From 7ea6224ed752678c869dae28eb4ae56c601be75f Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Thu, 27 Sep 2012 10:37:56 -0700 Subject: [PATCH] When collecting files for a geo submission, group on library id instead of the previous grouping on lane. --- htsworkflow/submission/geo.py | 8 ++++---- htsworkflow/templates/geo_fastqs.sparql | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/htsworkflow/submission/geo.py b/htsworkflow/submission/geo.py index 097bea1..ef8d945 100644 --- a/htsworkflow/submission/geo.py +++ b/htsworkflow/submission/geo.py @@ -131,10 +131,10 @@ class GEOSubmission(Submission): data = {} for k, v in row.items(): data[k] = v - lane = str(data['lane']) - lanes.setdefault(lane, []).append(data) + library = str(data['library']) + lanes.setdefault(library, []).append(data) result = [] - for lane, files in lanes.items(): + for library, files in lanes.items(): if len(files) > 2: errmsg = "Don't know what to do with more than 2 raw files" raise ValueError(errmsg) @@ -143,7 +143,7 @@ class GEOSubmission(Submission): elif len(files) == 1: is_paired = False elif len(files) == 0: - raise RuntimeError("Empty lane list discovered") + raise RuntimeError("Empty library list discovered") files = self._format_filename(files, is_paired) files = self._format_flowcell_type(files, is_paired) files = self._format_read_length(files, is_paired) diff --git a/htsworkflow/templates/geo_fastqs.sparql b/htsworkflow/templates/geo_fastqs.sparql index 428cef7..8f19c99 100644 --- a/htsworkflow/templates/geo_fastqs.sparql +++ b/htsworkflow/templates/geo_fastqs.sparql @@ -5,7 +5,7 @@ PREFIX ncbiTaxon: PREFIX geoSoft: PREFIX dc: -select distinct ?lane ?filename, ?md5sum, ?file_type ?file_type_label ?flowcell_id ?read_length ?flowcell_type ?image_software ?image_version ?basecall_software ?basecall_version ?sequencer_model +select distinct ?library ?filename, ?md5sum, ?file_type ?file_type_label ?flowcell_id ?read_length ?flowcell_type ?image_software ?image_version ?basecall_software ?basecall_version ?sequencer_model WHERE { <{{submission}}> ucscDaf:has_file ?file ; submissionOntology:library ?library ; -- 2.30.2