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test_artifact.py
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# -----------------------------------------------------------------------------
# Copyright (c) 2014--, The Qiita Development Team.
#
# Distributed under the terms of the BSD 3-clause License.
#
# The full license is in the file LICENSE, distributed with this software.
# -----------------------------------------------------------------------------
from unittest import TestCase, main
from tempfile import mkstemp, mkdtemp
from datetime import datetime
from os import close, remove
from os.path import exists, join, basename, dirname, abspath
from shutil import copyfile
from functools import partial
from json import dumps
import pandas as pd
import networkx as nx
from biom import example_table as et
from biom.util import biom_open
from qiita_core.util import qiita_test_checker
from qiita_core.testing import wait_for_processing_job
import qiita_db as qdb
from qiita_ware.private_plugin import _delete_analysis_artifacts
class ArtifactTestsReadOnly(TestCase):
def test_iter(self):
obs = list(qdb.artifact.Artifact.iter_by_visibility('public'))
self.assertEqual(obs, [])
obs = list(qdb.artifact.Artifact.iter_by_visibility('private'))
exp = [qdb.artifact.Artifact(1),
qdb.artifact.Artifact(2),
qdb.artifact.Artifact(3),
qdb.artifact.Artifact(4),
qdb.artifact.Artifact(5),
qdb.artifact.Artifact(6),
qdb.artifact.Artifact(7)]
self.assertEqual(obs, exp)
exp.extend([qdb.artifact.Artifact(8), qdb.artifact.Artifact(9)])
self.assertEqual(list(qdb.artifact.Artifact.iter()), exp)
def test_create_type(self):
obs = qdb.artifact.Artifact.types()
exp = [['BIOM', 'BIOM table', False, False, True],
['Demultiplexed', 'Demultiplexed and QC sequences', True, True,
False],
['FASTA', None, False, False, False],
['FASTA_Sanger', None, False, False, False],
['FASTQ', None, False, False, True],
['SFF', None, False, False, False],
['per_sample_FASTQ', None, True, False, True],
['beta_div_plots', 'Qiime 1 beta diversity results', False,
False, False],
['rarefaction_curves', 'Rarefaction curves', False, False,
False],
['taxa_summary', 'Taxa summary plots', False, False, False]]
self.assertCountEqual(obs, exp)
qdb.artifact.Artifact.create_type(
"NewType", "NewTypeDesc", False, False, False,
[("log", False), ("raw_forward_seqs", True)])
obs = qdb.artifact.Artifact.types()
exp = [['BIOM', 'BIOM table', False, False, True],
['Demultiplexed', 'Demultiplexed and QC sequences', True, True,
False],
['FASTA', None, False, False, False],
['FASTA_Sanger', None, False, False, False],
['FASTQ', None, False, False, True],
['SFF', None, False, False, False],
['per_sample_FASTQ', None, True, False, True],
['beta_div_plots', 'Qiime 1 beta diversity results', False,
False, False],
['rarefaction_curves', 'Rarefaction curves', False, False,
False],
['taxa_summary', 'Taxa summary plots', False, False, False],
['NewType', 'NewTypeDesc', False, False, False]]
self.assertCountEqual(obs, exp)
self.assertTrue(exists(qdb.util.get_mountpoint('NewType')[0][1]))
with self.assertRaises(qdb.exceptions.QiitaDBDuplicateError):
qdb.artifact.Artifact.create_type(
"NewType", "NewTypeDesc", False, False, False,
[("log", False), ("raw_forward_seqs", True)])
def test_name(self):
self.assertEqual(qdb.artifact.Artifact(1).name, "Raw data 1")
self.assertEqual(qdb.artifact.Artifact(2).name, "Demultiplexed 1")
self.assertEqual(qdb.artifact.Artifact(3).name, "Demultiplexed 2")
self.assertEqual(qdb.artifact.Artifact(4).name, "BIOM")
def test_timestamp(self):
self.assertEqual(qdb.artifact.Artifact(1).timestamp,
datetime(2012, 10, 1, 9, 30, 27))
self.assertEqual(qdb.artifact.Artifact(2).timestamp,
datetime(2012, 10, 1, 10, 30, 27))
self.assertEqual(qdb.artifact.Artifact(3).timestamp,
datetime(2012, 10, 1, 11, 30, 27))
self.assertEqual(qdb.artifact.Artifact(4).timestamp,
datetime(2012, 10, 2, 17, 30, 00))
def test_processing_parameters(self):
self.assertIsNone(qdb.artifact.Artifact(1).processing_parameters)
obs = qdb.artifact.Artifact(2).processing_parameters
exp = qdb.software.Parameters.load(
qdb.software.Command(1),
values_dict={'max_barcode_errors': '1.5', 'sequence_max_n': '0',
'max_bad_run_length': '3', 'rev_comp': 'False',
'phred_quality_threshold': '3', 'input_data': '1',
'rev_comp_barcode': 'False',
'rev_comp_mapping_barcodes': 'False',
'min_per_read_length_fraction': '0.75',
'barcode_type': 'golay_12',
'phred_offset': 'auto'})
self.assertEqual(obs, exp)
obs = qdb.artifact.Artifact(3).processing_parameters
exp = qdb.software.Parameters.load(
qdb.software.Command(1),
