Create script to migrate SemanticDomains lists in the CombineDatabase (…

…#1738)

README.md

@@ -219,6 +219,13 @@ To upgrade all pinned dependencies:
 python -m piptools compile --upgrade dev-requirements.in
 ```
 
+To upgrade the pinned dependencies for the Maintenance container:
+
+```bash
+cd maintenance
+python -m piptools compile --upgrade requirements.in
+```
+
 ## Available Scripts
 
 ### Running in Development

dev-requirements.in

@@ -29,6 +29,7 @@ jinja2-base64-filters
 humanfriendly
 kubernetes
 pyopenssl
+pymongo
 
 # Kubernetes Installation.
 pyyaml

dev-requirements.txt

@@ -4,63 +4,63 @@
 #
 #    pip-compile dev-requirements.in
 #
-attrs==21.4.0
+attrs==22.1.0
     # via
     #   flake8-bugbear
     #   flake8-eradicate
 beautifulsoup4==4.11.1
     # via mkdocs-htmlproofer-plugin
-black==22.6.0
+black==22.8.0
     # via -r dev-requirements.in
 cachetools==5.2.0
     # via google-auth
-certifi==2022.6.15
+certifi==2022.9.14
     # via
     #   kubernetes
     #   requests
 cffi==1.15.1
     # via cryptography
-charset-normalizer==2.1.0
+charset-normalizer==2.1.1
     # via requests
 click==8.1.3
     # via
     #   black
     #   mkdocs
 colorama==0.4.5
     # via -r dev-requirements.in
-cryptography==37.0.4
+cryptography==38.0.1
     # via pyopenssl
-distlib==0.3.5
+distlib==0.3.6
     # via virtualenv
 eradicate==2.1.0
     # via flake8-eradicate
-filelock==3.7.1
+filelock==3.8.0
     # via
     #   tox
     #   virtualenv
-flake8==4.0.1
+flake8==5.0.4
     # via
     #   -r dev-requirements.in
     #   flake8-broken-line
     #   flake8-bugbear
     #   flake8-comprehensions
     #   flake8-eradicate
     #   pep8-naming
-flake8-broken-line==0.4.0
+flake8-broken-line==0.5.0
     # via -r dev-requirements.in
-flake8-bugbear==22.7.1
+flake8-bugbear==22.9.11
     # via -r dev-requirements.in
 flake8-comprehensions==3.10.0
     # via -r dev-requirements.in
-flake8-eradicate==1.2.1
+flake8-eradicate==1.4.0
     # via -r dev-requirements.in
 ghp-import==2.1.0
     # via mkdocs
-google-auth==2.9.1
+google-auth==2.11.1
     # via kubernetes
 humanfriendly==10.0
     # via -r dev-requirements.in
-idna==3.3
+idna==3.4
     # via requests
 importlib-metadata==4.12.0
     # via mkdocs
@@ -86,7 +86,7 @@ markdown==3.3.7
     #   pymdown-extensions
 markupsafe==2.1.1
     # via jinja2
-mccabe==0.6.1
+mccabe==0.7.0
     # via flake8
 mergedeep==1.3.4
     # via mkdocs
@@ -96,7 +96,7 @@ mkdocs==1.3.1
     #   mkdocs-material
 mkdocs-htmlproofer-plugin==0.8.0
     # via -r dev-requirements.in
-mkdocs-material==8.3.9
+mkdocs-material==8.5.3
     # via -r dev-requirements.in
 mkdocs-material-extensions==1.0.3
     # via mkdocs-material
@@ -106,15 +106,15 @@ mypy-extensions==0.4.3
     # via
     #   black
     #   mypy
-oauthlib==3.2.0
+oauthlib==3.2.1
     # via requests-oauthlib
 packaging==21.3
     # via
     #   mkdocs
     #   tox
-pathspec==0.9.0
+pathspec==0.10.1
     # via black
-pep8-naming==0.13.1
+pep8-naming==0.13.2
     # via -r dev-requirements.in
 platformdirs==2.5.2
     # via
@@ -130,16 +130,18 @@ pyasn1==0.4.8
     #   rsa
 pyasn1-modules==0.2.8
     # via google-auth
-pycodestyle==2.8.0
+pycodestyle==2.9.1
