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Merged
merged 7 commits into from
Nov 18, 2015
Merged

Fixing more tests #1532

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bdad3e0
Fixing software
josenavas Nov 12, 2015
e066080
Fixing portal
josenavas Nov 12, 2015
7938843
Fixing test_sql.py
josenavas Nov 12, 2015
89c9248
Fixing utils
josenavas Nov 12, 2015
73596ea
fixing style
josenavas Nov 12, 2015
a6ee948
Merge branch 'artifact' of https://github.com/biocore/qiita into arti…
josenavas Nov 18, 2015
8f02f44
Addressing comments
josenavas Nov 18, 2015
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Fixing software
  • Loading branch information
@josenavas
josenavas committed Nov 12, 2015
commit bdad3e0dee146efb7a3e7a5617294c0e000cd7ac
7 changes: 4 additions & 3 deletions qiita_db/software.py
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Original file line number Diff line number Diff line change
Expand Up @@ -282,15 +282,16 @@ def commands(self):

Returns
-------
list of int
The command identifiers
list of qiita_db.software.Command
The commands attached to this software package
"""
with qdb.sql_connection.TRN:
sql = """SELECT command_id
FROM qiita.software_command
WHERE software_id = %s"""
qdb.sql_connection.TRN.add(sql, [self.id])
return qdb.sql_connection.TRN.execute_fetchflatten()
return [Command(cid)
for cid in qdb.sql_connection.TRN.execute_fetchflatten()]

@property
def publications(self):
Expand Down
93 changes: 52 additions & 41 deletions qiita_db/test/test_software.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,27 +9,28 @@
from unittest import TestCase, main

from qiita_core.util import qiita_test_checker
from qiita_db.software import Command, Software, Parameters
from qiita_db.exceptions import QiitaDBDuplicateError
import qiita_db as qdb


@qiita_test_checker()
class CommandTests(TestCase):
def setUp(self):
self.software = Software(1)
self.software = qdb.software.Software(1)

def test_exists(self):
self.assertFalse(Command.exists(self.software, "donotexists"))
self.assertTrue(Command.exists(self.software, "split_libraries.py"))
self.assertFalse(qdb.software.Command.exists(
self.software, "donotexists"))
self.assertTrue(qdb.software.Command.exists(
self.software, "split_libraries.py"))

def test_create_error_duplicate(self):
with self.assertRaises(QiitaDBDuplicateError):
Command.create(
with self.assertRaises(qdb.exceptions.QiitaDBDuplicateError):
qdb.software.Command.create(
self.software, "Test Command", "This is a command for testing",
"split_libraries.py", "preprocessed_spectra_params")

def test_create(self):
obs = Command.create(
obs = qdb.software.Command.create(
self.software, "Test Command", "This is a command for testing",
"test_command.py", "preprocessed_spectra_params")
self.assertEqual(obs.name, "Test Command")
Expand All @@ -38,33 +39,35 @@ def test_create(self):
self.assertEqual(obs.parameters_table, "preprocessed_spectra_params")

def test_name(self):
self.assertEqual(Command(1).name, "Split libraries FASTQ")
self.assertEqual(Command(2).name, "Split libraries")
self.assertEqual(qdb.software.Command(1).name, "Split libraries FASTQ")
self.assertEqual(qdb.software.Command(2).name, "Split libraries")

def test_description(self):
self.assertEqual(
Command(1).description,
qdb.software.Command(1).description,
"Demultiplexes and applies quality control to FASTQ data")
self.assertEqual(
Command(2).description,
qdb.software.Command(2).description,
"Demultiplexes and applies quality control to FASTA data")

def test_cli(self):
self.assertEqual(Command(1).cli, "split_libraries_fastq.py")
self.assertEqual(Command(2).cli, "split_libraries.py")
self.assertEqual(qdb.software.Command(1).cli,
"split_libraries_fastq.py")
self.assertEqual(qdb.software.Command(2).cli, "split_libraries.py")

def test_parameters_table(self):
self.assertEqual(Command(1).parameters_table,
self.assertEqual(qdb.software.Command(1).parameters_table,
"preprocessed_sequence_illumina_params")
self.assertEqual(Command(2).parameters_table,
self.assertEqual(qdb.software.Command(2).parameters_table,
"preprocessed_sequence_454_params")


@qiita_test_checker()
class SoftwareTests(TestCase):
def test_create(self):
obs = Software.create("New Software", "0.1.0",
"This is adding a new software for testing")
obs = qdb.software.Software.create(
"New Software", "0.1.0",
"This is adding a new software for testing")
self.assertEqual(obs.name, "New Software")
self.assertEqual(obs.version, "0.1.0")
self.assertEqual(obs.description,
Expand All @@ -74,36 +77,38 @@ def test_create(self):

def test_create_with_publications(self):
exp_publications = [['10.1000/nmeth.f.101', '12345678']]
obs = Software.create("Published Software", "1.0.0",
"Another testing software",
publications=exp_publications)
obs = qdb.software.Software.create(
"Published Software", "1.0.0", "Another testing software",
publications=exp_publications)
self.assertEqual(obs.name, "Published Software")
self.assertEqual(obs.version, "1.0.0")
self.assertEqual(obs.description, "Another testing software")
self.assertEqual(obs.commands, [])
self.assertEqual(obs.publications, exp_publications)

