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b/qiita_db/test/test_artifact.py |
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# ----------------------------------------------------------------------------- |
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# Copyright (c) 2014--, The Qiita Development Team. |
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# |
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# Distributed under the terms of the BSD 3-clause License. |
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# |
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# The full license is in the file LICENSE, distributed with this software. |
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# ----------------------------------------------------------------------------- |
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from unittest import TestCase, main |
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from tempfile import mkstemp, mkdtemp |
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from datetime import datetime |
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from os import close, remove |
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from os.path import exists, join, basename, dirname, abspath |
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from shutil import copyfile |
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from functools import partial |
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from json import dumps |
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import pandas as pd |
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import networkx as nx |
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from biom import example_table as et |
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from biom.util import biom_open |
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from qiita_core.util import qiita_test_checker |
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from qiita_core.testing import wait_for_processing_job |
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import qiita_db as qdb |
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class ArtifactTestsReadOnly(TestCase): |
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def test_iter(self): |
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obs = list(qdb.artifact.Artifact.iter_by_visibility('public')) |
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self.assertEqual(obs, []) |
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obs = list(qdb.artifact.Artifact.iter_by_visibility('private')) |
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exp = [qdb.artifact.Artifact(1), |
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qdb.artifact.Artifact(2), |
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qdb.artifact.Artifact(3), |
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qdb.artifact.Artifact(4), |
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qdb.artifact.Artifact(5), |
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qdb.artifact.Artifact(6), |
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qdb.artifact.Artifact(7)] |
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self.assertEqual(obs, exp) |
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exp.extend([qdb.artifact.Artifact(8), qdb.artifact.Artifact(9)]) |
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self.assertEqual(list(qdb.artifact.Artifact.iter()), exp) |
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def test_create_type(self): |
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obs = qdb.artifact.Artifact.types() |
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exp = [['BIOM', 'BIOM table', False, False, True], |
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['Demultiplexed', 'Demultiplexed and QC sequences', True, True, |
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False], |
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['FASTA', None, False, False, False], |
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['FASTA_Sanger', None, False, False, False], |
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['FASTQ', None, False, False, True], |
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['SFF', None, False, False, False], |
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['per_sample_FASTQ', None, True, False, True], |
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['beta_div_plots', 'Qiime 1 beta diversity results', False, |
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False, False], |
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['rarefaction_curves', 'Rarefaction curves', False, False, |
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False], |
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['taxa_summary', 'Taxa summary plots', False, False, False]] |
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self.assertCountEqual(obs, exp) |
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qdb.artifact.Artifact.create_type( |
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"NewType", "NewTypeDesc", False, False, False, |
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[("log", False), ("raw_forward_seqs", True)]) |
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obs = qdb.artifact.Artifact.types() |
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exp = [['BIOM', 'BIOM table', False, False, True], |
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['Demultiplexed', 'Demultiplexed and QC sequences', True, True, |
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False], |
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['FASTA', None, False, False, False], |
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['FASTA_Sanger', None, False, False, False], |
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['FASTQ', None, False, False, True], |
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['SFF', None, False, False, False], |
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['per_sample_FASTQ', None, True, False, True], |
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['beta_div_plots', 'Qiime 1 beta diversity results', False, |
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False, False], |
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['rarefaction_curves', 'Rarefaction curves', False, False, |
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False], |
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['taxa_summary', 'Taxa summary plots', False, False, False], |
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['NewType', 'NewTypeDesc', False, False, False]] |
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self.assertCountEqual(obs, exp) |
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self.assertTrue(exists(qdb.util.get_mountpoint('NewType')[0][1])) |
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with self.assertRaises(qdb.exceptions.QiitaDBDuplicateError): |
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qdb.artifact.Artifact.create_type( |
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"NewType", "NewTypeDesc", False, False, False, |
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[("log", False), ("raw_forward_seqs", True)]) |
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def test_name(self): |
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self.assertEqual(qdb.artifact.Artifact(1).name, "Raw data 1") |
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self.assertEqual(qdb.artifact.Artifact(2).name, "Demultiplexed 1") |
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self.assertEqual(qdb.artifact.Artifact(3).name, "Demultiplexed 2") |
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self.assertEqual(qdb.artifact.Artifact(4).name, "BIOM") |
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def test_timestamp(self): |
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self.assertEqual(qdb.artifact.Artifact(1).timestamp, |
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datetime(2012, 10, 1, 9, 30, 27)) |
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self.assertEqual(qdb.artifact.Artifact(2).timestamp, |
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datetime(2012, 10, 1, 10, 30, 27)) |
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self.assertEqual(qdb.artifact.Artifact(3).timestamp, |
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datetime(2012, 10, 1, 11, 30, 27)) |
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self.assertEqual(qdb.artifact.Artifact(4).timestamp, |
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datetime(2012, 10, 2, 17, 30, 00)) |
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def test_processing_parameters(self): |
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self.assertIsNone(qdb.artifact.Artifact(1).processing_parameters) |
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obs = qdb.artifact.Artifact(2).processing_parameters |
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exp = qdb.software.Parameters.load( |
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qdb.software.Command(1), |
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values_dict={'max_barcode_errors': '1.5', 'sequence_max_n': '0', |
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'max_bad_run_length': '3', 'rev_comp': 'False', |
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'phred_quality_threshold': '3', 'input_data': '1', |
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'rev_comp_barcode': 'False', |
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'rev_comp_mapping_barcodes': 'False', |
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'min_per_read_length_fraction': '0.75', |
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'barcode_type': 'golay_12', |
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'phred_offset': 'auto'}) |
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self.assertEqual(obs, exp) |
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obs = qdb.artifact.Artifact(3).processing_parameters |
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exp = qdb.software.Parameters.load( |
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qdb.software.Command(1), |
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values_dict={'max_barcode_errors': '1.5', 'sequence_max_n': '0', |
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'max_bad_run_length': '3', 'rev_comp': 'False', |
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'phred_quality_threshold': '3', 'input_data': '1', |
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'rev_comp_barcode': 'False', |
