Merge branch 'dev' into f-date-query-lte-gte

.docker/Dockerfile

 FROM debian:buster
-RUN apt-get update && \
-	apt-get install curl mariadb-client make unzip -y
+RUN apt-get update \
+    && \
+    apt-get install -y \
+        curl \
+		mariadb-client \
+		make \
+		unzip \
+        python3-lxml \
+        python3-pip \
+		python3-sqlparse \
+		python3-sphinx \
+		python3-recommonmark \
+		doxygen
+RUN pip3 install breathe

.gitignore

+# -*- mode:conf; -*-
+
 # dot files
 .*
 !/.gitignore
@@ -7,3 +9,8 @@
 # dumps
 *.dump.sql
 libs/*
+
+# Generated files
+_doxygen/
+_generated/
+/build/
\ No newline at end of file

.gitlab-ci.yml

@@ -76,3 +76,21 @@ build-testenv:
       --cache-from $CI_REGISTRY_IMAGE 
       -t $CI_REGISTRY_IMAGE .
     - docker push $CI_REGISTRY_IMAGE
+
+# Build the sphinx documentation and make it ready for deployment by Gitlab Pages
+# documentation:
+#   stage: deploy
+
+# Special job for serving a static website. See https://docs.gitlab.com/ee/ci/yaml/README.html#pages
+pages:
+  tags: [ docker ]
+  stage: deploy
+  only:
+    - dev
+  script:
+    - echo "Deploying"
+    - make doc
+    - cp -r build/doc/html public
+  artifacts:
+    paths:
+      - public

CHANGELOG.md

@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added ###
 
 * Added a `_get_head_iversion` for non-api usage.
+* Automated documentation builds: `make doc`
 
 ### Changed ###
 

makefile → Makefile

@@ -69,3 +69,8 @@ test-docker:
 test-docker-stop:
 	docker kill caosdb-mysqlserver-test
 	docker container rm caosdb-mysqlserver-test
+
+# Compile the standalone documentation
+.PHONY: doc
+doc:
+	$(MAKE) -C doc html

README_SETUP.md

@@ -81,3 +81,17 @@ with the then current version of the stored entities.
 * Run `make test`.
     * Alternatively, to run the tests in a containerized MariaDB instance, run `make test-docker`,
       followed by `make test-docker-stop`.
+
+# Documentation #
+
+Build documentation in `build/` with `make doc`.
+
+## Requirements ##
+
+- sphinx
+- sphinx-autoapi
+- python3-sqlparse
+- doxygen
+- python3-lxml
+- breathe (Doxygen extension for Sphinx)
+- recommonmark

doc/Makefile

+# ** header v3.0
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2020 Daniel Hornung <d.hornung@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+# ** end header
+
+# This Makefile is a wrapper for sphinx scripts.
+#
+# It is based upon the autocreated makefile for Sphinx documentation.
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?= -a
+SPHINXBUILD   ?= sphinx-build
+SPHINXAPIDOC  ?= ./scripts/sql2sphinx.py
+SQL_BASEFILES  = ../procedures/*.sql
+SOURCEDIR      = .
+BUILDDIR       = ../build/doc
+
+.PHONY: doc-help Makefile apidoc doxygen
+
+# Put it first so that "make" without argument is like "make help".
+doc-help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile doxygen
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+#	sphinx-build -M html . ../../build/doc
+
+apidoc:
+	@mkdir -p _generated
+	@$(SPHINXAPIDOC) --input $(wildcard $(SQL_BASEFILES)) > _generated/sql_sources.hh
+
+# Extract comments from sql files.
+doxygen: apidoc
+	doxygen

doc/concepts.rst

+========================
+The concepts of pycaosdb
+========================
+
+Some text...
+

