Issue31 ontologies wout aeon

.flake8

@@ -14,7 +14,6 @@ exclude =
     dist,
     build,
     prototypes,
-    test_*,
     cli_args.py
     notebooks
 max-complexity = 10

.github/workflows/main.yml

@@ -5,16 +5,15 @@ name: ontology2smw build
 
 on:
   push:
-    branches: [ master ]
+    branches: [ master, issue31_ontologies_wout_aeon ]
   pull_request:
-    branches: [ master ]
-
+    branches: [ master, issue31_ontologies_wout_aeon ]
 jobs:
   build:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, windows-latest]
+        os: [ubuntu-latest, windows-latest, macOS-latest]
         python-version: [3.6, 3.7, 3.8]
 #        exclude:
 #          - os: windows-latest
@@ -31,11 +30,6 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Display Python version
       run: python -V
-#    - name: Install dependencies
-#      run: |
-#        python -m pip install --upgrade pip
-#        pip install pytest
-#        pip install -r requirements.txt
     - name: install application
       run: |
         python setup.py install
@@ -45,6 +39,3 @@ jobs:
     - name: run application
       run: |
         ontology2smw --format ttl --ontology https://raw.githubusercontent.com/tibonto/aeon/master/aeon.ttl
-#    - name: Test with pytest
-#      run: |
-#        pytest

.github/workflows/pytest.yml

@@ -0,0 +1,34 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+name: pytest
+
+on:
+  push:
+    branches: [ master, issue31_ontologies_wout_aeon ]
+  pull_request:
+    branches: [ master, issue31_ontologies_wout_aeon ]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: [3.6, 3.7, 3.8]
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: install application
+      run: |
+        python setup.py install
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest
+        pip install -r requirements.txt
+    - name: pytest
+      run: |
+        pytest -m "not smw"

.gitignore

@@ -13,3 +13,4 @@ confident2wikidata_mapping.yml
 /.tox/
 /vm/.vagrant/
 /notebooks/
+/report.txt

README.md

@@ -1,4 +1,6 @@
 ![ontology2smw build](https://github.com/TIBHannover/ontology2smw/workflows/ontology2smw%20build/badge.svg)
+![pytest](https://github.com/TIBHannover/ontology2smw/workflows/pytest/badge.svg)
+
 # Ontology to SMW
 _**Automating an RDF ontology import into Semantic Mediawiki**_
 
@@ -10,13 +12,10 @@ the wiki pages, which point to IRIs of the imported ontology(s).
 The process of importing is simple, but time consuming. Hence making it a perfect candidate for an automated process, 
 which can be run at anytime a new version of the ontology is published, hence this python script.
 
-**In order for the terms of an ontology to be imported to SMW instance they should include the property
-`aeon:SMW_datatype` and the appropriate [SMW datatype](https://www.semantic-mediawiki.org/wiki/Help:List_of_datatypes) or Category for Classes**
-
 ![ontology2smw import workflow](docs/ontology2smw_aeon.svg?raw=true)
 
 Supports:
-* python3.6, python3.7, python3.8 
+* python3.6, python3.7, python3.8
 
 
 ## Install:
@@ -33,6 +32,7 @@ pip install --upgrade setuptools
 python setup.py install
 ```
 
+
 ## Run:
 
 **Run:**
@@ -43,12 +43,10 @@ Using a remote ontology:<br/>`ontology2smw --format ttl --ontology https://raw.g
 
 Writing to wiki pages:<br/>`ontology2smw --format ttl --ontology https://raw.githubusercontent.com/tibonto/aeon/master/aeon.ttl --write` 
 
-Using local ontology:<br/>`ontology2smw --format ttl --ontology XYZ.ttl`
-
-
 Asking for help:<br/>`ontology2smw --help`
 ```bash
-usage: __main__.py [-h] [-w] [-o ONTOLOGY] [-f {application/rdf+xml,ttl}]
+usage: ontology2smw [-h] [-w] [-o ONTOLOGY] [-f {rdf,ttl}] [-v] [-r]
+
 