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'rev_comp_mapping_barcodes': 'True', |
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'min_per_read_length_fraction': '0.75', |
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'barcode_type': 'golay_12', |
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'phred_offset': 'auto'}) |
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self.assertEqual(obs, exp) |
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def test_visibility(self): |
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self.assertEqual(qdb.artifact.Artifact(1).visibility, "private") |
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def test_artifact_type(self): |
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self.assertEqual(qdb.artifact.Artifact(1).artifact_type, "FASTQ") |
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self.assertEqual(qdb.artifact.Artifact(2).artifact_type, |
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"Demultiplexed") |
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self.assertEqual(qdb.artifact.Artifact(3).artifact_type, |
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"Demultiplexed") |
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self.assertEqual(qdb.artifact.Artifact(4).artifact_type, "BIOM") |
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def test_data_type(self): |
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self.assertEqual(qdb.artifact.Artifact(1).data_type, "18S") |
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self.assertEqual(qdb.artifact.Artifact(2).data_type, "18S") |
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self.assertEqual(qdb.artifact.Artifact(3).data_type, "18S") |
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self.assertEqual(qdb.artifact.Artifact(4).data_type, "18S") |
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def test_can_be_submitted_to_ebi(self): |
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self.assertFalse(qdb.artifact.Artifact(1).can_be_submitted_to_ebi) |
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self.assertTrue(qdb.artifact.Artifact(2).can_be_submitted_to_ebi) |
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self.assertTrue(qdb.artifact.Artifact(3).can_be_submitted_to_ebi) |
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self.assertFalse(qdb.artifact.Artifact(4).can_be_submitted_to_ebi) |
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def test_is_submitted_to_ebi(self): |
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self.assertTrue(qdb.artifact.Artifact(2).is_submitted_to_ebi) |
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self.assertFalse(qdb.artifact.Artifact(3).is_submitted_to_ebi) |
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with self.assertRaises( |
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qdb.exceptions.QiitaDBOperationNotPermittedError): |
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qdb.artifact.Artifact(1).is_submitted_to_ebi |
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with self.assertRaises( |
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qdb.exceptions.QiitaDBOperationNotPermittedError): |
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qdb.artifact.Artifact(4).is_submitted_to_ebi |
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def test_ebi_run_accessions(self): |
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exp = {'1.SKB1.640202': 'ERR0000001', |
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'1.SKB2.640194': 'ERR0000002', |
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'1.SKB3.640195': 'ERR0000003', |
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'1.SKB4.640189': 'ERR0000004', |
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'1.SKB5.640181': 'ERR0000005', |
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'1.SKB6.640176': 'ERR0000006', |
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'1.SKB7.640196': 'ERR0000007', |
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'1.SKB8.640193': 'ERR0000008', |
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'1.SKB9.640200': 'ERR0000009', |
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'1.SKD1.640179': 'ERR0000010', |
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'1.SKD2.640178': 'ERR0000011', |
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'1.SKD3.640198': 'ERR0000012', |
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'1.SKD4.640185': 'ERR0000013', |
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'1.SKD5.640186': 'ERR0000014', |
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'1.SKD6.640190': 'ERR0000015', |
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'1.SKD7.640191': 'ERR0000016', |
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'1.SKD8.640184': 'ERR0000017', |
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'1.SKD9.640182': 'ERR0000018', |
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'1.SKM1.640183': 'ERR0000019', |
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'1.SKM2.640199': 'ERR0000020', |
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'1.SKM3.640197': 'ERR0000021', |
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'1.SKM4.640180': 'ERR0000022', |
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'1.SKM5.640177': 'ERR0000023', |
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'1.SKM6.640187': 'ERR0000024', |
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'1.SKM7.640188': 'ERR0000025', |
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'1.SKM8.640201': 'ERR0000026', |
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'1.SKM9.640192': 'ERR0000027'} |
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self.assertEqual(qdb.artifact.Artifact(2).ebi_run_accessions, exp) |
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self.assertEqual(qdb.artifact.Artifact(3).ebi_run_accessions, dict()) |
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with self.assertRaises( |
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qdb.exceptions.QiitaDBOperationNotPermittedError): |
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qdb.artifact.Artifact(1).ebi_run_accessions |
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with self.assertRaises( |
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qdb.exceptions.QiitaDBOperationNotPermittedError): |
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qdb.artifact.Artifact(4).ebi_run_accessions |
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def test_can_be_submitted_to_vamps(self): |
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self.assertFalse(qdb.artifact.Artifact(1).can_be_submitted_to_vamps) |
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self.assertTrue(qdb.artifact.Artifact(2).can_be_submitted_to_vamps) |
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self.assertTrue(qdb.artifact.Artifact(3).can_be_submitted_to_vamps) |
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self.assertFalse(qdb.artifact.Artifact(4).can_be_submitted_to_vamps) |
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def test_is_submitted_to_vamps(self): |
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with self.assertRaises( |
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qdb.exceptions.QiitaDBOperationNotPermittedError): |
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self.assertFalse(qdb.artifact.Artifact(1).is_submitted_to_vamps) |
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self.assertFalse(qdb.artifact.Artifact(2).is_submitted_to_vamps) |
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self.assertFalse(qdb.artifact.Artifact(3).is_submitted_to_vamps) |
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with self.assertRaises( |
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qdb.exceptions.QiitaDBOperationNotPermittedError): |
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self.assertFalse(qdb.artifact.Artifact(4).is_submitted_to_vamps) |
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def test_filepaths(self): |
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db_test_raw_dir = qdb.util.get_mountpoint('raw_data')[0][1] |
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path_builder = partial(join, db_test_raw_dir) |
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exp_fps = [{'fp_id': 1, |
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'fp': path_builder("1_s_G1_L001_sequences.fastq.gz"), |
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'fp_type': "raw_forward_seqs", |
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'checksum': '2125826711', |
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'fp_size': 58}, |
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{'fp_id': 2, |
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'fp': path_builder( |
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"1_s_G1_L001_sequences_barcodes.fastq.gz"), |
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'fp_type': "raw_barcodes", |
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'checksum': '2125826711', |
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'fp_size': 58}] |
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self.assertEqual(qdb.artifact.Artifact(1).filepaths, exp_fps) |
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def test_parents(self): |
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self.assertEqual(qdb.artifact.Artifact(1).parents, []) |
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exp_parents = [qdb.artifact.Artifact(1)] |
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self.assertEqual(qdb.artifact.Artifact(2).parents, exp_parents) |
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self.assertEqual(qdb.artifact.Artifact(3).parents, exp_parents) |
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exp_parents = [qdb.artifact.Artifact(2)] |
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self.assertEqual(qdb.artifact.Artifact(4).parents, exp_parents) |
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def test_create_lineage_graph_from_edge_list_empty(self): |
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tester = qdb.artifact.Artifact(1) |
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obs = tester._create_lineage_graph_from_edge_list([]) |
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self.assertTrue(isinstance(obs, nx.DiGraph)) |
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self.assertCountEqual(obs.nodes(), [tester]) |
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self.assertCountEqual(obs.edges(), []) |
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def test_create_lineage_graph_from_edge_list(self): |
