Add docs

.readthedocs.yml

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+version: 2
+
+sphinx:
+  configuration: docs/conf.py
+
+formats: all
+
+python:
+  version: 3.7
+  install:
+    - requirements: docs/requirements.txt

LICENSE

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+MIT License
+
+Copyright (c) <YEAR> <COPYRIGHT HOLDER>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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 # FIP Wizard Documentation
 
+[![Documentation Status](https://readthedocs.org/projects/fip-wizard/badge/?version=latest)](https://fip-wizard.readthedocs.io/en/latest/?badge=latest)
+
+
 Technical documentation for FIP Wizard.

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/_static/style.css

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+.wy-side-nav-search {
+  background-color: #01518E;
+  color: #ffffff;
+}

docs/about/about.rst

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+****************
+About FIP Wizard
+****************
+
+What FIP Wizard?
+================
+
+**FIP Wizard** is a toolset to facilitate the capture of data in FAIR Convergence Matrix questionnaire prompting communities to explicitly declare their FAIR Implementation Profiles. These profiles can be then stored and published as nanopublications.
+
+The toolset can be deployed wherever the user wants. It can be deployed in a cloud provider, on a server or on a local machine. Naturally, the first two options can be made accessible anywhere on the Web while the third option is normally for testing and demonstration purposes only.
+
+
+Demo instance
+=============
+
+You can explore and try out *FIP Wizard* using our instance:
+
+- `FIP Wizard fip-wizard.ds-wizard.org <https://fip-wizard.ds-wizard.org>`_

docs/about/components.rst

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+**********
+Components
+**********
+
+FIP Wizard consists of the following services:
+
+- `Data Stewardship Wizard (DSW) <https://ds-wizard.org>`_ adjusted to serve as FIP Wizard for creating FAIR Implementation Profiles for the communities.
+- AllegroGraph triple store for storing the FIP nanopublications,
+- MongoDB used by DSW to store data,
+- Submission Service that handles storing FIPs in triple store,
+- RabbitMQ for queueing generation of a FIP to a RDF document using DSW document worker,
+- (optionally) Nginx proxy for :ref:`production-deployment`.

docs/about/usage-scenarios.rst

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+***************
+Usage Scenarios
+***************
+
+The **FIP Wizard** can be used in the following scenarios:
+
+FAIR Implementation Profile
+---------------------------
+
+In this scenario, we will use FIP Wizard to create and update FAIR Implementation Profile of a community and submit it to the triple store as a nanopublication.
+
+These use cases are require user to be logged in in FIP Wizard:
+
+Create FIP
+~~~~~~~~~~
+
+1. Select :guilabel:`Create a FIP` from the left menu
+2. Fill-in the name and press :guilabel:`Save` button
+3. Fill FIP Questionnaire with your community data, the changes will be saved automatically
+
+Update FIP
+~~~~~~~~~~
+
+1. Select :guilabel:`Projects` from the left menu
+2. Find by name the FIP you want to edit
+3. Fill FIP with new data you have, the changes will be saved automatically
+
+Submit FIP
+~~~~~~~~~~
+
+1. Open FIP you want to submit
+2. Go to :guilabel:`Documents`
+3. Press :guilabel:`New document`
+4. Press :guilabel:`Create` (optionally, you can change the document name, e.g. "My community - v0.1")
+5. Press three dots on the right for the new document and press :guilabel:`Submit`
+6. Select the triple store you want to use and press :guilabel:`Submit`

docs/conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'FIP Wizard'
+copyright = '2020, FIP Team'
+author = 'FIP Team'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx_copybutton'
+]
+
+# Add any paths that contain templates here, relative to this directory.
+# templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# html_logo = '_static/logo.png'
+# html_favicon = '_static/favicon.ico'
+html_theme_options = {
+    'logo_only': False,
+    'display_version': True,
+}
+html_css_files = [
+    'style.css',
+]

