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tedinburghtedinburgh
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Merge pull request #35 from ISARICResearch/public-projects
allow public projects
2 parents 183505e + 524ec72 commit 1fb09b8

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‎.gitignore‎

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# logs
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app.log*
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#public project dir
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public-projects/*
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]

‎Dockerfile‎

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WORKDIR /app
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# Upgrade pip and install pip-tools first
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RUN pip install --upgrade pip setuptools wheel
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RUN pip install pip-tools
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RUN pip install "pip<25" "setuptools<80" wheel
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RUN pip install "pip-tools==7.5.1"
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COPY pyproject.toml ./
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‎projects/ARChetypeCRF_dengue_synthetic/config_file.json‎

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{
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"project_name": "ARChetype CRF Dengue (Synthetic)",
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"project_name": "(Analysis) ARChetype CRF Dengue",
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"api_url": "https://ncov.medsci.ox.ac.uk/api/",
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"api_key": "481093EAF0FD7947B1B40E53C374E350",
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"map_layout_center_latitude": 6,

‎projects/ARChetypeCRF_h5nx_synthetic/config_file.json‎

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{
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"project_name": "ARChetype CRF H5Nx (Synthetic)",
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"project_name": "(Analysis) ARChetype CRF H5Nx",
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"api_url": "https://ncov.medsci.ox.ac.uk/api/",
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"api_key": "825EE199496BE8F41B1CDBE335FBFB78",
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"map_layout_center_latitude": 6,

‎projects/ARChetypeCRF_h5nx_synthetic_mf/config_file.json‎

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{
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"project_name": "H5Nx Synthetic data",
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"project_name": "(Analysis) H5Nx Synthetic data",
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"api_url": "https://ncov.medsci.ox.ac.uk/api/",
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"api_key": "0D855E040CB0A5DEC78BCA9137BB65B3",
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"vertex_dataframes_path": "vertex_patient_level_data/",

‎projects/ARChetypeCRF_mpox_synthetic/config_file.json‎

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{
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"project_name": "ARChetype CRF mpox (Synthetic)",
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"project_name": "(Analysis) ARChetype CRF mpox",
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"api_url": "https://ncov.medsci.ox.ac.uk/api/",
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"api_key": "27B9F4C93C8C2BCDB4EFCA9DA8717DC0",
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"map_layout_center_latitude": 6,

‎projects/Bubo_Images/characteristics/fig_upset_CharacteristicsConfirme_day11_data___0.csv‎

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index,count,label,short_label
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unilateral,9,unilateral,unilateral
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homogenous cortex,6,homogenous cortex,homogenous cortex
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oval shape,6,oval shape,oval shape
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distinct hilum,5,distinct hilum,distinct hilum
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peri-nodal reaction,5,peri-nodal reaction,peri-nodal reaction
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distinct capsule,5,distinct capsule,distinct capsule
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blurred capsule,4,blurred capsule,blurred capsule
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round shape,3,round shape,round shape
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hypervascularity,2,hypervascularity,hypervascularity
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coalescence,1,coalescence,coalescence

‎projects/Bubo_Images/characteristics/fig_upset_CharacteristicsConfirme_day11_data___1.csv‎

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index,count,label
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"('unilateral', 'distinct hilum', 'homogenous cortex', 'oval shape', 'distinct capsule')",3,"('unilateral', 'distinct hilum', 'homogenous cortex', 'oval shape', 'distinct capsule')"
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"('unilateral', 'distinct hilum', 'homogenous cortex', 'peri-nodal reaction', 'oval shape', 'distinct capsule')",1,"('unilateral', 'distinct hilum', 'homogenous cortex', 'peri-nodal reaction', 'oval shape', 'distinct capsule')"
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"('unilateral', 'homogenous cortex', 'hypervascularity', 'peri-nodal reaction', 'oval shape', 'blurred capsule')",1,"('unilateral', 'homogenous cortex', 'hypervascularity', 'peri-nodal reaction', 'oval shape', 'blurred capsule')"
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"('unilateral', 'distinct hilum', 'homogenous cortex', 'round shape', 'distinct capsule')",1,"('unilateral', 'distinct hilum', 'homogenous cortex', 'round shape', 'distinct capsule')"
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"('unilateral', 'peri-nodal reaction', 'coalescence', 'round shape', 'blurred capsule')",1,"('unilateral', 'peri-nodal reaction', 'coalescence', 'round shape', 'blurred capsule')"
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"('unilateral', 'hypervascularity', 'peri-nodal reaction', 'round shape', 'blurred capsule')",1,"('unilateral', 'hypervascularity', 'peri-nodal reaction', 'round shape', 'blurred capsule')"
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"('unilateral', 'peri-nodal reaction', 'oval shape', 'blurred capsule')",1,"('unilateral', 'peri-nodal reaction', 'oval shape', 'blurred capsule')"

‎projects/Bubo_Images/characteristics/fig_upset_CharacteristicsConfirme_day11_metadata.json‎

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{
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"fig_id": "characteristics/fig_upset_CharacteristicsConfirme_day11",
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"fig_name": "fig_upset",
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"fig_arguments": {
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"title": "Intersection sizes of bubo characteristics",
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"suffix": "characteristics",
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"filepath": "",
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"save_inputs": false,
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"graph_id": "fig_upset_CharacteristicsConfirme_day11",
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"graph_label": "Day11: Cas confirmé",
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"graph_about": "Upset plot of sonographic characteristics detected among confirmed cases on D11"
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},
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"fig_data": [
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"characteristics/fig_upset_CharacteristicsConfirme_day11_data___0.csv",
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"characteristics/fig_upset_CharacteristicsConfirme_day11_data___1.csv"
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]
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}

‎projects/Bubo_Images/characteristics/fig_upset_CharacteristicsConfirme_day1_data___0.csv‎

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index,count,label,short_label
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unilateral,10,unilateral,unilateral
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oval shape,6,oval shape,oval shape
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homogenous cortex,5,homogenous cortex,homogenous cortex
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distinct capsule,5,distinct capsule,distinct capsule
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distinct hilum,4,distinct hilum,distinct hilum
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peri-nodal reaction,4,peri-nodal reaction,peri-nodal reaction
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blurry capsule,4,blurry capsule,blurry capsule
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round shape,3,round shape,round shape
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hypervascularity,2,hypervascularity,hypervascularity
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necrosis,1,necrosis,necrosis
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coalescence,1,coalescence,coalescence

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