def test_CreateFromSeqRecord(self):
with GeneSequenceApp.app.test_request_context("/"):
GeneSequenceApp.app.preprocess_request()
with open(__location__ + "/testfiles/422900759.pickle", 'rb') as f:
record = pickle.load(f)
GenBankEntry.create_from_seqrecord(record, "")
entry = Sequence.create_from_seqrecord(record)
self.assertEqual(entry.Sequence, str(record.seq))
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 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 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
def render_genbank_view():
entries = GenBankEntry.all()
get_module_logger().info("Rendering table for {} GenBank entries.".format(len(entries)))
return render_template("genbank.view.template.html", title = "GenBank Interface", genbank_entries = entries)
def setUp(self):
self.db_fd, GeneSequenceApp.app.config['DATABASE'] = tempfile.mkstemp()
self.app = GeneSequenceApp.app.test_client()
GeneSequenceApp.db.create_if_not_exists(True)
GenBankEntry.fill_db_with_test_data()
self.fill_db_with_test_data()
