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Merged
merged 9 commits into from
Jun 20, 2014
Merged

Load processed data #129

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e5c4fd0
Add get_processed_params_tables util
Jun 20, 2014
b35662a
Merge branch 'master' of https://github.com/biocore/qiita into load_p…
Jun 20, 2014
a0274e5
Add load_processed_data command and tests
Jun 20, 2014
397bc5e
Fix processed_filepath table
Jun 20, 2014
a682de3
Fix handling of preprocessed_data_id
Jun 20, 2014
563dc68
Add second biom table to test
Jun 20, 2014
58b3d37
Add CLI support for passing processed_date
Jun 20, 2014
0624a85
Uppercase portions of SQL commands
Jun 20, 2014
067767b
Remove prep_x and sample_y from the SQL export
Jun 20, 2014
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Add second biom table to test
  • Loading branch information
Adam Robbins-Pianka committed Jun 20, 2014
commit 563dc68dd9a36d06aaab255098fd21b48c9ea776
21 changes: 15 additions & 6 deletions qiita_db/test/test_commands.py
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Original file line number Diff line number Diff line change
Expand Up @@ -154,12 +154,17 @@ class TestLoadProcessedDataFromCmd(TestCase):
def setUp(self):
fd, self.otu_table_fp = mkstemp(suffix='_otu_table.biom')
close(fd)
fd, self.otu_table_2_fp = mkstemp(suffix='_otu_table2.biom')
close(fd)

with open(self.otu_table_fp, "w") as f:
f.write("\n")
with open(self.otu_table_2_fp, "w") as f:
f.write("\n")

self.files_to_remove = []
self.files_to_remove.append(self.otu_table_fp)
self.files_to_remove.append(self.otu_table_2_fp)

self.db_test_processed_data_dir = join(get_db_files_base_dir(),
'processed_data')
Expand All @@ -170,8 +175,8 @@ def tearDown(self):
remove(fp)

def test_load_processed_data_from_cmd(self):
filepaths = [self.otu_table_fp]
filepath_types = ['biom']
filepaths = [self.otu_table_fp, self.otu_table_2_fp]
filepath_types = ['biom', 'biom']

initial_processed_data_count = get_count('qiita.processed_data')
initial_processed_fp_count = get_count('qiita.processed_filepath')
Expand All @@ -183,19 +188,23 @@ def test_load_processed_data_from_cmd(self):
self.files_to_remove.append(
join(self.db_test_processed_data_dir,
'%d_%s' % (processed_data_id, basename(self.otu_table_fp))))
self.files_to_remove.append(
join(self.db_test_processed_data_dir,
'%d_%s' % (processed_data_id,
basename(self.otu_table_2_fp))))

self.assertTrue(check_count('qiita.processed_data',
initial_processed_data_count + 1))
self.assertTrue(check_count('qiita.processed_filepath',
initial_processed_fp_count + 1))
initial_processed_fp_count + 2))
self.assertTrue(check_count('qiita.filepath',
initial_fp_count + 1))
initial_fp_count + 2))

# Ensure that the ValueError is raised when a filepath_type is not
# provided for each and every filepath
with self.assertRaises(ValueError):
load_processed_data_cmd(filepaths, [], 'processed_params_uclust',
1, 1, None)
load_processed_data_cmd(filepaths, filepath_types[:-1],
'processed_params_uclust', 1, 1, None)


CONFIG_1 = """[required]
Expand Down