These resources are for those under development or in a testing phase. They can be turned off at runtime to prohibit risky operations.
A collection of reports useful when verifying that data in the SeqWare meta db is correct.
GET /x/report/reversehierarchy/{file-swa}
Produces a text representation of a reverse hierarchy tree starting at a file (indicated by the provided file-swa). The tree includes all the processing nodes that led to the creation of the file as well as all the links (sequencer_run, lane, ius, sample, experiment, study) to those processing nodes.
This report is useful for answering the question: What steps led to the creation of this file?
Status: 200 OKFILE SWA: 182467 FILE NAME: SWID_9858_PCSI_0106_Ly_R_PE_190_WG_110916_L004_R1_001.fastq.gz.annotated.bam Processing Children: 1
PicardAddReadGroups SWA: 182453
PicardSortNovoalign SWA: 182409
PicardConvertNovoalign SWA: 182388
Novoalign SWA: 181997
WORKFLOW GenomicAlignmentNovoalign 0.10.1 SWA: 23341
BCLToFastq SWA: 178878
LINK IUS SWA: 9858
Bustard SWA: 178810
LINK Lane SWA: 9857
WORKFLOW CASAVA-RTA 1.8.2-1 SWA: 37743
PicardSortNovoalign SWA: 182432
PicardConvertNovoalign SWA: 182388
Novoalign SWA: 181997
WORKFLOW GenomicAlignmentNovoalign 0.10.1 SWA: 23341
BCLToFastq SWA: 178878
LINK IUS SWA: 9858
Bustard SWA: 178810
LINK Lane SWA: 9857
WORKFLOW CASAVA-RTA 1.8.2-1 SWA: 37743GET /x/report/filelinkreport/{file-swa}
Every file must be associated with at least one processing node and this node in turn must be linked (either directly or through a parent) to one of the following: sequencer_run, lane, ius, sample, experiment or study.
This report includes all files included in the given list of file-swas (file SeqWare accesssions) and notes the number of links that exist for that file. An orphaned files is inidicated when the total number of links for the file is zero (0). Most files will have 1 or 2 links. Files with more than 2 links are not necessarily incorrectly linked, but are worthy of investigation to ensure they are correctness.
You can provide a list of file-swas to report on.
182467,186014,25877If no file-swa is provided the report will be generated for all the files in the seqware meta db. A report that includes all the files will take a long time to produce.
Status: 200 OK
total_links #SRL SeqRunSWAs #LL LaneSWAs #IL IusSWAs #SaL SampleSWAs #EL ExpSWAs #StL StudySWAs file_SWA file_name
1 0 0 1 15687 0 0 0 25877 s_7_2_sequence.txt
2 0 1 24648 1 15687 0 0 0 186014 s_5_1_sequence.txt