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tester = qdb.artifact.Artifact(1) |
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obs = tester._create_lineage_graph_from_edge_list( |
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[(1, 2), (2, 4), (1, 3), (3, 4)]) |
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self.assertTrue(isinstance(obs, nx.DiGraph)) |
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exp = [qdb.artifact.Artifact(1), qdb.artifact.Artifact(2), |
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qdb.artifact.Artifact(3), qdb.artifact.Artifact(4)] |
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self.assertCountEqual(obs.nodes(), exp) |
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exp = [(qdb.artifact.Artifact(1), qdb.artifact.Artifact(2)), |
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(qdb.artifact.Artifact(2), qdb.artifact.Artifact(4)), |
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(qdb.artifact.Artifact(1), qdb.artifact.Artifact(3)), |
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(qdb.artifact.Artifact(3), qdb.artifact.Artifact(4))] |
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self.assertCountEqual(obs.edges(), exp) |
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def test_ancestors(self): |
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obs = qdb.artifact.Artifact(1).ancestors |
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self.assertTrue(isinstance(obs, nx.DiGraph)) |
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obs_nodes = obs.nodes() |
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self.assertCountEqual(obs_nodes, [qdb.artifact.Artifact(1)]) |
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obs_edges = obs.edges() |
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self.assertCountEqual(obs_edges, []) |
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obs = qdb.artifact.Artifact(2).ancestors |
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self.assertTrue(isinstance(obs, nx.DiGraph)) |
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obs_nodes = obs.nodes() |
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exp_nodes = [qdb.artifact.Artifact(1), qdb.artifact.Artifact(2)] |
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self.assertCountEqual(obs_nodes, exp_nodes) |
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obs_edges = obs.edges() |
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exp_edges = [(qdb.artifact.Artifact(1), qdb.artifact.Artifact(2))] |
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self.assertCountEqual(obs_edges, exp_edges) |
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obs = qdb.artifact.Artifact(3).ancestors |
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self.assertTrue(isinstance(obs, nx.DiGraph)) |
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obs_nodes = obs.nodes() |
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exp_nodes = [qdb.artifact.Artifact(1), qdb.artifact.Artifact(3)] |
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self.assertCountEqual(obs_nodes, exp_nodes) |
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obs_edges = obs.edges() |
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exp_edges = [(qdb.artifact.Artifact(1), qdb.artifact.Artifact(3))] |
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self.assertCountEqual(obs_edges, exp_edges) |
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obs = qdb.artifact.Artifact(4).ancestors |
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self.assertTrue(isinstance(obs, nx.DiGraph)) |
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obs_nodes = obs.nodes() |
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exp_nodes = [qdb.artifact.Artifact(1), qdb.artifact.Artifact(2), |
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qdb.artifact.Artifact(4)] |
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self.assertCountEqual(obs_nodes, exp_nodes) |
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obs_edges = obs.edges() |
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exp_edges = [(qdb.artifact.Artifact(1), qdb.artifact.Artifact(2)), |
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(qdb.artifact.Artifact(2), qdb.artifact.Artifact(4))] |
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self.assertCountEqual(obs_edges, exp_edges) |
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def test_descendants(self): |
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obs = qdb.artifact.Artifact(1).descendants |
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self.assertTrue(isinstance(obs, nx.DiGraph)) |
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obs_nodes = obs.nodes() |
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exp_nodes = [qdb.artifact.Artifact(1), qdb.artifact.Artifact(2), |
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qdb.artifact.Artifact(3), qdb.artifact.Artifact(4), |
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|
312 |
qdb.artifact.Artifact(5), qdb.artifact.Artifact(6)] |
|
|
313 |
self.assertCountEqual(obs_nodes, exp_nodes) |
|
|
314 |
obs_edges = obs.edges() |
|
|
315 |
exp_edges = [(qdb.artifact.Artifact(1), qdb.artifact.Artifact(2)), |
|
|
316 |
(qdb.artifact.Artifact(1), qdb.artifact.Artifact(3)), |
|
|
317 |
(qdb.artifact.Artifact(2), qdb.artifact.Artifact(4)), |
|
|
318 |
(qdb.artifact.Artifact(2), qdb.artifact.Artifact(5)), |
|
|
319 |
(qdb.artifact.Artifact(2), qdb.artifact.Artifact(6))] |
|
|
320 |
self.assertCountEqual(obs_edges, exp_edges) |
|
|
321 |
|
|
|
322 |
obs = qdb.artifact.Artifact(2).descendants |
|
|
323 |
self.assertTrue(isinstance(obs, nx.DiGraph)) |
|
|
324 |
obs_nodes = obs.nodes() |
|
|
325 |
exp_nodes = [qdb.artifact.Artifact(2), qdb.artifact.Artifact(4), |
|
|
326 |
qdb.artifact.Artifact(5), qdb.artifact.Artifact(6)] |
|
|
327 |
self.assertCountEqual(obs_nodes, exp_nodes) |
|
|
328 |
obs_edges = obs.edges() |
|
|
329 |
exp_edges = [(qdb.artifact.Artifact(2), qdb.artifact.Artifact(4)), |
|
|
330 |
(qdb.artifact.Artifact(2), qdb.artifact.Artifact(5)), |
|
|
331 |
(qdb.artifact.Artifact(2), qdb.artifact.Artifact(6))] |
|
|
332 |
self.assertCountEqual(obs_edges, exp_edges) |
|
|
333 |
|
|
|
334 |
obs = qdb.artifact.Artifact(3).descendants |
|
|
335 |
self.assertTrue(isinstance(obs, nx.DiGraph)) |
|
|
336 |
obs_nodes = obs.nodes() |
|
|
337 |
self.assertCountEqual(obs_nodes, [qdb.artifact.Artifact(3)]) |
|
|
338 |
obs_edges = obs.edges() |
|
|
339 |
self.assertCountEqual(obs_edges, []) |
|
|
340 |
|
|
|
341 |
obs = qdb.artifact.Artifact(4).descendants |
|
|
342 |
self.assertTrue(isinstance(obs, nx.DiGraph)) |
|
|
343 |
obs_nodes = obs.nodes() |
|
|
344 |
self.assertCountEqual(obs_nodes, [qdb.artifact.Artifact(4)]) |
|
|
345 |
obs_edges = obs.edges() |
|
|
346 |
self.assertCountEqual(obs_edges, []) |
|
|
347 |
|
|
|
348 |
def test_descendants_with_jobs(self): |
|
|
349 |
A = qdb.artifact.Artifact |
|
|
350 |
obs = A(1).descendants_with_jobs |
|
|
351 |
self.assertTrue(isinstance(obs, nx.DiGraph)) |
|
|
352 |
obs_nodes = obs.nodes() |
|
|
353 |
|
|
|
354 |
# Add an HTML summary job in one artifact in a non-success statuts, to |
|
|
355 |
# make sure that it doesn't get returned in the graph |
|
|
356 |
html_job = qdb.processing_job.ProcessingJob.create( |
|
|
357 |
qdb.user.User('test@foo.bar'), |
|
|
358 |
qdb.software.Parameters.load( |
|
|
359 |
qdb.software.Command.get_html_generator(A(6).artifact_type), |
|
|
360 |
values_dict={'input_data': 6})) |
|
|
361 |
html_job._set_status('running') |
|
|
362 |
# as jobs are created at random we will only check that the artifacts |
|
|
363 |
# are there and that the number of jobs matches |
|
|
364 |
exp_nodes = [('artifact', A(1)), ('artifact', A(2)), |
|
|
365 |
('artifact', A(3)), ('artifact', A(4)), |
|
|
366 |
('artifact', A(5)), ('artifact', A(6))] |
|
|
367 |
for e in exp_nodes: |
|
|
368 |
self.assertIn(e, obs_nodes) |
|
|
369 |
self.assertEqual(5, len([e for dt, e in obs_nodes if dt == 'job'])) |
|
|
370 |
obs_edges = obs.edges() |
|
|
371 |
# as jobs are created at random we will only check the number of pairs |
|
|
372 |
# matches and they are instances of what we expect |
|
|
373 |
self.assertEqual(10, len(obs_edges)) |
|
|
374 |
self.assertEqual(2, len([x for x, y in obs_edges |
|
|
375 |
if x[1] == A(1) and y[0] == 'job'])) |
|
|
376 |
self.assertEqual(3, len([x for x, y in obs_edges |
|
|
377 |
if x[1] == A(2) and y[0] == 'job'])) |
|
|
378 |
self.assertEqual(1, len([y for x, y in obs_edges |
|
|
379 |
if y[1] == A(2) and x[0] == 'job'])) |
|
|
380 |
self.assertEqual(1, len([y for x, y in obs_edges |
|
|
381 |
if y[1] == A(3) and x[0] == 'job'])) |
|
|
382 |
self.assertEqual(1, len([y for x, y in obs_edges |
|
|
383 |
if y[1] == A(4) and x[0] == 'job'])) |
|
|
384 |
self.assertEqual(1, len([y for x, y in obs_edges |
|
|
385 |
if y[1] == A(5) and x[0] == 'job'])) |
|
|
386 |
self.assertEqual(1, len([y for x, y in obs_edges |
|
|
387 |
if y[1] == A(6) and x[0] == 'job'])) |
|
|
388 |
|
|
|
389 |
obs = A(3).descendants |
|
|
390 |
self.assertTrue(isinstance(obs, nx.DiGraph)) |
|
|
391 |
obs_nodes = obs.nodes() |
|
|
392 |
self.assertCountEqual(obs_nodes, [A(3)]) |
|
|
393 |
obs_edges = obs.edges() |
|
|
394 |
self.assertCountEqual(obs_edges, []) |
|
|
395 |
|
|
|
396 |
# Create a workflow starting in the artifact 1, so we can test that |
|
|
397 |
# "in construction" jobs also show up correctly |
|
|
398 |
json_str = ( |
|
|
399 |
'{"input_data": 1, "max_barcode_errors": 1.5, ' |
|
|
400 |
'"barcode_type": "8", "max_bad_run_length": 3, ' |
|
|
401 |
'"rev_comp": false, "phred_quality_threshold": 3, ' |
|
|
402 |
'"rev_comp_barcode": false, "rev_comp_mapping_barcodes": false, ' |
|
|
403 |
'"min_per_read_length_fraction": 0.75, "sequence_max_n": 0, ' |
|
|
404 |
'"phred_offset": "auto"}') |
|
|
405 |
params = qdb.software.Parameters.load(qdb.software.Command(1), |
|
|
406 |
json_str=json_str) |
|
|
407 |
wf = qdb.processing_job.ProcessingWorkflow.from_scratch( |
|
|
408 |
qdb.user.User('test@foo.bar'), params, name='Test WF') |
|
|
409 |
parent = list(wf.graph.nodes())[0] |
|
|
410 |
wf.add(qdb.software.DefaultParameters(10), |
|
|
411 |
connections={parent: {'demultiplexed': 'input_data'}}) |
|
|
412 |
obs = A(1).descendants_with_jobs |
|
|
413 |
obs_edges = obs.edges() |
|
|
414 |
# We have 4 more edges than before. From artifact 1 to parent job, |
|
|
415 |
# from parent job to output, from output to child job, and from child |
|
|
416 |
# job to child output |
|
|
417 |
self.assertEqual(len(obs_edges), 14) |
|
|
418 |
# We will check that the edges related with the "type" nodes (i.e. |
|
|
419 |
# the outputs of the jobs in construction) are present |
|