values_dict={'max_barcode_errors': '1.5', 'sequence_max_n': '0',
'max_bad_run_length': '3', 'rev_comp': 'False',
'phred_quality_threshold': '3', 'input_data': '1',
'rev_comp_barcode': 'False',
'rev_comp_mapping_barcodes': 'True',
'min_per_read_length_fraction': '0.75',
'barcode_type': 'golay_12',
'phred_offset': 'auto'})
self.assertEqual(obs, exp)
def test_visibility(self):
self.assertEqual(qdb.artifact.Artifact(1).visibility, "private")
def test_artifact_type(self):
self.assertEqual(qdb.artifact.Artifact(1).artifact_type, "FASTQ")
self.assertEqual(qdb.artifact.Artifact(2).artifact_type,
"Demultiplexed")
self.assertEqual(qdb.artifact.Artifact(3).artifact_type,
"Demultiplexed")
self.assertEqual(qdb.artifact.Artifact(4).artifact_type, "BIOM")
def test_data_type(self):
self.assertEqual(qdb.artifact.Artifact(1).data_type, "18S")
self.assertEqual(qdb.artifact.Artifact(2).data_type, "18S")
self.assertEqual(qdb.artifact.Artifact(3).data_type, "18S")
self.assertEqual(qdb.artifact.Artifact(4).data_type, "18S")
def test_can_be_submitted_to_ebi(self):
self.assertFalse(qdb.artifact.Artifact(1).can_be_submitted_to_ebi)
self.assertTrue(qdb.artifact.Artifact(2).can_be_submitted_to_ebi)
self.assertTrue(qdb.artifact.Artifact(3).can_be_submitted_to_ebi)
self.assertFalse(qdb.artifact.Artifact(4).can_be_submitted_to_ebi)
def test_is_submitted_to_ebi(self):
self.assertTrue(qdb.artifact.Artifact(2).is_submitted_to_ebi)
self.assertFalse(qdb.artifact.Artifact(3).is_submitted_to_ebi)
with self.assertRaises(
qdb.exceptions.QiitaDBOperationNotPermittedError):
qdb.artifact.Artifact(1).is_submitted_to_ebi
with self.assertRaises(
qdb.exceptions.QiitaDBOperationNotPermittedError):
qdb.artifact.Artifact(4).is_submitted_to_ebi
def test_ebi_run_accessions(self):
exp = {'1.SKB1.640202': 'ERR0000001',
'1.SKB2.640194': 'ERR0000002',
'1.SKB3.640195': 'ERR0000003',
'1.SKB4.640189': 'ERR0000004',
'1.SKB5.640181': 'ERR0000005',
'1.SKB6.640176': 'ERR0000006',
'1.SKB7.640196': 'ERR0000007',
'1.SKB8.640193': 'ERR0000008',
'1.SKB9.640200': 'ERR0000009',
'1.SKD1.640179': 'ERR0000010',
'1.SKD2.640178': 'ERR0000011',
'1.SKD3.640198': 'ERR0000012',
'1.SKD4.640185': 'ERR0000013',
'1.SKD5.640186': 'ERR0000014',
'1.SKD6.640190': 'ERR0000015',
'1.SKD7.640191': 'ERR0000016',
'1.SKD8.640184': 'ERR0000017',
'1.SKD9.640182': 'ERR0000018',
'1.SKM1.640183': 'ERR0000019',
'1.SKM2.640199': 'ERR0000020',
'1.SKM3.640197': 'ERR0000021',
'1.SKM4.640180': 'ERR0000022',
'1.SKM5.640177': 'ERR0000023',
'1.SKM6.640187': 'ERR0000024',
'1.SKM7.640188': 'ERR0000025',
'1.SKM8.640201': 'ERR0000026',
'1.SKM9.640192': 'ERR0000027'}
self.assertEqual(qdb.artifact.Artifact(2).ebi_run_accessions, exp)
self.assertEqual(qdb.artifact.Artifact(3).ebi_run_accessions, dict())
with self.assertRaises(
qdb.exceptions.QiitaDBOperationNotPermittedError):
qdb.artifact.Artifact(1).ebi_run_accessions
with self.assertRaises(
qdb.exceptions.QiitaDBOperationNotPermittedError):
qdb.artifact.Artifact(4).ebi_run_accessions
def test_can_be_submitted_to_vamps(self):
self.assertFalse(qdb.artifact.Artifact(1).can_be_submitted_to_vamps)
self.assertTrue(qdb.artifact.Artifact(2).can_be_submitted_to_vamps)
self.assertTrue(qdb.artifact.Artifact(3).can_be_submitted_to_vamps)
self.assertFalse(qdb.artifact.Artifact(4).can_be_submitted_to_vamps)
def test_is_submitted_to_vamps(self):
with self.assertRaises(
qdb.exceptions.QiitaDBOperationNotPermittedError):
self.assertFalse(qdb.artifact.Artifact(1).is_submitted_to_vamps)
self.assertFalse(qdb.artifact.Artifact(2).is_submitted_to_vamps)
self.assertFalse(qdb.artifact.Artifact(3).is_submitted_to_vamps)
with self.assertRaises(
qdb.exceptions.QiitaDBOperationNotPermittedError):
self.assertFalse(qdb.artifact.Artifact(4).is_submitted_to_vamps)
def test_filepaths(self):
db_test_raw_dir = qdb.util.get_mountpoint('raw_data')[0][1]
path_builder = partial(join, db_test_raw_dir)
exp_fps = [{'fp_id': 1,
'fp': path_builder("1_s_G1_L001_sequences.fastq.gz"),
'fp_type': "raw_forward_seqs",
'checksum': '2125826711',
'fp_size': 58},
{'fp_id': 2,
'fp': path_builder(
"1_s_G1_L001_sequences_barcodes.fastq.gz"),
'fp_type': "raw_barcodes",
'checksum': '2125826711',
'fp_size': 58}]
self.assertEqual(qdb.artifact.Artifact(1).filepaths, exp_fps)
def test_parents(self):
self.assertEqual(qdb.artifact.Artifact(1).parents, [])
exp_parents = [qdb.artifact.Artifact(1)]
self.assertEqual(qdb.artifact.Artifact(2).parents, exp_parents)
self.assertEqual(qdb.artifact.Artifact(3).parents, exp_parents)
exp_parents = [qdb.artifact.Artifact(2)]
self.assertEqual(qdb.artifact.Artifact(4).parents, exp_parents)
