def test_call(self):
def validate_func(a, b, c, d):
return 42
def html_generator_func(a, b, c, d):
return 42
# Test the install procedure
atypes = [QiitaArtifactType('Name', 'Description', False, True, False,
[('plain_text', False)])]
tester = QiitaTypePlugin("NewPlugin", "1.0.0", "Description",
validate_func, html_generator_func, atypes)
# Generate the config file for the new plugin
tester.generate_config('ls', 'echo',
server_cert=self.server_cert)
# Ask Qiita to reload the plugins
self.qclient.post('/apitest/reload_plugins/')
# Install the current plugin
tester("https://localhost:21174", 'register', 'ignored')
# Check that it has been installed
obs = self.qclient.get('/qiita_db/plugins/NewPlugin/1.0.0/')
self.assertEqual(obs['name'], 'NewPlugin')
self.assertEqual(obs['version'], '1.0.0')
def test_generate_config(self):
def validate_func(a, b, c, d):
return 42
def html_generator_func(a, b, c, d):
return 42
atypes = [QiitaArtifactType('Name', 'Description', False, True, False,
[('plain_text', False)])]
tester = QiitaTypePlugin("NewPlugin", "1.0.0", "Description",
validate_func, html_generator_func, atypes)
tester.generate_config('ls', 'echo')
self.assertTrue(exists(tester.conf_fp))
with open(tester.conf_fp, 'U') as f:
conf = f.readlines()
exp_lines = ['[main]\n',
'NAME = NewPlugin\n',
'VERSION = 1.0.0\n',
'DESCRIPTION = Description\n',
'ENVIRONMENT_SCRIPT = ls\n',
'START_SCRIPT = echo\n',
'PLUGIN_TYPE = artifact definition\n',
'PUBLICATIONS = \n',
'\n',
'[oauth2]\n',
'SERVER_CERT = \n']
# We will test the last 2 lines independently since they're variable
# in each test run
self.assertEqual(conf[:-2], exp_lines)
self.assertTrue(conf[-2].startswith('CLIENT_ID = '))
self.assertTrue(conf[-1].startswith('CLIENT_SECRET = '))
def test_init(self):
def validate_func(a, b, c, d):
return 42
def html_generator_func(a, b, c, d):
return 42
atypes = [QiitaArtifactType('Name', 'Description', False, True, False,
[('plain_text', False)])]
obs = QiitaTypePlugin("NewPlugin", "1.0.0", "Description",
validate_func, html_generator_func,
atypes)
self.assertEqual(obs.name, "NewPlugin")
self.assertEqual(obs.version, "1.0.0")
self.assertEqual(obs.description, "Description")
self.assertEqual(set(obs.task_dict.keys()),
{'Validate', 'Generate HTML summary'})
self.assertEqual(obs.task_dict['Validate'].function, validate_func)
self.assertEqual(obs.task_dict['Generate HTML summary'].function,
html_generator_func)
self.assertEqual(obs.artifact_types, atypes)
self.assertEqual(basename(obs.conf_fp), 'NewPlugin_1.0.0.conf')
# can_be_submitted_to_vamps, is_user_uploadable,
# filepath_types):
QiitaArtifactType('SFF', 'Raw SFF files', False, False, True,
[('raw_sff', True)]),
QiitaArtifactType('FASTA_Sanger', 'Raw fasta files from Sanger sequencing',
False, False, False, [('raw_fasta', True)]),
QiitaArtifactType('FASTQ', 'Raw fastq files, with or without paired ends',
False, False, True, [('raw_forward_seqs', True),
('raw_reverse_seqs', False),
('raw_barcodes', True)]),
QiitaArtifactType('FASTA', 'Raw fasta files', False, False, True,
[('raw_fasta', True), ('raw_qual', False)]),
QiitaArtifactType('FASTA_preprocessed', 'preprocessed fasta files', False,
False, False, [('preprocessed_fasta', True),
('log', False)]),
QiitaArtifactType('per_sample_FASTQ', 'Raw per sample FASTQ files', False,
False, True, [('raw_forward_seqs', True),
('raw_reverse_seqs', False)]),
QiitaArtifactType('Demultiplexed',
'Demultiplexed and QC sequeunces with QIIME labels',
True, True, False, [('preprocessed_fasta', True),
('preprocessed_fastq', True),
('preprocessed_demux', False),
('log', False)]),
]
