update docs for pori_python and update the required libraries

Author: sshugsc

docker-compose.dev.yml

@@ -36,13 +36,8 @@ services:
     networks:
       - app-network
     volumes:
-      - source: ./databases/orientdb/data
-        target: /orientdb/databases
-        type: bind
-      - source: ./databases/orientdb/backup
-        target: /orientdb/backup
-        type: bind
-    user: "${UID}:${GID}"
+      - orientdb_data:/orientdb/databases
+      - orientdb_backup:/orientdb/backup
   graphkb_api:
     image: bcgsc/pori-graphkb-api:latest
     ports:
@@ -140,7 +135,7 @@ services:
     image: bcgsc/pori-ipr-api:latest
     command: npm start
     ports:
-      - 8082:8082
+      - 8082:8080
     environment:
       IPR_DATABASE_HOSTNAME: ipr_db
       IPR_DATABASE_NAME: ipr_demo
@@ -191,3 +186,6 @@ services:
 networks:
   app-network:
     driver: bridge
+volumes:
+  orientdb_data:
+  orientdb_backup:

docs/build_external.sh

@@ -4,28 +4,15 @@
 # clone the IPR python adapter if it does not exist, otherwise update
 if ! [ -d docs/_pori_ipr_python ];
 then
-    git clone https://github.com/bcgsc/pori_ipr_python.git docs/_pori_ipr_python
-    echo "hide: true" > docs/_pori_ipr_python/.pages
+    git clone https://github.com/bcgsc/pori_python.git docs/_pori_python
+    echo "hide: true" > docs/_pori_python/.pages
 else
-    cd docs/_pori_ipr_python
+    cd docs/_pori_python
     git checkout master
     git pull
     cd ../..
 fi
 
-# clone the GraphKB Python adapter if it does not exist, otherwise update
-if ! [ -d docs/_pori_graphkb_python ];
-then
-    git clone https://github.com/bcgsc/pori_graphkb_python.git docs/_pori_graphkb_python
-    echo "hide: true" > docs/_pori_graphkb_python/.pages
-else
-    cd docs/_pori_graphkb_python
-    git checkout master
-    git pull
-    cd ../..
-fi
-
-
 # clone the loaders repo if it does not exist, otherwise update
 if ! [ -d docs/graphkb/_pori_graphkb_loader ];
 then
@@ -40,8 +27,8 @@ fi
 
 # now build the reference python module API files
 markdown_refdocs \
-    docs/_pori_graphkb_python/graphkb \
-    docs/_pori_ipr_python/ipr  \
+    docs/_pori_python/pori_python/graphkb \
+    docs/_pori_python/pori_python/ipr  \
     -o docs/developer_reference \
     --link
 

docs/index.md

@@ -5,7 +5,6 @@ software designed to support scalable precision oncology. The platform has two m
 a graph knowledge base ([GraphKB](./graphkb)) and an integrated pipeline reporting application ([IPR](./ipr)). This site
 contains central documentation for the platform as well as setup and installation instructions.
 
-Click on the menu icon (:material-menu:) to see a full table of contents for this site.
 
 ![pori server stack](./images/pori-server-stack.png)
 

docs/ipr_spec_tables.py

@@ -79,7 +79,7 @@ def spec_to_md(spec, optional_only=False, ignore_nested=False):
     return result
 
 
-specfile = os.path.join(os.path.dirname(__file__), '_pori_ipr_python/ipr/content.spec.json')
+specfile = os.path.join(os.path.dirname(__file__), '_pori_python/pori_python/ipr/content.spec.json')
 with open(specfile, 'r') as fh:
     spec = json.load(fh)
 

docs/repos.md

@@ -76,17 +76,9 @@ A developer reference for these packages including the function signatures and p
 
 <div class='projects' markdown='1'>
 
-- ### [GraphKB Python Adapter](https://github.com/bcgsc/pori_graphkb_python)
+- ### [Pori Python Adapter](https://github.com/bcgsc/pori_python)
 