def test_create_lineage_graph_from_edge_list_empty(self):
tester = qdb.artifact.Artifact(1)
obs = tester._create_lineage_graph_from_edge_list([])
self.assertTrue(isinstance(obs, nx.DiGraph))
self.assertCountEqual(obs.nodes(), [tester])
self.assertCountEqual(obs.edges(), [])
def test_create_lineage_graph_from_edge_list(self):
tester = qdb.artifact.Artifact(1)
obs = tester._create_lineage_graph_from_edge_list(
[(1, 2), (2, 4), (1, 3), (3, 4)])
self.assertTrue(isinstance(obs, nx.DiGraph))
exp = [qdb.artifact.Artifact(1), qdb.artifact.Artifact(2),
qdb.artifact.Artifact(3), qdb.artifact.Artifact(4)]
self.assertCountEqual(obs.nodes(), exp)
exp = [(qdb.artifact.Artifact(1), qdb.artifact.Artifact(2)),
(qdb.artifact.Artifact(2), qdb.artifact.Artifact(4)),
(qdb.artifact.Artifact(1), qdb.artifact.Artifact(3)),
(qdb.artifact.Artifact(3), qdb.artifact.Artifact(4))]
self.assertCountEqual(obs.edges(), exp)
def test_ancestors(self):
obs = qdb.artifact.Artifact(1).ancestors
self.assertTrue(isinstance(obs, nx.DiGraph))
obs_nodes = obs.nodes()
self.assertCountEqual(obs_nodes, [qdb.artifact.Artifact(1)])
obs_edges = obs.edges()
self.assertCountEqual(obs_edges, [])
obs = qdb.artifact.Artifact(2).ancestors
self.assertTrue(isinstance(obs, nx.DiGraph))
obs_nodes = obs.nodes()
exp_nodes = [qdb.artifact.Artifact(1), qdb.artifact.Artifact(2)]
self.assertCountEqual(obs_nodes, exp_nodes)
obs_edges = obs.edges()
exp_edges = [(qdb.artifact.Artifact(1), qdb.artifact.Artifact(2))]
self.assertCountEqual(obs_edges, exp_edges)
obs = qdb.artifact.Artifact(3).ancestors
self.assertTrue(isinstance(obs, nx.DiGraph))
obs_nodes = obs.nodes()
exp_nodes = [qdb.artifact.Artifact(1), qdb.artifact.Artifact(3)]
self.assertCountEqual(obs_nodes, exp_nodes)
obs_edges = obs.edges()
exp_edges = [(qdb.artifact.Artifact(1), qdb.artifact.Artifact(3))]
self.assertCountEqual(obs_edges, exp_edges)
obs = qdb.artifact.Artifact(4).ancestors
self.assertTrue(isinstance(obs, nx.DiGraph))
obs_nodes = obs.nodes()
exp_nodes = [qdb.artifact.Artifact(1), qdb.artifact.Artifact(2),
qdb.artifact.Artifact(4)]
self.assertCountEqual(obs_nodes, exp_nodes)
obs_edges = obs.edges()
exp_edges = [(qdb.artifact.Artifact(1), qdb.artifact.Artifact(2)),
(qdb.artifact.Artifact(2), qdb.artifact.Artifact(4))]
self.assertCountEqual(obs_edges, exp_edges)
def test_descendants(self):
obs = qdb.artifact.Artifact(1).descendants
self.assertTrue(isinstance(obs, nx.DiGraph))
obs_nodes = obs.nodes()
exp_nodes = [qdb.artifact.Artifact(1), qdb.artifact.Artifact(2),
qdb.artifact.Artifact(3), qdb.artifact.Artifact(4),
qdb.artifact.Artifact(5), qdb.artifact.Artifact(6)]
self.assertCountEqual(obs_nodes, exp_nodes)
obs_edges = obs.edges()
exp_edges = [(qdb.artifact.Artifact(1), qdb.artifact.Artifact(2)),
(qdb.artifact.Artifact(1), qdb.artifact.Artifact(3)),
(qdb.artifact.Artifact(2), qdb.artifact.Artifact(4)),
(qdb.artifact.Artifact(2), qdb.artifact.Artifact(5)),
(qdb.artifact.Artifact(2), qdb.artifact.Artifact(6))]
self.assertCountEqual(obs_edges, exp_edges)
obs = qdb.artifact.Artifact(2).descendants
self.assertTrue(isinstance(obs, nx.DiGraph))
obs_nodes = obs.nodes()
exp_nodes = [qdb.artifact.Artifact(2), qdb.artifact.Artifact(4),
qdb.artifact.Artifact(5), qdb.artifact.Artifact(6)]
self.assertCountEqual(obs_nodes, exp_nodes)
obs_edges = obs.edges()
exp_edges = [(qdb.artifact.Artifact(2), qdb.artifact.Artifact(4)),
(qdb.artifact.Artifact(2), qdb.artifact.Artifact(5)),
(qdb.artifact.Artifact(2), qdb.artifact.Artifact(6))]
self.assertCountEqual(obs_edges, exp_edges)
obs = qdb.artifact.Artifact(3).descendants
self.assertTrue(isinstance(obs, nx.DiGraph))
obs_nodes = obs.nodes()
self.assertCountEqual(obs_nodes, [qdb.artifact.Artifact(3)])
obs_edges = obs.edges()
self.assertCountEqual(obs_edges, [])
obs = qdb.artifact.Artifact(4).descendants
self.assertTrue(isinstance(obs, nx.DiGraph))
obs_nodes = obs.nodes()
self.assertCountEqual(obs_nodes, [qdb.artifact.Artifact(4)])
obs_edges = obs.edges()
self.assertCountEqual(obs_edges, [])
def test_descendants_with_jobs(self):
A = qdb.artifact.Artifact
obs = A(1).descendants_with_jobs
self.assertTrue(isinstance(obs, nx.DiGraph))
obs_nodes = obs.nodes()
# Add an HTML summary job in one artifact in a non-success statuts, to
# make sure that it doesn't get returned in the graph
html_job = qdb.processing_job.ProcessingJob.create(
qdb.user.User('test@foo.bar'),
qdb.software.Parameters.load(
qdb.software.Command.get_html_generator(A(6).artifact_type),
values_dict={'input_data': 6}))
html_job._set_status('running')
