Merge pull request #1 from lpoaura/develop

v0.0.1

.gitignore

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+
+# Created by https://www.gitignore.io/api/code,python
+# Edit at https://www.gitignore.io/?templates=code,python
+
+### Code ###
+.vscode/*
+!.vscode/settings.json
+!.vscode/tasks.json
+!.vscode/launch.json
+!.vscode/extensions.json
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# End of https://www.gitignore.io/api/code,python
+

CHANGELOG.md

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+# v0.0.1 
+
+Pemière pre-release avec un premier lot de fonctions:
+* Extraction de données à partir d'une couche de zonages
+* Création d'un tableau de synthèse par taxons à partir d'une couche de zonages
+* Création d'un graphique de synthèse d'état des connaissances par groupes taxonomiques à partir d'une couche de zonages
+
+

README.md

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+# Scripts de processing framework de la LPO AuRA
+
+Ce plugin ajoute à QGIS des scripts d'exploitation des données naturalistes de
+la [LPO Auvergne-Rhône-Alpes](https://auvergne-rhone-alpes.lpo.fr/) à QGIS.
+
+## Licence
+
+## Equipe
+
+* @eguilley (LPO Auvergne-Rhône-Alpes)
+* @lpofredc (@lpofredc - LPO Auvergne-Rhône-Alpes)
+* @jgirardclaudon (@lpojgc LPO Auvergne-Rhône-Alpes)
+
+![logoLPO AuRA](https://raw.githubusercontent.com/lpoaura/biodivsport-widget/master/images/LPO_AuRA_l250px.png)
+
+

VERSION

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+v0.0.1

common_functions.py

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+# -*- coding: utf-8 -*-
+
+"""
+/***************************************************************************
+        ScriptsLPO : common_functions.py
+        -------------------
+        Date                 : 2020-04-16
+        Copyright            : (C) 2020 by Elsa Guilley (LPO AuRA)
+        Email                : lpo-aura@lpo.fr
+ ***************************************************************************/
+
+/***************************************************************************
+ *                                                                         *
+ *   This program is free software; you can redistribute it and/or modify  *
+ *   it under the terms of the GNU General Public License as published by  *
+ *   the Free Software Foundation; either version 2 of the License, or     *
+ *   (at your option) any later version.                                   *
+ *                                                                         *
+ ***************************************************************************/
+"""
+
+__author__ = 'Elsa Guilley (LPO AuRA)'
+__date__ = '2020-04-16'
+__copyright__ = '(C) 2020 by Elsa Guilley (LPO AuRA)'
+
+# This will get replaced with a git SHA1 when you do a git archive
+__revision__ = '$Format:%H$'
+
+from qgis.utils import iface
+from qgis.gui import QgsMessageBar
+
+from qgis.PyQt.QtCore import QVariant
+from qgis.core import (QgsWkbTypes,
+                       QgsField,
+                       QgsProcessingException,
+                       Qgis)
+import processing
+
+
+def simplify_name(string):
+    """
+    Simplify a layer name written by the user.
+    """
+    translation_table = str.maketrans(
+        'àâäéèêëîïôöùûüŷÿç~- ',
+        'aaaeeeeiioouuuyyc___',
+        "2&'([{|}])`^\/@+-=*°$£%§#.?!;:<>"
+    )
+    return string.lower().translate(translation_table)
+
+# def check_layer_geometry(layer):
+#     """
+#     Check if the input vector layer is a polygon layer.
+#     """
+#     if QgsWkbTypes.displayString(layer.wkbType()) not in ['Polygon', 'MultiPolygon']:
+#         iface.messageBar().pushMessage("Erreur", "La zone d'étude fournie n'est pas valide ! Veuillez sélectionner une couche vecteur de type POLYGONE.", level=Qgis.Critical, duration=10)
+#         raise QgsProcessingException("La zone d'étude fournie n'est pas valide ! Veuillez sélectionner une couche vecteur de type POLYGONE.")
+#     return None
+
+def check_layer_is_valid(feedback, layer):
+    """
+    Check if the input vector layer is valid.
+    """
+    if not layer.isValid():
+        raise QgsProcessingException(""""La couche PostGIS chargée n'est pas valide !
+            Checkez les logs de PostGIS pour visualiser les messages d'erreur.""")
+    else:
+        #iface.messageBar().pushMessage("Info", "La couche PostGIS demandée est valide, la requête SQL a été exécutée avec succès !", level=Qgis.Info, duration=10)
+        feedback.pushInfo("La couche PostGIS demandée est valide, la requête SQL a été exécutée avec succès !")
+    return None
+
+def construct_sql_array_polygons(layer):
+    """
+    Construct the sql array containing the input vector layer's features geometry.
+    """
+    # Initialization of the sql array containing the study area's features geometry
+    array_polygons = "array["
+    # Retrieve the CRS of the layer
+    crs = layer.sourceCrs().authid().split(':')[1]
+    # For each entity in the study area...
+    for feature in layer.getFeatures():
+        # Retrieve the geometry
+        area = feature.geometry() # QgsGeometry object
+        # Retrieve the geometry type (single or multiple)
+        geomSingleType = QgsWkbTypes.isSingleType(area.wkbType())
+        # Increment the sql array
+        if geomSingleType:
+            array_polygons += "ST_transform(ST_PolygonFromText('{}', {}), 2154), ".format(area.asWkt(), crs)
+        else:
+            array_polygons += "ST_transform(ST_MPolyFromText('{}', {}), 2154), ".format(area.asWkt(), crs)
+    # Remove the last "," in the sql array which is useless, and end the array
+    array_polygons = array_polygons[:len(array_polygons)-2] + "]"
+    return array_polygons
+
+def load_layer(context, layer):
+    """
+    Load a layer in the current project.
+    """
+    root = context.project().layerTreeRoot()
+    plugin_lpo_group = root.findGroup('Résultats plugin LPO')
+    if not plugin_lpo_group:
+        plugin_lpo_group = root.insertGroup(0, 'Résultats plugin LPO')
+    context.project().addMapLayer(layer, False)
+    plugin_lpo_group.addLayer(layer)
+    ### Variant
+    # context.temporaryLayerStore().addMapLayer(layer)
+    # context.addLayerToLoadOnCompletion(
+    #     layer.id(),
+    #     QgsProcessingContext.LayerDetails("Données d'observations", context.project(), self.OUTPUT)
+    # )
+
+def execute_sql_queries(context, feedback, connection, queries):
+    """
+    Execute several sql queries.
+    """
+    for query in queries:
+        processing.run(
+            'qgis:postgisexecutesql',
+            {
+                'DATABASE': connection,
+                'SQL': query
+            },
+            is_child_algorithm=True,
+            context=context,
+            feedback=feedback
+        )
+        feedback.pushInfo('Requête SQL exécutée avec succès !')
+    return None
+
+def format_layer_export(layer):
+    """
+    Create new valid fields for the sink.
+    """
+    old_fields = layer.fields()
+    new_fields = layer.fields()
+    new_fields.clear()
+    invalid_formats = ["_text", "jsonb"]
+    for field in old_fields:
+        if field.typeName() in invalid_formats:
+            new_fields.append(QgsField(field.name(), QVariant.String, "str"))
+        else:
+            new_fields.append(field)
+    # for i,field in enumerate(new_fields):
+    #     feedback.pushInfo('Elt : {}- {} {}'.format(i, field.name(), field.typeName()))
+    return new_fields