureLayout, - selected, - reversed, - } = props - - const screenWidth = (region.end - region.start) / bpPerPx - const width = Math.max(featureLayout.absolute.width, 1) - const { left } = featureLayout.absolute - let { top, height } = featureLayout.absolute - if (isUTR(feature)) { - top += ((1 - utrHeightFraction) / 2) * height - height *= utrHeightFraction - } - - // @ts-ignore - const color = readConfObject(config, (isUTR(feature) ? 'color3' : 'color1'), { feature }) - - let emphasizedColor - try { - emphasizedColor = emphasize(color, 0.3) - } catch (error) { - emphasizedColor = color - } - const color2 = readConfObject(config, 'color2', { feature }) - - if (left + width < 0) { - return null - } - const leftWithinBlock = Math.max(left, 0) - const diff = leftWithinBlock - left - const widthWithinBlock = Math.max(1, Math.min(width - diff, screenWidth)) - - return ( - <> - - - ) -} - -export default observer(Diamond) diff --git a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantRenderer/components/ExtendedVariantRendering.tsx b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantRenderer/components/ExtendedVariantRendering.tsx deleted file mode 100644 index 22fa99691..000000000 --- a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantRenderer/components/ExtendedVariantRendering.tsx +++ /dev/null @@ -1,44 +0,0 @@ -import { SvgFeatureRendererReactComponent } from '@jbrowse/plugin-svg'; -import { observer } from 'mobx-react'; -import React from 'react'; -import { deserializeFilters } from '../../InfoFilterWidget/filterUtil'; -import Diamond from './Diamond'; -import { passesInfoFilters, passesSampleFilters } from '../../../../../utils'; -import { VcfFeature } from '@jbrowse/plugin-variants'; - -export function ExtendedVariantRendering(props) { - const { features, rendererConfig } = props - const { activeSamples, infoFilters } = rendererConfig - - let expandedFilters = [] - if (infoFilters.toJSON()) { - expandedFilters = deserializeFilters(infoFilters.toJSON()) - } - - const sampleFilters = activeSamples.value ? activeSamples.value.split(',') : null - - function diamondValidator(feature: VcfFeature) { - return feature.get('type') === "SNV"; - } - - function isFeatureDisplayed(feature: VcfFeature) { - return passesInfoFilters(feature, expandedFilters) && passesSampleFilters(feature, sampleFilters) - } - - function getDiamondValidator() { - return { - glyph: Diamond, - validator: diamondValidator - } - } - - return ( - - ) -} - -export default observer(ExtendedVariantRendering) \ No newline at end of file diff --git a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantRenderer/configSchema.ts b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantRenderer/configSchema.ts deleted file mode 100644 index acc492b20..000000000 --- a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantRenderer/configSchema.ts +++ /dev/null @@ -1,42 +0,0 @@ -import { ConfigurationSchema } from '@jbrowse/core/configuration'; -import { svgFeatureRendererConfigSchema} from '@jbrowse/plugin-svg' - -import { generateSchemeJexl } from "../ColorWidget/colorUtil"; - -export default ConfigurationSchema( - 'ExtendedVariantRenderer', - { - palette: { - type: 'string', - description: 'The names of the palette to use for coloring features', - defaultValue: 'IMPACT', - }, - infoFilters: { - type: 'stringArray', - description: 'the active filter set by the user', - defaultValue: [] - }, - activeSamples: { - type: 'string', - defaultValue: '', - description: 'comma-delineated string of sample IDs to filter' - }, - supportsLuceneIndex: { - type: 'boolean', - defaultValue: false - } - }, - { - explicitlyTyped: true, - baseConfiguration: svgFeatureRendererConfigSchema, - preProcessSnapshot: s => { - const snap = JSON.parse(JSON.stringify(s)) - snap.palette = snap.palette || 'IMPACT' - if (snap.palette) { - snap.color1 = generateSchemeJexl(snap.palette) - } - - return {...snap} - } - } -) diff --git a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantRenderer/index.ts b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantRenderer/index.ts deleted file mode 100644 index 8432ff2e7..000000000 --- a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantRenderer/index.ts +++ /dev/null @@ -1,8 +0,0 @@ -import BoxRendererType from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType'; - -export { default as ReactComponent } from './components/ExtendedVariantRendering' -export { default as configSchema } from './configSchema' - -export class ExtendedVariantRenderer extends BoxRendererType { - supportsSVG = true -} \ No newline at end of file diff --git a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantWidget/ExtendedVariantWidget.tsx b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantWidget/ExtendedVariantWidget.tsx index 107a19976..974b455ed 100644 --- a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantWidget/ExtendedVariantWidget.tsx +++ b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantWidget/ExtendedVariantWidget.tsx @@ -105,8 +105,10 @@ export default jbrowse => { for (let display of displays){ const tempProp = [] for (let propertyName of display.properties){ - // This value is not in the header, and is probably injected programmatically, so skip: - if (!featureInfoFields[propertyName]) { + // This value is not in the header, and is probably injected programmatically, so skip. + // Only apply this guard when featureInfoFields is actually populated (non-empty); + // when metadata is unavailable we still want to render configured sections. + if (Object.keys(featureInfoFields).length > 0 && !featureInfoFields[propertyName]) { continue } @@ -333,10 +335,12 @@ export default jbrowse => { const { model } = props const detailsConfig = JSON.parse(JSON.stringify(model.detailsConfig || {})) const feature = model.featureData - const featureInfoFields = feature.parser.metadata.INFO + const featureInfoFields = feature.vcfMetadataInfo || feature.parser?.metadata?.INFO || {} const [infoFields, setInfoFields] = useState>(null) const feat = JSON.parse(JSON.stringify(feature)) + + delete feat["vcfMetadataInfo"] const { samples } = feat feat["samples"] = null @@ -374,7 +378,7 @@ export default jbrowse => { delete feat["INFO"]["ANN"] } - const sections = detailsConfig.sections || inferSections(feat, infoFields) + const sections = detailsConfig.sections?.length > 0 ? detailsConfig.sections : inferSections(feat, infoFields) const displays = makeDisplays(feat, sections, featureInfoFields, infoFields) // If a given INFO field is used in a specific section, dont include in the catch-all INFO section: diff --git a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/InfoFilterWidget/InfoFilterWidget.tsx b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/InfoFilterWidget/InfoFilterWidget.tsx index e224cbe67..981d8076d 100644 --- a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/InfoFilterWidget/InfoFilterWidget.tsx +++ b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/InfoFilterWidget/InfoFilterWidget.tsx @@ -47,7 +47,7 @@ export default jbrowse => { // @ts-ignore const displays = readConfObject(track, 'displays') - const initialFilters = displays[0].renderer.infoFilters || [] + const initialFilters = displays[0].infoFilters || [] const [infoFilters, setInfoFilters] = React.useState(initialFilters) const [hasSubmitted, setHasSubmitted] = React.useState(false) @@ -85,13 +85,13 @@ export default jbrowse => { return } - track.displays[0].renderer.infoFilters.set([...infoFilters]) + track.displays[0].infoFilters.set([...infoFilters]) const m = getSession(model) as SessionWithWidgets m.hideWidget(model) } const clearFilters = (event) => { - track.displays[0].renderer.infoFilters.set([]) + track.displays[0].infoFilters.set([]) const m = getSession(model) as SessionWithWidgets m.hideWidget(model) } diff --git a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/SampleFilterWidget/SampleFilterWidget.tsx b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/SampleFilterWidget/SampleFilterWidget.tsx index e681ae050..c7aae3702 100644 --- a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/SampleFilterWidget/SampleFilterWidget.tsx +++ b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/SampleFilterWidget/SampleFilterWidget.tsx @@ -45,20 +45,20 @@ export default jbrowse => { // @ts-ignore const displays = readConfObject(track, ['displays']) || [] - const [sampleFilter, setSampleFilter] = useState(replaceCommaWithNewline(displays[0].renderer.activeSamples) || '') + const [sampleFilter, setSampleFilter] = useState(replaceCommaWithNewline(displays[0].activeSamples) || '') const handleSampleFilterChange = (event) => { setSampleFilter(event.target.value) } const handleSampleFilterSubmit = (event) => { - track.displays[0].renderer.activeSamples.set(parseSampleCSV(sampleFilter)) + track.displays[0].activeSamples.set(parseSampleCSV(sampleFilter)) const m = getSession(model) as SessionWithWidgets m.hideWidget(model) } const clearFilters = (event) => { - track.displays[0].renderer.activeSamples.set('') + track.displays[0].activeSamples.set('') const m = getSession(model) as SessionWithWidgets m.hideWidget(model) } diff --git a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/index.ts b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/index.ts index f2166e50a..6bb66ce9d 100644 --- a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/index.ts +++ b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/index.ts @@ -1,5 +1,6 @@ import Plugin from '@jbrowse/core/Plugin'; import PluginManager from '@jbrowse/core/PluginManager'; +import { LinearBasicDisplayComponent } from '@jbrowse/plugin-linear-genome-view'; import ExtendedVariantWidget from './ExtendedVariantWidget'; import ExtendedVariantDisplay from './ExtendedVariantDisplay'; import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'; @@ -8,16 +9,49 @@ import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'; import { configSchema as EVAdapterConfigSchema, EVAdapterClass } from './ExtendedVariantAdapter'; -import { - configSchema as EVRendererConfigSchema, - ExtendedVariantRenderer, - ReactComponent as EVRendererReactComponent -} from './ExtendedVariantRenderer'; - import { default as createExtendedVariantTrackConfig } from './configSchema'; import InfoFilterWidget from './InfoFilterWidget'; import ColorWidget from './ColorWidget'; import SampleFilterWidget from './SampleFilterWidget'; +import GlyphType from '@jbrowse/core/pluggableElementTypes/GlyphType'; +import { readConfObject } from '@jbrowse/core/configuration'; +import { emphasize } from '@jbrowse/core/util/color'; +import jexl from '@jbrowse/jexl'; +import { deserializeFilters } from './InfoFilterWidget/filterUtil'; +import { passesInfoFilters, passesSampleFilters } from '../../../utils'; + +const utrHeightFraction = 0.65 + +function isUTR(feature: any) { + return /(\bUTR|_UTR|untranslated[_\s]region)\b/.test( + feature?.get?.('type') || '', + ) +} + +function evaluateInfoFilters(feature: any, serializedFilters: any) { + try { + const filters = typeof serializedFilters === 'string' + ? JSON.parse(serializedFilters) + : serializedFilters + const expandedFilters = deserializeFilters(filters) + return passesInfoFilters(feature, expandedFilters) + } catch (e) { + console.error(e) + return true + } +} + +function evaluateSampleFilters(feature: any, serializedSampleFilters: any) { + try { + const sampleFilters = typeof serializedSampleFilters === 'string' + ? JSON.parse(serializedSampleFilters) + : serializedSampleFilters + return passesSampleFilters(feature, sampleFilters) + } catch (e) { + console.error(e) + return true + } +} export default class ExtendedVariantPlugin extends Plugin { name = 'ExtendedVariantPlugin' @@ -28,17 +62,6 @@ export default class ExtendedVariantPlugin extends Plugin { const WidgetType = jbrequire('@jbrowse/core/pluggableElementTypes/WidgetType') const TrackType = jbrequire('@jbrowse/core/pluggableElementTypes/TrackType') const LGVPlugin = pluginManager.getPlugin('LinearGenomeViewPlugin',) as import('@jbrowse/plugin-linear-genome-view').default - const { BaseLinearDisplayComponent } = LGVPlugin.exports - - pluginManager.addRendererType( - () => - new ExtendedVariantRenderer({ - name: 'ExtendedVariantRenderer', - ReactComponent: EVRendererReactComponent, - configSchema: EVRendererConfigSchema, - pluginManager, - }), - ) pluginManager.addAdapterType(() => new AdapterType({ @@ -69,10 +92,68 @@ export default class ExtendedVariantPlugin extends Plugin { stateModel, trackType: 'ExtendedVariantTrack', viewType: 'LinearGenomeView', - ReactComponent: BaseLinearDisplayComponent, + // Use LinearBasicDisplayComponent so canvas floating labels are rendered. + // BaseLinearDisplayComponent alone does not mount FloatingLabels. + ReactComponent: LinearBasicDisplayComponent, }) }) + pluginManager.addGlyphType( + () => + new GlyphType({ + name: 'SNVGlyph', + displayName: 'SNV Diamond', + draw: (ctx: any) => { + const { ctx: context, featureLayout, feature, config } = ctx + const selected = !!ctx?.selected + const rendererConfig: any = config + const { x, y, width } = featureLayout + + let top = y + let height = featureLayout.height + if (isUTR(feature)) { + top += ((1 - utrHeightFraction) / 2) * height + height *= utrHeightFraction + } + + const centerX = x + width / 2 + const centerY = top + height / 2 + const halfWidth = height / 2 + const halfHeight = height / 2 + + const color = (readConfObject as any)( + rendererConfig, + isUTR(feature) ? 