# as jobs are created at random we will only check that the artifacts
# are there and that the number of jobs matches
exp_nodes = [('artifact', A(1)), ('artifact', A(2)),
('artifact', A(3)), ('artifact', A(4)),
('artifact', A(5)), ('artifact', A(6))]
for e in exp_nodes:
self.assertIn(e, obs_nodes)
self.assertEqual(5, len([e for dt, e in obs_nodes if dt == 'job']))
obs_edges = obs.edges()
# as jobs are created at random we will only check the number of pairs
# matches and they are instances of what we expect
self.assertEqual(10, len(obs_edges))
self.assertEqual(2, len([x for x, y in obs_edges
if x[1] == A(1) and y[0] == 'job']))
self.assertEqual(3, len([x for x, y in obs_edges
if x[1] == A(2) and y[0] == 'job']))
self.assertEqual(1, len([y for x, y in obs_edges
if y[1] == A(2) and x[0] == 'job']))
self.assertEqual(1, len([y for x, y in obs_edges
if y[1] == A(3) and x[0] == 'job']))
self.assertEqual(1, len([y for x, y in obs_edges
if y[1] == A(4) and x[0] == 'job']))
self.assertEqual(1, len([y for x, y in obs_edges
if y[1] == A(5) and x[0] == 'job']))
self.assertEqual(1, len([y for x, y in obs_edges
if y[1] == A(6) and x[0] == 'job']))
obs = A(3).descendants
self.assertTrue(isinstance(obs, nx.DiGraph))
obs_nodes = obs.nodes()
self.assertCountEqual(obs_nodes, [A(3)])
obs_edges = obs.edges()
self.assertCountEqual(obs_edges, [])
# Create a workflow starting in the artifact 1, so we can test that
# "in construction" jobs also show up correctly
json_str = (
'{"input_data": 1, "max_barcode_errors": 1.5, '
'"barcode_type": "8", "max_bad_run_length": 3, '
'"rev_comp": false, "phred_quality_threshold": 3, '
'"rev_comp_barcode": false, "rev_comp_mapping_barcodes": false, '
'"min_per_read_length_fraction": 0.75, "sequence_max_n": 0, '
'"phred_offset": "auto"}')
params = qdb.software.Parameters.load(qdb.software.Command(1),
json_str=json_str)
wf = qdb.processing_job.ProcessingWorkflow.from_scratch(
qdb.user.User('test@foo.bar'), params, name='Test WF')
parent = list(wf.graph.nodes())[0]
wf.add(qdb.software.DefaultParameters(10),
connections={parent: {'demultiplexed': 'input_data'}})
obs = A(1).descendants_with_jobs
obs_edges = obs.edges()
# We have 4 more edges than before. From artifact 1 to parent job,
# from parent job to output, from output to child job, and from child
# job to child output
self.assertEqual(len(obs_edges), 14)
# We will check that the edges related with the "type" nodes (i.e.
# the outputs of the jobs in construction) are present
self.assertEqual(1, len([y for x, y in obs_edges if x[0] == 'type']))
self.assertEqual(2, len([y for x, y in obs_edges if y[0] == 'type']))
def test_children(self):
exp = [qdb.artifact.Artifact(2), qdb.artifact.Artifact(3)]
self.assertEqual(qdb.artifact.Artifact(1).children, exp)
exp = [qdb.artifact.Artifact(4), qdb.artifact.Artifact(5),
qdb.artifact.Artifact(6)]
self.assertEqual(qdb.artifact.Artifact(2).children, exp)
self.assertEqual(qdb.artifact.Artifact(3).children, [])
self.assertEqual(qdb.artifact.Artifact(4).children, [])
def test_youngest_artifact(self):
exp = qdb.artifact.Artifact(6)
self.assertEqual(qdb.artifact.Artifact(1).youngest_artifact, exp)
self.assertEqual(qdb.artifact.Artifact(2).youngest_artifact, exp)
self.assertEqual(qdb.artifact.Artifact(3).youngest_artifact,
qdb.artifact.Artifact(3))
self.assertEqual(qdb.artifact.Artifact(6).youngest_artifact, exp)
def test_prep_templates(self):
self.assertEqual(
qdb.artifact.Artifact(1).prep_templates,
[qdb.metadata_template.prep_template.PrepTemplate(1)])
self.assertEqual(
qdb.artifact.Artifact(2).prep_templates,
[qdb.metadata_template.prep_template.PrepTemplate(1)])
self.assertEqual(
qdb.artifact.Artifact(3).prep_templates,
[qdb.metadata_template.prep_template.PrepTemplate(1)])
self.assertEqual(
qdb.artifact.Artifact(4).prep_templates,
[qdb.metadata_template.prep_template.PrepTemplate(1)])
def test_study(self):
self.assertEqual(qdb.artifact.Artifact(1).study, qdb.study.Study(1))
self.assertIsNone(qdb.artifact.Artifact(9).study)
def test_analysis(self):
self.assertEqual(qdb.artifact.Artifact(9).analysis,
qdb.analysis.Analysis(1))
self.assertIsNone(qdb.artifact.Artifact(1).analysis)
def test_merging_scheme(self):
self.assertEqual(qdb.artifact.Artifact(1).merging_scheme, ('', ''))
self.assertEqual(qdb.artifact.Artifact(2).merging_scheme,
('Split libraries FASTQ | N/A', 'N/A'))
self.assertEqual(qdb.artifact.Artifact(3).merging_scheme,
('Split libraries FASTQ | N/A', 'N/A'))
self.assertEqual(qdb.artifact.Artifact(4).merging_scheme,
('Pick closed-reference OTUs | Split libraries FASTQ',
'QIIMEq2 v1.9.1'))
self.assertEqual(qdb.artifact.Artifact(5).merging_scheme,
('Pick closed-reference OTUs | Split libraries FASTQ',
