--- markdown: advanced toc_includes_sections: true is_dynamic: true title: Metadata - Experimental Resources --- Overview ---------- These resources are for those under development or in a testing phase. They can be turned off at runtime to prohibit risky operations. ## Validation Report API A collection of reports useful when verifying that data in the SeqWare meta db is correct. ### File reverse hierarchy display 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? #### Response <%= headers 200 %>

FILE 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: 37743
### File link report GET /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. #### Input You can provide a list of file-swas to report on.

182467,186014,25877
If 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. #### Response <%= headers 200 %>
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