# Initialize the plugin
plugin = QiitaTypePlugin('Sequencing Data Type', '2022.07',
'Sequencing artifact types plugin', validate,
generate_html_summary, artifact_types)
# -----------------------------------------------------------------------------
# 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 qiita_client import QiitaTypePlugin, QiitaArtifactType
from .validate import validate
from .summary import generate_html_summary
# Define the supported artifact types
artifact_types = [
QiitaArtifactType('BIOM', 'BIOM table', False, False, True,
[('biom', True), ('directory', False), ('log', False),
('preprocessed_fasta', False), ('plain_text', False),
('qza', False)])
]
# Initialize the plugin
plugin = QiitaTypePlugin('BIOM type', '2.1.4 - Qiime2',
'The Biological Observation Matrix format', validate,
generate_html_summary, artifact_types)
# -----------------------------------------------------------------------------
# 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 qiita_client import QiitaTypePlugin, QiitaArtifactType
from .validate import validate
from .summary import generate_html_summary
# Define the supported artifact types
artifact_types = [
QiitaArtifactType(
'distance_matrix', 'Distance matrix holding pairwise distance between '
'samples', False, False, False, [('plain_text', True)]),
QiitaArtifactType('ordination_results', 'Ordination results', False, False,
False, [('plain_text', True)]),
QiitaArtifactType('alpha_vector', 'Alpha Diversity per sample results',
False, False, False, [('plain_text', True)])
]
# Initialize the plugin
plugin = QiitaTypePlugin('Diversity types', '0.1.0',
'Diversity artifacts type plugin', validate,
generate_html_summary, artifact_types)
# -----------------------------------------------------------------------------
# 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 qiita_client import QiitaTypePlugin, QiitaArtifactType
from .validate import validate
# Define the supported artifact types
artifact_types = [
QiitaArtifactType('q2_visualization', 'Qiime 2 visualization',
False, False, [('qzv', True)])]
# The visualization is the summary itself, so we don't need a
# generate_html_summary function. However, the plugins requires to
# register a function for it
def generate_html_summary(qclient, job_id, parameters, out_dir):
return True, None, ""
# Initialize the plugin
plugin = QiitaTypePlugin('Visualization types', '0.1.0',
'Visualization artifacts type plugin',
validate, generate_html_summary,
artifact_types)
from .validate import validate
from .summary import generate_html_summary
# DEfine the supported artifact types
artifact_types = [
QiitaArtifactType('SFF', 'Raw SFF files', False, False,
[('raw_sff', True)]),
QiitaArtifactType('FASTA_Sanger', 'Raw fasta files from Sanger sequencing',
False, False, [('raw_fasta', True)]),
QiitaArtifactType('FASTQ', 'Raw fastq files, with or without paired ends',
False, False, [('raw_forward_seqs', True),
('raw_reverse_seqs', False),
('raw_barcodes', True)]),
QiitaArtifactType('FASTA', 'Raw fasta files', False, False,
[('raw_fasta', True), ('raw_qual', False)]),
QiitaArtifactType('per_sample_FASTQ', 'Raw per sample FASTQ files', False,
False, [('raw_forward_seqs', True),
('raw_reverse_seqs', False)]),
QiitaArtifactType('Demultiplexed',
'Demultiplexed and QC sequeunces with QIIME labels',
True, True, [('preprocessed_fasta', True),
('preprocessed_fastq', True),
('preprocessed_demux', False),
('log', False)]),
]
# Initialize the plugin
plugin = QiitaTypePlugin('Target Gene type', '0.1.0',
'Target gene artifact types plugin',
validate, generate_html_summary, artifact_types)