Merge f710394 into 2196214

CHANGES.rst

@@ -1,6 +1,18 @@
 Changes
 =======
 
+Version master (UNRELEASED)
+---------------------------
+
+- Encrypts user tokens.
+- Adds initial central workflow status transitions logic.
+- Factors out user tokens from User table to UserToken table.
+- Adds audit table and logic to register actions.
+- Adds new column ``workspace_path`` to the Workflow table.
+- Adds fixtures for better testing models.
+- Amends database host configuration to respect REANA component prefixing.
+- Add Black formatter support.
+
 Version 0.6.0 (2019-12-19)
 --------------------------
 

README.rst

@@ -20,6 +20,9 @@
 .. image:: https://img.shields.io/github/license/reanahub/reana-db.svg
       :target: https://github.com/reanahub/reana-db/blob/master/LICENSE
 
+.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
+   :target: https://github.com/psf/black
+
 About
 -----
 

docs/conf.py

@@ -34,36 +34,36 @@
 # needs_sphinx = '1.0'
 
 # Do not warn on external images.
-suppress_warnings = ['image.nonlocal_uri']
+suppress_warnings = ["image.nonlocal_uri"]
 
 # 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.ext.autodoc',
-    'sphinx.ext.coverage',
-    'sphinx.ext.doctest',
-    'sphinx.ext.graphviz',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.viewcode',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.coverage",
+    "sphinx.ext.doctest",
+    "sphinx.ext.graphviz",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.viewcode",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = 'reana'
-copyright = '2018, 2019 info@reana.io'
-author = 'info@reana.io'
+project = "reana"
+copyright = "2018, 2019 info@reana.io"
+author = "info@reana.io"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -73,9 +73,9 @@
 
 # Get the version string. Cannot be done with import!
 g = {}
-with open(os.path.join('..', 'reana_db', 'version.py'), 'rt') as fp:
+with open(os.path.join("..", "reana_db", "version.py"), "rt") as fp:
     exec(fp.read(), g)
-    version = g['__version__']
+    version = g["__version__"]
 
 # The full version, including alpha/beta/rc tags.
 release = version
@@ -90,10 +90,10 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
@@ -104,52 +104,52 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+html_theme = "alabaster"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
 #
 html_theme_options = {
-    'logo': 'logo-reana.png',
-    'description': """<p>REANA-DB is a component of the <a
+    "logo": "logo-reana.png",
+    "description": """<p>REANA-DB is a component of the <a
                       href="http://www.reana.io">REANA</a> reusable and
                       reproducible research data analysis
                       platform.</p><p>It contains REANA database models and
                       utilities.</p>""",
-    'github_user': 'reanahub',
-    'github_repo': 'reana-db',
-    'github_button': False,
-    'github_banner': True,
-    'show_powered_by': False,
-    'extra_nav_links': {
-        'REANA@DockerHub': 'https://hub.docker.com/u/reanahub/',
-        'REANA@GitHub': 'https://github.com/reanahub',
-        'REANA@Twitter': 'https://twitter.com/reanahub',
-        'REANA@Web': 'http://www.reana.io',
-    }
+    "github_user": "reanahub",
+    "github_repo": "reana-db",
+    "github_button": False,
+    "github_banner": True,
+    "show_powered_by": False,
+    "extra_nav_links": {
+        "REANA@DockerHub": "https://hub.docker.com/u/reanahub/",
+        "REANA@GitHub": "https://github.com/reanahub",
+        "REANA@Twitter": "https://twitter.com/reanahub",
+        "REANA@Web": "http://www.reana.io",
+    },
 }
 
 # 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_static_path = ["_static"]
 
 # Custom sidebar templates, maps document names to template names.
 html_sidebars = {
-    '**': [
-        'about.html',
-        'navigation.html',
-        'relations.html',
-        'searchbox.html',
-        'donate.html',
+    "**": [
+        "about.html",
+        "navigation.html",
+        "relations.html",
+        "searchbox.html",
+        "donate.html",
     ]
 }
 
 # -- Options for HTMLHelp output ------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'reanadoc'
+htmlhelp_basename = "reanadoc"
 