'QIIMEq2 v1.9.1'))
def test_jobs(self):
# Returning all jobs
obs = qdb.artifact.Artifact(1).jobs(show_hidden=True)
exp = [
qdb.processing_job.ProcessingJob(
'6d368e16-2242-4cf8-87b4-a5dc40bb890b'),
qdb.processing_job.ProcessingJob(
'4c7115e8-4c8e-424c-bf25-96c292ca1931'),
qdb.processing_job.ProcessingJob(
'063e553b-327c-4818-ab4a-adfe58e49860'),
qdb.processing_job.ProcessingJob(
'bcc7ebcd-39c1-43e4-af2d-822e3589f14d'),
qdb.processing_job.ProcessingJob(
'b72369f9-a886-4193-8d3d-f7b504168e75')]
# there are some extra jobs randomly generated, not testing those
for e in exp:
self.assertIn(e, obs)
# Returning only jobs visible by the user
obs = qdb.artifact.Artifact(1).jobs()
exp = [
qdb.processing_job.ProcessingJob(
'6d368e16-2242-4cf8-87b4-a5dc40bb890b'),
qdb.processing_job.ProcessingJob(
'4c7115e8-4c8e-424c-bf25-96c292ca1931'),
qdb.processing_job.ProcessingJob(
'b72369f9-a886-4193-8d3d-f7b504168e75')]
for e in exp:
self.assertIn(e, obs)
def test_jobs_cmd(self):
cmd = qdb.software.Command(1)
obs = qdb.artifact.Artifact(1).jobs(cmd=cmd, show_hidden=True)
exp = [
qdb.processing_job.ProcessingJob(
'6d368e16-2242-4cf8-87b4-a5dc40bb890b'),
qdb.processing_job.ProcessingJob(
'4c7115e8-4c8e-424c-bf25-96c292ca1931'),
qdb.processing_job.ProcessingJob(
'063e553b-327c-4818-ab4a-adfe58e49860'),
qdb.processing_job.ProcessingJob(
'b72369f9-a886-4193-8d3d-f7b504168e75')
]
# there are some extra jobs randomly generated, not testing those
for e in exp:
self.assertIn(e, obs)
obs = qdb.artifact.Artifact(1).jobs(cmd=cmd)
exp = [
qdb.processing_job.ProcessingJob(
'6d368e16-2242-4cf8-87b4-a5dc40bb890b'),
qdb.processing_job.ProcessingJob(
'4c7115e8-4c8e-424c-bf25-96c292ca1931'),
qdb.processing_job.ProcessingJob(
'b72369f9-a886-4193-8d3d-f7b504168e75')
]
cmd = qdb.software.Command(2)
obs = qdb.artifact.Artifact(1).jobs(cmd=cmd, show_hidden=True)
exp = [qdb.processing_job.ProcessingJob(
'bcc7ebcd-39c1-43e4-af2d-822e3589f14d')]
self.assertEqual(obs, exp)
obs = qdb.artifact.Artifact(1).jobs(cmd=cmd)
self.assertEqual(obs, [])
def test_jobs_status(self):
obs = qdb.artifact.Artifact(1).jobs(status='success')
exp = [
qdb.processing_job.ProcessingJob(
'6d368e16-2242-4cf8-87b4-a5dc40bb890b'),
qdb.processing_job.ProcessingJob(
'4c7115e8-4c8e-424c-bf25-96c292ca1931'),
qdb.processing_job.ProcessingJob(
'b72369f9-a886-4193-8d3d-f7b504168e75')
]
# there are some extra jobs randomly generated, not testing those
for e in exp:
self.assertIn(e, obs)
obs = qdb.artifact.Artifact(1).jobs(status='running', show_hidden=True)
exp = [qdb.processing_job.ProcessingJob(
'bcc7ebcd-39c1-43e4-af2d-822e3589f14d')]
self.assertEqual(obs, exp)
obs = qdb.artifact.Artifact(1).jobs(status='running')
self.assertEqual(obs, [])
obs = qdb.artifact.Artifact(1).jobs(status='queued', show_hidden=True)
exp = [qdb.processing_job.ProcessingJob(
'063e553b-327c-4818-ab4a-adfe58e49860')]
self.assertEqual(obs, exp)
obs = qdb.artifact.Artifact(1).jobs(status='queued')
self.assertEqual(obs, [])
def test_jobs_cmd_and_status(self):
cmd = qdb.software.Command(1)
obs = qdb.artifact.Artifact(1).jobs(cmd=cmd, status='success')
exp = [
qdb.processing_job.ProcessingJob(
'6d368e16-2242-4cf8-87b4-a5dc40bb890b'),
qdb.processing_job.ProcessingJob(
'4c7115e8-4c8e-424c-bf25-96c292ca1931'),
qdb.processing_job.ProcessingJob(
'b72369f9-a886-4193-8d3d-f7b504168e75')
]
# there are some extra jobs randomly generated, not testing those
for e in exp:
self.assertIn(e, obs)
obs = qdb.artifact.Artifact(1).jobs(cmd=cmd, status='queued',
show_hidden=True)
exp = [qdb.processing_job.ProcessingJob(
'063e553b-327c-4818-ab4a-adfe58e49860')]
self.assertEqual(obs, exp)
obs = qdb.artifact.Artifact(1).jobs(cmd=cmd, status='queued')
self.assertEqual(obs, [])
cmd = qdb.software.Command(2)
obs = qdb.artifact.Artifact(1).jobs(cmd=cmd, status='queued')
exp = []
self.assertEqual(obs, exp)
def test_get_commands(self):
# we will check only ids for simplicity
# checking processing artifacts
obs = [c.id for c in qdb.artifact.Artifact(1).get_commands]
self.assertEqual(obs, [1])
obs = [c.id for c in qdb.artifact.Artifact(2).get_commands]
self.assertEqual(obs, [3])
# this is a biom in processing, so no commands should be available
obs = [c.id for c in qdb.artifact.Artifact(6).get_commands]
self.assertEqual(obs, [])
# checking analysis object - this is a biom in analysis, several
# commands should be available
obs = [c.id for c in qdb.artifact.Artifact(8).get_commands]
self.assertEqual(obs, [9, 10, 11, 12])
@qiita_test_checker()
class ArtifactTests(TestCase):
def setUp(self):
