Uncouple plugin #3
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sjanssen2
commented
Nov 3, 2025
qtp_sequencing/tests/test_plugin.py
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| # as we access functions directly, plugin configuration is not parsed, | ||
| # thus resort to environment variable here | ||
| self.qclient._plugincoupling = environ.get( | ||
| 'QIITA_PLUGINCOUPLING', BaseQiitaPlugin._DEFAULT_PLUGIN_COUPLINGS) | ||
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should now be in PluginTestCase
qtp_sequencing/tests/test_summary.py
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| # as we access functions directly, plugin configuration is not parsed, | ||
| # thus resort to environment variable here | ||
| self.qclient._plugincoupling = environ.get( | ||
| 'QIITA_PLUGINCOUPLING', BaseQiitaPlugin._DEFAULT_PLUGIN_COUPLINGS) | ||
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should now be in PluginTestCase
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| # as we access functions directly, plugin configuration is not parsed, | ||
| # thus resort to environment variable here | ||
| self.qclient._plugincoupling = environ.get( | ||
| 'QIITA_PLUGINCOUPLING', BaseQiitaPlugin._DEFAULT_PLUGIN_COUPLINGS) | ||
|
|
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should now be in PluginTestCase
sjanssen2
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Nov 3, 2025
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| def _deposite_in_qiita_basedir(qclient, fps, update_fp_only=False): | ||
| """Push a file to qiita main AND adapts given filepath accordingly. | ||
| A helper function to fix file paths in tests such that they point to the | ||
| expected BASE_DATA_DIR. This becomes necessary when uncoupling the plugin | ||
| filesystem as some methods now actually fetches expected files from | ||
| BASE_DATA_DIR. | ||
| Parameters | ||
| ---------- | ||
| qclient : qiita_client.QiitaClient | ||
| The Qiita server client | ||
| fps : str or [str] | ||
| Filepath or list of filepaths to file(s) that shall be part of | ||
| BASE_DATA_DIR, but currently points to some tmp file for testing. | ||
| update_fp_only : bool | ||
| Some tests operate on filepaths only - files do not actually need to | ||
| exist. Thus, we don't need to tranfer a file. | ||
| """ | ||
| if qclient._plugincoupling == 'filesystem': | ||
| return fps | ||
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| # use artifact 1 info to determine BASA_DATA_DIR, as we know that the | ||
| # filepath ends with ....raw_data/1_s_G1_L001_sequences.fastq.gz, thus | ||
| # BASE_DATA_DIR must be the prefix, e.g. /qiita_data/ | ||
| ainfo = qclient.get('/qiita_db/artifacts/1/') | ||
| base_data_dir = ainfo['files']['raw_forward_seqs'][0]['filepath'][ | ||
| :(-1 * len('raw_data/1_s_G1_L001_sequences.fastq.gz'))] | ||
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| if isinstance(fps, str): | ||
| if not update_fp_only: | ||
| qclient.push_file_to_central(fps) | ||
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| return join(base_data_dir, relpath(fps, sep)) | ||
| elif isinstance(fps, list): | ||
| for fp in fps: | ||
| if not update_fp_only: | ||
| qclient.push_file_to_central(fp) |
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better more the whole function to qiita_client/testing.py
qtp_sequencing/tests/test_plugin.py
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| from time import sleep | ||
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| from qiita_client.testing import PluginTestCase | ||
| from qiita_client.plugin import BaseQiitaPlugin |
qtp_sequencing/tests/test_plugin.py
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| from qiita_client.plugin import BaseQiitaPlugin | ||
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| from qtp_sequencing import plugin | ||
| from qtp_sequencing.tests.test_validate import _deposite_in_qiita_basedir |
qtp_sequencing/tests/test_plugin.py
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| files = {'raw_forward_seqs': [fp], | ||
| 'raw_barcodes': [fp2]} | ||
| files = {'raw_forward_seqs': [ | ||
| _deposite_in_qiita_basedir(self.qclient, fp)], |
qtp_sequencing/tests/test_plugin.py
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| files = {'raw_forward_seqs': [ | ||
| _deposite_in_qiita_basedir(self.qclient, fp)], | ||
| 'raw_barcodes': [ | ||
| _deposite_in_qiita_basedir(self.qclient, fp2)]} |
| "1.SKB3.640195": {"not_a_run_prefix": "prefix2"}} | ||
| files = {'preprocessed_fastq': [f1, f2, f3]} | ||
| files = {'preprocessed_fastq': | ||
| _deposite_in_qiita_basedir(self.qclient, [f1, f2, f3])} |
| (f2 + '.gz', 'preprocessed_fastq'), | ||
| (f3 + '.gz', 'preprocessed_fastq')] | ||
| filepaths = [ | ||
| (_deposite_in_qiita_basedir(self.qclient, x + '.gz', True), |
| "1.SKB3.640195": {"not_a_run_prefix": "prefix2"}} | ||
| files = {'preprocessed_fastq': raw_files} | ||
| files = {'preprocessed_fastq': | ||
| _deposite_in_qiita_basedir(self.qclient, raw_files)} |
| self.assertTrue(obs_success) | ||
| filepaths = [('%s.gz' % x, 'preprocessed_fastq') for x in raw_files] | ||
| filepaths = [ | ||
| (_deposite_in_qiita_basedir(self.qclient, '%s.gz' % x, True), |
| "1.SKB6.640176": {"run_prefix": "s4"}} | ||
| files = {'preprocessed_fastq': [fastq_fp]} | ||
| files = {'preprocessed_fastq': | ||
| [_deposite_in_qiita_basedir(self.qclient, fastq_fp)]} |
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