doc/conf.py

+# -*- coding: utf-8 -*-
+#
+# 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('../caosdb'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'caosdb-mysqlbackend'
+copyright = '2020, IndiScale GmbH'
+author = 'Daniel Hornung'
+
+# The short X.Y version
+version = '0.X.Y'
+# The full version, including alpha/beta/rc tags
+release = '0.x.y-beta-rc2'
+
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# 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.todo',
+    'breathe',
+    'sphinx.ext.todo',
+    "sphinx.ext.autodoc",
+    "recommonmark",            # For markdown files.
+     # 'autoapi.extension',
+    # 'sphinx.ext.intersphinx',
+    # 'sphinx.ext.napoleon',     # For Google style docstrings
+]
+
+# Add any paths that contain templates here, relative to this directory.
+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'
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# 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 = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = None
+
+
+# -- 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 = '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 = {}
+
+# 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']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'caosdb-mysqlbackenddoc'
+
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+    # 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',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'caosdb-mysqlbackend.tex', 'caosdb-mysqlbackend Documentation',
+     'IndiScale GmbH', '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, 'caosdb-mysqlbackend', 'caosdb-mysqlbackend Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'caosdb-mysqlbackend', 'caosdb-mysqlbackend Documentation',
+     author, 'caosdb-mysqlbackend', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+# -- Options for Epub output -------------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = project
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ['search.html']
+
+
+# -- Extension configuration -------------------------------------------------
+
+# -- Options for breathe ---------------------------------------------------
+# See also https://breathe.readthedocs.io/en/latest/quickstart.html
+
+breathe_projects = {
+    "mysqlbackend": "./_doxygen/xml"
+}
+breathe_default_project = "mysqlbackend"
+
+# -- Options for intersphinx extension ---------------------------------------
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'https://docs.python.org/': None}
+
+# TODO Which options do we want?
+autodoc_default_options = {
+    'members': None,
+    'undoc-members': None,
+}

doc/functions.rst

+==============================
+The (documented) SQL Functions
+==============================
+
+.. doxygenindex::

doc/getting_started.md

+# Getting started with pycaosdb #
+
+1. Install
+2. import
+3. enjoy

doc/index.rst

+
+Welcome to caosdb-server's documentation!
+=========================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+   :hidden:
+
+   Getting started <getting_started>
+   Concepts <concepts>
+   tutorials
+   API documentation<functions>
+
+Welcome to the MySQL/MariaDB backend of CaosDB!
+
+This documentation helps you to :doc:`get started<getting_started>`, explains the most important
+:doc:`concepts<concepts>` and offers a range of :doc:`tutorials<tutorials>`.
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`search`

