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SmartDataAnalytics / BioKEEN

A computational library for learning and evaluating biological knowledge graph embeddings - please see the main PyKEEN repo at https://github.com/pykeen/pykeen/
https://github.com/pykeen/pykeen/
MIT License
46 stars 4 forks source link

mirtarbase #8

Closed mali-git closed 5 years ago

mali-git commented 5 years ago

"bio2bel_mirtarbase does not produce BEL"

cthoyt commented 5 years ago

I still think we've already fixed this, and it's a problem with an old version of the installation.

I just added a piece of logging that looks up the version number of the currently installed bio2bel_mirtarbase and prints it. Please send the output of pip freeze and the error message in full.

mali-git commented 5 years ago

I still think we've already fixed this, and it's a problem with an old version of the installation.

I just added a piece of logging that looks up the version number of the currently installed bio2bel_mirtarbase and prints it. Please send the output of pip freeze and the error message in full.

Output of pip freeze:

alabaster==0.7.12 asn1crypto==0.24.0 Babel==2.6.0 bio2bel==0.2.0 bio2bel-hgnc==0.2.0 bio2bel-mirtarbase==0.1.2 bio2bel-wikipathways==0.2.0 -e git+https://github.com/SmartDataAnalytics/BioKEEN.git@ab7287ca6b2aa4a6a00621b34ee1d9ef60e89181#egg=biokeen bumpversion==0.5.3 certifi==2018.10.15 cffi==1.11.5 chardet==3.0.4 Click==7.0 click-plugins==1.0.4 compath-resources==0.0.7 compath-utils==0.2.1 configparser==3.5.0 cryptography==2.4.2 dataclasses==0.6 decorator==4.3.0 docutils==0.14 easy-config==0.2.0 enum34==1.1.6 filelock==3.0.10 flasgger==0.9.2 Flask==1.0.2 Flask-Cors==3.0.7 idna==2.7 ijson==2.3 imagesize==1.1.0 isodate==0.6.0 itsdangerous==1.1.0 Jinja2==2.10 jsonschema==2.6.0 MarkupSafe==1.1.0 mistune==0.8.4 mock==2.0.0 ndex2==2.0.0.8 networkx==2.2 numpy==1.15.4 packaging==18.0 pandas==0.23.4 passlib==1.7.1 pbr==5.1.1 Pillow==5.3.0 pluggy==0.8.0 prompt-toolkit==2.0.7 py==1.7.0 PyBEL==0.12.2 pycparser==2.19 Pygments==2.2.0 PyHGNC==0.2.4 pykeen==0.0.13.dev0 PyMySQL==0.9.2 pyparsing==2.3.0 pysolr==3.8.1 python-dateutil==2.7.5 pytz==2018.7 PyYAML==3.13 rdflib==4.2.2 requests==2.20.1 requests-file==1.4.3 requests-toolbelt==0.8.0 scikit-learn==0.19.1 scipy==1.1.0 six==1.11.0 snowballstemmer==1.2.1 Sphinx==1.8.2 sphinxcontrib-websupport==1.1.0 SQLAlchemy==1.2.14 toml==0.10.0 torch==0.4.0 torchvision==0.2.1 tox==3.5.3 tqdm==4.28.1 urllib3==1.24.1 virtualenv==16.1.0 wcwidth==0.1.7 Werkzeug==0.14.1 WTForms==2.2.1 xlrd==1.1.0

Error message:

🍩 imported bio2bel_mirtarbase Traceback (most recent call last): File "/Users/mehdi/virtual_envs/BioKEEN/bin/biokeen", line 11, in load_entry_point('biokeen', 'console_scripts', 'biokeen')() File "/Users/mehdi/virtual_envs/BioKEEN/lib/python3.6/site-packages/click/core.py", line 764, in call return self.main(args, kwargs) File "/Users/mehdi/virtual_envs/BioKEEN/lib/python3.6/site-packages/click/core.py", line 717, in main rv = self.invoke(ctx) File "/Users/mehdi/virtual_envs/BioKEEN/lib/python3.6/site-packages/click/core.py", line 1137, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/Users/mehdi/virtual_envs/BioKEEN/lib/python3.6/site-packages/click/core.py", line 956, in invoke return ctx.invoke(self.callback, ctx.params) File "/Users/mehdi/virtual_envs/BioKEEN/lib/python3.6/site-packages/click/core.py", line 555, in invoke return callback(args, **kwargs) File "/Users/mehdi/PycharmProjects/BioKEEN/src/biokeen/cli.py", line 106, in start config = prompt_config(connection, rebuild) File "/Users/mehdi/PycharmProjects/BioKEEN/src/biokeen/cli.py", line 52, in prompt_config config[TRAINING_SET_PATH] = install_bio2bel_module(name=database_name, connection=connection, rebuild=rebuild) File "/Users/mehdi/PycharmProjects/BioKEEN/src/biokeen/cli_utils/bio_2_bel_utils.py", line 71, in install_bio2bel_module version = pkg_resources.get_distribution("construct").version File "/Users/mehdi/virtual_envs/BioKEEN/lib/python3.6/site-packages/pkg_resources/init.py", line 479, in get_distribution dist = get_provider(dist) File "/Users/mehdi/virtual_envs/BioKEEN/lib/python3.6/site-packages/pkg_resources/init.py", line 355, in get_provider return working_set.find(moduleOrReq) or require(str(moduleOrReq))[0] File "/Users/mehdi/virtual_envs/BioKEEN/lib/python3.6/site-packages/pkg_resources/init.py", line 898, in require needed = self.resolve(parse_requirements(requirements)) File "/Users/mehdi/virtual_envs/BioKEEN/lib/python3.6/site-packages/pkg_resources/init.py", line 784, in resolve raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'construct' distribution was not found and is required by the application

cthoyt commented 5 years ago

Okay. We still need to make a new release for miRTarBase, but for some reason the unit tests aren't passing anymore :/