'color3' : 'color1', + { feature }, + ) || '#800080' + const color2 = (readConfObject as any)(rendererConfig, 'color2', { feature }) || '#4B0082' + + let emphasizedColor + try { + emphasizedColor = emphasize(color, 0.3) + } catch (error) { + emphasizedColor = color + } + + context.fillStyle = selected ? emphasizedColor : color + context.beginPath() + context.moveTo(centerX, centerY - halfHeight) // top + context.lineTo(centerX + halfWidth, centerY) // right + context.lineTo(centerX, centerY + halfHeight) // bottom + context.lineTo(centerX - halfWidth, centerY) // left + context.closePath() + context.fill() + + if (selected) { + context.strokeStyle = color2 + context.lineWidth = 1 + context.stroke() + } + }, + match: feature => feature.get('type') === 'SNV', + }) + ) + pluginManager.addWidgetType(() => { const { configSchema, @@ -144,6 +225,11 @@ export default class ExtendedVariantPlugin extends Plugin { pluginManager.jexl.addFunction('formatWithCommas', (val) => { return val ? Number(val).toLocaleString() : val }) + + jexl.addFunction('passesInfoFilters', evaluateInfoFilters) + jexl.addFunction('passesSampleFilters', evaluateSampleFilters) + pluginManager.jexl.addFunction('passesInfoFilters', evaluateInfoFilters) + pluginManager.jexl.addFunction('passesSampleFilters', evaluateSampleFilters) } configure(pluginManager: PluginManager) { diff --git a/jbrowse/src/client/JBrowse/Browser/plugins/LogSession/index.ts b/jbrowse/src/client/JBrowse/Browser/plugins/LogSession/index.ts index 96fe00325..b9cfb7e73 100644 --- a/jbrowse/src/client/JBrowse/Browser/plugins/LogSession/index.ts +++ b/jbrowse/src/client/JBrowse/Browser/plugins/LogSession/index.ts @@ -1,6 +1,6 @@ import Plugin from '@jbrowse/core/Plugin' import InfoIcon from '@mui/icons-material/Info' -import { getSnapshot } from "mobx-state-tree"; +import { getSnapshot } from "@jbrowse/mobx-state-tree" import { getSession } from '@jbrowse/core/util' export default class LogSession extends Plugin { diff --git a/jbrowse/src/client/JBrowse/Search/components/StandaloneSearchComponent.tsx b/jbrowse/src/client/JBrowse/Search/components/StandaloneSearchComponent.tsx index eef531ee6..69a1f0ea8 100644 --- a/jbrowse/src/client/JBrowse/Search/components/StandaloneSearchComponent.tsx +++ b/jbrowse/src/client/JBrowse/Search/components/StandaloneSearchComponent.tsx @@ -1,8 +1,13 @@ import React from 'react'; -import { RefNameAutocomplete } from '@jbrowse/plugin-linear-genome-view'; -import { fetchResults } from '@jbrowse/plugin-linear-genome-view/esm/LinearGenomeView/components/util'; +import { RefNameAutocomplete, fetchResults } from '@jbrowse/plugin-linear-genome-view'; import { ParsedLocString, parseLocString } from '@jbrowse/core/util'; +import { dedupe } from '@jbrowse/core/util' +import type { SearchScope } from '@jbrowse/core/TextSearch/TextSearchManager' +import type { Assembly } from '@jbrowse/core/assemblyManager/assembly' +import type { TextSearchManager } from '@jbrowse/core/util' +import type { SearchType } from '@jbrowse/core/data_adapters/BaseAdapter' + export default function StandaloneSearchComponent(props: { session: any, selectedRegion: string, assemblyName: string, onSelect: (queryString: string, parsedLocString: ParsedLocString, errors?: string[]) => void, forVariantTable?: boolean, fieldMinWidth?: number}) { const { session, selectedRegion, assemblyName, onSelect, forVariantTable, fieldMinWidth = 175 } = props diff --git a/jbrowse/src/client/JBrowse/VariantSearch/VariantSearch.tsx b/jbrowse/src/client/JBrowse/VariantSearch/VariantSearch.tsx index a0332e66f..9956218c7 100644 --- a/jbrowse/src/client/JBrowse/VariantSearch/VariantSearch.tsx +++ b/jbrowse/src/client/JBrowse/VariantSearch/VariantSearch.tsx @@ -1,6 +1,6 @@ import React, { useEffect, useState } from 'react'; import { observer } from 'mobx-react'; -import { getEnv } from 'mobx-state-tree'; +import { getEnv } from '@jbrowse/mobx-state-tree'; import { createTheme } from '@mui/material/styles'; import { parseLocString } from '@jbrowse/core/util'; import { readConfObject } from '@jbrowse/core/configuration'; diff --git a/jbrowse/src/client/JBrowse/VariantSearch/components/VariantTableWidget.tsx b/jbrowse/src/client/JBrowse/VariantSearch/components/VariantTableWidget.tsx index 98f6ac0f9..7326c16bc 100644 --- a/jbrowse/src/client/JBrowse/VariantSearch/components/VariantTableWidget.tsx +++ b/jbrowse/src/client/JBrowse/VariantSearch/components/VariantTableWidget.tsx @@ -155,7 +155,7 @@ const VariantTableWidget = observer(props => { const [anchorEl, setAnchorEl] = React.useState(null) const open = Boolean(anchorEl); - const [hoverTimeout, setHoverTimeout] = React.useState(null); + const [hoverTimeout, setHoverTimeout] = React.useState(null); const handlePopoverOpen = (event: React.MouseEvent) => { clearHoverTimeout() diff --git a/jbrowse/src/client/JBrowse/VariantTable/VariantTable.tsx b/jbrowse/src/client/JBrowse/VariantTable/VariantTable.tsx index f9f9b0b4d..b7f02bab9 100644 --- a/jbrowse/src/client/JBrowse/VariantTable/VariantTable.tsx +++ b/jbrowse/src/client/JBrowse/VariantTable/VariantTable.tsx @@ -1,6 +1,6 @@ import React, { useEffect, useState } from 'react'; import { observer } from 'mobx-react'; -import { getEnv, IAnyStateTreeNode } from 'mobx-state-tree'; +import { getEnv, IAnyStateTreeNode } from '@jbrowse/mobx-state-tree'; import { createTheme } from '@mui/material/styles'; import { readConfObject } from '@jbrowse/core/configuration'; import { createJBrowseTheme } from '@jbrowse/core/ui'; diff --git a/jbrowse/src/client/JBrowse/VariantTable/components/VariantTableWidget.tsx b/jbrowse/src/client/JBrowse/VariantTable/components/VariantTableWidget.tsx index 33f61a49d..abbc8bb2b 100644 --- a/jbrowse/src/client/JBrowse/VariantTable/components/VariantTableWidget.tsx +++ b/jbrowse/src/client/JBrowse/VariantTable/components/VariantTableWidget.tsx @@ -110,15 +110,15 @@ const VariantTableWidget = observer(props => { const rawFeatures = await lastValueFrom(featObservable) const filteredFeatures = filterFeatures(rawFeatures, - getConf(track, ['displays', '0', 'renderer', 'activeSamples']), - getConf(track, ['displays', '0', 'renderer', 'infoFilters']) + getConf(track, ['displays', '0', 'activeSamples']), + getConf(track, ['displays', '0', 'infoFilters']) ) // Maintain a cached list of all non-WT samples at this position: filteredFeatures.forEach(variant => { if (!variant.get('INFO')['variableSamples']) { variant.get('INFO')['variableSamples'] = [] - const genotypes = variant.get('GENOTYPES')() + const genotypes = variant.get('genotypes') Object.keys(genotypes).forEach(function(sampleId) { const gt = genotypes[sampleId] ? genotypes[sampleId] : null if (isVariant(gt)) { @@ -322,7 +322,7 @@ const VariantTableWidget = observer(props => { } // @ts-ignore - const supportsLuceneIndex = getConf(track, ['displays', '0', 'renderer', 'supportsLuceneIndex']) + const supportsLuceneIndex = getConf(track, ['displays', '0', 'supportsLuceneIndex']) const showDetailsWidget = (rowIdx: number) => { const feature = features[rowIdx] const trackId = getConf(track, ['trackId']) @@ -453,11 +453,11 @@ const VariantTableWidget = observer(props => {
