updating the readscount script

I need to check wether I sould use the epplogger or the default logging, but that's how it's done in the others epps from maya and johannes, so I guess that's oay
We are actively discussing this point.
Currently, there are two fields for the sample status at sample level :
"Status (Manual)" and "Status (Auto)"

Status manual will be left for the lab people to fill if they assume it's
done. Status auto will keep displaying In Progress, because that is what
the rules end up to. This behavior is related to the following usage case :

You have 200 samples that you just sequenced. 100 of them have enough
reads, and the scripts marks them "Finished". 50 of them have almost enough
reads, so the lab person marks them "Finished" too. the last 50 will be
resequenced. The next time you click the button, all the samples will be
updated, so if you changed the "Status (Auto)", it would be overwritten.

With the current implementation, what the lab person wrote keeps written,
and we still get to know the status for every sample.

Is that okay ?


On Tue, Oct 7, 2014 at 9:54 AM, senthil10 <notifications@github.com> wrote:

> In scripts/readscount.py:
>
> >  SUMMARY = {'356' : 'Project Summary 1.3'}
> >  SEQUENCING = {'38' : 'Illumina Sequencing (Illumina SBS) 4.0','46' : 'MiSeq Run (MiSeq) 4.0'}
> >  def main(lims, args, logger):
> > -   p = Process(lims,id = args.pid)
> > -   for output_artifact in p.all_outputs():
> > -       if output_artifact.type=='Analyte' and len(output_artifact.samples)==1:
> > -           sample=output_artifact.samples[0]
> > -           sample.udf['Total Reads (M)']=sumreads(sample)
> > -           logging.info("Total reads is {0} for sample {1}".format(sample.udf['Total Reads (M)'],sample.name))
> > +    p = Process(lims,id = args.pid)
> > +    for output_artifact in p.all_outputs():
> > +        if output_artifact.type=='Analyte' and len(output_artifact.samples)==1:
> > +            sample=output_artifact.samples[0]
> > +            sample.udf['Total Reads (M)']=sumreads(sample)
> > +            logging.info("Total reads is {0} for sample {1}".format(sample.udf['Total Reads (M)'],sample.name))
> > +            try:
> > +                if sample.udf['Reads min'] > sample.udf['Total Reads (M)']:
> > +                    sample.udf['Status (Auto)']="In Progress"
>
> @Galithil <https://github.com/Galithil> : Just a clarification, In some
> cases the "total reads" for a sample might be low than "Minimum reads" even
> after all the sequencing attempts. So for those cases, will it be modified
> manually in LIMS by application specialist ?
>
> —
> Reply to this email directly or view it on GitHub
> <https://github.com/SciLifeLab/genologics/pull/70/files#r18505175>.
>