def render_sequence_add(): form_to_validate = SequenceEntryForm(GenBankEntry.all()) if form_to_validate.validate_on_submit(): try: Sequence.add(form.genbank_id.data, form.sequence.data) except: return render_template("sequence.view.template.html", title = "Sequences") else: return render_template("sequence.form.template.html", title = "Add new sequence", form=form_to_validate)
def render_sequences_view(genbank_id): if GenBankEntry.exists(genbank_id): sequences = Sequence.get_for_genbank_id(genbank_id) return render_template( "sequence.view.template.html", title = "Sequences", genbank_id=genbank_id, sequences=sequences) else: return render_template( "sequence.view.template.html", title = "Sequences", genbank_id=genbank_id, sequences=sequences)
def try_add_from_genbank(id, silk_type): get_module_logger().info("Calling entrez for ID {}".format(id)) fasta = entrez_get_fasta_seqrecord(id) success = False if fasta is not None: get_module_logger().info("Data for ID {} found. Trying to add to database.".format(id)) try: get_module_logger().info("Creating GenBankEntry.") GenBankEntry.create_from_seqrecord(fasta, silk_type) get_module_logger().info("Creating Sequence.") Sequence.create_from_seqrecord(fasta) success = True except: raise else: get_module_logger().info("Data for ID {} not found.") return success