# Generate some files for a root artifact
fd, self.fp1 = mkstemp(suffix='_seqs.fastq')
close(fd)
with open(self.fp1, 'w') as f:
f.write("@HWI-ST753:189:D1385ACXX:1:1101:1214:1906 1:N:0:\n"
"NACGTAGGGTGCAAGCGTTGTCCGGAATNA\n"
"+\n"
"#1=DDFFFHHHHHJJJJJJJJJJJJGII#0\n")
fd, self.fp2 = mkstemp(suffix='_barcodes.fastq')
close(fd)
with open(self.fp2, 'w') as f:
f.write("@HWI-ST753:189:D1385ACXX:1:1101:1214:1906 2:N:0:\n"
"NNNCNNNNNNNNN\n"
"+\n"
"#############\n")
self.filepaths_root = [(self.fp1, 1), (self.fp2, 3)]
# Generate some files for a processed artifact
fd, self.fp3 = mkstemp(suffix='_seqs.fna')
close(fd)
with open(self.fp3, 'w') as f:
f.write(">1.sid_r4_0 M02034:17:000000000-A5U18:1:1101:15370:1394 "
"1:N:0:1 orig_bc=CATGAGCT new_bc=CATGAGCT bc_diffs=0\n"
"GTGTGCCAGCAGCCGCGGTAATACGTAGGG\n")
self.filepaths_processed = [(self.fp3, 4)]
# Generate some file for a BIOM
fd, self.fp4 = mkstemp(suffix='_table.biom')
with biom_open(self.fp4, 'w') as f:
et.to_hdf5(f, "test")
self.filepaths_biom = [(self.fp4, 7)]
# Create a new prep template
metadata_dict = {
'SKB8.640193': {'center_name': 'ANL',
'primer': 'GTGCCAGCMGCCGCGGTAA',
'barcode': 'GTCCGCAAGTTA',
'run_prefix': "s_G1_L001_sequences",
'platform': 'Illumina',
'instrument_model': 'Illumina MiSeq',
'library_construction_protocol': 'AAAA',
'target_subfragment': 'V4',
'target_gene': '16S rRNA',
'experiment_design_description': 'BBBB'}}
metadata = pd.DataFrame.from_dict(metadata_dict, orient='index',
dtype=str)
self.prep_template = \
qdb.metadata_template.prep_template.PrepTemplate.create(
metadata, qdb.study.Study(1), "16S")
self.prep_template_2 = \
qdb.metadata_template.prep_template.PrepTemplate.create(
metadata, qdb.study.Study(1), "16S")
self._clean_up_files = [self.fp1, self.fp2, self.fp3, self.fp4]
# per_sample_FASTQ Metagenomic example
self.prep_template_per_sample_fastq = \
qdb.metadata_template.prep_template.PrepTemplate.create(
metadata, qdb.study.Study(1), "Metagenomic")
fd, self.fwd = mkstemp(prefix='SKB8.640193', suffix='_R1.fastq')
close(fd)
with open(self.fwd, 'w') as f:
f.write("@HWI-ST753:189:D1385ACXX:1:1101:1214:1906 1:N:0:\n"
"NACGTAGGGTGCAAGCGTTGTCCGGAATNA\n"
"+\n"
"#1=DDFFFHHHHHJJJJJJJJJJJJGII#0\n")
fd, self.rev = mkstemp(prefix='SKB8.640193', suffix='_R2.fastq')
close(fd)
with open(self.rev, 'w') as f:
f.write("@HWI-ST753:189:D1385ACXX:1:1101:1214:1906 1:N:0:\n"
"NACGTAGGGTGCAAGCGTTGTCCGGAATNA\n"
"+\n"
"#1=DDFFFHHHHHJJJJJJJJJJJJGII#0\n")
self._clean_up_files.extend([self.fwd, self.rev])
self.user = qdb.user.User('test@foo.bar')
def tearDown(self):
for f in self._clean_up_files:
if exists(f):
remove(f)
def test_copy(self):
src = qdb.artifact.Artifact.create(
self.filepaths_root, "FASTQ", prep_template=self.prep_template)
before = datetime.now()
obs = qdb.artifact.Artifact.copy(src, self.prep_template_2)
self.assertTrue(before < obs.timestamp < datetime.now())
self.assertIsNone(obs.processing_parameters)
self.assertEqual(obs.visibility, 'sandbox')
self.assertEqual(obs.artifact_type, src.artifact_type)
self.assertEqual(obs.data_type, self.prep_template.data_type())
self.assertEqual(obs.can_be_submitted_to_ebi,
src.can_be_submitted_to_ebi)
self.assertEqual(obs.can_be_submitted_to_vamps,
src.can_be_submitted_to_vamps)
db_dir = qdb.util.get_mountpoint(src.artifact_type)[0][1]
path_builder = partial(join, db_dir, str(obs.id))
exp_fps = []
for x in src.filepaths:
new_fp = path_builder(basename(x['fp']))
exp_fps.append((new_fp, x['fp_type']))
self._clean_up_files.append(new_fp)
self.assertEqual([(x['fp'], x['fp_type'])
for x in obs.filepaths], exp_fps)
self.assertEqual(obs.parents, [])
self.assertEqual(obs.prep_templates, [self.prep_template_2])
self.assertEqual(obs.study, qdb.study.Study(1))
def test_create_error(self):
# no filepaths
with self.assertRaises(qdb.exceptions.QiitaDBArtifactCreationError):
qdb.artifact.Artifact.create(
[], "FASTQ", prep_template=self.prep_template)
# prep template and parents
with self.assertRaises(qdb.exceptions.QiitaDBArtifactCreationError):
qdb.artifact.Artifact.create(
self.filepaths_root, "FASTQ", prep_template=self.prep_template,
parents=[qdb.artifact.Artifact(1)])
# analysis and prep_template
with self.assertRaises(qdb.exceptions.QiitaDBArtifactCreationError):
qdb.artifact.Artifact.create(
self.filepaths_root, "BIOM", prep_template=self.prep_template,
analysis=qdb.analysis.Analysis(1))
# Analysis and parents
with self.assertRaises(qdb.exceptions.QiitaDBArtifactCreationError):
qdb.artifact.Artifact.create(
self.filepaths_root, "BIOM",
parents=[qdb.artifact.Artifact(1)],
analysis=qdb.analysis.Analysis(1))
