Exemple #1
0
    def edit(self, id):
        """
        Edits an assay.
        """
        assay_q = Session.query(Assay)
        assay = assay_q.filter_by(id=id).first()
        dye_field = fl.assay_dye_field(assay.dye)
        quencher_field = fl.assay_quencher_field(assay.quencher)
        secondary_structure = fl.tertiary_field(assay.secondary_structure)

        if assay is None:
            abort(404)
        else:
            c.assay = assay

        owner_field = fl.person_field(c.assay.owner_id)
        c.form = h.LiteralFormSelectPatch(
            value={
                "dye": dye_field["value"],
                "quencher": quencher_field["value"],
                "owner_id": unicode(owner_field["value"]),
                "secondary_structure": secondary_structure["value"],
            },
            option={
                "chromosome": [("", "--")] + [(chr, chr) for chr in Chromosome.chrom_list],
                "owner_id": owner_field["options"],
                "dye": dye_field["options"],
                "quencher": quencher_field["options"],
                "secondary_structure": secondary_structure["options"],
            },
        )
        values = {
            "name": assay.name,
            "gene": assay.gene,
            "owner_id": unicode(assay.owner_id),
            "primer_fwd": assay.primer_fwd,
            "primer_rev": assay.primer_rev,
            "chromosome": assay.chromosome,
            "probe_pos": assay.probe_pos,
            "probe_seq": assay.probe_seq,
            "dye": assay.dye,
            "quencher": assay.quencher,
            "secondary_structure": secondary_structure["value"],
            "amplicon_width": assay.amplicon_width,
            "snp_rsid": assay.snp_rsid,
            "notes": assay.notes,
            "reference_source": assay.reference_source,
            "optimal_anneal_temp": assay.optimal_anneal_temp,
        }

        if assay.assay_type == Assay.TYPE_LOCATION:
            c.selectedTab = 1
        elif assay.assay_type == Assay.TYPE_SNP:
            c.selectedTab = 2
        else:
            c.selectedTab = 0
        return htmlfill.render(render("/assay/edit.html"), values)
Exemple #2
0
    def new(self):
        dye_field = fl.assay_dye_field()
        quencher_field = fl.assay_quencher_field()
        owner_field = fl.person_field()
        secondary_structure = fl.tertiary_field()
        c.form = h.LiteralFormSelectPatch(
            value={
                "dye": dye_field["value"],
                "quencher": quencher_field["value"],
                "owner_id": owner_field["value"],
                "secondary_structure": secondary_structure["value"],
            },
            option={
                "chromosome": [("", "--")] + [(chr, chr) for chr in Chromosome.chrom_list],
                "owner_id": [("", "--")] + owner_field["options"],
                "dye": dye_field["options"],
                "quencher": quencher_field["options"],
                "secondary_structure": secondary_structure["options"],
            },
        )

        return render("/assay/new.html")