Feat taxref/search: add parameter "fields"

Use query string parameter "fields" to add taxref fields into the
response body.
Fields must be separate by comma.
Improve documentation for /taxref/search webservice.

Close #243.

apptax/taxonomie/routestaxref.py

@@ -44,18 +44,27 @@ def getTaxrefBibtaxonList():
 
 @adresses.route("/search/<field>/<ilike>", methods=["GET"])
 def getSearchInField(field, ilike):
-    """
-    Get the first 20 result of Taxref table for a given field with an ilike query
-    Use trigram algo to add relevance
-
-    :params field: a Taxref column
-    :type field: str
-    :param ilike: the ilike where expression to filter
-    :type ilike:str
-
-    :query str add_rank: join on table BibTaxrefRank and add the column 'nom_rang' to the result
-    :query str rank_limit: return only the taxon where rank <= of the given rank (id_rang of BibTaxrefRang table)
-    :returns: Array of dict
+    """.. http:get:: /taxref/search/(str:field)/(str:ilike)
+    .. :quickref: Taxref;
+    
+    Retourne les 20 premiers résultat de la table "taxref" pour une 
+    requête sur le champ `field` avec ILIKE et la valeur `ilike` fournie.
+    L'algorithme Trigramme est utilisé pour établir la correspondance.
+
+    :query fields: Permet de récupérer des champs suplémentaire de la
+        table "taxref" dans la réponse. Séparer les noms des champs par 
+        des virgules.
+    :query is_inbibnom: Ajoute une jointure sur la table "bib_noms".
+    :query add_rank: Ajoute une jointure sur la table "bib_taxref_rangs" 
+        et la colonne nom_rang aux résultats.
+    :query rank_limit: Retourne seulement les taxons dont le rang est 
+        supérieur ou égal au rang donné. Le rang passé doit être une 
+        valeur de la colonne "id_rang" de la table "bib_taxref_rangs".
+
+    :statuscode 200: Tableau de dictionnaires correspondant aux résultats
+        de la recherche dans la table "taxref".
+    :statuscode 500: Aucun rang ne correspond à la valeur fournie.
+                     Aucune colonne ne correspond à la valeur fournie.
     """
     taxrefColumns = Taxref.__table__.columns
     if field in taxrefColumns:
@@ -73,6 +82,16 @@ def getSearchInField(field, ilike):
             .order_by(desc("idx_trgm"))
         )
 
+        if request.args.get("fields"):
+            fields = request.args["fields"].split(",")
+            for field in fields:
+                if field in taxrefColumns:
+                    column = taxrefColumns[field]
+                    q = q.add_columns(column)
+                else:
+                    msg = f"No column found in Taxref for {field}"
+                    return jsonify(msg), 500
+
         if request.args.get("is_inbibnoms"):
             q = q.join(BibNoms, BibNoms.cd_nom == Taxref.cd_nom)
         join_on_bib_rang = False

docs/api/Makefile

@@ -0,0 +1,20 @@
+# 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     = source
+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/api/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/api/source/apptax.log.rst

@@ -0,0 +1,29 @@
+apptax.log package
+==================
+
+Submodules
+----------
+
+apptax.log.logmanager module
+----------------------------
+
+.. automodule:: apptax.log.logmanager
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+apptax.log.models module
+------------------------
+
+.. automodule:: apptax.log.models
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: apptax.log
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/api/source/apptax.rst

@@ -0,0 +1,39 @@
+apptax package
+==============
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   apptax.log
+   apptax.taxonomie
+   apptax.utils
+
+Submodules
+----------
+
+apptax.database module
+----------------------
+
+.. automodule:: apptax.database
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+apptax.index module
+-------------------
+
+.. automodule:: apptax.index
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: apptax
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/api/source/apptax.taxonomie.rst

@@ -0,0 +1,77 @@
+apptax.taxonomie package
+========================
+
+Submodules
+----------
+
+apptax.taxonomie.filemanager module
+-----------------------------------
+
+.. automodule:: apptax.taxonomie.filemanager
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+apptax.taxonomie.models module
+------------------------------
+
+.. automodule:: apptax.taxonomie.models
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+apptax.taxonomie.routesbibattributs module
+------------------------------------------
+
+.. automodule:: apptax.taxonomie.routesbibattributs
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+apptax.taxonomie.routesbiblistes module
+---------------------------------------
+
+.. automodule:: apptax.taxonomie.routesbiblistes
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+apptax.taxonomie.routesbibnoms module
+-------------------------------------
+
+.. automodule:: apptax.taxonomie.routesbibnoms
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+apptax.taxonomie.routesbibtypesmedia module
+-------------------------------------------
+
+.. automodule:: apptax.taxonomie.routesbibtypesmedia
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+apptax.taxonomie.routestaxref module
+------------------------------------
+
+.. automodule:: apptax.taxonomie.routestaxref
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+apptax.taxonomie.routestmedias module
+-------------------------------------
+
+.. automodule:: apptax.taxonomie.routestmedias
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: apptax.taxonomie
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/api/source/apptax.utils.rst

@@ -0,0 +1,45 @@
+apptax.utils package
+====================
+
+Submodules
+----------
+
+apptax.utils.genericfunctions module
+------------------------------------
+
+.. automodule:: apptax.utils.genericfunctions
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+apptax.utils.genericmodels module
+---------------------------------
+
+.. automodule:: apptax.utils.genericmodels
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+apptax.utils.routesconfig module
+--------------------------------
+
+.. automodule:: apptax.utils.routesconfig
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+apptax.utils.utilssqlalchemy module
+-----------------------------------
+
+.. automodule:: apptax.utils.utilssqlalchemy
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: apptax.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/api/source/conf.py

@@ -0,0 +1,67 @@
+# 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 = 'TaxHub'
+copyright = '2020, GeoNature contributors'
+author = 'GeoNature contributors'
+
+# The full version, including alpha/beta/rc tags
+release = '1.7.4.dev0'
+
+
+# -- 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.ext.autodoc",
+    "sphinx.ext.viewcode",
+    "sphinxcontrib.httpdomain",
+    "sphinxcontrib.autohttp.flask",
+    "sphinxcontrib.autohttp.flaskqref",
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# 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 = []
+
+
+# -- 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'
+
+# 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']

docs/api/source/index.rst

@@ -0,0 +1,20 @@
+.. TaxHub documentation master file, created by
+   sphinx-quickstart on Tue Oct  6 15:43:23 2020.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to TaxHub's documentation!
+==================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`