|
420 |
self.assertEqual(1, len([y for x, y in obs_edges if x[0] == 'type'])) |
|
|
421 |
self.assertEqual(2, len([y for x, y in obs_edges if y[0] == 'type'])) |
|
|
422 |
|
|
|
423 |
def test_children(self): |
|
|
424 |
exp = [qdb.artifact.Artifact(2), qdb.artifact.Artifact(3)] |
|
|
425 |
self.assertEqual(qdb.artifact.Artifact(1).children, exp) |
|
|
426 |
exp = [qdb.artifact.Artifact(4), qdb.artifact.Artifact(5), |
|
|
427 |
qdb.artifact.Artifact(6)] |
|
|
428 |
self.assertEqual(qdb.artifact.Artifact(2).children, exp) |
|
|
429 |
self.assertEqual(qdb.artifact.Artifact(3).children, []) |
|
|
430 |
self.assertEqual(qdb.artifact.Artifact(4).children, []) |
|
|
431 |
|
|
|
432 |
def test_youngest_artifact(self): |
|
|
433 |
exp = qdb.artifact.Artifact(6) |
|
|
434 |
self.assertEqual(qdb.artifact.Artifact(1).youngest_artifact, exp) |
|
|
435 |
self.assertEqual(qdb.artifact.Artifact(2).youngest_artifact, exp) |
|
|
436 |
self.assertEqual(qdb.artifact.Artifact(3).youngest_artifact, |
|
|
437 |
qdb.artifact.Artifact(3)) |
|
|
438 |
self.assertEqual(qdb.artifact.Artifact(6).youngest_artifact, exp) |
|
|
439 |
|
|
|
440 |
def test_prep_templates(self): |
|
|
441 |
self.assertEqual( |
|
|
442 |
qdb.artifact.Artifact(1).prep_templates, |
|
|
443 |
[qdb.metadata_template.prep_template.PrepTemplate(1)]) |
|
|
444 |
self.assertEqual( |
|
|
445 |
qdb.artifact.Artifact(2).prep_templates, |
|
|
446 |
[qdb.metadata_template.prep_template.PrepTemplate(1)]) |
|
|
447 |
self.assertEqual( |
|
|
448 |
qdb.artifact.Artifact(3).prep_templates, |
|
|
449 |
[qdb.metadata_template.prep_template.PrepTemplate(1)]) |
|
|
450 |
self.assertEqual( |
|
|
451 |
qdb.artifact.Artifact(4).prep_templates, |
|
|
452 |
[qdb.metadata_template.prep_template.PrepTemplate(1)]) |
|
|
453 |
|
|
|
454 |
def test_study(self): |
|
|
455 |
self.assertEqual(qdb.artifact.Artifact(1).study, qdb.study.Study(1)) |
|
|
456 |
self.assertIsNone(qdb.artifact.Artifact(9).study) |
|
|
457 |
|
|
|
458 |
def test_analysis(self): |
|
|
459 |
self.assertEqual(qdb.artifact.Artifact(9).analysis, |
|
|
460 |
qdb.analysis.Analysis(1)) |
|
|
461 |
self.assertIsNone(qdb.artifact.Artifact(1).analysis) |
|
|
462 |
|
|
|
463 |
def test_merging_scheme(self): |
|
|
464 |
self.assertEqual(qdb.artifact.Artifact(1).merging_scheme, ('', '')) |
|
|
465 |
self.assertEqual(qdb.artifact.Artifact(2).merging_scheme, |
|
|
466 |
('Split libraries FASTQ | N/A', 'N/A')) |
|
|
467 |
self.assertEqual(qdb.artifact.Artifact(3).merging_scheme, |
|
|
468 |
('Split libraries FASTQ | N/A', 'N/A')) |
|
|
469 |
self.assertEqual(qdb.artifact.Artifact(4).merging_scheme, |
|
|
470 |
('Pick closed-reference OTUs | Split libraries FASTQ', |
|
|
471 |
'QIIMEq2 v1.9.1')) |
|
|
472 |
self.assertEqual(qdb.artifact.Artifact(5).merging_scheme, |
|
|
473 |
('Pick closed-reference OTUs | Split libraries FASTQ', |
|
|
474 |
'QIIMEq2 v1.9.1')) |
|
|
475 |
|
|
|
476 |
def test_jobs(self): |
|
|
477 |
# Returning all jobs |
|
|
478 |
obs = qdb.artifact.Artifact(1).jobs(show_hidden=True) |
|
|
479 |
exp = [ |
|
|
480 |
qdb.processing_job.ProcessingJob( |
|
|
481 |
'6d368e16-2242-4cf8-87b4-a5dc40bb890b'), |
|
|
482 |
qdb.processing_job.ProcessingJob( |
|
|
483 |
'4c7115e8-4c8e-424c-bf25-96c292ca1931'), |
|
|
484 |
qdb.processing_job.ProcessingJob( |
|
|
485 |
'063e553b-327c-4818-ab4a-adfe58e49860'), |
|
|
486 |
qdb.processing_job.ProcessingJob( |
|
|
487 |
'bcc7ebcd-39c1-43e4-af2d-822e3589f14d'), |
|
|
488 |
qdb.processing_job.ProcessingJob( |
|
|
489 |
'b72369f9-a886-4193-8d3d-f7b504168e75')] |
|
|
490 |
|
|
|
491 |
# there are some extra jobs randomly generated, not testing those |
|
|
492 |
for e in exp: |
|
|
493 |
self.assertIn(e, obs) |
|
|
494 |
|
|
|
495 |
# Returning only jobs visible by the user |
|
|
496 |
obs = qdb.artifact.Artifact(1).jobs() |
|
|
497 |
exp = [ |
|
|
498 |
qdb.processing_job.ProcessingJob( |
|
|
499 |
'6d368e16-2242-4cf8-87b4-a5dc40bb890b'), |
|
|
500 |
qdb.processing_job.ProcessingJob( |
|
|
501 |
'4c7115e8-4c8e-424c-bf25-96c292ca1931'), |
|
|
502 |
qdb.processing_job.ProcessingJob( |
|
|
503 |
'b72369f9-a886-4193-8d3d-f7b504168e75')] |
|
|
504 |
|
|
|
505 |
for e in exp: |
|
|
506 |
self.assertIn(e, obs) |
|
|
507 |
|
|
|
508 |
def test_jobs_cmd(self): |
|
|
509 |
cmd = qdb.software.Command(1) |
|
|
510 |
obs = qdb.artifact.Artifact(1).jobs(cmd=cmd, show_hidden=True) |
|
|
511 |
exp = [ |
|
|
512 |
qdb.processing_job.ProcessingJob( |
|
|
513 |
'6d368e16-2242-4cf8-87b4-a5dc40bb890b'), |
|
|
514 |
qdb.processing_job.ProcessingJob( |
|
|
515 |
'4c7115e8-4c8e-424c-bf25-96c292ca1931'), |
|
|
516 |
qdb.processing_job.ProcessingJob( |
|
|
517 |
'063e553b-327c-4818-ab4a-adfe58e49860'), |
|
|
518 |
qdb.processing_job.ProcessingJob( |
|
|
519 |
'b72369f9-a886-4193-8d3d-f7b504168e75') |
|
|
520 |
] |
|
|
521 |
# there are some extra jobs randomly generated, not testing those |
|
|
522 |
for e in exp: |
|
|
523 |
self.assertIn(e, obs) |
|
|
524 |
|
|
|
525 |
obs = qdb.artifact.Artifact(1).jobs(cmd=cmd) |
|
|
526 |
exp = [ |
|
|
527 |
qdb.processing_job.ProcessingJob( |
|
|
528 |
'6d368e16-2242-4cf8-87b4-a5dc40bb890b'), |
|
|
529 |
qdb.processing_job.ProcessingJob( |
|
|
530 |
'4c7115e8-4c8e-424c-bf25-96c292ca1931'), |
|
|
531 |
qdb.processing_job.ProcessingJob( |
|
|
532 |
'b72369f9-a886-4193-8d3d-f7b504168e75') |
|
|
533 |
] |
|
|
534 |
|
|
|
535 |
cmd = qdb.software.Command(2) |
|
|
536 |
obs = qdb.artifact.Artifact(1).jobs(cmd=cmd, show_hidden=True) |
|
|
537 |
exp = [qdb.processing_job.ProcessingJob( |
|
|
538 |
'bcc7ebcd-39c1-43e4-af2d-822e3589f14d')] |
|
|
539 |
self.assertEqual(obs, exp) |
|
|
540 |
|
|
|
541 |
obs = qdb.artifact.Artifact(1).jobs(cmd=cmd) |
|
|
542 |
self.assertEqual(obs, []) |
|
|
543 |
|
|
|
544 |
def test_jobs_status(self): |
|
|
545 |
obs = qdb.artifact.Artifact(1).jobs(status='success') |
|
|
546 |
exp = [ |
|
|
547 |
qdb.processing_job.ProcessingJob( |
|
|
548 |
'6d368e16-2242-4cf8-87b4-a5dc40bb890b'), |
|
|
549 |
qdb.processing_job.ProcessingJob( |
|
|
550 |
'4c7115e8-4c8e-424c-bf25-96c292ca1931'), |
|
|
551 |
qdb.processing_job.ProcessingJob( |
|
|
552 |
'b72369f9-a886-4193-8d3d-f7b504168e75') |
|
|
553 |
] |
|
|
554 |
# there are some extra jobs randomly generated, not testing those |
|
|
555 |
for e in exp: |
|
|
556 |
self.assertIn(e, obs) |
|
|
557 |
|
|
|
558 |
obs = qdb.artifact.Artifact(1).jobs(status='running', show_hidden=True) |
|
|
559 |
exp = [qdb.processing_job.ProcessingJob( |
|
|
560 |
'bcc7ebcd-39c1-43e4-af2d-822e3589f14d')] |
|
|
561 |
self.assertEqual(obs, exp) |
|
|
562 |
|
|
|
563 |
obs = qdb.artifact.Artifact(1).jobs(status='running') |
|
|
564 |
self.assertEqual(obs, []) |
|
|
565 |
|
|
|
566 |
obs = qdb.artifact.Artifact(1).jobs(status='queued', show_hidden=True) |
|
|
567 |
exp = [qdb.processing_job.ProcessingJob( |
|
|
568 |
'063e553b-327c-4818-ab4a-adfe58e49860')] |
|
|
569 |
self.assertEqual(obs, exp) |
|
|
570 |
|
|
|
571 |
obs = qdb.artifact.Artifact(1).jobs(status='queued') |
|
|
572 |
self.assertEqual(obs, []) |
|
|
573 |
|
|
|
574 |
def test_jobs_cmd_and_status(self): |
|
|
575 |
cmd = qdb.software.Command(1) |
|
|
576 |
obs = qdb.artifact.Artifact(1).jobs(cmd=cmd, status='success') |
|
|
577 |
exp = [ |
|
|
578 |
qdb.processing_job.ProcessingJob( |
|
|
579 |
'6d368e16-2242-4cf8-87b4-a5dc40bb890b'), |
|
|
580 |
qdb.processing_job.ProcessingJob( |
|
|
581 |
'4c7115e8-4c8e-424c-bf25-96c292ca1931'), |
|
|
582 |
qdb.processing_job.ProcessingJob( |
|
|
583 |
'b72369f9-a886-4193-8d3d-f7b504168e75') |
|
|
584 |
] |
|
|
585 |
# there are some extra jobs randomly generated, not testing those |
|
|
586 |
for e in exp: |
|
|
587 |
self.assertIn(e, obs) |
|
|
588 |
|
|
|
589 |
obs = qdb.artifact.Artifact(1).jobs(cmd=cmd, status='queued', |
|
|
590 |
show_hidden=True) |
|
|
591 |
exp = [qdb.processing_job.ProcessingJob( |
|
|
592 |
'063e553b-327c-4818-ab4a-adfe58e49860')] |
|
|
593 |
self.assertEqual(obs, exp) |
|
|
594 |
|
|
|
595 |
obs = qdb.artifact.Artifact(1).jobs(cmd=cmd, status='queued') |
|
|
596 |
self.assertEqual(obs, []) |
|
|
597 |
|
|
|
598 |
cmd = qdb.software.Command(2) |
|
|
599 |
obs = qdb.artifact.Artifact(1).jobs(cmd=cmd, status='queued') |
|
|
600 |
exp = [] |
|
|
601 |
self.assertEqual(obs, exp) |
|
|
602 |
|
|
|
603 |
def test_get_commands(self): |
|
|
604 |
# we will check only ids for simplicity |
|
|
605 |
# checking processing artifacts |
|
|
606 |
obs = [c.id for c in qdb.artifact.Artifact(1).get_commands] |
|
|
607 |
self.assertEqual(obs, [1]) |
|
|
608 |
obs = [c.id for c in qdb.artifact.Artifact(2).get_commands] |
|
|
609 |
self.assertEqual(obs, [3]) |
|
|
610 |
# this is a biom in processing, so no commands should be available |
|
|
611 |
obs = [c.id for c in qdb.artifact.Artifact(6).get_commands] |
|
|
612 |
self.assertEqual(obs, []) |
|
|
613 |
|
|
|
614 |
# checking analysis object - this is a biom in analysis, several |
|
|
615 |
# commands should be available |
|
|
616 |
obs = [c.id for c in qdb.artifact.Artifact(8).get_commands] |
|
|
617 |
self.assertEqual(obs, [9, 10, 11, 12]) |
|
|
618 |
|
|
|
619 |
|
|
|
620 |
@qiita_test_checker() |
|
|
621 |
class ArtifactTests(TestCase): |
|
|
622 |
def setUp(self): |
|
|
623 |
# Generate some files for a root artifact |
|
|
624 |
fd, self.fp1 = mkstemp(suffix='_seqs.fastq') |
|
|
625 |
close(fd) |
|
|
626 |
with open(self.fp1, 'w') as f: |
|
|
627 |
f.write("@HWI-ST753:189:D1385ACXX:1:1101:1214:1906 1:N:0:\n" |
|
|
628 |
"NACGTAGGGTGCAAGCGTTGTCCGGAATNA\n" |
|
|
629 |
"+\n" |
|
|
630 |
"#1=DDFFFHHHHHJJJJJJJJJJJJGII#0\n") |
|
|
631 |
|
|
|
632 |
fd, self.fp2 = mkstemp(suffix='_barcodes.fastq') |
|
|
633 |
close(fd) |
|
|
634 |
with open(self.fp2, 'w') as f: |
|
|
635 |
f.write("@HWI-ST753:189:D1385ACXX:1:1101:1214:1906 2:N:0:\n" |
|
|
636 |
"NNNCNNNNNNNNN\n" |
|
|
637 |
"+\n" |
|
|
638 |
"#############\n") |
|
|
639 |
self.filepaths_root = [(self.fp1, 1), (self.fp2, 3)] |
|
|
640 |
|
|
|
641 |
# Generate some files for a processed artifact |
|
|
642 |
fd, self.fp3 = mkstemp(suffix='_seqs.fna') |
|
|
643 |
close(fd) |
|
|
644 |
with open(self.fp3, 'w') as f: |
|
|
645 |
f.write(">1.sid_r4_0 M02034:17:000000000-A5U18:1:1101:15370:1394 " |
|
|
646 |
"1:N:0:1 orig_bc=CATGAGCT new_bc=CATGAGCT bc_diffs=0\n" |
|
|
647 |
"GTGTGCCAGCAGCCGCGGTAATACGTAGGG\n") |
|
|
648 |
self.filepaths_processed = [(self.fp3, 4)] |
|
|
649 |
|
|
|
650 |
# Generate some file for a BIOM |
|
|
651 |
fd, self.fp4 = mkstemp(suffix='_table.biom') |
|
|
652 |
with biom_open(self.fp4, 'w') as f: |
|
|
653 |
et.to_hdf5(f, "test") |
|
|
654 |
self.filepaths_biom = [(self.fp4, 7)] |
|
|
655 |
|
|
|
656 |
# Create a new prep template |
|
|
657 |
metadata_dict = { |
|
|
658 |
'SKB8.640193': {'center_name': 'ANL', |
|
|
659 |
'primer': 'GTGCCAGCMGCCGCGGTAA', |
|
|
660 |
'barcode': 'GTCCGCAAGTTA', |
|
|
661 |
'run_prefix': "s_G1_L001_sequences", |
