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RyanJFieldRyanJField
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Merge remote-tracking branch 'origin/main' into feature/github-actions
2 parents e4bfe04 + ff30db5 commit 29e3041

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+135
-65
lines changed

‎.github/workflows/fair-data-registry.yaml

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fi
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- name: Run Tests
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run: |
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python -m pip install -r local-requirements.txt
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python -m pip install -r requirements.txt
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DJANGO_SETTINGS_MODULE=drams.test-settings coverage run --omit=drams,scripts,tools manage.py test
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- name: Generate XML
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run: coverage xml

‎CITATION.cff

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@@ -30,6 +30,6 @@ license: "BSD-2-Clause"
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message: "If you use this software, please cite it using these metadata."
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repository-code: "https://github.com/FAIRDataPipeline/data-registry/"
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title: "The FAIR Data Registry"
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version: "v1.1.1"
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version: "v1.2.0"
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doi: "10.5281/zenodo.5562750"
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date-released: "2023-02-03"

‎Vagrantfile

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@@ -35,7 +35,7 @@ source "$FAIR_HOME"/venv/bin/activate
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# see https://www.virtualbox.org/ticket/8761
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# a work around for this is to use the --ignore-installed option for pip
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python -m pip install --upgrade pip wheel --ignore-installed
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python -m pip install -r "$FAIR_HOME"/local-requirements.txt --ignore-installed
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python -m pip install -r "$FAIR_HOME"/requirements.txt --ignore-installed
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export DJANGO_SETTINGS_MODULE="drams.vagrant-settings"
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export DJANGO_SUPERUSER_USERNAME=admin

‎codemeta.json

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{
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"@context": "https://w3id.org/codemeta/3.0",
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"type": "SoftwareSourceCode",
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"applicationCategory": "Software",
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"author": [
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{
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"id": "_:author_1",
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"type": "Person",
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"familyName": "Blackwell",
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"givenName": "Richard"
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},
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{
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"id": "_:author_2",
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"type": "Person",
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"familyName": "Brett",
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"givenName": "Alys"
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},
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{
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"id": "_:author_3",
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"type": "Person",
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"familyName": "Cook",
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"givenName": "James"
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},
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{
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"id": "_:author_4",
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"type": "Person",
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"familyName": "Cumming",
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"givenName": "Nathan"
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},
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{
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"id": "http://orcid.org/0000-0002-4424-9890",
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"type": "Person",
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"affiliation": {
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"type": "Organization",
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"name": "University of Glasgow"
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},
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"familyName": "Field",
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"givenName": "Ryan"
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},
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{
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"id": "http://orcid.org/0000-0003-3499-8262",
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"type": "Person",
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"familyName": "Gonzalez-Beltran",
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"givenName": "Alejandra"
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},
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{
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"id": "_:author_7",
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"type": "Person",
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"familyName": "Hollocombe",
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"givenName": "Jonathan"
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},
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{
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"id": "_:author_8",
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"type": "Person",
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"familyName": "Lahiff",
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"givenName": "Andrew"
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},
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{
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"id": "_:author_9",
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"type": "Person",
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"affiliation": {
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"type": "Organization",
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"name": "University of Glasgow"
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},
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"familyName": "Reeve",
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"givenName": "Richard"
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},
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{
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"id": "_:author_10",
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"type": "Person",
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"familyName": "Wilson",
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"givenName": "Anthony"
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},
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{
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"id": "_:author_11",
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"type": "Person",
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"familyName": "Zarebski",
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"givenName": "Kristian"
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}
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],
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"codeRepository": "git+https://github.com/FAIRDataPipeline/data-registry.git",
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"dateCreated": "2020-05-07",
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"dateModified": "2024-02-23",
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"datePublished": "2021-06-22",
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"description": "The FAIR data registry is a component of the FAIR data pipeline that maintains a metadata catalogue for different data types utilised and generated within a typical epidemiological modelling workflow.",
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"downloadUrl": "https://github.com/FAIRDataPipeline/data-registry/archive/refs/tags/v1.1.1.tar.gz",
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"identifier": "10.5281/zenodo.5562749",
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"isPartOf": "https://www.fairdatapipeline.org",
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"keywords": [
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"FAIR",
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"REST",
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"Django",
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"Data Pipeline"
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],
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"license": "https://spdx.org/licenses/GPL-3.0+",
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"name": "FAIR Data Registry",
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"operatingSystem": [
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"Linux",
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"Windows",
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"MacOS"
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],
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"programmingLanguage": "Python 3",
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"releaseNotes": "Full Changelog: https://github.com/FAIRDataPipeline/data-registry/compare/v1.1.0...v1.1.1",
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"softwareRequirements": "Django",
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"version": "1.1.1",
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"codemeta:contIntegration": {
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"id": "https://github.com/FAIRDataPipeline/data-registry/actions"
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},
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"continuousIntegration": "https://github.com/FAIRDataPipeline/data-registry/actions",
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"developmentStatus": "active",
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"issueTracker": "https://github.com/FAIRDataPipeline/data-registry/issues"
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}