# no prep template no parents no analysis
with self.assertRaises(qdb.exceptions.QiitaDBArtifactCreationError):
qdb.artifact.Artifact.create(self.filepaths_root, "FASTQ")
# parents no processing parameters
with self.assertRaises(qdb.exceptions.QiitaDBArtifactCreationError):
qdb.artifact.Artifact.create(
self.filepaths_root, "FASTQ",
parents=[qdb.artifact.Artifact(1)])
# analysis no data type
with self.assertRaises(qdb.exceptions.QiitaDBArtifactCreationError):
qdb.artifact.Artifact.create(
self.filepaths_root, "BIOM", analysis=qdb.analysis.Analysis(1))
# prep template and processing parameters
parameters = qdb.software.Parameters.from_default_params(
qdb.software.DefaultParameters(1), {'input_data': 1})
with self.assertRaises(qdb.exceptions.QiitaDBArtifactCreationError):
qdb.artifact.Artifact.create(
self.filepaths_root, "FASTQ", prep_template=self.prep_template,
processing_parameters=parameters)
# prep template and data type
with self.assertRaises(qdb.exceptions.QiitaDBArtifactCreationError):
qdb.artifact.Artifact.create(
self.filepaths_root, "FASTQ", prep_template=self.prep_template,
data_type="Multiomic")
# different data types
new = qdb.artifact.Artifact.create(
self.filepaths_root, "FASTQ", prep_template=self.prep_template)
parameters = qdb.software.Parameters.from_default_params(
qdb.software.DefaultParameters(1), {'input_data': 1})
with self.assertRaises(qdb.exceptions.QiitaDBArtifactCreationError):
qdb.artifact.Artifact.create(
self.filepaths_processed, "Demultiplexed",
parents=[qdb.artifact.Artifact(1), new],
processing_parameters=parameters)
def test_create_root(self):
before = datetime.now()
obs = qdb.artifact.Artifact.create(
self.filepaths_root, "FASTQ", prep_template=self.prep_template,
name='Test artifact')
self.assertEqual(obs.name, 'Test artifact')
self.assertTrue(before < obs.timestamp < datetime.now())
self.assertIsNone(obs.processing_parameters)
self.assertEqual(obs.visibility, 'sandbox')
self.assertEqual(obs.artifact_type, "FASTQ")
self.assertEqual(obs.data_type, self.prep_template.data_type())
self.assertFalse(obs.can_be_submitted_to_ebi)
self.assertFalse(obs.can_be_submitted_to_vamps)
db_fastq_dir = qdb.util.get_mountpoint('FASTQ')[0][1]
path_builder = partial(join, db_fastq_dir, str(obs.id))
exp_fps = [
(path_builder(basename(self.fp1)), "raw_forward_seqs"),
(path_builder(basename(self.fp2)), "raw_barcodes")]
self.assertEqual([(x['fp'], x['fp_type'])
for x in obs.filepaths], exp_fps)
self.assertEqual(obs.parents, [])
self.assertEqual(obs.prep_templates, [self.prep_template])
with self.assertRaises(
qdb.exceptions.QiitaDBOperationNotPermittedError):
obs.ebi_run_accessions
with self.assertRaises(
qdb.exceptions.QiitaDBOperationNotPermittedError):
obs.is_submitted_to_vamps
self.assertEqual(obs.study, qdb.study.Study(1))
self.assertIsNone(obs.analysis)
def test_create_root_analysis(self):
before = datetime.now()
obs = qdb.artifact.Artifact.create(
self.filepaths_biom, "BIOM", name='Test artifact analysis',
analysis=qdb.analysis.Analysis(1), data_type="16S")
self.assertEqual(obs.name, 'Test artifact analysis')
self.assertTrue(before < obs.timestamp < datetime.now())
self.assertIsNone(obs.processing_parameters)
self.assertEqual(obs.visibility, 'sandbox')
self.assertEqual(obs.artifact_type, "BIOM")
self.assertEqual(obs.data_type, "16S")
self.assertFalse(obs.can_be_submitted_to_ebi)
self.assertFalse(obs.can_be_submitted_to_vamps)
db_fastq_dir = qdb.util.get_mountpoint('BIOM')[0][1]
path_builder = partial(join, db_fastq_dir, str(obs.id))
exp_fps = [(path_builder(basename(self.fp4)), "biom")]
self.assertEqual([(x['fp'], x['fp_type'])
for x in obs.filepaths], exp_fps)
self.assertEqual(obs.parents, [])
self.assertEqual(obs.prep_templates, [])
with self.assertRaises(
qdb.exceptions.QiitaDBOperationNotPermittedError):
obs.ebi_run_accessions
with self.assertRaises(
qdb.exceptions.QiitaDBOperationNotPermittedError):
obs.is_submitted_to_vamps
self.assertIsNone(obs.study)
self.assertEqual(obs.analysis, qdb.analysis.Analysis(1))
# testing that it can be deleted
qdb.artifact.Artifact.delete(obs.id)
def test_create_processed(self):
# make a copy of files for the can_be_submitted_to_ebi tests
lcopy = self.fp3 + '.fna'
self._clean_up_files.append(lcopy)
copyfile(self.fp3, lcopy)
exp_params = qdb.software.Parameters.from_default_params(
qdb.software.DefaultParameters(1), {'input_data': 1})
before = datetime.now()
obs = qdb.artifact.Artifact.create(
self.filepaths_processed, "Demultiplexed",
parents=[qdb.artifact.Artifact(1)],
processing_parameters=exp_params)
self.assertEqual(obs.name, 'noname')
self.assertTrue(before < obs.timestamp < datetime.now())