|
|
662 |
'platform': 'Illumina', |
|
|
663 |
'instrument_model': 'Illumina MiSeq', |
|
|
664 |
'library_construction_protocol': 'AAAA', |
|
|
665 |
'target_subfragment': 'V4', |
|
|
666 |
'target_gene': '16S rRNA', |
|
|
667 |
'experiment_design_description': 'BBBB'}} |
|
|
668 |
metadata = pd.DataFrame.from_dict(metadata_dict, orient='index', |
|
|
669 |
dtype=str) |
|
|
670 |
self.prep_template = \ |
|
|
671 |
qdb.metadata_template.prep_template.PrepTemplate.create( |
|
|
672 |
metadata, qdb.study.Study(1), "16S") |
|
|
673 |
self.prep_template_2 = \ |
|
|
674 |
qdb.metadata_template.prep_template.PrepTemplate.create( |
|
|
675 |
metadata, qdb.study.Study(1), "16S") |
|
|
676 |
|
|
|
677 |
self._clean_up_files = [self.fp1, self.fp2, self.fp3, self.fp4] |
|
|
678 |
|
|
|
679 |
# per_sample_FASTQ Metagenomic example |
|
|
680 |
|
|
|
681 |
self.prep_template_per_sample_fastq = \ |
|
|
682 |
qdb.metadata_template.prep_template.PrepTemplate.create( |
|
|
683 |
metadata, qdb.study.Study(1), "Metagenomic") |
|
|
684 |
fd, self.fwd = mkstemp(prefix='SKB8.640193', suffix='_R1.fastq') |
|
|
685 |
close(fd) |
|
|
686 |
with open(self.fwd, 'w') as f: |
|
|
687 |
f.write("@HWI-ST753:189:D1385ACXX:1:1101:1214:1906 1:N:0:\n" |
|
|
688 |
"NACGTAGGGTGCAAGCGTTGTCCGGAATNA\n" |
|
|
689 |
"+\n" |
|
|
690 |
"#1=DDFFFHHHHHJJJJJJJJJJJJGII#0\n") |
|
|
691 |
fd, self.rev = mkstemp(prefix='SKB8.640193', suffix='_R2.fastq') |
|
|
692 |
close(fd) |
|
|
693 |
with open(self.rev, 'w') as f: |
|
|
694 |
f.write("@HWI-ST753:189:D1385ACXX:1:1101:1214:1906 1:N:0:\n" |
|
|
695 |
"NACGTAGGGTGCAAGCGTTGTCCGGAATNA\n" |
|
|
696 |
"+\n" |
|
|
697 |
"#1=DDFFFHHHHHJJJJJJJJJJJJGII#0\n") |
|
|
698 |
|
|
|
699 |
self._clean_up_files.extend([self.fwd, self.rev]) |
|
|
700 |
|
|
|
701 |
self.user = qdb.user.User('test@foo.bar') |
|
|
702 |
|
|
|
703 |
def tearDown(self): |
|
|
704 |
for f in self._clean_up_files: |
|
|
705 |
if exists(f): |
|
|
706 |
remove(f) |
|
|
707 |
|
|
|
708 |
def test_copy(self): |
|
|
709 |
src = qdb.artifact.Artifact.create( |
|
|
710 |
self.filepaths_root, "FASTQ", prep_template=self.prep_template) |
|
|
711 |
before = datetime.now() |
|
|
712 |
obs = qdb.artifact.Artifact.copy(src, self.prep_template_2) |
|
|
713 |
|
|
|
714 |
self.assertTrue(before < obs.timestamp < datetime.now()) |
|
|
715 |
self.assertIsNone(obs.processing_parameters) |
|
|
716 |
self.assertEqual(obs.visibility, 'sandbox') |
|
|
717 |
self.assertEqual(obs.artifact_type, src.artifact_type) |
|
|
718 |
self.assertEqual(obs.data_type, self.prep_template.data_type()) |
|
|
719 |
self.assertEqual(obs.can_be_submitted_to_ebi, |
|
|
720 |
src.can_be_submitted_to_ebi) |
|
|
721 |
self.assertEqual(obs.can_be_submitted_to_vamps, |
|
|
722 |
src.can_be_submitted_to_vamps) |
|
|
723 |
|
|
|
724 |
db_dir = qdb.util.get_mountpoint(src.artifact_type)[0][1] |
|
|
725 |
path_builder = partial(join, db_dir, str(obs.id)) |
|
|
726 |
exp_fps = [] |
|
|
727 |
for x in src.filepaths: |
|
|
728 |
new_fp = path_builder(basename(x['fp'])) |
|
|
729 |
exp_fps.append((new_fp, x['fp_type'])) |
|
|
730 |
self._clean_up_files.append(new_fp) |
|
|
731 |
|
|
|
732 |
self.assertEqual([(x['fp'], x['fp_type']) |
|
|
733 |
for x in obs.filepaths], exp_fps) |
|
|
734 |
self.assertEqual(obs.parents, []) |
|
|
735 |
self.assertEqual(obs.prep_templates, [self.prep_template_2]) |
|
|
736 |
|
|
|
737 |
self.assertEqual(obs.study, qdb.study.Study(1)) |
|
|
738 |
|
|
|
739 |
def test_create_error(self): |
|
|
740 |
# no filepaths |
|
|
741 |
with self.assertRaises(qdb.exceptions.QiitaDBArtifactCreationError): |
|
|
742 |
qdb.artifact.Artifact.create( |
|
|
743 |
[], "FASTQ", prep_template=self.prep_template) |
|
|
744 |
|
|
|
745 |
# prep template and parents |
|
|
746 |
with self.assertRaises(qdb.exceptions.QiitaDBArtifactCreationError): |
|
|
747 |
qdb.artifact.Artifact.create( |
|
|
748 |
self.filepaths_root, "FASTQ", prep_template=self.prep_template, |
|
|
749 |
parents=[qdb.artifact.Artifact(1)]) |
|
|
750 |
|
|
|
751 |
# analysis and prep_template |
|
|
752 |
with self.assertRaises(qdb.exceptions.QiitaDBArtifactCreationError): |
|
|
753 |
qdb.artifact.Artifact.create( |
|
|
754 |
self.filepaths_root, "BIOM", prep_template=self.prep_template, |
|
|
755 |
analysis=qdb.analysis.Analysis(1)) |
|
|
756 |
|
|
|
757 |
# Analysis and parents |
|
|
758 |
with self.assertRaises(qdb.exceptions.QiitaDBArtifactCreationError): |
|
|
759 |
qdb.artifact.Artifact.create( |
|
|
760 |
self.filepaths_root, "BIOM", |
|
|
761 |
parents=[qdb.artifact.Artifact(1)], |
|
|
762 |
analysis=qdb.analysis.Analysis(1)) |
|
|
763 |
|
|
|
764 |
# no prep template no parents no analysis |
|
|
765 |
with self.assertRaises(qdb.exceptions.QiitaDBArtifactCreationError): |
|
|
766 |
qdb.artifact.Artifact.create(self.filepaths_root, "FASTQ") |
|
|
767 |
|
|
|
768 |
# parents no processing parameters |
|
|
769 |
with self.assertRaises(qdb.exceptions.QiitaDBArtifactCreationError): |
|
|
770 |
qdb.artifact.Artifact.create( |
|
|
771 |
self.filepaths_root, "FASTQ", |
|
|
772 |
parents=[qdb.artifact.Artifact(1)]) |
|
|
773 |
|
|
|
774 |
# analysis no data type |
|
|
775 |
with self.assertRaises(qdb.exceptions.QiitaDBArtifactCreationError): |
|
|
776 |
qdb.artifact.Artifact.create( |
|
|
777 |
self.filepaths_root, "BIOM", analysis=qdb.analysis.Analysis(1)) |
|
|
778 |
|
|
|
779 |
# prep template and processing parameters |
|
|
780 |
parameters = qdb.software.Parameters.from_default_params( |
|
|
781 |
qdb.software.DefaultParameters(1), {'input_data': 1}) |
|
|
782 |
with self.assertRaises(qdb.exceptions.QiitaDBArtifactCreationError): |
|
|
783 |
qdb.artifact.Artifact.create( |
|
|
784 |
self.filepaths_root, "FASTQ", prep_template=self.prep_template, |
|
|
785 |
processing_parameters=parameters) |
|
|
786 |
|
|
|
787 |
# prep template and data type |
|
|
788 |
with self.assertRaises(qdb.exceptions.QiitaDBArtifactCreationError): |
|
|
789 |
qdb.artifact.Artifact.create( |
|
|
790 |
self.filepaths_root, "FASTQ", prep_template=self.prep_template, |
|
|
791 |
data_type="Multiomic") |
|
|
792 |
|
|
|
793 |
# different data types |
|
|
794 |
new = qdb.artifact.Artifact.create( |
|
|
795 |
self.filepaths_root, "FASTQ", prep_template=self.prep_template) |
|
|
796 |
parameters = qdb.software.Parameters.from_default_params( |
|
|
797 |
qdb.software.DefaultParameters(1), {'input_data': 1}) |
|
|
798 |
with self.assertRaises(qdb.exceptions.QiitaDBArtifactCreationError): |
|
|
799 |
qdb.artifact.Artifact.create( |
|
|
800 |
self.filepaths_processed, "Demultiplexed", |
|
|
801 |
parents=[qdb.artifact.Artifact(1), new], |
|
|
802 |
processing_parameters=parameters) |
|
|
803 |
|
|
|
804 |
def test_create_root(self): |
|
|
805 |
before = datetime.now() |
|
|
806 |
obs = qdb.artifact.Artifact.create( |
|
|
807 |
self.filepaths_root, "FASTQ", prep_template=self.prep_template, |
|
|
808 |
name='Test artifact') |
|
|
809 |
self.assertEqual(obs.name, 'Test artifact') |
|
|
810 |
self.assertTrue(before < obs.timestamp < datetime.now()) |
|
|
811 |
self.assertIsNone(obs.processing_parameters) |
|
|
812 |
self.assertEqual(obs.visibility, 'sandbox') |
|
|
813 |
self.assertEqual(obs.artifact_type, "FASTQ") |
|
|
814 |
self.assertEqual(obs.data_type, self.prep_template.data_type()) |
|
|
815 |
self.assertFalse(obs.can_be_submitted_to_ebi) |
|
|
816 |
self.assertFalse(obs.can_be_submitted_to_vamps) |
|
|
817 |
|
|
|
818 |
db_fastq_dir = qdb.util.get_mountpoint('FASTQ')[0][1] |
|
|
819 |
path_builder = partial(join, db_fastq_dir, str(obs.id)) |
|
|
820 |
exp_fps = [ |
|
|
821 |
(path_builder(basename(self.fp1)), "raw_forward_seqs"), |
|
|
822 |
(path_builder(basename(self.fp2)), "raw_barcodes")] |
|
|
823 |
self.assertEqual([(x['fp'], x['fp_type']) |
|
|
824 |
for x in obs.filepaths], exp_fps) |
|
|
825 |
self.assertEqual(obs.parents, []) |
|
|
826 |
self.assertEqual(obs.prep_templates, [self.prep_template]) |
|
|
827 |
|
|
|
828 |
with self.assertRaises( |
|
|
829 |
qdb.exceptions.QiitaDBOperationNotPermittedError): |
|
|
830 |
obs.ebi_run_accessions |
|
|
831 |
|
|
|
832 |
with self.assertRaises( |
|
|
833 |
qdb.exceptions.QiitaDBOperationNotPermittedError): |
|
|
834 |
obs.is_submitted_to_vamps |
|
|
835 |
|
|
|
836 |
self.assertEqual(obs.study, qdb.study.Study(1)) |
|
|
837 |
self.assertIsNone(obs.analysis) |
|
|
838 |
|
|
|
839 |
def test_create_root_analysis(self): |
|
|
840 |
before = datetime.now() |
|
|
841 |
obs = qdb.artifact.Artifact.create( |
|
|
842 |
self.filepaths_biom, "BIOM", name='Test artifact analysis', |
|
|
843 |
analysis=qdb.analysis.Analysis(1), data_type="16S") |
|
|
844 |
self.assertEqual(obs.name, 'Test artifact analysis') |
|
|
845 |
self.assertTrue(before < obs.timestamp < datetime.now()) |
|
|
846 |
self.assertIsNone(obs.processing_parameters) |
|
|
847 |
self.assertEqual(obs.visibility, 'sandbox') |
|
|
848 |
self.assertEqual(obs.artifact_type, "BIOM") |
|
|
849 |
self.assertEqual(obs.data_type, "16S") |
|
|
850 |
self.assertFalse(obs.can_be_submitted_to_ebi) |
|
|
851 |
self.assertFalse(obs.can_be_submitted_to_vamps) |
|
|
852 |
|
|
|
853 |
db_fastq_dir = qdb.util.get_mountpoint('BIOM')[0][1] |
|
|
854 |
path_builder = partial(join, db_fastq_dir, str(obs.id)) |
|
|
855 |
exp_fps = [(path_builder(basename(self.fp4)), "biom")] |
|
|
856 |
self.assertEqual([(x['fp'], x['fp_type']) |
|
|
857 |
for x in obs.filepaths], exp_fps) |
|
|
858 |
self.assertEqual(obs.parents, []) |
|
|
859 |
self.assertEqual(obs.prep_templates, []) |
|
|
860 |
|
|
|
861 |
with self.assertRaises( |
|
|
862 |
qdb.exceptions.QiitaDBOperationNotPermittedError): |
|
|
863 |
obs.ebi_run_accessions |
|
|
864 |
|
|
|
865 |
with self.assertRaises( |
|
|
866 |
qdb.exceptions.QiitaDBOperationNotPermittedError): |
|
|
867 |
obs.is_submitted_to_vamps |
|
|
868 |
|
|
|
869 |
self.assertIsNone(obs.study) |
|
|
870 |
self.assertEqual(obs.analysis, qdb.analysis.Analysis(1)) |
|
|
871 |
|
|
|
872 |
# testing that it can be deleted |
|
|
873 |
qdb.artifact.Artifact.delete(obs.id) |
|
|
874 |
|
|
|
875 |
def test_create_processed(self): |
|
|
876 |
# make a copy of files for the can_be_submitted_to_ebi tests |
|
|
877 |
lcopy = self.fp3 + '.fna' |
|
|
878 |
self._clean_up_files.append(lcopy) |
|
|
879 |
copyfile(self.fp3, lcopy) |
|
|
880 |
|
|
|
881 |
exp_params = qdb.software.Parameters.from_default_params( |
|
|
882 |
qdb.software.DefaultParameters(1), {'input_data': 1}) |
|
|
883 |
before = datetime.now() |
|
|
884 |
obs = qdb.artifact.Artifact.create( |
|
|
885 |
self.filepaths_processed, "Demultiplexed", |
|
|
886 |
parents=[qdb.artifact.Artifact(1)], |
|
|
887 |
processing_parameters=exp_params) |
|
|
888 |
self.assertEqual(obs.name, 'noname') |
|
|
889 |
self.assertTrue(before < obs.timestamp < datetime.now()) |
|
|
890 |
self.assertEqual(obs.processing_parameters, exp_params) |
|
|
891 |