- + - + handleMenuClick(e, setAnchorFilterMenu)} handleClose={(e) => handleMenuClose(setAnchorFilterMenu)} > @@ -466,11 +466,11 @@ const VariantTableWidget = observer(props => { - + - {supportsLuceneIndex ? + {supportsLuceneIndex ? : null} diff --git a/jbrowse/src/client/JBrowse/utils.ts b/jbrowse/src/client/JBrowse/utils.ts index ad1870022..f2ce9d0d3 100644 --- a/jbrowse/src/client/JBrowse/utils.ts +++ b/jbrowse/src/client/JBrowse/utils.ts @@ -1,5 +1,5 @@ import { isEmptyObject } from 'jquery'; -import jexl from 'jexl'; +import jexl from '@jbrowse/jexl'; import { createViewState, loadPlugins } from '@jbrowse/react-linear-genome-view2'; import { ActionURL, Ajax } from '@labkey/api'; import { @@ -33,7 +33,7 @@ export function passesInfoFilters(feature, filters) { filterObj.jexlExpression = filterObj.jexlExpression.replace('variant', 'data') } - if (!jexl.evalSync(filterObj.jexlExpression, feature)){ + if (!jexl.eval(filterObj.jexlExpression, feature)){ return false } } catch (e){ @@ -44,7 +44,7 @@ export function passesInfoFilters(feature, filters) { return true } -export function passesSampleFilters(variant : VcfFeature, sampleIDs){ +export function passesSampleFilters(variant: VcfFeature, sampleIDs){ if (!sampleIDs || sampleIDs.length === 0) { return true } @@ -60,7 +60,7 @@ export function passesSampleFilters(variant : VcfFeature, sampleIDs){ return false } - const genotypes = variant.get('GENOTYPES')() + const genotypes = variant.get('genotypes') if (!genotypes || isEmptyObject(genotypes)) { return false } @@ -174,7 +174,7 @@ function applyUrlParams(json, queryParam) { let found = false for (const track of json.tracks) { if (track.trackId?.toLowerCase() === trackId?.toLowerCase() || track.name?.toLowerCase() === trackId?.toLowerCase() || track.trackId?.toLowerCase().includes(trackId?.toLowerCase())) { - track.displays[0].renderer.activeSamples = sampleList.join(',') + track.displays[0].activeSamples = sampleList.join(',') found = true break } @@ -198,7 +198,7 @@ function applyUrlParams(json, queryParam) { let found = false for (const track of json.tracks) { if (track.trackId?.toLowerCase() === trackId?.toLowerCase() || track.name?.toLowerCase() === trackId?.toLowerCase() || track.trackId?.toLowerCase().includes(trackId?.toLowerCase())) { - track.displays[0].renderer.infoFilters = [...infoFilterList] + track.displays[0].infoFilters = [...infoFilterList] found = true break } @@ -276,11 +276,11 @@ function serializeSampleFilters(track) { return undefined } - if (!track.configuration.displays[0].renderer.activeSamples.value) { + if (!track.configuration.displays[0].activeSamples.value) { return undefined } - return track.configuration.trackId + ":" + track.configuration.displays[0].renderer.activeSamples.value + return track.configuration.trackId + ":" + track.configuration.displays[0].activeSamples.value } function serializeInfoFilters(track) { @@ -288,11 +288,11 @@ function serializeInfoFilters(track) { return undefined } - if (!track.configuration.displays[0].renderer.infoFilters.valueJSON || isEmptyObject(track.configuration.displays[0].renderer.infoFilters.valueJSON) || !track.configuration.displays[0].renderer.infoFilters.valueJSON.length) { + if (!track.configuration.displays[0].infoFilters.valueJSON || isEmptyObject(track.configuration.displays[0].infoFilters.valueJSON) || !track.configuration.displays[0].infoFilters.valueJSON.length) { return undefined } - return track.configuration.trackId + ":" + encodeURIComponent(track.configuration.displays[0].renderer.infoFilters.valueJSON) + return track.configuration.trackId + ":" + encodeURIComponent(track.configuration.displays[0].infoFilters.valueJSON) } function handleFailure(error, sessionId?, trackId?, isTable?, reloadOnFailure = true) { diff --git a/jbrowse/src/org/labkey/jbrowse/JBrowseController.java b/jbrowse/src/org/labkey/jbrowse/JBrowseController.java index d7c75b483..1831d7763 100644 --- a/jbrowse/src/org/labkey/jbrowse/JBrowseController.java +++ b/jbrowse/src/org/labkey/jbrowse/JBrowseController.java @@ -715,10 +715,10 @@ else if (MGAP.equalsIgnoreCase(form.getSession())) else if (MGAP_FILTERED.equalsIgnoreCase(form.getSession())) { resp = getDemoSession("external/mGAPSession.json"); - resp.getJSONArray("tracks").getJSONObject(0).getJSONArray("displays").getJSONObject(0).getJSONObject("renderer").put("activeSamples", "m00004,m00005"); - resp.getJSONArray("tracks").getJSONObject(0).getJSONArray("displays").getJSONObject(0).getJSONObject("renderer").put("palette", "AF"); - resp.getJSONArray("tracks").getJSONObject(0).getJSONArray("displays").getJSONObject(0).getJSONObject("renderer").put("supportsLuceneIndex", true); - resp.getJSONArray("tracks").getJSONObject(0).getJSONArray("displays").getJSONObject(0).getJSONObject("renderer").put("infoFilters", new JSONArray(){{ + resp.getJSONArray("tracks").getJSONObject(0).getJSONArray("displays").getJSONObject(0).put("activeSamples", "m00004,m00005"); + resp.getJSONArray("tracks").getJSONObject(0).getJSONArray("displays").getJSONObject(0).put("palette", "AF"); + resp.getJSONArray("tracks").getJSONObject(0).getJSONArray("displays").getJSONObject(0).put("supportsLuceneIndex", true); + resp.getJSONArray("tracks").getJSONObject(0).getJSONArray("displays").getJSONObject(0).put("infoFilters", new JSONArray(){{ put("AF:gt:0.1"); }}); diff --git a/jbrowse/src/org/labkey/jbrowse/JBrowseModule.java b/jbrowse/src/org/labkey/jbrowse/JBrowseModule.java index 15feab9e5..945d451aa 100644 --- a/jbrowse/src/org/labkey/jbrowse/JBrowseModule.java +++ b/jbrowse/src/org/labkey/jbrowse/JBrowseModule.java @@ -117,6 +117,7 @@ public void doStartupAfterSpringConfig(ModuleContext moduleContext) // These are all part of the JBrowse demo data: ContentSecurityPolicyFilter.registerAllowedSources(this.getClass().getName(), Directive.Connection, "https://jbrowse.org", "https://s3.amazonaws.com", "https://ftp.ncbi.nlm.nih.gov"); ContentSecurityPolicyFilter.registerAllowedSources(this.getClass().getName(), Directive.Style, "https://www.gstatic.com"); + ContentSecurityPolicyFilter.registerAllowedSources(this.getClass().getName(), Directive.Font, "https://www.gstatic.com", "https://fonts.googleapis.com"); ContextListener.addShutdownListener(new JBrowseLuceneSearch.ShutdownHandler()); } diff --git a/jbrowse/src/org/labkey/jbrowse/model/JsonFile.java b/jbrowse/src/org/labkey/jbrowse/model/JsonFile.java index 756e22cd6..6c56553c0 100644 --- a/jbrowse/src/org/labkey/jbrowse/model/JsonFile.java +++ b/jbrowse/src/org/labkey/jbrowse/model/JsonFile.java @@ -551,17 +551,11 @@ private JSONObject getVcfTrack(Logger log, ExpData targetFile, ReferenceGenome r put("displayId", getJsonTrackId() + "-ExtendedVariantDisplay"); put("maxFeatureScreenDensity", 100); put("mouseover", "jexl:'Position: ' + formatWithCommas(get(feature,'POS'))"); - put("renderer", new JSONObject(){{ - put("type", "ExtendedVariantRenderer"); - if (shouldHaveFreeTextSearch()) - { - put("supportsLuceneIndex", true); - } - //put("showLabels", false); - //put("labels", new