docs/deployment/configuration.rst

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+.. _configuration:
+
+**********************
+Advanced Configuration
+**********************
+
+To work with *FIP Wizard* you are not required to change anything in the included ``docker-compose.yml`` nor configuration files. For some specific use cases you might want to make some of the following changes.
+
+Persistence
+===========
+
+In the basic setup, persistence is assured using mounted folders (bind mounts):
+
+- ``./mongo/data`` - for MongoDB
+- ``./allegrograph/data`` - for AllegroGraph triple store (used as nanopublications data storage)
+
+This allows you to easily work with data used by *FIP Wizard*. For example, you can clear those folders (while it is not running) to start over. In some cases you might want to use `Docker volumes <https://docs.docker.com/storage/volumes/>`_ instead. Using Docker volumes is recommended when using Docker for Windows due to common problems related to mounting Windows folders into Linux containers.
+
+.. code-block:: yaml
+
+   # ...
+
+   mongo:
+     image: mongo:4.2.3
+     restart: always
+     ports:
+       - 27017:27017
+     environment:
+       MONGO_INITDB_DATABASE: wizard
+     volumes:
+       - mongo-data:/data/db  # <- USING DOCKER VOLUME
+       - ./mongo/init-mongo.js:/docker-entrypoint-initdb.d/init-mongo.js:ro
+
+   # ...
+
+   agraph:
+     image: franzinc/agraph:v7.0.1
+     restart: always
+     ports:
+       - 10000-10035:10000-10035
+     hostname: agraph
+     shm_size: '1gb'
+     volumes:
+       - agraph-data:/agraph/data    # <- USING DOCKER VOLUME
+       - ./allegrograph/agraph.cfg:/agraph/etc/agraph.cfg
+
+   # ...
+
+   volumes:
+     mongo-data:
+     agraph-data:
+
+
+To avoid persistence totally (i.e. all data will be lost after ``docker-compose down``). Just comment out or delete lines related to mounting volumes in ``docker-compose.yml```:
+
+.. code-block:: yaml
+
+   # ...
+
+   mongo:
+     image: mongo:4.2.3
+     restart: always
+     ports:
+       - 27017:27017
+     environment:
+       MONGO_INITDB_DATABASE: wizard
+     volumes:
+       # - mongo-data:/data/db  # <-
+       - ./mongo/init-mongo.js:/docker-entrypoint-initdb.d/init-mongo.js:ro
+
+   # ...
+
+   agraph:
+     image: franzinc/agraph:v7.0.1
+     restart: always
+     ports:
+       - 10000-10035:10000-10035
+     hostname: agraph
+     shm_size: '1gb'
+     volumes:
+       # - agraph-data:/agraph/data    # <- 
+       - ./allegrograph/agraph.cfg:/agraph/etc/agraph.cfg
+
+
+.. IMPORTANT::
+
+   Data backups are your responsibility. It is recommended to backup regularly all mounted volumes and store such backups in different site(s).
+
+
+Changing ports
+==============
+
+If you need to change ports because you already use those for other services, you just need to adjust the mappings in ``docker-compose.yml`` file. For example, if you want to access MongoDB on other port than ``27017`` change the mapping ``27017:27017`` to something else, e.g. ``27020:27017``.
+
+.. code-block:: yaml
+
+   # ...
+
+   mongo:
+     image: mongo:4.2.3
+     restart: always
+     ports:
+       - 27020:27017
+     environment:
+       MONGO_INITDB_DATABASE: wizard
+     volumes:
+       # ...
+       - ./mongo/init-mongo.js:/docker-entrypoint-initdb.d/init-mongo.js:ro
+
+
+
+FIP Wizard emails
+=================
+
+There is optional configuration in ``dsw-server/application.yml`` related to email server. You need that to enable:
+
+- User registrations with email-based verification: upon registration a verification email is sent, otherwise administrator have to set new accounts as *Active* manually in users administration.
+- Password recovery: when someone forgots password, they can ask for reset link that will be sent to their email address, otherwise it can be again changes only by administrators.
+
+To make those emails working, fill the configuration with your SMTP server and accoung. We recommend using secured emails with SSL/TLS or STARTTLS. For more information, visit `DSW documentation <https://docs.ds-wizard.org/en/latest/admin/configuration.html#mail>`_.
+
+.. NOTE::
+
+   Registrations can be turned off using :guilabel:`Settings` and :guilabel:`Authentication`.