self.assertEqual(obs.visibility, 'private') |
|
|
892 |
self.assertEqual(obs.artifact_type, "Demultiplexed") |
|
|
893 |
self.assertEqual(obs.data_type, qdb.artifact.Artifact(1).data_type) |
|
|
894 |
self.assertTrue(obs.can_be_submitted_to_ebi) |
|
|
895 |
self.assertTrue(obs.can_be_submitted_to_vamps) |
|
|
896 |
self.assertFalse(obs.is_submitted_to_vamps) |
|
|
897 |
|
|
|
898 |
db_demultiplexed_dir = qdb.util.get_mountpoint('Demultiplexed')[0][1] |
|
|
899 |
path_builder = partial(join, db_demultiplexed_dir, str(obs.id)) |
|
|
900 |
exp_fps = [(path_builder(basename(self.fp3)), |
|
|
901 |
"preprocessed_fasta")] |
|
|
902 |
self.assertEqual([(x['fp'], x['fp_type']) |
|
|
903 |
for x in obs.filepaths], exp_fps) |
|
|
904 |
self.assertEqual(obs.parents, [qdb.artifact.Artifact(1)]) |
|
|
905 |
self.assertEqual( |
|
|
906 |
obs.prep_templates, |
|
|
907 |
[qdb.metadata_template.prep_template.PrepTemplate(1)]) |
|
|
908 |
self.assertEqual(obs.ebi_run_accessions, dict()) |
|
|
909 |
self.assertEqual(obs.study, qdb.study.Study(1)) |
|
|
910 |
self.assertFalse(exists(self.filepaths_processed[0][0])) |
|
|
911 |
self.assertIsNone(obs.analysis) |
|
|
912 |
|
|
|
913 |
# let's create another demultiplexed on top of the previous one to |
|
|
914 |
# test can_be_submitted_to_ebi |
|
|
915 |
exp_params = qdb.software.Parameters.from_default_params( |
|
|
916 |
qdb.software.DefaultParameters(1), {'input_data': obs.id}) |
|
|
917 |
new = qdb.artifact.Artifact.create( |
|
|
918 |
[(lcopy, 4)], "Demultiplexed", parents=[obs], |
|
|
919 |
processing_parameters=exp_params) |
|
|
920 |
self.assertFalse(new.can_be_submitted_to_ebi) |
|
|
921 |
|
|
|
922 |
def test_create_copy_files(self): |
|
|
923 |
exp_params = qdb.software.Parameters.from_default_params( |
|
|
924 |
qdb.software.DefaultParameters(1), {'input_data': 1}) |
|
|
925 |
before = datetime.now() |
|
|
926 |
obs = qdb.artifact.Artifact.create( |
|
|
927 |
self.filepaths_processed, "Demultiplexed", |
|
|
928 |
parents=[qdb.artifact.Artifact(1)], |
|
|
929 |
processing_parameters=exp_params, move_files=False) |
|
|
930 |
self.assertEqual(obs.name, 'noname') |
|
|
931 |
self.assertTrue(before < obs.timestamp < datetime.now()) |
|
|
932 |
self.assertEqual(obs.processing_parameters, exp_params) |
|
|
933 |
self.assertEqual(obs.visibility, 'private') |
|
|
934 |
self.assertEqual(obs.artifact_type, "Demultiplexed") |
|
|
935 |
self.assertEqual(obs.data_type, qdb.artifact.Artifact(1).data_type) |
|
|
936 |
self.assertTrue(obs.can_be_submitted_to_ebi) |
|
|
937 |
self.assertTrue(obs.can_be_submitted_to_vamps) |
|
|
938 |
self.assertFalse(obs.is_submitted_to_vamps) |
|
|
939 |
|
|
|
940 |
db_demultiplexed_dir = qdb.util.get_mountpoint('Demultiplexed')[0][1] |
|
|
941 |
path_builder = partial(join, db_demultiplexed_dir, str(obs.id)) |
|
|
942 |
exp_fps = [(path_builder(basename(self.fp3)), |
|
|
943 |
"preprocessed_fasta")] |
|
|
944 |
self.assertEqual([(x['fp'], x['fp_type']) |
|
|
945 |
for x in obs.filepaths], exp_fps) |
|
|
946 |
self.assertEqual(obs.parents, [qdb.artifact.Artifact(1)]) |
|
|
947 |
self.assertEqual( |
|
|
948 |
obs.prep_templates, |
|
|
949 |
[qdb.metadata_template.prep_template.PrepTemplate(1)]) |
|
|
950 |
self.assertEqual(obs.ebi_run_accessions, dict()) |
|
|
951 |
self.assertEqual(obs.study, qdb.study.Study(1)) |
|
|
952 |
self.assertTrue(exists(self.filepaths_processed[0][0])) |
|
|
953 |
self.assertIsNone(obs.analysis) |
|
|
954 |
|
|
|
955 |
def test_create_biom(self): |
|
|
956 |
before = datetime.now() |
|
|
957 |
cmd = qdb.software.Command(3) |
|
|
958 |
exp_params = qdb.software.Parameters.from_default_params( |
|
|
959 |
next(cmd.default_parameter_sets), {'input_data': 1}) |
|
|
960 |
obs = qdb.artifact.Artifact.create( |
|
|
961 |
self.filepaths_biom, "BIOM", parents=[qdb.artifact.Artifact(2)], |
|
|
962 |
processing_parameters=exp_params) |
|
|
963 |
self.assertEqual(obs.name, 'noname') |
|
|
964 |
self.assertTrue(before < obs.timestamp < datetime.now()) |
|
|
965 |
self.assertEqual(obs.processing_parameters, exp_params) |
|
|
966 |
self.assertEqual(obs.visibility, 'private') |
|
|
967 |
self.assertEqual(obs.artifact_type, 'BIOM') |
|
|
968 |
self.assertEqual(obs.data_type, qdb.artifact.Artifact(2).data_type) |
|
|
969 |
self.assertFalse(obs.can_be_submitted_to_ebi) |
|
|
970 |
self.assertFalse(obs.can_be_submitted_to_vamps) |
|
|
971 |
with self.assertRaises( |
|
|
972 |
qdb.exceptions.QiitaDBOperationNotPermittedError): |
|
|
973 |
obs.ebi_run_accessions |
|
|
974 |
|
|
|
975 |
with self.assertRaises( |
|
|
976 |
qdb.exceptions.QiitaDBOperationNotPermittedError): |
|
|
977 |
obs.is_submitted_to_vamps |
|
|
978 |
|
|
|
979 |
db_biom_dir = qdb.util.get_mountpoint('BIOM')[0][1] |
|
|
980 |
path_builder = partial(join, db_biom_dir, str(obs.id)) |
|
|
981 |
exp_fps = [(path_builder(basename(self.fp4)), 'biom')] |
|
|
982 |
self.assertEqual([(x['fp'], x['fp_type']) |
|
|
983 |
for x in obs.filepaths], exp_fps) |
|
|
984 |
self.assertEqual(obs.parents, [qdb.artifact.Artifact(2)]) |
|
|
985 |
self.assertEqual(obs.prep_templates, |
|
|
986 |
[qdb.metadata_template.prep_template.PrepTemplate(1)]) |
|
|
987 |
self.assertEqual(obs.study, qdb.study.Study(1)) |
|
|
988 |
self.assertIsNone(obs.analysis) |
|
|
989 |
|
|
|
990 |
def test_delete_error_public(self): |
|
|
991 |
test = qdb.artifact.Artifact.create( |
|
|
992 |
self.filepaths_root, "FASTQ", prep_template=self.prep_template) |
|
|
993 |
test.visibility = "public" |
|
|
994 |
self._clean_up_files.extend([x['fp'] for x in test.filepaths]) |
|
|
995 |
with self.assertRaises(qdb.exceptions.QiitaDBArtifactDeletionError): |
|
|
996 |
qdb.artifact.Artifact.delete(test.id) |
|
|
997 |
|
|
|
998 |
def test_delete_error_has_children(self): |
|
|
999 |
with self.assertRaises(qdb.exceptions.QiitaDBArtifactDeletionError): |
|
|
1000 |
qdb.artifact.Artifact.delete(1) |
|
|
1001 |
|
|
|
1002 |
def test_delete_error_analyzed(self): |
|
|
1003 |
with self.assertRaises(qdb.exceptions.QiitaDBArtifactDeletionError): |
|
|
1004 |
qdb.artifact.Artifact.delete(4) |
|
|
1005 |
|
|
|
1006 |
def test_delete_error_ebi(self): |
|
|
1007 |
parameters = qdb.software.Parameters.from_default_params( |
|
|
1008 |
qdb.software.DefaultParameters(1), {'input_data': 1}) |
|
|
1009 |
obs = qdb.artifact.Artifact.create( |
|
|
1010 |
self.filepaths_processed, "Demultiplexed", |
|
|
1011 |
parents=[qdb.artifact.Artifact(1)], |
|
|
1012 |
processing_parameters=parameters) |
|
|
1013 |
obs.ebi_run_accessions = {'1.SKB1.640202': 'ERR1000001', |
|
|
1014 |
'1.SKB2.640194': 'ERR1000002'} |
|
|
1015 |
self._clean_up_files.extend([x['fp'] for x in obs.filepaths]) |
|
|
1016 |
with self.assertRaises(qdb.exceptions.QiitaDBArtifactDeletionError): |
|
|
1017 |
qdb.artifact.Artifact.delete(obs.id) |
|
|
1018 |
|
|
|
1019 |
def test_delete_error_vamps(self): |
|
|
1020 |
parameters = qdb.software.Parameters.from_default_params( |
|
|
1021 |
qdb.software.DefaultParameters(1), {'input_data': 1}) |
|
|
1022 |
obs = qdb.artifact.Artifact.create( |
|
|
1023 |
self.filepaths_processed, "Demultiplexed", |
|
|
1024 |
parents=[qdb.artifact.Artifact(1)], |
|
|
1025 |
processing_parameters=parameters) |
|
|
1026 |
obs.is_submitted_to_vamps = True |
|
|
1027 |
self._clean_up_files.extend([x['fp'] for x in obs.filepaths]) |
|
|
1028 |
with self.assertRaises(qdb.exceptions.QiitaDBArtifactDeletionError): |
|
|
1029 |
qdb.artifact.Artifact.delete(obs.id) |
|
|
1030 |
|
|
|
1031 |
def test_delete_in_construction_job(self): |
|
|
1032 |
test = qdb.artifact.Artifact.create( |
|
|
1033 |
self.filepaths_root, 'FASTQ', prep_template=self.prep_template) |
|
|
1034 |
self._clean_up_files.extend([x['fp'] for x in test.filepaths]) |
|
|
1035 |
json_str = ( |
|
|
1036 |
'{"input_data": %d, "max_barcode_errors": 1.5, ' |
|
|
1037 |
'"barcode_type": "golay_12", "max_bad_run_length": 3, ' |
|
|
1038 |
'"rev_comp": false, "phred_quality_threshold": 3, ' |
|
|
1039 |
'"rev_comp_barcode": false, "rev_comp_mapping_barcodes": false, ' |
|
|
1040 |
'"min_per_read_length_fraction": 0.75, "sequence_max_n": 0, ' |
|
|
1041 |
'"phred_offset": ""}' % test.id) |
|
|
1042 |
qdb.processing_job.ProcessingJob.create( |
|
|
1043 |
self.user, |
|
|
1044 |
qdb.software.Parameters.load(qdb.software.Command(1), |
|
|
1045 |
json_str=json_str)) |
|
|
1046 |
uploads_fp = join(qdb.util.get_mountpoint("uploads")[0][1], |
|
|
1047 |
str(test.study.id)) |
|
|
1048 |
self._clean_up_files.extend( |
|
|
1049 |
[join(uploads_fp, basename(x['fp'])) for x in test.filepaths]) |
|
|
1050 |
|
|
|
1051 |
qdb.artifact.Artifact.delete(test.id) |
|
|
1052 |
|
|
|
1053 |
with self.assertRaises(qdb.exceptions.QiitaDBUnknownIDError): |
|
|
1054 |
qdb.artifact.Artifact(test.id) |
|
|
1055 |
|
|
|
1056 |
def test_delete_error_running_job(self): |
|
|
1057 |
test = qdb.artifact.Artifact.create( |
|
|
1058 |
self.filepaths_root, 'FASTQ', prep_template=self.prep_template) |
|
|
1059 |
self._clean_up_files.extend([x['fp'] for x in test.filepaths]) |
|
|
1060 |
json_str = ( |
|
|
1061 |
'{"input_data": %d, "max_barcode_errors": 1.5, ' |
|
|
1062 |
'"barcode_type": "golay_12", "max_bad_run_length": 3, ' |
|
|
1063 |
'"rev_comp": false, "phred_quality_threshold": 3, ' |
|
|
1064 |
'"rev_comp_barcode": false, "rev_comp_mapping_barcodes": false, ' |
|
|
1065 |
'"min_per_read_length_fraction": 0.75, "sequence_max_n": 0, ' |
|
|
1066 |
'"phred_offset": ""}' % test.id) |
|
|
1067 |
job = qdb.processing_job.ProcessingJob.create( |
|
|
1068 |
self.user, |
|
|
1069 |
qdb.software.Parameters.load(qdb.software.Command(1), |
|
|
1070 |
json_str=json_str)) |
|
|
1071 |
job._set_status('running') |
|
|
1072 |
with self.assertRaises(qdb.exceptions.QiitaDBArtifactDeletionError): |
|
|
1073 |
qdb.artifact.Artifact.delete(test.id) |
|
|
1074 |
|
|
|
1075 |
def test_delete(self): |
|
|
1076 |
test = qdb.artifact.Artifact.create( |
|
|
1077 |
self.filepaths_root, "FASTQ", prep_template=self.prep_template) |
|
|
1078 |
|
|
|
1079 |
uploads_fp = join(qdb.util.get_mountpoint("uploads")[0][1], |
|
|
1080 |
str(test.study.id)) |
|
|
1081 |
self._clean_up_files.extend( |
|
|
1082 |
[join(uploads_fp, basename(x['fp'])) for x in test.filepaths]) |
|
|
1083 |
|
|
|
1084 |
qdb.artifact.Artifact.delete(test.id) |
|
|
1085 |
|
|
|
1086 |
with self.assertRaises(qdb.exceptions.QiitaDBUnknownIDError): |
|
|
1087 |
qdb.artifact.Artifact(test.id) |
|
|
1088 |
|
|
|
1089 |
# Analysis artifact |
|
|
1090 |
parameters = qdb.software.Parameters.from_default_params( |
|
|
1091 |
qdb.software.DefaultParameters(1), {'input_data': 1}) |
|
|
1092 |
test = qdb.artifact.Artifact.create( |
|
|
1093 |
self.filepaths_processed, "Demultiplexed", |
|
|
1094 |
parents=[qdb.artifact.Artifact(9)], |
|
|
1095 |
processing_parameters=parameters) |
|
|
1096 |
|
|
|
1097 |
self._clean_up_files.extend( |
|
|
1098 |
