From 72daaea8379a3af4afca5bb63d389435ec4017d8 Mon Sep 17 00:00:00 2001 From: Scott Christley Date: Mon, 14 Sep 2026 14:20:01 -0500 Subject: [PATCH 1/4] update igblast --- app/scripts/config/AnalysisConfig.js | 4 ++-- app/vdjserver-schema | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/app/scripts/config/AnalysisConfig.js b/app/scripts/config/AnalysisConfig.js index 4585ec3..db4374b 100644 --- a/app/scripts/config/AnalysisConfig.js +++ b/app/scripts/config/AnalysisConfig.js @@ -115,9 +115,9 @@ var AnalysisConfig = { "igblast": { "vdjserver:name":"IgBlast", "activity": { - "igblast-ls6-0.10": { + "igblast-ls6-0.11": { "vdjserver:app:name": "igblast-ls6", - "vdjserver:app:version": "0.10", + "vdjserver:app:version": "0.11", "vdjserver:app:default": true } }, diff --git a/app/vdjserver-schema b/app/vdjserver-schema index 5459c75..8bbce5f 160000 --- a/app/vdjserver-schema +++ b/app/vdjserver-schema @@ -1 +1 @@ -Subproject commit 5459c75e4498ffa35c4f227a6f7fceabc0774340 +Subproject commit 8bbce5f7fb0f79eca744ea9c47bd5c2298cf1988 From 89f0b1e18451ce2c511d78d679c3f3bf9b54201a Mon Sep 17 00:00:00 2001 From: Scott Christley Date: Fri, 18 Sep 2026 17:05:51 -0500 Subject: [PATCH 2/4] mapping for single FASTQ files --- app/scripts/config/AnalysisConfig.js | 2 +- app/scripts/models/AnalysisDocument.js | 22 ++++++++++++++++++++-- 2 files changed, 21 insertions(+), 3 deletions(-) diff --git a/app/scripts/config/AnalysisConfig.js b/app/scripts/config/AnalysisConfig.js index db4374b..54525ff 100644 --- a/app/scripts/config/AnalysisConfig.js +++ b/app/scripts/config/AnalysisConfig.js @@ -91,7 +91,7 @@ var AnalysisConfig = { "vdjserver:activity:uses": { "JobFiles": [ 'archive' ], "SequenceFASTQ": [ 'sequence_reads', 'sequence_single_read', 'sequence_quality' ], - "SequenceFASTA": [ 'sequence_reads', 'sequence_single_read' ], + "SequenceFASTA": [ 'sequence_reads' ], "SequenceQualityFiles": [ 'sequence_quality'], "SequenceForwardPairedFiles": ['sequence_forward_paired_reads'], "SequenceReversePairedFiles": ['sequence_reverse_paired_reads'] , diff --git a/app/scripts/models/AnalysisDocument.js b/app/scripts/models/AnalysisDocument.js index 835bcfe..1274afe 100644 --- a/app/scripts/models/AnalysisDocument.js +++ b/app/scripts/models/AnalysisDocument.js @@ -164,6 +164,25 @@ AnalysisDocument.prototype.expand_airr_types = async function(project_metadata) let use_type = app['vdjserver:activity:uses'][input_name][ut]; console.log(input_name, use_type); switch(use_type) { + case 'sequence_single_read': + for (let i in rep['sample']) { + let seqfiles = rep['sample'][i]['sequencing_files']; + //console.log(seqfiles); + if (seqfiles['filename'] && seqfiles['file_type'] == 'fastq') { + found = true; + new_entity_id.push('vdjserver:project_file:' + seqfiles['filename']); + let extra = {}; + extra[input_name] = seqfiles['filename']; + extra['airr:Repertoire'] = rep['repertoire_id'] + new_uses_id.push('vdjserver:app:inputs:' + activity_id + ':' + seqfiles['filename']); + if (project_file_map[seqfiles['filename']]) { + extra['vdjserver:uuid'] = project_file_map[seqfiles['filename']]; + } + extras.push(extra); + } + } + break; + case 'sequence_forward_paired_reads': // identifiers use the forward read file for (let i in rep['sample']) { @@ -225,7 +244,7 @@ AnalysisDocument.prototype.expand_airr_types = async function(project_metadata) case 'sequence': for (let i in rep['sample']) { let seqfiles = rep['sample'][i]['sequencing_files']; - console.log(seqfiles); + //console.log(seqfiles); if (seqfiles['filename'] && seqfiles['file_type'] == 'fasta') { found = true; new_entity_id.push('vdjserver:project_file:' + seqfiles['filename']); @@ -241,7 +260,6 @@ AnalysisDocument.prototype.expand_airr_types = async function(project_metadata) } break; - case 'sequence_single_read': case 'sequence_quality': case 'sequence_reads': case 'archive': From 0f893c14a547b0d890bd1615117730c8e88391f4 Mon Sep 17 00:00:00 2001 From: Scott Christley Date: Sun, 20 Sep 2026 21:00:57 -0500 Subject: [PATCH 3/4] new app versions --- app/scripts/config/AnalysisConfig.js | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/app/scripts/config/AnalysisConfig.js b/app/scripts/config/AnalysisConfig.js index 54525ff..5891df3 100644 --- a/app/scripts/config/AnalysisConfig.js +++ b/app/scripts/config/AnalysisConfig.js @@ -169,9 +169,9 @@ var AnalysisConfig = { "repcalc": { "vdjserver:name":"RepCalc", "activity": { - "repcalc2-ls6-0.9": { + "repcalc2-ls6-0.10": { "vdjserver:app:name": "repcalc2-ls6", - "vdjserver:app:version": "0.9", + "vdjserver:app:version": "0.10", "vdjserver:app:default": true } }, @@ -204,9 +204,9 @@ var AnalysisConfig = { "cellranger": { "vdjserver:name":"Cell Ranger", "activity": { - "cellranger-ls6-10.0.0": { + "cellranger-ls6-0.2": { "vdjserver:app:name": "cellranger-ls6", - "vdjserver:app:version": "10.0.0", + "vdjserver:app:version": "0.2", "vdjserver:app:default": true } }, From 307725b50b6e8f08d994c727f66c2ccae27122cf Mon Sep 17 00:00:00 2001 From: Scott Christley Date: Sun, 20 Sep 2026 21:02:06 -0500 Subject: [PATCH 4/4] new version --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 5df3507..0c7fcfd 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "vdjserver-api", - "version": "2.13.1", + "version": "2.14.0", "description": "VDJServer Web Services", "author": [ {