                    ___    
                  { . . } 
@@ -61,8 +59,12 @@ optional arguments:
   -w, --write           writes the output to wiki or file. Default: False (dry-run).
   -o ONTOLOGY, --ontology ONTOLOGY
                         Ontology file or URI. Default: https://raw.githubusercontent.com/tibonto/aeon/master/aeon.ttl 
-  -f {application/rdf+xml,ttl}, --format {application/rdf+xml,ttl}
+  -f {rdf,ttl}, --format {rdf,ttl}
                         Ontology format. Default value: ttl
+  -v, --verbose         Verbose output. Default: False.
+  -r, --report          Save report in file report.txt Default: False.
+
+
 ```
 
 <!--
@@ -92,18 +94,19 @@ Details for that wiki, VM, bot username and password are set in `wikidetails.yml
 
 
 
-### Test on local Virtual Machine
+### Try on local Virtual Machine
 In order to test ontology2smw in action in a isolated virtual 
 environment, the repository includes a Ansible playbook which creates a VM with Mediawiki installed, and also creates a Bot account for wiki user Admin.
 
 The playbook sets Mediawiki with:
 * URL: http://192.168.100.100/w
 * SemanticMediawiki extension
 * bot account for Admin, with details (in wikidetail.yml):
-   * user: Admin 
-   * user password: adminpassword
-   * bot: Admin@ontology2smwbot
-   * bot password: botpasswordbotpasswordbotpassword
+   * wiki user: Admin 
+   * wiki user password: adminpassword
+   * wiki bot: Admin@ontology2smwbot
+   * wiki bot password: botpasswordbotpasswordbotpassword
+
 
 Requirements:
 * [VirtualBox](https://www.virtualbox.org/)
@@ -130,23 +133,17 @@ cd ontology2smw
 pip install -r requirements.txt
 python -m ontology2smw
 ```
-
-
-## Properties from other ontologies
-...
-
-## queries with [ARQ](https://jena.apache.org/documentation/query/)
-`arq --data=aeon/aeon.ttl   --query=ontology2smw/queries/ontology.rq`
 
-`arq --data=aeon/aeon.ttl   --query=ontology2smw/queries/query_classes.rq`
+## Test 
 
-`arq --data=aeon/aeon.ttl   --query=ontology2smw/queries/query_properties.rq`
+**Tox:** automated testing on py36, py37, py38
+`tox -p all -v`
 
+* pytest
+* flake8s
+* test coverage report
 
-# Other Scripts
-## confident2wikidata_mapping.py
-Script to make a YAML file that holds the mapping of AEON/ConfIDent properties to Wikidata properties, 
-by parsing the annotation properties aeon:WikidataLabel and aeon:WikidatURI from the recent ontology TTL.
 
-    :param  source          The URL of the recent aeon ontology (defaults to AEON/ConfIDent branch)
-    :param  outfile_path     The file path of the YAML generated by the script
+**pytest**
+* without running target VM running Mediawiki + SMW `pytest -m "not smw"`
+* with VM running Mediawiki + SMW `pytest` for all the tests

docs/function_calls.md

@@ -3,15 +3,15 @@ BEFORE REFACTORING
     * (loop): 
         * def append_smw_import_content
             * instantiate_smwimport
-                * def query_ontology  KEEP
+                * def get_ontology_details  KEEP
     * def create_smw_import_pages
 
 
 AFTER REFACTORING
 
 * def sparql2smwpage
     * (loop): 
-        * def query_ontology  KEEP
+        * def get_ontology_details  KEEP
     * def create_smw_import_pages
 
 

ontology2smw/__main__.py

@@ -15,7 +15,7 @@ def main():
         writetowiki_decision()
 
     sparql2smwpage(
-        sparql_fn='ontology2smw/queries/query_classes_properties.rq',
+        sparql_fn='ontology2smw/queries/ontology_terms.rq',
         format_=args.format,
         source=args.ontology,
     )