doc/scripts/sql2sphinx.py

+#!/usr/bin/env python3
+
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2020 IndiScale GmbH <www.indiscale.com>
+# Copyright (C) 2020 Daniel Hornung <d.hornung@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+
+"""Convert an SQL script to a Python with the same function signatures."""
+
+import argparse
+import sys
+
+import sqlparse
+
+
+MAINPAGE = """
+
+/*! \\mainpage This autogenerated documentation from SQL.
+ *
+ * \\section function Global functions
+ *
+ * \\htmlonly The functions are listed <A href="globals.html">here</A>.\\endhtmlonly
+ */
+
+"""
+
+
+def _parse_file(filename):
+    """Parse and convert the file."""
+    with open(filename, "r") as sqf:
+        sql = sqlparse.parsestream(sqf)
+        statements = list(sql)
+
+    for stat in statements:
+        sublists = list(stat.get_sublists())
+        for i, ident in enumerate(sublists):
+            if not (i > 0 and isinstance(ident, sqlparse.sql.Identifier)
+                    and isinstance(sublists[i-1], sqlparse.sql.Comment)):
+                continue
+            comment = sublists[i-1]
+            after_comment = stat.tokens[stat.tokens.index(comment) + 1]
+            if not after_comment.value == "CREATE":
+                # print(after_comment.value)
+                continue
+
+            print("/" * 78)
+            print("// taken from {filename}".format(filename=filename))
+            print("/" * 78)
+            # print(type(ident))
+            # print(ident)
+            # print(ident.tokens[-1])
+            # print(ident.tokens[-1].tokens[1].tokens)
+            _print_header(comment.value, ident)
+
+
+def _strip_whitespace(tokens):
+    """Remove whitespace tokens from the tokens list and return that."""
+    to_delete = []
+    for i, tok in enumerate(tokens):
+        if isinstance(tok, sqlparse.sql.Token) and tok.ttype in (
+                sqlparse.tokens.Whitespace, sqlparse.tokens.Newline):
+            to_delete.append(i)
+    while to_delete:
+        tokens.pop(to_delete.pop())
+    return tokens
+
+
+def _print_header(comment, ident, outfile=sys.stdout):
+    """Print a C header with the given comment and identifier.
+
+Parameters
+----------
+comment : str
+
+ident : sqlparse.sql.Identifier
+    """
+    func = ident.token_matching(lambda tok: isinstance(tok, sqlparse.sql.Function), idx=0)
+    _strip_whitespace(func.tokens)
+    name, paren = func.tokens[0:2]
+    assert isinstance(paren, sqlparse.sql.Parenthesis)
+
+    args = []
+    # if name.value == "insert_single_child_version":
+    #     from IPython import embed; embed()
+    _strip_whitespace(paren.tokens)
+
+    # Expand nested elements
+    to_expand = {}
+    for tok in paren.tokens:
+        if isinstance(tok, sqlparse.sql.IdentifierList):
+            to_expand[tok] = _strip_whitespace(tok.tokens)
+    for old in to_expand:
+        pivot = paren.tokens.index(old)
+        paren.tokens = paren.tokens[:pivot] + to_expand[old] + paren.tokens[pivot+1:]
+
+
+    start = 0
+    end = 0
+    while end + 1 < len(paren.tokens):
+        start = end + 1
+        punct = paren.token_matching(lambda t: t.ttype == sqlparse.tokens.Punctuation, idx=end+1)
+        if not punct:
+            continue
+        end = paren.tokens.index(punct)
+        if start == end:
+            continue
+        tokens = paren.tokens[start: end]
+        arg_name = _arg_from_tokens(tokens)
+        args.append(arg_name)
+    print(comment.strip(), file=outfile)
+    print("void {name}(void* {args});\n".format(name=name, args=", void* ".join(args)),
+          file=outfile)
+
+
+def _arg_from_tokens(tokens):
+    """Extract and return an argument name."""
+    # Remove content of functions
+    for i, tok in enumerate(tokens):
+        if isinstance(tok, sqlparse.sql.Function):
+            tokens[i] = tok.token_first()
+
+    arg_name = "_".join([tok.value for tok in tokens])
+    return arg_name.strip()
+
+
+def _parse_arguments():
+    """Parse the arguments."""
+    parser = argparse.ArgumentParser(description='')
+    parser.add_argument('-i', '--input', help="Input file(s)", required=True, nargs="+")
+
+    return parser.parse_args()
+
+
+def main():
+    """The main function of this script."""
+    args = _parse_arguments()
+    print(MAINPAGE)
+    for filename in args.input:
+        _parse_file(filename=filename)
+
+
+if __name__ == "__main__":
+    main()

procedures/insertIsaCache.sql

@@ -24,20 +24,21 @@
 DROP PROCEDURE IF EXISTS db_2_0.insertIsa;
 DELIMITER //
 
-/* Insert an "is a" relation
-
-This procedure fills the isa_cache table.  All passed entities must be existing
-in entities.id.
-
-Parameters
-==========
-
-c : UNSIGNED
-The child entity
-
-p : UNSIGNED
-The parent entity
-*/
+/**
+ * Insert an "is a" relation
+ *
+ * This procedure fills the isa_cache table.  All passed entities must be existing
+ * in entities.id.
+ *
+ * Parameters
+ * ==========
+ * 
+ * c : UNSIGNED
+ * The child entity
+ * 
+ * p : UNSIGNED
+ * The parent entity
+ */
 CREATE PROCEDURE db_2_0.insertIsa(IN c INT UNSIGNED, IN p INT UNSIGNED)
 insert_is_a_proc: BEGIN