JSONObject(){{ - // put("description", "jexl:get(feature,'POS')"); - //}}); - }}); + + if (shouldHaveFreeTextSearch()) + { + put("supportsLuceneIndex", true); + } JSONObject json = getExtraTrackConfig(); if (json != null && json.has("additionalFeatureMsg")) diff --git a/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java b/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java index 6b339bcd5..28ec3cbd3 100644 --- a/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java +++ b/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java @@ -48,6 +48,7 @@ import org.labkey.test.util.ext4cmp.Ext4FieldRef; import org.labkey.test.util.external.labModules.LabModuleHelper; import org.openqa.selenium.By; +import org.openqa.selenium.JavascriptExecutor; import org.openqa.selenium.Keys; import org.openqa.selenium.WebElement; import org.openqa.selenium.interactions.Actions; @@ -141,19 +142,19 @@ private void testColorWidget() // We expect IMPACT to be the default scheme assertElementPresent(Locator.tagWithText("td", "HIGH")); assertBoxWithColorPresent("#ff0000"); // red - waitForElement(Locator.tagWithAttribute("polygon", "fill", "red")); + waitForCanvasColorPresent("#ff0000"); assertElementPresent(Locator.tagWithText("td", "MODERATE")); assertBoxWithColorPresent("#DAA520"); //"goldenrod" - assertElementPresent(Locator.tagWithAttribute("polygon", "fill", "goldenrod")); + waitForCanvasColorPresent("#daa520"); assertElementPresent(Locator.tagWithText("td", "LOW")); assertBoxWithColorPresent("#049931"); - assertElementPresent(Locator.tagWithAttribute("polygon", "fill", "#049931")); + waitForCanvasColorPresent("#049931"); assertElementPresent(Locator.tagWithText("td", "Other")); assertBoxWithColorPresent("#808080"); //gray - assertElementPresent(Locator.tagWithAttribute("polygon", "fill", "gray")); + waitForCanvasColorPresent("#808080"); // Now toggle to Allele Freq.: waitAndClick(Locator.tagWithText("div", "Predicted Impact")); @@ -164,7 +165,7 @@ private void testColorWidget() clickDialogButton("Apply"); - waitForElement(Locator.tagWithAttribute("polygon", "fill", "#2425E0")); + waitForCanvasColorPresent("#2425e0"); } private void assertBoxWithColorPresent(final String expectedColor) @@ -184,6 +185,48 @@ private void clickDialogButton(String text) waitAndClick(Locator.XPathLocator.tagWithClass("button", "MuiButtonBase-root").withText(text)); } + private void waitForCanvasColorPresent(final String expectedColor) + { + final long timeoutMs = WAIT_FOR_JAVASCRIPT; + final long start = System.currentTimeMillis(); + + while (System.currentTimeMillis() - start < timeoutMs) + { + if (isCanvasColorPresent(expectedColor)) + return; + + sleep(250); + } + + Assert.fail("Unable to find color in any canvas: " + expectedColor); + } + + private boolean isCanvasColorPresent(final String expectedColor) + { + final String script = "const expected = (arguments[0] || '').toLowerCase();\n" + + "const toHex = (v) => v.toString(16).padStart(2, '0');\n" + + "const canvases = Array.from(document.querySelectorAll('canvas'));\n" + + "for (const canvas of canvases) {\n" + + " try {\n" + + " const ctx = canvas.getContext('2d');\n" + + " if (!ctx || canvas.width === 0 || canvas.height === 0) continue;\n" + + " const data = ctx.getImageData(0, 0, canvas.width, canvas.height).data;\n" + + " for (let i = 0; i < data.length; i += 4) {\n" + + " const a = data[i + 3];\n" + + " if (!a) continue;\n" + + " const hex = '#' + toHex(data[i]) + toHex(data[i + 1]) + toHex(data[i + 2]);\n" + + " if (hex === expected) return true;\n" + + " }\n" + + " } catch (e) {\n" + + " // Ignore canvases we cannot sample\n" + + " }\n" + + "}\n" + + "return false;"; + + Object ret = ((JavascriptExecutor) getDriver()).executeScript(script, expectedColor); + return ret instanceof Boolean && (Boolean) ret; + } + private void testBrowserNavToVariantTable() throws Exception { beginAt("/" + getProjectName() + "/jbrowse-jbrowse.view?session=mgap"); @@ -201,7 +244,7 @@ private void testDefaultColorApplied() waitForJBrowseToLoad(); // Indicates AF scheme applied: - waitForElement(Locator.tagWithAttribute("polygon", "fill", "#9A1764")); + waitForCanvasColorPresent("#9a1764"); openTrackMenuItem("Color Selection"); waitForElement(Locator.tagWithText("h6", "Color Schemes")); @@ -217,7 +260,7 @@ private void testDefaultColorApplied() clickDialogButton("Apply"); // Indicates the IMPACT scheme applies: - waitForElement(Locator.tagWithAttribute("polygon", "fill", "gray")); + waitForCanvasColorPresent("#808080"); } private void testAFColor() @@ -237,7 +280,7 @@ private void testAFColor() assertBoxWithColorPresent("#808080"); //gray clickDialogButton("Apply"); - waitForElement(Locator.tagWithAttribute("polygon", "fill", "#9A1764")); + waitForCanvasColorPresent("#9a1764"); } private void testFilterWidget() @@ -292,7 +335,7 @@ private void testFilterWidget() sleep(1000); // NOTE: depending on the size of the view area, this can vary. This is more a factor of the environment that actual behavior - Assert.assertEquals("Incorrect number of variants", 87.0, getTotalVariantFeatures(), 1.0); + Assert.assertEquals("Incorrect number of variants", 96.0, getTotalVariantFeatures(), 1.0); // bottom filter UI waitForElement(Locator.tagContainingText("button", "mGAP: Showing sites where").containing("AF < 0.02")); @@ -311,7 +354,7 @@ private void testLoadingConfigFilters(){ getDriver().findElements(getVariantWithinTrack("mgap_hg38", "SNV T -> G")); getDriver().findElements(getVariantWithinTrack("mgap_hg38", "SNV A -> T")); - Assert.assertEquals("Incorrect number of variants", 7, getTotalVariantFeatures()); + Assert.assertEquals("Incorrect number of variants", 9, getTotalVariantFeatures()); // bottom filter UI waitForElement(Locator.tagContainingText("button", "mGAP: Showing sites with a variant in any of:").containing("m00004,m00005")); @@ -339,7 +382,7 @@ private void testSampleFilters() getDriver().findElements(getVariantWithinTrack("mgap_hg38", "SNV A -> T")); // NOTE: depending on the size of the view area, this can vary. This is more a factor of the environment that actual behavior - Assert.assertEquals("Incorrect number of variants", 37.0, getTotalVariantFeatures(), 1); + Assert.assertEquals("Incorrect number of variants", 42.0, getTotalVariantFeatures(), 1); openTrackMenuItem("Filter By Sample"); waitForElement(Locator.tagWithText("h6", "Filter By Sample")); @@ -348,7 +391,7 @@ private void testSampleFilters() Locator.findElements(getDriver(), textArea).get(0).sendKeys("m00010"); clickDialogButton("Apply"); - Assert.assertEquals("Incorrect number of variants", 3, getTotalVariantFeatures()); + Assert.assertEquals("Incorrect number of variants", 4, getTotalVariantFeatures()); } private void testInferredDetails() @@ -509,9 +552,6 @@ private void testGenotypeFrequencies() assertElementPresent(Locator.tagWithText("td", "3041")); assertElementPresent(Locator.tagWithText("span", "Genotype