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Merge pull request #10 from ZhixuNi/master
Updated UI for Linker and Converter
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| @@ -0,0 +1,11 @@ | ||
| name: Lint | ||
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| on: [push, pull_request] | ||
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| jobs: | ||
| lint: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - uses: actions/setup-python@v2 | ||
| - uses: psf/black@master |
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@@ -11,24 +11,20 @@ jobs: | |
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| os: [ubuntu-latest, macos-latest, windows-latest] | ||
| python-version: [3.7, 3.8] | ||
| os: [ubuntu-20.04, ubuntu-latest, macos-latest, windows-latest] | ||
| python-version: [3.7] | ||
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| name: Test Python ${{ matrix.python-version }} | ||
| name: Test Python ${{ matrix.python-version }} on ${{ matrix.os }} | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - name: Set up Python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v2 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| architecture: x64 | ||
| - name: Install dependencies | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install -r requirements.txt | ||
| - name: Black Code Formatter | ||
| uses: lgeiger/[email protected] | ||
| - name: Test with pytest | ||
| run: | | ||
| pip install codecov pytest pytest-cov | ||
| pytest --cov=./ | ||
| - uses: actions/checkout@v2 | ||
| - name: Set up Python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v2 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| architecture: x64 | ||
| - name: GitHub Action for pytest | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install -r requirements.txt | ||
| pip install codecov pytest pytest-cov | ||
| pytest ./ | ||
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| Original file line number | Diff line number | Diff line change |
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@@ -13,6 +13,7 @@ | |
| # For more info please contact: | ||
| # Developer Zhixu Ni [email protected] | ||
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| class LynxObject(object): | ||
| def __init__(self, lynx_id: str): | ||
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@@ -14,6 +14,7 @@ | |
| # Developer Zhixu Ni [email protected] | ||
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| import json | ||
| import os | ||
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| from lynx.utils.cfg_reader import app_cfg_info | ||
| from lynx.utils.params_loader import ( | ||
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@@ -33,6 +34,15 @@ | |
| default_alias_file = get_abs_path(app_cfg_info["defined_alias"]) | ||
| default_kegg_file = get_abs_path(app_cfg_info["resource_kegg"]) | ||
| default_lion_file = get_abs_path(app_cfg_info["resource_lion"]) | ||
| default_temp_folder = app_cfg_info.get("temp_folder", r"lynx/temp") | ||
| default_temp_max_days = int(app_cfg_info.get("temp_max_days", "3")) | ||
| default_temp_max_files = int(app_cfg_info.get("temp_max_files", "99")) | ||
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| if os.path.isdir(default_temp_folder): | ||
| pass | ||
| else: | ||
| os.mkdir(default_temp_folder) | ||
| default_temp_folder = get_abs_path(default_temp_folder) | ||
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| with open(default_cv_file, "r") as cv_js: | ||
| cv_alias_json = json.load(cv_js) | ||
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@@ -53,6 +63,10 @@ | |
| with open(default_lion_file, "r") as lion_json_obj: | ||
| lion_ids = json.load(lion_json_obj) | ||
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| default_template_files = { | ||
| "LipidLynxX_Linker_Template.csv": "lynx/static/files/LipidLynxX_Linker_Template.csv" | ||
| } | ||
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| lipid_level_lst = ["B", "D", "S"] | ||
| mod_level_lst = ["0", "1", "2", "3", "4", "5"] | ||
| db_level_lst = [".0", "0.1", "0.2"] | ||
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