[join(uploads_fp, basename(x['fp'])) for x in test.filepaths]) |
|
|
1099 |
qdb.artifact.Artifact.delete(test.id) |
|
|
1100 |
|
|
|
1101 |
with self.assertRaises(qdb.exceptions.QiitaDBUnknownIDError): |
|
|
1102 |
qdb.artifact.Artifact(test.id) |
|
|
1103 |
|
|
|
1104 |
def test_delete_with_html(self): |
|
|
1105 |
|
|
|
1106 |
# creating a single file html_summary |
|
|
1107 |
fd, html_fp = mkstemp(suffix=".html") |
|
|
1108 |
close(fd) |
|
|
1109 |
self.filepaths_root.append((html_fp, 'html_summary')) |
|
|
1110 |
self._clean_up_files.append(html_fp) |
|
|
1111 |
|
|
|
1112 |
# creating a folder with a file for html_summary_dir |
|
|
1113 |
summary_dir = mkdtemp() |
|
|
1114 |
open(join(summary_dir, 'index.html'), 'w').write('this is a test') |
|
|
1115 |
self.filepaths_root.append((summary_dir, 'html_summary_dir')) |
|
|
1116 |
self._clean_up_files.append(summary_dir) |
|
|
1117 |
|
|
|
1118 |
test = qdb.artifact.Artifact.create( |
|
|
1119 |
self.filepaths_root, "FASTQ", prep_template=self.prep_template) |
|
|
1120 |
|
|
|
1121 |
uploads_fp = join(qdb.util.get_mountpoint("uploads")[0][1], |
|
|
1122 |
str(test.study.id)) |
|
|
1123 |
|
|
|
1124 |
self._clean_up_files.extend( |
|
|
1125 |
[join(uploads_fp, basename(x['fp'])) for x in test.filepaths]) |
|
|
1126 |
|
|
|
1127 |
qdb.artifact.Artifact.delete(test.id) |
|
|
1128 |
|
|
|
1129 |
with self.assertRaises(qdb.exceptions.QiitaDBUnknownIDError): |
|
|
1130 |
qdb.artifact.Artifact(test.id) |
|
|
1131 |
|
|
|
1132 |
self.assertFalse(exists(join(uploads_fp, basename(html_fp)))) |
|
|
1133 |
self.assertFalse(exists(join(uploads_fp, basename(summary_dir)))) |
|
|
1134 |
|
|
|
1135 |
def test_delete_with_jobs(self): |
|
|
1136 |
test = qdb.artifact.Artifact.create( |
|
|
1137 |
self.filepaths_root, "FASTQ", prep_template=self.prep_template) |
|
|
1138 |
uploads_fp = join(qdb.util.get_mountpoint("uploads")[0][1], |
|
|
1139 |
str(test.study.id)) |
|
|
1140 |
self._clean_up_files.extend( |
|
|
1141 |
[join(uploads_fp, basename(x['fp'])) for x in test.filepaths]) |
|
|
1142 |
|
|
|
1143 |
json_str = ( |
|
|
1144 |
'{"input_data": %d, "max_barcode_errors": 1.5, ' |
|
|
1145 |
'"barcode_type": "golay_12", "max_bad_run_length": 3, ' |
|
|
1146 |
'"rev_comp": false, "phred_quality_threshold": 3, ' |
|
|
1147 |
'"rev_comp_barcode": false, "rev_comp_mapping_barcodes": false, ' |
|
|
1148 |
'"min_per_read_length_fraction": 0.75, "sequence_max_n": 0, ' |
|
|
1149 |
'"phred_offset": ""}' % test.id) |
|
|
1150 |
job = qdb.processing_job.ProcessingJob.create( |
|
|
1151 |
self.user, |
|
|
1152 |
qdb.software.Parameters.load(qdb.software.Command(1), |
|
|
1153 |
json_str=json_str)) |
|
|
1154 |
job._set_status('success') |
|
|
1155 |
|
|
|
1156 |
qdb.artifact.Artifact.delete(test.id) |
|
|
1157 |
|
|
|
1158 |
with self.assertRaises(qdb.exceptions.QiitaDBUnknownIDError): |
|
|
1159 |
qdb.artifact.Artifact(test.id) |
|
|
1160 |
|
|
|
1161 |
# Check that the job still exists, so we cap keep track of system usage |
|
|
1162 |
qdb.processing_job.ProcessingJob(job.id) |
|
|
1163 |
|
|
|
1164 |
def test_being_deleted_by(self): |
|
|
1165 |
test = qdb.artifact.Artifact.create( |
|
|
1166 |
self.filepaths_root, "FASTQ", prep_template=self.prep_template) |
|
|
1167 |
uploads_fp = join(qdb.util.get_mountpoint("uploads")[0][1], |
|
|
1168 |
str(test.study.id)) |
|
|
1169 |
self._clean_up_files.extend( |
|
|
1170 |
[join(uploads_fp, basename(x['fp'])) for x in test.filepaths]) |
|
|
1171 |
|
|
|
1172 |
# verifying that there are no jobs in the list |
|
|
1173 |
self.assertIsNone(test.being_deleted_by) |
|
|
1174 |
|
|
|
1175 |
# creating new deleting job |
|
|
1176 |
qiita_plugin = qdb.software.Software.from_name_and_version( |
|
|
1177 |
'Qiita', 'alpha') |
|
|
1178 |
cmd = qiita_plugin.get_command('delete_artifact') |
|
|
1179 |
params = qdb.software.Parameters.load( |
|
|
1180 |
cmd, values_dict={'artifact': test.id}) |
|
|
1181 |
job = qdb.processing_job.ProcessingJob.create(self.user, params, True) |
|
|
1182 |
job._set_status('running') |
|
|
1183 |
|
|
|
1184 |
# verifying that there is a job and is the same than above |
|
|
1185 |
self.assertEqual(job, test.being_deleted_by) |
|
|
1186 |
|
|
|
1187 |
# let's set it as error and now we should not have it anymore |
|
|
1188 |
job._set_error('Killed by admin') |
|
|
1189 |
self.assertIsNone(test.being_deleted_by) |
|
|
1190 |
|
|
|
1191 |
# now, let's actually remove |
|
|
1192 |
job = qdb.processing_job.ProcessingJob.create(self.user, params, True) |
|
|
1193 |
job.submit() |
|
|
1194 |
# let's wait for job |
|
|
1195 |
wait_for_processing_job(job.id) |
|
|
1196 |
|
|
|
1197 |
with self.assertRaises(qdb.exceptions.QiitaDBUnknownIDError): |
|
|
1198 |
qdb.artifact.Artifact(test.id) |
|
|
1199 |
|
|
|
1200 |
def test_delete_as_output_job(self): |
|
|
1201 |
fd, fp = mkstemp(suffix='_table.biom') |
|
|
1202 |
self._clean_up_files.append(fp) |
|
|
1203 |
close(fd) |
|
|
1204 |
with open(fp, 'w') as f: |
|
|
1205 |
f.write('\n') |
|
|
1206 |
data = {'OTU table': {'filepaths': [(fp, 'biom')], |
|
|
1207 |
'artifact_type': 'BIOM'}} |
|
|
1208 |
job = qdb.processing_job.ProcessingJob.create( |
|
|
1209 |
self.user, |
|
|
1210 |
qdb.software.Parameters.load( |
|
|
1211 |
qdb.software.Command.get_validator('BIOM'), |
|
|
1212 |
values_dict={'files': dumps({'biom': [fp]}), |
|
|
1213 |
'artifact_type': 'BIOM', |
|
|
1214 |
'template': 1, |
|
|
1215 |
'provenance': dumps( |
|
|
1216 |
{'job': "bcc7ebcd-39c1-43e4-af2d-822e3589f14d", |
|
|
1217 |
'cmd_out_id': 3, 'name': 'test-delete'})} |
|
|
1218 |
) |
|
|
1219 |
) |
|
|
1220 |
parent = qdb.processing_job.ProcessingJob( |
|
|
1221 |
"bcc7ebcd-39c1-43e4-af2d-822e3589f14d") |
|
|
1222 |
parent._set_validator_jobs([job]) |
|
|
1223 |
job._set_status('running') |
|
|
1224 |
job.complete(True, artifacts_data=data) |
|
|
1225 |
job = qdb.processing_job.ProcessingJob( |
|
|
1226 |
"bcc7ebcd-39c1-43e4-af2d-822e3589f14d") |
|
|
1227 |
job.release_validators() |
|
|
1228 |
artifact = job.outputs['OTU table'] |
|
|
1229 |
self._clean_up_files.extend([x['fp'] for x in artifact.filepaths]) |
|
|
1230 |
|
|
|
1231 |
qdb.artifact.Artifact.delete(artifact.id) |
|
|
1232 |
|
|
|
1233 |
with self.assertRaises(qdb.exceptions.QiitaDBUnknownIDError): |
|
|
1234 |
qdb.artifact.Artifact(artifact.id) |
|
|
1235 |
|
|
|
1236 |
def test_name_setter(self): |
|
|
1237 |
a = qdb.artifact.Artifact(1) |
|
|
1238 |
self.assertEqual(a.name, "Raw data 1") |
|
|
1239 |
a.name = "new name" |
|
|
1240 |
self.assertEqual(a.name, "new name") |
|
|
1241 |
|
|
|
1242 |
def test_visibility_setter(self): |
|
|
1243 |
a = qdb.artifact.Artifact.create( |
|
|
1244 |
self.filepaths_root, "FASTQ", prep_template=self.prep_template) |
|
|
1245 |
|
|
|
1246 |
self.assertEqual(a.visibility, "sandbox") |
|
|
1247 |
a.visibility = "awaiting_approval" |
|
|
1248 |
self.assertEqual(a.visibility, "awaiting_approval") |
|
|
1249 |
a.visibility = "private" |
|
|
1250 |
self.assertEqual(a.visibility, "private") |
|
|
1251 |
a.visibility = "public" |
|
|
1252 |
self.assertEqual(a.visibility, "public") |
|
|
1253 |
|
|
|
1254 |
# Testing that the visibility inference works as expected |
|
|
1255 |
# The current artifact network that we have in the db looks as follows: |
|
|
1256 |
# /- 4 (private) |
|
|
1257 |
# /- 2 (private) -|- 5 (private) |
|
|
1258 |
# 1 (private) -| \- 6 (private) |
|
|
1259 |
# \- 3 (private) |
|
|
1260 |
# By changing the visibility of 4 to public, the visibility of all |
|
|
1261 |
# should change |
|
|
1262 |
a1 = qdb.artifact.Artifact(1) |
|
|
1263 |
a2 = qdb.artifact.Artifact(2) |
|
|
1264 |
a3 = qdb.artifact.Artifact(3) |
|
|
1265 |
a4 = qdb.artifact.Artifact(4) |
|
|
1266 |
a5 = qdb.artifact.Artifact(5) |
|
|
1267 |
a6 = qdb.artifact.Artifact(6) |
|
|
1268 |
|
|
|
1269 |
a4.visibility = 'public' |
|
|
1270 |
|
|
|
1271 |
self.assertEqual(a1.visibility, "public") |
|
|
1272 |
self.assertEqual(a2.visibility, "public") |
|
|
1273 |
self.assertEqual(a3.visibility, "public") |
|
|
1274 |
self.assertEqual(a4.visibility, "public") |
|
|
1275 |
self.assertEqual(a5.visibility, "public") |
|
|
1276 |
self.assertEqual(a6.visibility, "public") |
|
|
1277 |
|
|
|
1278 |
# Same if we go back |
|
|
1279 |
a4.visibility = 'private' |
|
|
1280 |
|
|
|
1281 |
self.assertEqual(a1.visibility, "private") |
|
|
1282 |
self.assertEqual(a2.visibility, "private") |
|
|
1283 |
self.assertEqual(a3.visibility, "private") |
|
|
1284 |
self.assertEqual(a4.visibility, "private") |
|
|
1285 |
self.assertEqual(a5.visibility, "private") |
|
|
1286 |
self.assertEqual(a6.visibility, "private") |
|
|
1287 |
|
|
|
1288 |
# testing human_reads_filter_method here as in the future we might |
|
|
1289 |
# want to check that this property is inherited as visibility is; |
|
|
1290 |
# however, for the time being we don't need to do that and there is |
|
|
1291 |
# no downside on adding it here. |
|
|
1292 |
mtd = 'The greatest human filtering method' |
|
|
1293 |
self.assertEqual(mtd, a1.human_reads_filter_method) |
|
|
1294 |
self.assertIsNone(a2.human_reads_filter_method) |
|
|
1295 |
self.assertIsNone(a3.human_reads_filter_method) |
|
|
1296 |
|
|
|
1297 |
# let's change some values |
|
|
1298 |
with self.assertRaisesRegex(ValueError, '"This should fail" is not a ' |
|
|
1299 |
'valid human_reads_filter_method'): |
|
|
1300 |
a2.human_reads_filter_method = 'This should fail' |
|
|
1301 |
self.assertIsNone(a2.human_reads_filter_method) |
|
|
1302 |
a2.human_reads_filter_method = mtd |
|
|
1303 |
self.assertEqual(mtd, a2.human_reads_filter_method) |
|
|
1304 |
self.assertIsNone(a3.human_reads_filter_method) |
|
|
1305 |
|
|
|
1306 |
def test_ebi_run_accessions_setter(self): |
|
|
1307 |
a = qdb.artifact.Artifact(3) |
|
|
1308 |
self.assertEqual(a.ebi_run_accessions, dict()) |
|
|
1309 |
new_vals = { |
|
|
1310 |
'1.SKB1.640202': 'ERR1000001', |
|
|
1311 |
'1.SKB2.640194': 'ERR1000002', |
|
|
1312 |
'1.SKB3.640195': 'ERR1000003', |
|
|
1313 |
'1.SKB4.640189': 'ERR1000004', |
|
|
1314 |
'1.SKB5.640181': 'ERR1000005', |
|
|
1315 |
'1.SKB6.640176': 'ERR1000006', |
|
|
1316 |
'1.SKB7.640196': 'ERR1000007', |
|
|
1317 |
'1.SKB8.640193': 'ERR1000008', |
|
|
1318 |
'1.SKB9.640200': 'ERR1000009', |
|
|
1319 |
'1.SKD1.640179': 'ERR1000010', |
|
|
1320 |
'1.SKD2.640178': 'ERR1000011', |
|
|
1321 |
'1.SKD3.640198': 'ERR1000012', |
|
|
1322 |
'1.SKD4.640185': 'ERR1000013', |
|
|
1323 |
'1.SKD5.640186': 'ERR1000014', |
|
|
1324 |
'1.SKD6.640190': 'ERR1000015', |
|
|
1325 |
'1.SKD7.640191': 'ERR1000016', |
|
|
1326 |
'1.SKD8.640184': 'ERR1000017', |
|
|
1327 |
'1.SKD9.640182': 'ERR1000018', |
|
|
1328 |
'1.SKM1.640183': 'ERR1000019', |
|
|
1329 |
'1.SKM2.640199': 'ERR1000020', |
|
|
1330 |
'1.SKM3.640197': 'ERR1000021', |
|
|
1331 |
'1.SKM4.640180': 'ERR1000022', |
|
|
1332 |
'1.SKM5.640177': 'ERR1000023', |
|
|