-    ![graphkb python](./images/graph-icon_outline.svg)
-
-    Python adapter package for querying the GraphKB API. See the related
-    [user manual](../graphkb/python/docs) for instructions on incorporating
-    this into custom scripts.
-
-- ### [IPR Python Adapter](https://github.com/bcgsc/pori_ipr_python)
-
-    ![ipr python](./images/wrench.svg)
+    ![pori python](./images/wrench.svg)
 
     Python adapter for generating reports uploaded to the IPR API. This python tool takes in variant inputs as tab-delimited files and annotates them using GraphKB. The resulting output is uploaded to IPR as a report. Additional report content such as images and metadata can be passed to be included in the report upload.
 

mkdocs.yml

@@ -18,8 +18,8 @@ markdown_extensions:
       check_paths: True
       base_path: .
   - pymdownx.emoji:
-      emoji_index: !!python/name:materialx.emoji.twemoji
-      emoji_generator: !!python/name:materialx.emoji.to_svg
+      emoji_index: !!python/name:material.extensions.emoji.twemoji
+      emoji_generator: !!python/name:material.extensions.emoji.to_svg
   - attr_list
   - markdown_include.include:
       base_path: docs

requirements.txt

@@ -1,81 +1,9 @@
-appdirs==1.4.4
-async-generator==1.10
-attrs==21.2.0
-black==21.5b2
-bleach==3.3.0
-bracex==2.1.1
-certifi==2020.12.5
-chardet==4.0.0
-click==7.1.2
-defusedxml==0.7.1
-entrypoints==0.3
-future==0.18.2
-ghp-import==2.0.2
-gitdb==4.0.7
-GitPython==3.1.17
-graphkb==1.5.4
-idna==2.10
-importlib-metadata==4.10.1
-ipython-genutils==0.2.0
-Jinja2==2.11.3
-joblib==1.0.1
-jsonschema==3.2.0
-jupyter-client==6.2.0
-jupyter-core==4.7.1
-jupyterlab-pygments==0.1.2
-jupytext==1.11.2
-livereload==2.6.3
-lunr==0.5.8
-Markdown==3.3.4
-markdown-include==0.6.0
-markdown-it-py==1.1.0
-markdown-refdocs==1.4.0
-MarkupSafe==1.1.1
-mdit-py-plugins==0.2.8
-mergedeep==1.3.4
-mistune==0.8.4
-mkdocs==1.2.3
-mkdocs-awesome-pages-plugin==2.5.0
+mkdocs==1.6.1
+mkdocs-material==9.6.17
+markdown-include==0.8.1
 mkdocs-exclude==1.0.2
-mkdocs-include-markdown-plugin==3.0.1
-mkdocs-material==8.1.8
-mkdocs-material-extensions==1.0.1
-mkdocs-redirects==1.0.3
-mknotebooks==0.7.0
-mypy==0.812
-mypy-extensions==0.4.3
-nbclient==0.5.3
-nbconvert==6.0.7
-nbformat==5.1.3
-nest-asyncio==1.5.1
-nltk==3.6.2
-packaging==20.9
-pandocfilters==1.4.3
-pathspec==0.8.1
-progressbar2==3.53.1
-Pygments==2.11.2
-pymdown-extensions==9.1
-pyparsing==2.4.7
-pyrsistent==0.17.3
-python-dateutil==2.8.1
-python-utils==2.5.6
-pytz==2021.1
-PyYAML==5.4.1
-pyyaml-env-tag==0.1
-pyzmq==22.1.0
-regex==2021.4.4
-requests==2.25.1
-six==1.15.0
-smmap==4.0.0
-testpath==0.5.0
-toml==0.10.2
-tornado==6.1
-tqdm==4.60.0
-traitlets==5.0.5
-typed-ast==1.4.3
-typing-extensions==3.7.4.3
-urllib3==1.26.5
-watchdog==2.1.6
-wcmatch==8.2
-webencodings==0.5.1
-zipp==3.4.1
+mkdocs-awesome-pages-plugin==2.10.1
+mkdocs-include-markdown-plugin==7.1.6
+mkdocs-redirects==1.2.2
+mknotebooks==0.8.0
+markdown_refdocs==1.4.1