self.assertEqual(obs.processing_parameters, exp_params)
self.assertEqual(obs.visibility, 'private')
self.assertEqual(obs.artifact_type, "Demultiplexed")
self.assertEqual(obs.data_type, qdb.artifact.Artifact(1).data_type)
self.assertTrue(obs.can_be_submitted_to_ebi)
self.assertTrue(obs.can_be_submitted_to_vamps)
self.assertFalse(obs.is_submitted_to_vamps)
db_demultiplexed_dir = qdb.util.get_mountpoint('Demultiplexed')[0][1]
path_builder = partial(join, db_demultiplexed_dir, str(obs.id))
exp_fps = [(path_builder(basename(self.fp3)),
"preprocessed_fasta")]
self.assertEqual([(x['fp'], x['fp_type'])
for x in obs.filepaths], exp_fps)
self.assertEqual(obs.parents, [qdb.artifact.Artifact(1)])
self.assertEqual(
obs.prep_templates,
[qdb.metadata_template.prep_template.PrepTemplate(1)])
self.assertEqual(obs.ebi_run_accessions, dict())
self.assertEqual(obs.study, qdb.study.Study(1))
self.assertFalse(exists(self.filepaths_processed[0][0]))
self.assertIsNone(obs.analysis)
# let's create another demultiplexed on top of the previous one to
# test can_be_submitted_to_ebi
exp_params = qdb.software.Parameters.from_default_params(
qdb.software.DefaultParameters(1), {'input_data': obs.id})
new = qdb.artifact.Artifact.create(
[(lcopy, 4)], "Demultiplexed", parents=[obs],
processing_parameters=exp_params)
self.assertFalse(new.can_be_submitted_to_ebi)
def test_create_copy_files(self):
exp_params = qdb.software.Parameters.from_default_params(
qdb.software.DefaultParameters(1), {'input_data': 1})
before = datetime.now()
obs = qdb.artifact.Artifact.create(
self.filepaths_processed, "Demultiplexed",
parents=[qdb.artifact.Artifact(1)],
processing_parameters=exp_params, move_files=False)
self.assertEqual(obs.name, 'noname')
self.assertTrue(before < obs.timestamp < datetime.now())
self.assertEqual(obs.processing_parameters, exp_params)
self.assertEqual(obs.visibility, 'private')
self.assertEqual(obs.artifact_type, "Demultiplexed")
self.assertEqual(obs.data_type, qdb.artifact.Artifact(1).data_type)
self.assertTrue(obs.can_be_submitted_to_ebi)
self.assertTrue(obs.can_be_submitted_to_vamps)
self.assertFalse(obs.is_submitted_to_vamps)
db_demultiplexed_dir = qdb.util.get_mountpoint('Demultiplexed')[0][1]
path_builder = partial(join, db_demultiplexed_dir, str(obs.id))
exp_fps = [(path_builder(basename(self.fp3)),
"preprocessed_fasta")]
self.assertEqual([(x['fp'], x['fp_type'])
for x in obs.filepaths], exp_fps)
self.assertEqual(obs.parents, [qdb.artifact.Artifact(1)])
self.assertEqual(
obs.prep_templates,
[qdb.metadata_template.prep_template.PrepTemplate(1)])
self.assertEqual(obs.ebi_run_accessions, dict())
self.assertEqual(obs.study, qdb.study.Study(1))
self.assertTrue(exists(self.filepaths_processed[0][0]))
self.assertIsNone(obs.analysis)
def test_create_biom(self):
before = datetime.now()
cmd = qdb.software.Command(3)
exp_params = qdb.software.Parameters.from_default_params(
next(cmd.default_parameter_sets), {'input_data': 1})
obs = qdb.artifact.Artifact.create(
self.filepaths_biom, "BIOM", parents=[qdb.artifact.Artifact(2)],
processing_parameters=exp_params)
self.assertEqual(obs.name, 'noname')
self.assertTrue(before < obs.timestamp < datetime.now())
self.assertEqual(obs.processing_parameters, exp_params)
self.assertEqual(obs.visibility, 'private')
self.assertEqual(obs.artifact_type, 'BIOM')
self.assertEqual(obs.data_type, qdb.artifact.Artifact(2).data_type)
self.assertFalse(obs.can_be_submitted_to_ebi)
self.assertFalse(obs.can_be_submitted_to_vamps)
with self.assertRaises(
qdb.exceptions.QiitaDBOperationNotPermittedError):
obs.ebi_run_accessions
with self.assertRaises(
qdb.exceptions.QiitaDBOperationNotPermittedError):
obs.is_submitted_to_vamps
db_biom_dir = qdb.util.get_mountpoint('BIOM')[0][1]
path_builder = partial(join, db_biom_dir, str(obs.id))
exp_fps = [(path_builder(basename(self.fp4)), 'biom')]
self.assertEqual([(x['fp'], x['fp_type'])
for x in obs.filepaths], exp_fps)
self.assertEqual(obs.parents, [qdb.artifact.Artifact(2)])
self.assertEqual(obs.prep_templates,
[qdb.metadata_template.prep_template.PrepTemplate(1)])
self.assertEqual(obs.study, qdb.study.Study(1))
self.assertIsNone(obs.analysis)
def test_delete_error_public(self):
test = qdb.artifact.Artifact.create(
self.filepaths_root, "FASTQ", prep_template=self.prep_template)
test.visibility = "public"
self._clean_up_files.extend([x['fp'] for x in test.filepaths])
with self.assertRaises(qdb.exceptions.QiitaDBArtifactDeletionError):
qdb.artifact.Artifact.delete(test.id)
def test_delete_error_has_children(self):
with self.assertRaises(qdb.exceptions.QiitaDBArtifactDeletionError):