 
 # -- Options for LaTeX output ---------------------------------------------
@@ -158,15 +158,12 @@
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -176,19 +173,15 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'reana.tex', 'reana Documentation',
-     'info@reana.io', 'manual'),
+    (master_doc, "reana.tex", "reana Documentation", "info@reana.io", "manual"),
 ]
 
 
 # -- Options for manual page output ---------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'reana', 'reana Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "reana", "reana Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output -------------------------------------------
@@ -197,7 +190,13 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'reana', 'reana Documentation',
-     author, 'reana', 'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "reana",
+        "reana Documentation",
+        author,
+        "reana",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]

pytest.ini

@@ -5,4 +5,4 @@
 # under the terms of the MIT License; see LICENSE file for more details.
 
 [pytest]
-addopts = --pep8 --ignore=docs --cov=reana_db --cov-report=term-missing
+addopts = --ignore=docs --cov=reana_db --cov-report=term-missing

reana_db/__init__.py

@@ -12,4 +12,4 @@
 
 from .version import __version__
 
-__all__ = ('__version__', )
+__all__ = ("__version__",)

reana_db/config.py

@@ -10,33 +10,37 @@
 
 import os
 
-DB_NAME = os.getenv('REANA_DB_NAME', 'reana')
+DB_NAME = os.getenv("REANA_DB_NAME", "reana")
 """Database name."""
 
-DB_USERNAME = os.getenv('REANA_DB_USERNAME', 'reana')
+DB_USERNAME = os.getenv("REANA_DB_USERNAME", "reana")
 """Database user name."""
 
-DB_PASSWORD = os.getenv('REANA_DB_PASSWORD', 'reana')
+DB_PASSWORD = os.getenv("REANA_DB_PASSWORD", "reana")
 """Database password."""
 
-DB_HOST = os.getenv('REANA_DB_HOST',
-                    f'{os.getenv("REANA_COMPONENT_PREFIX")}-db')
+DB_HOST = os.getenv(
+    "REANA_DB_HOST", "{}-db".format(os.getenv("REANA_COMPONENT_PREFIX"))
+)
 """Database service host."""
 # Loading REANA_COMPONENT_PREFIX from environment because REANA-DB
 # doesn't depend on REANA-Commons, the package which loads this config.
 
-DB_PORT = os.getenv('REANA_DB_PORT', '5432')
+DB_PORT = os.getenv("REANA_DB_PORT", "5432")
 """Database service port."""
 
-DB_SECRET_KEY = os.getenv('REANA_SECRET_KEY', 'reana')
+DB_SECRET_KEY = os.getenv("REANA_SECRET_KEY", "reana")
 """Database encryption secret key."""
 
-SQLALCHEMY_DATABASE_URI = \
-    os.getenv(
-        'REANA_SQLALCHEMY_DATABASE_URI',
-        'postgresql+psycopg2://{username}:{password}'
-        '@{host}:{port}/{db}'.format(
-            username=DB_USERNAME, password=DB_PASSWORD, host=DB_HOST,
-            port=DB_PORT, db=DB_NAME
-        ))
+SQLALCHEMY_DATABASE_URI = os.getenv(
+    "REANA_SQLALCHEMY_DATABASE_URI",
+    "postgresql+psycopg2://{username}:{password}"
+    "@{host}:{port}/{db}".format(
+        username=DB_USERNAME,
+        password=DB_PASSWORD,
+        host=DB_HOST,
+        port=DB_PORT,
+        db=DB_NAME,
+    ),
+)
 """SQLAlchemy database location."""

reana_db/database.py

@@ -19,15 +19,14 @@
 from reana_db.models import Base  # isort:skip  # noqa
 
 engine = create_engine(SQLALCHEMY_DATABASE_URI)
-Session = scoped_session(sessionmaker(autocommit=False,
-                                      autoflush=False,
-                                      bind=engine))
+Session = scoped_session(sessionmaker(autocommit=False, autoflush=False, bind=engine))
 Base.query = Session.query_property()
 
 
 def init_db():
     """Initialize the DB."""
     import reana_db.models
+
     if not database_exists(engine.url):
         create_database(engine.url)
     Base.metadata.create_all(bind=engine)