def test_name(self):
self.assertEqual(Software(1).name, "QIIME")
self.assertEqual(qdb.software.Software(1).name, "QIIME")

def test_version(self):
self.assertEqual(Software(1).version, "1.9.1")
self.assertEqual(qdb.software.Software(1).version, "1.9.1")

def test_description(self):
exp = ("Quantitative Insights Into Microbial Ecology (QIIME) is an "
"open-source bioinformatics pipeline for performing microbiome "
"analysis from raw DNA sequencing data")
self.assertEqual(Software(1).description, exp)
self.assertEqual(qdb.software.Software(1).description, exp)

def test_commands(self):
self.assertEqual(Software(1).commands, [1, 2, 3])
exp = [qdb.software.Command(1), qdb.software.Command(2),
qdb.software.Command(3)]
self.assertEqual(qdb.software.Software(1).commands, exp)

def test_publications(self):
self.assertEqual(Software(1).publications,
self.assertEqual(qdb.software.Software(1).publications,
[['10.1038/nmeth.f.303', '20383131']])

def test_add_publications(self):
tester = Software(1)
tester = qdb.software.Software(1)
self.assertEqual(tester.publications,
[['10.1038/nmeth.f.303', '20383131']])
tester.add_publications([['10.1000/nmeth.f.101', '12345678']])
Expand All @@ -115,22 +120,22 @@ def test_add_publications(self):
@qiita_test_checker()
class ParametersTests(TestCase):
def test_init(self):
obs = Parameters(1, Command(1))
obs = qdb.software.Parameters(1, qdb.software.Command(1))
self.assertEqual(obs.id, 1)
self.assertEqual(obs._table, "preprocessed_sequence_illumina_params")
self.assertEqual(obs.command, Command(1))
self.assertEqual(obs.command, qdb.software.Command(1))

def test_exists(self):
cmd = Command(1)
obs = Parameters.exists(
cmd = qdb.software.Command(1)
obs = qdb.software.Parameters.exists(
cmd, max_bad_run_length=3, min_per_read_length_fraction=0.75,
sequence_max_n=0, rev_comp_barcode=False,
rev_comp_mapping_barcodes=False, rev_comp=False,
phred_quality_threshold=3, barcode_type="golay_12",
max_barcode_errors=1.5)
self.assertTrue(obs)

obs = Parameters.exists(
obs = qdb.software.Parameters.exists(
cmd, max_bad_run_length=3, min_per_read_length_fraction=0.75,
sequence_max_n=0, rev_comp_barcode=False,
rev_comp_mapping_barcodes=False, rev_comp=False,
Expand All @@ -139,8 +144,8 @@ def test_exists(self):
self.assertFalse(obs)

def test_create(self):
cmd = Command(1)
obs = Parameters.create(
cmd = qdb.software.Command(1)
obs = qdb.software.Parameters.create(
"test_create", cmd, max_bad_run_length=3,
min_per_read_length_fraction=0.75, sequence_max_n=0,
rev_comp_barcode=False, rev_comp_mapping_barcodes=False,
Expand All @@ -158,31 +163,37 @@ def test_create(self):
self.assertEqual(obs.command, cmd)

def test_iter(self):
cmd = Command(1)
obs = list(Parameters.iter(cmd))
exp = [Parameters(i, cmd) for i in range(1, 8)]
cmd = qdb.software.Command(1)
obs = list(qdb.software.Parameters.iter(cmd))
exp = [qdb.software.Parameters(i, cmd) for i in range(1, 8)]
self.assertEqual(obs, exp)

def test_name(self):
self.assertEqual(Parameters(1, Command(1)).name, "Defaults")
self.assertEqual(
qdb.software.Parameters(1, qdb.software.Command(1)).name,
"Defaults")

def test_values(self):
exp = {'min_per_read_length_fraction': 0.75,
'max_barcode_errors': 1.5, 'max_bad_run_length': 3,
'rev_comp': False, 'phred_quality_threshold': 3,
'rev_comp_barcode': False, 'sequence_max_n': 0,
'barcode_type': 'golay_12', 'rev_comp_mapping_barcodes': False}
self.assertEqual(Parameters(1, Command(1)).values, exp)
self.assertEqual(
qdb.software.Parameters(1, qdb.software.Command(1)).values, exp)

def test_to_str(self):
exp = ("--barcode_type 'golay_12' --max_bad_run_length '3' "
"--max_barcode_errors '1.5' "
"--min_per_read_length_fraction '0.75' "
"--phred_quality_threshold '3' --sequence_max_n '0'")
self.assertEqual(Parameters(1, Command(1)).to_str(), exp)
self.assertEqual(
qdb.software.Parameters(1, qdb.software.Command(1)).to_str(), exp)

def test_command(self):
self.assertEqual(Parameters(1, Command(1)).command, Command(1))
self.assertEqual(
qdb.software.Parameters(1, qdb.software.Command(1)).command,
qdb.software.Command(1))

if __name__ == '__main__':
main()