Frequency (2329)")); assertElementPresent(Locator.tagWithText("a", "Click here to view sample-level genotypes")); - while (isTextPresent("Loading")){ - sleep(10); - } waitForElement(Locator.tagWithAttributeContaining("div","id","reactgooglegraph")); } @@ -1209,8 +1249,6 @@ private void testTrixSearch(String sessionId) throws Exception searchBox.sendKeys(Keys.ENTER); }); - waitForJBrowseToLoad(); - waitForElement(Locator.tagWithText("span", "fakeData.gff").withClass("MuiTypography-root")); waitForElement(Locator.tagWithText("span", "fakeData.bed").withClass("MuiTypography-root")); diff --git a/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTestHelper.java b/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTestHelper.java index de884641b..95290fc73 100644 --- a/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTestHelper.java +++ b/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTestHelper.java @@ -143,10 +143,15 @@ public static By getVariantWithinTrack(BaseWebDriverTest test, String trackId, S { Locator.XPathLocator l = getTrackLocator(test, trackId, true); test.waitForElementToDisappear(Locator.tagWithText("p", "Loading")); - l = l.append(Locator.xpath("//*[name()='text' and contains(text(), '" + variantText + "')]")).notHidden().parent(); - if (appendPolygon){ - l = l.append("/*[name()='polygon']"); - } + + String normalizedVariantText = variantText.replaceFirst("^(?i)(SNV|deletion|insertion|indel|MNV|DEL|INS)\\s+", ""); + String textPredicate = normalizedVariantText.equals(variantText) + ? "contains(normalize-space(.), '" + variantText + "')" + : "(contains(normalize-space(.), '" + variantText + "') or contains(normalize-space(.), '" + normalizedVariantText + "'))"; + + String canvasPath = "//div[contains(@data-feature-id,'vcf-') and " + textPredicate + "]" + + "[not(ancestor-or-self::*[contains(@style,'display: none')])]"; + l = l.append(Locator.xpath(canvasPath)).notHidden(); test.waitForElement(l); @@ -155,24 +160,24 @@ public static By getVariantWithinTrack(BaseWebDriverTest test, String trackId, S public static void waitForJBrowseToLoad(BaseWebDriverTest test) { - test.waitForElementToDisappear(Locator.tagWithText("p", "Loading...")); //the initial message before getSession - test.waitForElement(Locator.tagWithAttribute("svg", "data-testid", "MenuIcon")); //this is the top-left icon - test.waitForElement(Locator.tagWithAttribute("button", "title", "close this track").notHidden()); + test.waitForElementToDisappear(Locator.tagWithText("p", "Loading..."), WebDriverWrapper.WAIT_FOR_PAGE); //the initial message before getSession + test.waitForElement(Locator.tagWithAttribute("button", "data-testid", "view_menu_icon"), WebDriverWrapper.WAIT_FOR_PAGE); //this is the top-left icon + test.waitForElement(Locator.tagWithAttribute("button", "title", "close this track").notHidden(), WebDriverWrapper.WAIT_FOR_PAGE); test.waitForElement(Locator.tagWithClassContaining("button", "MuiButtonBase-root").notHidden(), WebDriverWrapper.WAIT_FOR_PAGE); //this is the icon from the track label - test.waitForElementToDisappear(Locator.tagWithText("div", "Loading")); //track data - test.waitForElementToDisappear(Locator.tagWithText("p", "Loading").withClass("MuiTypography-root")); // the track data + Locator.XPathLocator trackContainer = Locator.tagWithAttributeContaining("div", "data-testid", "trackRenderingContainer-"); + test.waitForElement(trackContainer.descendant(Locator.tagWithAttributeContaining("canvas", "data-testid", "_done")), WebDriverWrapper.WAIT_FOR_PAGE); //track data } public static long getTotalVariantFeatures(BaseWebDriverTest test) { final Long winWidth = test.executeScript("return window.outerWidth", Long.class); final Long winHeight = test.executeScript("return window.outerHeight", Long.class); - final Locator l = Locator.tagWithAttribute("svg", "data-testid", "svgfeatures").append(Locator.tag("polygon")); + final Locator l = Locator.tagWithAttributeContaining("div", "data-feature-id", "vcf-"); try { - // NOTE: JBrowse renders features using multiple blocks per track, and these tracks can redundantly render identical features on top of one another. - // Counting unique locations is indirect, but should result in unique features + // NOTE: with canvas rendering, SVG polygons are no longer present. We count visible feature wrappers + // and de-duplicate by feature id to avoid overcounting duplicates across render blocks. return doVariantCount(test, l, winWidth, winHeight); } catch (StaleElementReferenceException e) @@ -186,9 +191,16 @@ public static long getTotalVariantFeatures(BaseWebDriverTest test) private static long doVariantCount(BaseWebDriverTest test, Locator l, long winWidth, long winHeight) { - return Locator.findElements(test.getDriver(), l).stream().filter(WebElement::isDisplayed).map(WebElement::getRect).distinct().filter( - // This is designed to limit to just elements within the viewport: - rec -> rec.x > 0 & rec.x <= winWidth & rec.y > 0 & rec.y <= winHeight - ).count(); + return Locator.findElements(test.getDriver(), l).stream() + .filter(WebElement::isDisplayed) + .filter(el -> { + var rec = el.getRect(); + // This is designed to limit to just elements within the viewport: + return rec.x > 0 && rec.x <= winWidth && rec.y > 0 && rec.y <= winHeight; + }) + .map(el -> el.getAttribute("data-feature-id")) + .filter(id -> id != null && id.contains("vcf-")) + .distinct() + .count(); } } diff --git a/singlecell/resources/chunks/ApplyKnownClonotypicData.R b/singlecell/resources/chunks/ApplyKnownClonotypicData.R index 4967ef43a..fa4f36ce8 100644 --- a/singlecell/resources/chunks/ApplyKnownClonotypicData.R +++ b/singlecell/resources/chunks/ApplyKnownClonotypicData.R @@ -11,7 +11,7 @@ for (datasetId in names(seuratObjects)) { printName(datasetId) seuratObj <- readSeuratRDS(seuratObjects[[datasetId]]) - seuratObj <- ApplyKnownClonotypicData(seuratObj, antigenInclusionList = antigenInclusionList, antigenExclusionList = antigenExclusionList, minActivationFrequency = minActivationFrequency) + seuratObj <- ApplyKnownClonotypicData(seuratObj, antigenInclusionList = antigenInclusionList, antigenExclusionList = antigenExclusionList, minActivationFrequency = minActivationFrequency, minFractionCloneActivated = minFractionCloneActivated) saveData(seuratObj, datasetId) # Cleanup diff --git a/singlecell/resources/chunks/ClassifyTNKByExpression.R b/singlecell/resources/chunks/ClassifyTNKByExpression.R index e7a00f83c..6b1570fe8 100644 --- a/singlecell/resources/chunks/ClassifyTNKByExpression.R +++ b/singlecell/resources/chunks/ClassifyTNKByExpression.R @@ -11,7 +11,7 @@ for (datasetId in names(seuratObjects)) { printName(datasetId) seuratObj <- readSeuratRDS(seuratObjects[[datasetId]]) - if (!'HasCDR3Data' %in% names(seuratObj@meta.data)) { + if (.ShouldReapplyTcr(seuratObj)) { seuratObj <- Rdiscvr::DownloadAndAppendTcrClonotypes(seuratObj) } diff --git a/singlecell/resources/chunks/Functions.R