Comments (3)
JonnyTran
commented on May 27, 2024
1
Removed the test_import_MiRTarBase automated test since MiRTarBase is not obtainable via ftp.
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JonnyTran
commented on May 27, 2024
The path at MiRTarBase(path="/data/datasets/Bioinformatics_ExternalData/miRTarBase/") is hard-coded to the directory at my local computer.
There are many bioinformatics datasets that are not publicly available via direct download (e.g. lncbase) and may require access permission. In that case, it is expected that the users would obtain the data themself then provide a path to their own local directory.
Since currently, it is difficult to get a reliable ftp download connection from the server at http://mirtarbase.mbc.nctu.edu.tw, I suggest we remove test_import_MiRTarBase from the automated test set that relies on ftp download.
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gawbul
commented on May 27, 2024
Tests all pass, though a few warnings:
$ OpenOmics [master] python -m pytest
============================================================================================================ test session starts =============================================================================================================
platform darwin -- Python 3.8.9, pytest-6.2.3, py-1.10.0, pluggy-0.13.1
rootdir: /Users/stephenmoss/Dropbox/Code/OpenOmics, configfile: setup.cfg
plugins: dash-1.20.0
collected 38 items
tests/test_annotations.py ......... [ 23%]
tests/test_disease.py .......... [ 50%]
tests/test_interaction.py ....... [ 68%]
tests/test_multiomics.py ... [ 76%]
tests/test_sequences.py ......... [100%]
============================================================================================================== warnings summary ==============================================================================================================
../../../.pyenv/versions/3.8.9/lib/python3.8/site-packages/_pytest/config/__init__.py:1233
/Users/stephenmoss/.pyenv/versions/3.8.9/lib/python3.8/site-packages/_pytest/config/__init__.py:1233: PytestConfigWarning: Unknown config option: collect_ignore
self._warn_or_fail_if_strict(f"Unknown config option: {key}\n")
openomics/database/ontology.py:235
/Users/stephenmoss/Dropbox/Code/OpenOmics/openomics/database/ontology.py:235: DeprecationWarning: invalid escape sequence \|
and annotation.str.contains("\||;", regex=True).any()):
tests/test_disease.py::test_import_HMDD
tests/test_disease.py::test_annotate_HMDD
/Users/stephenmoss/.pyenv/versions/3.8.9/lib/python3.8/encodings/unicode_escape.py:26: DeprecationWarning: invalid escape sequence '\ '
return codecs.unicode_escape_decode(input, self.errors)[0]
tests/test_disease.py::test_import_HMDD
tests/test_disease.py::test_annotate_HMDD
/Users/stephenmoss/.pyenv/versions/3.8.9/lib/python3.8/encodings/unicode_escape.py:26: DeprecationWarning: invalid escape sequence '\s'
return codecs.unicode_escape_decode(input, self.errors)[0]
tests/test_interaction.py::test_import_LncRNA2Target
tests/test_interaction.py::test_get_interactions_lnc2target
/Users/stephenmoss/Dropbox/Code/OpenOmics/openomics/database/interaction.py:479: FutureWarning: Your version of xlrd is 1.2.0. In xlrd >= 2.0, only the xls format is supported. As a result, the openpyxl engine will be used if it is installed and the engine argument is not specified. Install openpyxl instead.
table = pd.read_excel(file_resources["lncRNA_target_from_low_throughput_experiments.xlsx"])
-- Docs: https://docs.pytest.org/en/stable/warnings.html
================================================================================================= 38 passed, 8 warnings in 603.78s (0:10:03) =================================================================================================
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Related Issues (15)
- AttributeError: '_io.TextIOWrapper' object has no attribute 'startswith' HOT 7
- Reviewer 1 - comment 2 - Cannot change the directory of downloaded Dataset files (using astropy) HOT 2
- Reviewer 2 - Installation instructions - Unable to install dependency HOT 2
- Reviewer 2 - Vignette - Unable to `import umap` due to dependencies with scipy on Python 3.9 HOT 2
- Review 2 - Automated tests - Failed builds in Travis CI HOT 10
- Review 2 - Documentations - Readthedocs documentations should be updated HOT 4
- Reviewer 1 - Documentation HOT 6
- Reviewer 1 - errors using the example code HOT 1
- Reviewer 1 - Installation HOT 2
- Unable to use load_data() for class Multiomics HOT 4
- Test Suite Errors HOT 1
- Bug: MalaCards integration not working because CSV is not working HOT 1
- Request: making OMIM integration
- Initial Update
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