     # via flake8
 pycparser==2.21
     # via cffi
-pyflakes==2.4.0
+pyflakes==2.5.0
     # via flake8
-pygments==2.12.0
+pygments==2.13.0
     # via mkdocs-material
 pymdown-extensions==9.5
     # via mkdocs-material
+pymongo==4.2.0
+    # via -r dev-requirements.in
 pyopenssl==22.0.0
     # via -r dev-requirements.in
 pyparsing==3.0.9
@@ -162,6 +164,7 @@ requests==2.28.1
     # via
     #   kubernetes
     #   mkdocs-htmlproofer-plugin
+    #   mkdocs-material
     #   requests-oauthlib
 requests-oauthlib==1.3.1
     # via kubernetes
@@ -173,40 +176,38 @@ six==1.16.0
     #   kubernetes
     #   python-dateutil
     #   tox
-    #   virtualenv
 soupsieve==2.3.2.post1
     # via beautifulsoup4
-toml==0.10.2
-    # via tox
 tomli==2.0.1
     # via
     #   black
     #   mypy
-tox==3.25.1
+    #   tox
+tox==3.26.0
     # via -r dev-requirements.in
-types-cryptography==3.3.21
+types-cryptography==3.3.23
     # via types-pyopenssl
-types-pyopenssl==22.0.4
+types-pyopenssl==22.0.10
     # via -r dev-requirements.in
 types-python-dateutil==2.8.19
     # via -r dev-requirements.in
-types-pyyaml==6.0.10
+types-pyyaml==6.0.11
     # via -r dev-requirements.in
-types-requests==2.28.3
+types-requests==2.28.11
     # via -r dev-requirements.in
-types-urllib3==1.26.16
+types-urllib3==1.26.24
     # via types-requests
 typing-extensions==4.3.0
     # via mypy
-urllib3==1.26.10
+urllib3==1.26.12
     # via
     #   kubernetes
     #   requests
-virtualenv==20.15.1
+virtualenv==20.16.5
     # via tox
 watchdog==2.1.9
     # via mkdocs
-websocket-client==1.3.3
+websocket-client==1.4.1
     # via kubernetes
 zipp==3.8.1
     # via importlib-metadata

maintenance/requirements.in

@@ -0,0 +1,4 @@
+humanfriendly
+kubernetes
+pyopenssl
+pymongo

maintenance/requirements.txt

@@ -1,3 +1,66 @@
+#
+# This file is autogenerated by pip-compile with python 3.10
+# To update, run:
+#
+#    pip-compile requirements.in
+#
+cachetools==5.2.0
+    # via google-auth
+certifi==2022.9.24
+    # via
+    #   kubernetes
+    #   requests
+cffi==1.15.1
+    # via cryptography
+charset-normalizer==2.1.1
+    # via requests
+cryptography==38.0.1
+    # via pyopenssl
+google-auth==2.11.1
+    # via kubernetes
 humanfriendly==10.0
-kubernetes==18.20.0
-pyopenssl==21.0.0
+    # via -r requirements.in
+idna==3.4
+    # via requests
+kubernetes==24.2.0
+    # via -r requirements.in
+oauthlib==3.2.1
+    # via requests-oauthlib
+pyasn1==0.4.8
+    # via
+    #   pyasn1-modules
+    #   rsa
+pyasn1-modules==0.2.8
+    # via google-auth
+pycparser==2.21
+    # via cffi
+pymongo==4.2.0
+    # via -r requirements.in
+pyopenssl==22.1.0
+    # via -r requirements.in
+python-dateutil==2.8.2
+    # via kubernetes
+pyyaml==6.0
+    # via kubernetes
+requests==2.28.1
+    # via
+    #   kubernetes
+    #   requests-oauthlib
+requests-oauthlib==1.3.1
+    # via kubernetes
+rsa==4.9
+    # via google-auth
+six==1.16.0
+    # via
+    #   google-auth
+    #   kubernetes
+    #   python-dateutil
+urllib3==1.26.12
+    # via
+    #   kubernetes
+    #   requests
+websocket-client==1.4.1
+    # via kubernetes
+
+# The following packages are considered to be unsafe in a requirements file:
+# setuptools