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