‎local-requirements.txt

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‎requirements.txt

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certifi==2020.4.5.1
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certifi
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chardet==3.0.4
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decorator==4.4.2
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defusedxml==0.6.0
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Django==4.2.6
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social-auth-app-django==5.4.0
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Django==4.2.16
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social-auth-app-django==5.4.1
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django-bootstrap-breadcrumbs==0.9.2
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django-extensions==3.2.3
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django-filter==2.3.0
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django-grappelli==3.0.8
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djangorestframework==3.14.0
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future==0.17.1
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gunicorn==20.0.4
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idna==2.9
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djangorestframework==3.15.2
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future~=0.17.1
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gunicorn==22.0.0
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idna==3.7
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isodate==0.6.0
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lxml>=4.9
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lxml~=5.0
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mysql-connector-python==8.0.20
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networkx==3.0
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oauthlib==3.1.0
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pytz==2020.1
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rdflib==6.0.1
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requests>=2.25.0
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requests-oauthlib==1.3.0
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six==1.16.0
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sqlparse==0.3.1
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requests-oauthlib~=1.3.0
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six~=1.16.0
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sqlparse==0.5.0
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urllib3>=1.26.5
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semver>=2.10.2
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django-crispy-forms==1.14.0
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crispy-bootstrap3==2022.1
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Markdown==3.5.1
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setuptools>54.2
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whitenoise==5.2.0
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whitenoise~=5.2.0
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coverage
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rocrate==0.7.0
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boto3>=1.24
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boto3~=1.24
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psycopg>=3.1

‎static/localregistry.bat

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:: Install Python Dependencies
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python -m pip install --upgrade pip wheel
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python -m pip install -r "%FAIR_HOME:"=%\local-requirements.txt"
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python -m pip install -r "%FAIR_HOME:"=%\requirements.txt"
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:: Change into FAIR HOME directory
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cd /d %FAIR_HOME%

‎static/localregistry.ps1

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# Install Python Dependencies
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python -m pip install --upgrade pip wheel
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python -m pip install -r "${FAIR_HOME}\local-requirements.txt"
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python -m pip install -r "${FAIR_HOME}\requirements.txt"
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$Env:DJANGO_SETTINGS_MODULE= "drams.local-settings"
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$Env:DJANGO_SUPERUSER_USERNAME= "admin"

‎static/localregistry.sh

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python3 -m venv "$FAIR_HOME"/venv
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source "$FAIR_HOME"/venv/bin/activate
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python -m pip install --upgrade pip wheel
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python -m pip install -r "$FAIR_HOME"/local-requirements.txt
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python -m pip install -r "$FAIR_HOME"/requirements.txt
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export DJANGO_SETTINGS_MODULE="drams.local-settings"
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export DJANGO_SUPERUSER_USERNAME=admin
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export DJANGO_SUPERUSER_PASSWORD=admin

‎static/remoteregistry.bat

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:: Install Python Dependencies
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python -m pip install --upgrade pip wheel
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python -m pip install -r "%FAIR_HOME:"=%\local-requirements.txt"
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python -m pip install -r "%FAIR_HOME:"=%\requirements.txt"
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:: Change into FAIR HOME directory
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cd /d %FAIR_HOME%

‎static/remoteregistry.ps1

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# Install Python Dependencies
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python -m pip install --upgrade pip wheel
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python -m pip install -r "${FAIR_HOME}\local-requirements.txt"
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python -m pip install -r "${FAIR_HOME}\requirements.txt"
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$Env:DJANGO_SETTINGS_MODULE= $DRAMS
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‎static/remoteregistry.sh

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python3 -m venv "$FAIR_HOME"/venv
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source "$FAIR_HOME"/venv/bin/activate
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python -m pip install --upgrade pip wheel
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python -m pip install -r "$FAIR_HOME"/local-requirements.txt
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python -m pip install -r "$FAIR_HOME"/requirements.txt
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export DJANGO_SETTINGS_MODULE=$DRAMS
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if [ ! -z $(echo ${USE_SUPERUSER} | xargs) ]; then
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export DJANGO_SUPERUSER_USERNAME=$SUPERUSER_USERNAME

‎static/temp/registry

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