arches-for-science 2.0.4

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Welcome to Arches for Science!

Arches for Science an Arches Application designed to help conservation scientists record, manage, and visualize laboratory data.

Please see the project page for more information on the Arches project.

Installation

If you are installing Arches for Science for the first time, you can install it as an Arches application into a project or run it directly as an Arches project. Running Arches for Science as a project can provide some convienience if you are a developer contributing to the Arches for Science project. Otherwise, we strongly recommend running Arches for Science as an Arches Application within a project because that will allow greater flexibility in customizing your project without the risk of conflicts when upgrading to the next version of Arches for Science.

If installing for development

Clone the arches-for-science repo and checkout the latest dev/x.x.x branch. Navigate to the arches-for-science directory from your terminal and run:

pip install -e .

Important: Installing the arches-for-science app will install Arches as a dependency. This may replace your current install of Arches with a version from PyPi. If you've installed Arches for development using the --editable -e flag, you'll need to re pip install arches after installing arches-for-science

If installing for deployment, run:

pip install arches-for-science

Project Configuration

1. If you don't already have an Arches project, you'll need to create one by following the instructions in the Arches documentation. Since Arches for Science uses Cantaloupe as its IIIF server, take notice of the Cantaloupe installation instructions, too.

2. When your project is ready, add "arches_templating", "arches_for_science", and "pgtrigger" to INSTALLED_APPS below the name of your project:

   INSTALLED_APPS = (
       ...
       "my_project_name",
       "arches_templating",
       "arches_for_science",
       "pgtrigger",
   )
   

3. Make sure the following settings are added to your project

   FUNCTION_LOCATIONS.append("arches_for_science.functions")
   
   TEMPLATES = build_templates_config(
       debug=DEBUG,
       app_root=APP_ROOT,
       context_processors=[
           "django.contrib.auth.context_processors.auth",
           "django.template.context_processors.debug",
           "django.template.context_processors.i18n",
           "django.template.context_processors.media",
           "django.template.context_processors.static",
           "django.template.context_processors.tz",
           "django.template.context_processors.request",
           "django.contrib.messages.context_processors.messages",
           "arches.app.utils.context_processors.livereload",
           "arches.app.utils.context_processors.map_info",
           "arches.app.utils.context_processors.app_settings",
           "arches_for_science.utils.context_processors.project_settings",
       ],
   )
   
   RENDERERS += [
       {
           "name": "xy-reader",
           "title": "XY Data File Reader",
           "description": "Use for all instrument outputs with x-y data",
           "id": "e93b7b27-40d8-4141-996e-e59ff08742f3",
           "iconclass": "fa fa-bolt",
           "component": "views/components/cards/file-renderers/xy-reader",
           "ext": "txt",
           "type": "text/plain",   
           "exclude": "",
       },
   ]
   
   XY_TEXT_FILE_FORMATS = ["txt"]
   
   X_FRAME_OPTIONS = "SAMEORIGIN"
   

4. Next ensure arches and arches_for_science are included as dependencies in package.json

   "dependencies": {
       "@uppy/aws-s3": "3.6.2",
       "@uppy/core": "3.13.0",
       "@uppy/dashboard": "3.9.0",
       "@uppy/drag-drop": "3.1.0",
       "@uppy/progress-bar": "3.1.1",
       "@uppy/companion-client": "3.1.3",
       "typescript": "5.6.2",
       "arches": "archesproject/arches#dev/7.6.x",
       "arches_for_science": "archesproject/arches-for-science#dev/2.0.x"
   }
   

5. Update urls.py to include the arches-for-science urls

   urlpatterns = [
       path("", include("arches.urls")),
       path("", include("arches_for_science.urls")),
       path("reports/", include("arches_templating.urls")),
   ] + static(settings.MEDIA_URL, document_root=settings.MEDIA_ROOT)
   

6. Install the arches application package (models and other data)

   python manage.py packages -o load_package -a arches_for_science -dev -y
   

7. Start your project

   python manage.py runserver
   

8. Next cd into your project's app directory (the one with package.json) install and build front-end dependencies:

   npm install
   npm run build_development