1333 |
'1.SKM6.640187': 'ERR1000024', |
|
|
1334 |
'1.SKM7.640188': 'ERR1000025', |
|
|
1335 |
'1.SKM8.640201': 'ERR1000026', |
|
|
1336 |
'1.SKM9.640192': 'ERR1000027'} |
|
|
1337 |
a.ebi_run_accessions = new_vals |
|
|
1338 |
self.assertEqual(a.ebi_run_accessions, new_vals) |
|
|
1339 |
|
|
|
1340 |
def test_is_submitted_to_vamps_setter(self): |
|
|
1341 |
a = qdb.artifact.Artifact(2) |
|
|
1342 |
self.assertFalse(a.is_submitted_to_vamps) |
|
|
1343 |
a.is_submitted_to_vamps = True |
|
|
1344 |
self.assertTrue(a.is_submitted_to_vamps) |
|
|
1345 |
|
|
|
1346 |
def test_html_summary_setter(self): |
|
|
1347 |
a = qdb.artifact.Artifact(1) |
|
|
1348 |
|
|
|
1349 |
# Check that returns None when it doesn't exist |
|
|
1350 |
self.assertIsNone(a.html_summary_fp) |
|
|
1351 |
|
|
|
1352 |
fd, fp = mkstemp(suffix=".html") |
|
|
1353 |
close(fd) |
|
|
1354 |
self._clean_up_files.append(fp) |
|
|
1355 |
|
|
|
1356 |
db_fastq_dir = qdb.util.get_mountpoint('FASTQ')[0][1] |
|
|
1357 |
path_builder = partial(join, db_fastq_dir, str(a.id)) |
|
|
1358 |
|
|
|
1359 |
# Check the setter works when the artifact does not have the summary |
|
|
1360 |
a.set_html_summary(fp) |
|
|
1361 |
exp1 = path_builder(basename(fp)) |
|
|
1362 |
self.assertEqual(a.html_summary_fp[1], exp1) |
|
|
1363 |
|
|
|
1364 |
fd, fp = mkstemp(suffix=".html") |
|
|
1365 |
close(fd) |
|
|
1366 |
self._clean_up_files.append(fp) |
|
|
1367 |
|
|
|
1368 |
dp = mkdtemp() |
|
|
1369 |
self._clean_up_files.append(dp) |
|
|
1370 |
|
|
|
1371 |
# Check the setter works when the artifact already has a summary |
|
|
1372 |
# and with a directory |
|
|
1373 |
a.set_html_summary(fp, support_dir=dp) |
|
|
1374 |
exp2 = path_builder(basename(fp)) |
|
|
1375 |
self.assertEqual(a.html_summary_fp[1], exp2) |
|
|
1376 |
self.assertFalse(exists(exp1)) |
|
|
1377 |
|
|
|
1378 |
# Check that the setter correctly removes the directory if a new |
|
|
1379 |
# summary is added. Magic number 0. There is only one html_summary_dir |
|
|
1380 |
# added on the previous test |
|
|
1381 |
old_dir_fp = [x['fp'] for x in a.filepaths |
|
|
1382 |
if x['fp_type'] == 'html_summary_dir'][0] |
|
|
1383 |
fd, fp = mkstemp(suffix='.html') |
|
|
1384 |
close(fd) |
|
|
1385 |
self._clean_up_files.append(fp) |
|
|
1386 |
a.set_html_summary(fp) |
|
|
1387 |
exp3 = path_builder(basename(fp)) |
|
|
1388 |
self.assertEqual(a.html_summary_fp[1], exp3) |
|
|
1389 |
self.assertFalse(exists(exp2)) |
|
|
1390 |
self.assertFalse(exists(old_dir_fp)) |
|
|
1391 |
summary_dir = [x['fp'] for x in a.filepaths |
|
|
1392 |
if x['fp_type'] == 'html_summary_dir'] |
|
|
1393 |
self.assertEqual(summary_dir, []) |
|
|
1394 |
|
|
|
1395 |
# let's check if we update, we do _not_ remove the files |
|
|
1396 |
a.set_html_summary(exp3) |
|
|
1397 |
self.assertTrue(exists(a.html_summary_fp[1])) |
|
|
1398 |
|
|
|
1399 |
def test_descendants_with_jobs_one_element(self): |
|
|
1400 |
artifact = qdb.artifact.Artifact.create( |
|
|
1401 |
self.filepaths_root, 'FASTQ', prep_template=self.prep_template) |
|
|
1402 |
|
|
|
1403 |
obs = self.prep_template.artifact.descendants_with_jobs.nodes() |
|
|
1404 |
exp = [('artifact', artifact)] |
|
|
1405 |
self.assertCountEqual(obs, exp) |
|
|
1406 |
|
|
|
1407 |
def test_has_human(self): |
|
|
1408 |
# testing a FASTQ artifact (1), should be False |
|
|
1409 |
self.assertFalse(qdb.artifact.Artifact(1).has_human) |
|
|
1410 |
|
|
|
1411 |
# create a per_sample_FASTQ |
|
|
1412 |
artifact = qdb.artifact.Artifact.create( |
|
|
1413 |
[(self.fwd, 1), (self.rev, 2)], "per_sample_FASTQ", |
|
|
1414 |
prep_template=self.prep_template_per_sample_fastq) |
|
|
1415 |
|
|
|
1416 |
# this should be False as there are no human samples |
|
|
1417 |
self.assertFalse(artifact.has_human) |
|
|
1418 |
|
|
|
1419 |
# let's make it True by making the samle human-* |
|
|
1420 |
df = pd.DataFrame.from_dict( |
|
|
1421 |
{'1.SKB8.640193': {'env_package': 'human-oral'}}, |
|
|
1422 |
orient='index', dtype=str) |
|
|
1423 |
artifact.study.sample_template.update(df) |
|
|
1424 |
|
|
|
1425 |
self.assertTrue(artifact.has_human) |
|
|
1426 |
|
|
|
1427 |
# now if we change the pt data_type to 16S |
|
|
1428 |
pt = artifact.prep_templates[0] |
|
|
1429 |
with qdb.sql_connection.TRN: |
|
|
1430 |
qdb.sql_connection.TRN.add( |
|
|
1431 |
f"""UPDATE qiita.prep_template |
|
|
1432 |
SET data_type_id = 1 |
|
|
1433 |
WHERE prep_template_id = {pt.id}""") |
|
|
1434 |
qdb.sql_connection.TRN.execute() |
|
|
1435 |
self.assertFalse(artifact.has_human) |
|
|
1436 |
|
|
|
1437 |
def test_descendants_with_jobs(self): |
|
|
1438 |
# let's tests that we can connect two artifacts with different root |
|
|
1439 |
# in the same analysis |
|
|
1440 |
# 1. make sure there are 3 nodes |
|
|
1441 |
a = qdb.artifact.Artifact(8) |
|
|
1442 |
self.assertEqual(len(a.descendants_with_jobs.nodes), 3) |
|
|
1443 |
self.assertEqual(len(a.analysis.artifacts), 2) |
|
|
1444 |
# 2. add a new root and make sure we see it |
|
|
1445 |
c = qdb.artifact.Artifact.create( |
|
|
1446 |
self.filepaths_root, "BIOM", analysis=a.analysis, |
|
|
1447 |
data_type="16S") |
|
|
1448 |
self.assertEqual(len(a.analysis.artifacts), 3) |
|
|
1449 |
# 3. add jobs conencting the new artifact to the other root |
|
|
1450 |
# - currently: |
|
|
1451 |
# a -> job -> b |
|
|
1452 |
# c |
|
|
1453 |
# - expected: |
|
|
1454 |
# a --> job -> b |
|
|
1455 |
# |-> job2 -> out |
|
|
1456 |
# ^ |
|
|
1457 |
# |-----|---> job1 -> out |
|
|
1458 |
# c ------------| |
|
|
1459 |
cmd = qdb.software.Command.create( |
|
|
1460 |
qdb.software.Software(1), |
|
|
1461 |
"CommandWithMultipleInputs", "", { |
|
|
1462 |
'input_x': ['artifact:["BIOM"]', None], |
|
|
1463 |
'input_y': ['artifact:["BIOM"]', None]}, {'out': 'BIOM'}) |
|
|
1464 |
params = qdb.software.Parameters.load( |
|
|
1465 |
cmd, values_dict={'input_x': a.children[0].id, 'input_y': c.id}) |
|
|
1466 |
wf = qdb.processing_job.ProcessingWorkflow.from_scratch( |
|
|
1467 |
self.user, params, name='Test WF') |
|
|
1468 |
job1 = list(wf.graph.nodes())[0] |
|
|
1469 |
|
|
|
1470 |
cmd_dp = qdb.software.DefaultParameters.create("", cmd) |
|
|
1471 |
wf.add(cmd_dp, req_params={'input_x': a.id, 'input_y': c.id}) |
|
|
1472 |
job2 = list(wf.graph.nodes())[1] |
|
|
1473 |
jobs = [j[1] for e in a.descendants_with_jobs.edges |
|
|
1474 |
for j in e if j[0] == 'job'] |
|
|
1475 |
self.assertIn(job1, jobs) |
|
|
1476 |
self.assertIn(job2, jobs) |
|
|
1477 |
|
|
|
1478 |
# 4. add job3 connecting job2 output with c as inputs |
|
|
1479 |
# - expected: |
|
|
1480 |
# a --> job -> b |
|
|
1481 |
# |-> job2 -> out -> job3 -> out |
|
|
1482 |
# ^ ^ |
|
|
1483 |
# | | |
|
|
1484 |
# | | |
|
|
1485 |
# |-----|---> job1 -> out |
|
|
1486 |
# c ------------| |
|
|
1487 |
wf.add(cmd_dp, connections={ |
|
|
1488 |
job1: {'out': 'input_x'}, job2: {'out': 'input_y'}}) |
|
|
1489 |
job3 = list(wf.graph.nodes())[2] |
|
|
1490 |
jobs = [j[1] for e in a.descendants_with_jobs.edges |
|
|
1491 |
for j in e if j[0] == 'job'] |
|
|
1492 |
self.assertIn(job3, jobs) |
|
|
1493 |
|
|
|
1494 |
|
|
|
1495 |
@qiita_test_checker() |
|
|
1496 |
class ArtifactArchiveTests(TestCase): |
|
|
1497 |
def test_archive(self): |
|
|
1498 |
A = qdb.artifact.Artifact |
|
|
1499 |
QE = qdb.exceptions.QiitaDBOperationNotPermittedError |
|
|
1500 |
|
|
|
1501 |
# check nodes, without any change |
|
|
1502 |
exp_nodes = [A(1), A(2), A(3), A(4), A(5), A(6)] |
|
|
1503 |
self.assertCountEqual(A(1).descendants.nodes(), exp_nodes) |
|
|
1504 |
obs_artifacts = len(qdb.util.get_artifacts_information([4, 5, 6, 8])) |
|
|
1505 |
self.assertEqual(4, obs_artifacts) |
|
|
1506 |
|
|
|
1507 |
# check errors |
|
|
1508 |
with self.assertRaisesRegex(QE, 'Only public artifacts can be ' |
|
|
1509 |
'archived'): |
|
|
1510 |
A.archive(1) |
|
|
1511 |
A(1).visibility = 'public' |
|
|
1512 |
|
|
|
1513 |
with self.assertRaisesRegex(QE, 'Only BIOM artifacts can be archived'): |
|
|
1514 |
A.archive(1) |
|
|
1515 |
|
|
|
1516 |
A(8).visibility = 'public' |
|
|
1517 |
with self.assertRaisesRegex(QE, 'Only non analysis artifacts can ' |
|
|
1518 |
'be archived'): |
|
|
1519 |
A.archive(8) |
|
|
1520 |
|
|
|
1521 |
for aid in range(5, 7): |
|
|
1522 |
ms = A(aid).merging_scheme |
|
|
1523 |
A.archive(aid) |
|
|
1524 |
self.assertEqual(ms, A(aid).merging_scheme) |
|
|
1525 |
exp_nodes.remove(A(aid)) |
|
|
1526 |
self.assertCountEqual(A(1).descendants.nodes(), exp_nodes) |
|
|
1527 |
|
|
|
1528 |
obs_artifacts = len(qdb.util.get_artifacts_information([4, 5, 6, 8])) |
|
|
1529 |
self.assertEqual(2, obs_artifacts) |
|
|
1530 |
|
|
|
1531 |
# in the tests above we generated and validated archived artifacts |
|
|
1532 |
# so this allows us to add tests to delete a prep-info with archived |
|
|
1533 |
# artifacts. The first bottleneck to do this is that this tests will |
|
|
1534 |
# actually remove files, which we will need for other tests so lets |
|
|
1535 |
# make a copy and then restore them |
|
|
1536 |
mfolder = dirname(dirname(abspath(__file__))) |
|
|
1537 |
mpath = join(mfolder, 'support_files', 'test_data') |
|
|
1538 |
mp = partial(join, mpath) |
|
|
1539 |
fps = [ |
|
|
1540 |
mp('processed_data/1_study_1001_closed_reference_otu_table.biom'), |
|
|
1541 |
mp('processed_data/' |
|
|
1542 |
'1_study_1001_closed_reference_otu_table_Silva.biom'), |
|
|
1543 |
mp('raw_data/1_s_G1_L001_sequences.fastq.gz'), |
|
|
1544 |
mp('raw_data/1_s_G1_L001_sequences_barcodes.fastq.gz')] |
|
|
1545 |
for fp in fps: |
|
|
1546 |
copyfile(fp, f'{fp}.bk') |
|
|
1547 |
|
|
|
1548 |
PT = qdb.metadata_template.prep_template.PrepTemplate |
|
|
1549 |
QEE = qdb.exceptions.QiitaDBExecutionError |
|
|
1550 |
pt = A(1).prep_templates[0] |
|
|
1551 |
# it should fail as this prep is public and have been submitted to ENA |
|
|
1552 |
with self.assertRaisesRegex(QEE, 'Cannot remove prep template 1'): |
|
|
1553 |
PT.delete(pt.id) |
|
|
1554 |
# now, remove those restrictions + analysis + linked artifacts |
|
|
1555 |
sql = "DELETE FROM qiita.artifact_processing_job" |
|
|
1556 |
qdb.sql_connection.perform_as_transaction(sql) |
|
|
1557 |
sql = "DELETE FROM qiita.ebi_run_accession" |
|
|
1558 |
qdb.sql_connection.perform_as_transaction(sql) |
|
|
1559 |
sql = "UPDATE qiita.artifact SET visibility_id = 1" |
|
|
1560 |
qdb.sql_connection.perform_as_transaction(sql) |
|
|
1561 |
qdb.analysis.Analysis.delete_analysis_artifacts(1) |
|
|
1562 |
qdb.analysis.Analysis.delete_analysis_artifacts(2) |
|
|
1563 |
qdb.analysis.Analysis.delete_analysis_artifacts(3) |
|
|
1564 |
for aid in [3, 2, 1]: |
|
|
1565 |
A.delete(aid) |
|
|
1566 |
|
|
|
1567 |
PT.delete(pt.id) |
|
|
1568 |
|
|
|
1569 |
# bringing back the filepaths |
|
|
1570 |
for fp in fps: |
|
|
1571 |
copyfile(f'{fp}.bk', fp) |
|
|
1572 |
|
|
|
1573 |
|
|
|
1574 |
if __name__ == '__main__': |
|
|
1575 |
main() |