b/singlecell/resources/chunks/Functions.R index 71b18e449..e37fb605e 100644 --- a/singlecell/resources/chunks/Functions.R +++ b/singlecell/resources/chunks/Functions.R @@ -191,3 +191,13 @@ if (Sys.getenv('SEURAT_MAX_THREADS') != '') { future::plan(strategy = fs, workers = mt) } + +.ShouldReapplyTcr <- function(seuratObj) { + return ( + !'HasCDR3Data' %in% names(seuratObj@meta.data) || + 'TRB_Segments' %in% names(seuratObj@meta.data) || + !'TRB_WithProductive' %in% names(seuratObj@meta.data) || + # This purpose of this is to catch a previous bug where every cell was tagged as (NP) + (sum(seuratObj@meta.data$TRB_WithProductive, pattern = '(NP)' == sum(!is.na(seuratObj@meta.data$TRB_WithProductive)))) + ) +} \ No newline at end of file diff --git a/singlecell/resources/chunks/IdentifyAndStoreActiveClonotypes.R b/singlecell/resources/chunks/IdentifyAndStoreActiveClonotypes.R index d6e8c2141..9f7d2e9be 100644 --- a/singlecell/resources/chunks/IdentifyAndStoreActiveClonotypes.R +++ b/singlecell/resources/chunks/IdentifyAndStoreActiveClonotypes.R @@ -11,7 +11,7 @@ for (datasetId in names(seuratObjects)) { printName(datasetId) seuratObj <- readSeuratRDS(seuratObjects[[datasetId]]) - if (! 'TRB_WithProductive' %in% names(seuratObj@meta.data)) { + if (.ShouldReapplyTcr(seuratObj)) { print('Re-running AppendTcr to add segment columns') seuratObj <- Rdiscvr::DownloadAndAppendTcrClonotypes(seuratObj, allowMissing = TRUE) } diff --git a/singlecell/resources/chunks/MergeSeurat.R b/singlecell/resources/chunks/MergeSeurat.R index 4fecab9cf..2c35f64f3 100644 --- a/singlecell/resources/chunks/MergeSeurat.R +++ b/singlecell/resources/chunks/MergeSeurat.R @@ -46,9 +46,9 @@ mergeBatchInMemory <- function(datasetIdToFilePath, saveFile) { saveRDS(CellMembrane::MergeSeuratObjs(toMerge, projectName = projectName, doGC = doDiet, errorOnBarcodeSuffix = errorOnBarcodeSuffix, expectedDefaultAssay = expectedDefaultAssay), file = saveFile) filesToDelete <<- c(filesToDelete, saveFile) - logger::log_info(paste0('mem used: ', R.utils::hsize(as.numeric(pryr::mem_used())))) + logger::log_info(paste0('mem used: ', R.utils::hsize(as.numeric(lobstr::mem_used())))) gc() - logger::log_info(paste0('after gc: ', R.utils::hsize(as.numeric(pryr::mem_used())))) + logger::log_info(paste0('after gc: ', R.utils::hsize(as.numeric(lobstr::mem_used())))) return(saveFile) } diff --git a/singlecell/resources/chunks/PredictTcellActivation.R b/singlecell/resources/chunks/PredictTcellActivation.R index 70e660433..ddfbea78a 100644 --- a/singlecell/resources/chunks/PredictTcellActivation.R +++ b/singlecell/resources/chunks/PredictTcellActivation.R @@ -11,7 +11,7 @@ for (datasetId in names(seuratObjects)) { printName(datasetId) seuratObj <- readSeuratRDS(seuratObjects[[datasetId]]) - if (! 'TRB_WithProductive' %in% names(seuratObj@meta.data)) { + if (.ShouldReapplyTcr(seuratObj)) { print('Re-running AppendTcr to add segment columns') seuratObj <- Rdiscvr::DownloadAndAppendTcrClonotypes(seuratObj, allowMissing = TRUE) } @@ -24,11 +24,6 @@ for (datasetId in names(seuratObjects)) { } } - if (! 'TRB_Segments' %in% names(seuratObj@meta.data)) { - print('Re-running AppendTcr to add segment columns') - seuratObj <- Rdiscvr::DownloadAndAppendTcrClonotypes(seuratObj, allowMissing = TRUE) - } - seuratObj <- RIRA::PredictTcellActivation(seuratObj) saveData(seuratObj, datasetId) diff --git a/singlecell/resources/chunks/SummarizeTCellActivation.R b/singlecell/resources/chunks/SummarizeTCellActivation.R index b03c351ee..ff62e17ea 100644 --- a/singlecell/resources/chunks/SummarizeTCellActivation.R +++ b/singlecell/resources/chunks/SummarizeTCellActivation.R @@ -11,7 +11,7 @@ for (datasetId in names(seuratObjects)) { printName(datasetId) seuratObj <- readSeuratRDS(seuratObjects[[datasetId]]) - if (!'HasCDR3Data' %in% names(seuratObj@meta.data)){ + if (.ShouldReapplyTcr(seuratObj)){ seuratObj <- seuratObj <- Rdiscvr::DownloadAndAppendTcrClonotypes(seuratObj, allowMissing = FALSE) } diff --git a/singlecell/resources/chunks/UpdateSeuratPrototype.R b/singlecell/resources/chunks/UpdateSeuratPrototype.R index 4d7f9e13e..ad6a7725a 100644 --- a/singlecell/resources/chunks/UpdateSeuratPrototype.R +++ b/singlecell/resources/chunks/UpdateSeuratPrototype.R @@ -21,16 +21,16 @@ for (datasetId in names(seuratObjects)) { seuratObj <- Rdiscvr::QueryAndApplyCdnaMetadata(seuratObj) } + if (applyTCR) { + seuratObj <- Rdiscvr::DownloadAndAppendTcrClonotypes(seuratObj, allowMissing = allowMissingTcr) + } + if (runRira) { seuratObj <- RIRA::Classify_ImmuneCells(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix) seuratObj <- RIRA::Classify_TNK(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix) seuratObj <- RIRA::Classify_Myeloid(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix) } - if (applyTCR) { - seuratObj <- Rdiscvr::DownloadAndAppendTcrClonotypes(seuratObj, allowMissing = allowMissingTcr) - } - if (runTNKClassification) { # ClassifyTNKByExpression will fail without this, so ignore allowMissingTcr if (!'HasCDR3Data' %in% names(seuratObj@meta.data)) { diff --git a/singlecell/resources/views/singleCellDataManagement.html b/singlecell/resources/views/singleCellDataManagement.html index 0c0393de9..d037300aa 100644 --- a/singlecell/resources/views/singleCellDataManagement.html +++ b/singlecell/resources/views/singleCellDataManagement.html @@ -120,6 +120,22 @@ 'query.sort': 'name' } ) + }, { + name: 'GEX Readsets Possibly Needing Archival', + url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, { + schemaName: 'sequenceanalysis', + queryName: 'sequence_readsets', + 'query.viewName': 'SRA Info', + 'query.totalForwardReads~isnonblank': null, + 'query.isArchived~eq': 0, + 'query.readdataWithoutSra~eq': 0, + 'query.outputFileTypes~contains': '10x Loupe', + 'query.application~contains': 'single', + 'query.status~isblank': null, + 'query.librarytype~contains': 'GEX', + 'query.sort': 'name' + } + ) }, { name: 'Analyses Using Old Readsets', url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, { diff --git a/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java b/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java index 7c3d2045f..6e8304383 100644 --- a/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java +++ b/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java @@ -283,7 +283,7 @@ public void complete(JobContext ctx, List inputs, List inputFiles, JobContext c List currentFiles; Set originalInputs = inputFiles.stream().map(SequenceOutputFile::getFile).collect(Collectors.toSet()); - Map inputFileMap = new HashMap<>(); if (_doProcessRawCounts) { currentFiles = processRawCounts(ctx, inputFiles, basename); @@ -417,7 +416,6 @@ else if (_doProcessRawCounts) distinctIds.add(datasetId); currentFiles.add(new SingleCellStep.SeuratObjectWrapper(datasetId, datasetId, so.getFile(), so)); - inputFileMap.put(so.getName(), so.getFile()); } } @@ -542,7 +540,7 @@ else if (step.createsSeuratObjects()) } finalMarkdown.chunks.add(new AbstractSingleCellPipelineStep.SessionInfoChunk()); - File finalMarkdownFile = new File(ctx.getOutputDir(), "final.rmd"); + File finalMarkdownFile = FileUtil.appendName(ctx.getOutputDir(), "final.rmd"); try (PrintWriter writer = PrintWriters.getPrintWriter(finalMarkdownFile)) { finalMarkdown.print(writer); @@ -553,7 +551,7 @@ else if (step.createsSeuratObjects()) } ctx.getJob().setStatus(PipelineJob.TaskStatus.running, "Creating Final HTML Report"); - File finalHtml = new File(ctx.getOutputDir(), "finalHtml.html"); + File finalHtml = FileUtil.appendName(ctx.getOutputDir(), "finalHtml.html"); List lines = new ArrayList<>(); lines.add("rmarkdown::render(output_file = '" + finalHtml.getName() + "', input = '" + finalMarkdownFile.getName() + "', intermediates_dir = '" + ctx.getWorkingDirectory() + "')"); AbstractSingleCellPipelineStep.executeR(ctx, AbstractCellMembraneStep.CONTAINER_NAME, "pandoc", lines, null, null, null); @@ -623,23 +621,10 @@ else if (inputFiles.size() == 1) //This indicates the job processed an input file, but did not create a new object (like running FindMarkers) boolean skipOutput = false; - if (inputFileMap.containsKey(output.getFile().getName())) + if (originalInputs.contains(output.getFile())) { - try - { - ctx.getLogger().debug("Comparing file context of output to determine if it matches input: " + output.getFile().getName()); - ctx.getLogger().debug("Original file: " + inputFileMap.get(output.getFile().getName())); - ctx.getLogger().debug("Pipeline output file: " + output.getFile()); - if (FileUtils.contentEquals(inputFileMap.get(output.getFile().getName()), output.getFile())) - { - ctx.getLogger().info("Sequence output is the same as an input, will not re-create output for seurat object: " + output.getFile().getPath()); - skipOutput = true; - } - } - catch (IOException e) - { - throw new PipelineJobException(e); - } + ctx.getLogger().info("Sequence output is the same as an input, will not re-create output for seurat object: " + output.getFile().getPath()); + skipOutput = true; } if (!skipOutput) @@ -692,7 +677,7 @@ private List processRawCounts(JobContext ctx List inputMatrices = new ArrayList<>(); inputFiles.forEach(x -> { String datasetName = ctx.getSequenceSupport().getCachedReadset(x.getReadset()).getName(); - File countsDir = new File(x.getFile().getParentFile(), "raw_feature_bc_matrix"); + File countsDir = FileUtil.appendName(x.getFile().getParentFile(), "raw_feature_bc_matrix"); if (!countsDir.exists()) { throw new IllegalArgumentException("Unable to find file: " + countsDir.getPath()); @@ -703,7 +688,7 @@ private List processRawCounts(JobContext ctx try { - File localCopy = new File(ctx.getOutputDir(), x.getRowid() + "_RawData"); + File localCopy = FileUtil.appendName(ctx.getOutputDir(), x.getRowid() + "_RawData"); if (localCopy.exists()) { ctx.getLogger().debug("Deleting directory: " + localCopy.getPath()); @@ -901,7 +886,7 @@ public void serializeTest() throws Exception r._stepOutputs.put(1, List.of(new SingleCellStep.SeuratObjectWrapper("datasetId", "datasetName", new File("seurat.rds"), so1))); File tmp = new File(System.getProperty("java.io.tmpdir")); - File f = FileUtil.getAbsoluteCaseSensitiveFile(new File(tmp, AbstractSingleCellHandler.Resumer.JSON_NAME)); + File f = FileUtil.getAbsoluteCaseSensitiveFile(FileUtil.appendName(tmp, AbstractSingleCellHandler.Resumer.JSON_NAME)); SequenceOutputFile so = new SequenceOutputFile(); so.setName("so1"); diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/ApplyKnownClonotypicData.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/ApplyKnownClonotypicData.java index ac631dde2..6a4b49820 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/ApplyKnownClonotypicData.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/ApplyKnownClonotypicData.java @@ -38,7 +38,12 @@ public Provider() put("minValue", 0); put("maxValue", 1.0); put("decimalPrecision", 4); - }}, 0) + }}, 0.0005), + SeuratToolParameter.create("minFractionCloneActivated", "Min Fraction Clone Activated", "If provided, only responses where the fraction of cells harboring that clone were activated will be included", "ldk-numberfield", new JSONObject(){{ + put("minValue", 0); + put("maxValue", 1.0); + put("decimalPrecision", 4); + }}, 0.05) ), List.of("/sequenceanalysis/field/TrimmingTextArea.js"), null); } diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CalculateGeneComponentScores.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CalculateGeneComponentScores.java index 81c72051a..8f4285ef3 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CalculateGeneComponentScores.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CalculateGeneComponentScores.java @@ -24,7 +24,7 @@ public Provider() super("CalculateGeneComponentScores", "Calculate Gene Module Scores", "RIRA", "This will generate UCell scores for a set of pre-defined gene modules", Arrays.asList( SeuratToolParameter.create("savedComponent", "Saved Component(s)", "This is the name of the saved component (from RIRA) to apply", "ldk-simplecombo", new JSONObject() {{ - put("storeValues", "Tcell_EffectorDifferentiation;TCR_EarlyStimulationComponent;CD4_Activation_Axis;PRF1_EffectorAxis"); + put("storeValues", "Tcell_EffectorDifferentiation;CD4_Activation_Axis"); put("multiSelect", true); put("allowBlank", false); put("joinReturnValue", true); diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/VireoHandler.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/VireoHandler.java index e7a6ae2f2..97db18625 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/VireoHandler.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/VireoHandler.java @@ -39,6 +39,7 @@ public class VireoHandler extends AbstractParameterizedOutputHandler { private static final String REF_VCF = "refVCF"; + private static final String SKIP_VCF_FOR_VIREO = "omitRefVcfForVireo"; public VireoHandler() { @@ -59,6 +60,10 @@ public VireoHandler() put("performGenomeFilter", false); put("doNotIncludeInTemplates", true); }}, null), + ToolParameterDescriptor.createExpDataParam(SKIP_VCF_FOR_VIREO, "Use Reference VCF for CellSnp-List Only", "If checked, the reference VCF will only be used for cellsnp-lite, not vireo", "checkbox", new JSONObject() + {{ + + }}, false), ToolParameterDescriptor.create("storeCellSnpVcf", "Store CellSnp-Lite VCF", "If checked, the cellsnp donor calls VCF will be stored as an output file", "checkbox", null, false) )); } @@ -280,8 +285,10 @@ public void processFilesRemote(List inputFiles, JobContext c } int vcfFile = ctx.getParams().optInt(REF_VCF, -1); + boolean skipVcfFileForVireo = ctx.getParams().optBoolean(SKIP_VCF_FOR_VIREO, false); + File refVcfSubset = null; - if (vcfFile > -1) + if (vcfFile > -1 && !skipVcfFileForVireo) { File vcf = ctx.getSequenceSupport().getCachedData(vcfFile); if (vcf == null || !vcf.exists())