Merge pull request #63 from usnistgov/fix/mongo-support

Update docker to Ubuntu 22, Python 3.10, MongoDB 7.0. Additional testing to be done as part of oar-pdr-py.
usnistgov · Jun 23, 2024 · 57ed4ae · 57ed4ae
2 parents a056b47 + 2ee0fe7
commit 57ed4ae
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diff --git a/docker/ejsonschema/Dockerfile b/docker/ejsonschema/Dockerfile
@@ -2,12 +2,12 @@ FROM oar-metadata/jqfromsrc:latest
 
 RUN apt-get update && apt-get install -y unzip uwsgi uwsgi-src \
                                          uuid-dev libcap-dev libpcre3-dev python3-distutils
-RUN PYTHON=python3.8 uwsgi --build-plugin "/usr/src/uwsgi/plugins/python python38" && \
-    mv python38_plugin.so /usr/lib/uwsgi/plugins/python38_plugin.so && \
-    chmod 644 /usr/lib/uwsgi/plugins/python38_plugin.so
+RUN PYTHON=python3 uwsgi --build-plugin "/usr/src/uwsgi/plugins/python python3" && \
+    mv python3_plugin.so /usr/lib/uwsgi/plugins/python3_plugin.so && \
+    chmod 644 /usr/lib/uwsgi/plugins/python3_plugin.so
 
-RUN update-alternatives --install /usr/lib/uwsgi/plugins/python3_plugin.so \
-    python_plugin.so /usr/lib/uwsgi/plugins/python38_plugin.so 1
+RUN update-alternatives --install /usr/lib/uwsgi/plugins/python_plugin.so \
+    python_plugin.so /usr/lib/uwsgi/plugins/python3_plugin.so 1
 
 RUN python -m pip install "setuptools<66.0.0"
 RUN python -m pip install json-spec jsonschema==2.4.0 requests \
@@ -17,16 +17,16 @@ RUN python -m pip install --no-dependencies jsonmerge==1.3.0
 WORKDIR /root
 
 RUN curl -L -o ejsonschema.zip \
-    https://github.com/usnistgov/ejsonschema/archive/master.zip && \
+    https://github.com/usnistgov/ejsonschema/archive/1.0rc4.zip && \
     unzip ejsonschema.zip && \
-    cd ejsonschema-master && \
-    python setup.py install --install-purelib=/usr/local/lib/python3.8/dist-packages
+    cd ejsonschema-1.0rc4 && \
+    python setup.py install --install-purelib=/usr/local/lib/python3.10/dist-packages
 
 RUN curl -L -o pynoid.zip \
     https://github.com/RayPlante/pynoid/archive/master.zip && \
     unzip pynoid.zip && \
     cd pynoid-master && \
-    python setup.py install --install-purelib=/usr/local/lib/python3.8/dist-packages
+    python setup.py install --install-purelib=/usr/local/lib/python3.10/dist-packages
 
 CMD ["bash"]
 
diff --git a/docker/pymongo/Dockerfile b/docker/pymongo/Dockerfile
@@ -1,14 +1,15 @@
-# This provides the base support for Python 3.8 and MongoDB 4.4 
+# This provides the base support for Python 3.10 and MongoDB 7.0
 
-FROM mongo:4.4
+FROM mongo:7.0-jammy
 # VOLUME /data
 MAINTAINER Ray Plante <[email protected]>
 COPY mongod.conf /etc/mongod.conf
 COPY mongod_ctl.sh /usr/local/bin
 
-RUN apt-get update && apt-get install -y ca-certificates locales python3.8 python3-pip python3.8-dev
-RUN update-alternatives --install /usr/bin/python python /usr/bin/python3.8 1; \
-    update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.8 1; \
+RUN apt-get update && apt-get install -y ca-certificates locales \
+                                         python3 python3-pip python3-dev python-is-python3
+RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 1; \
+    update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3 1; \
     update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 1
 RUN locale-gen en_US.UTF-8
 

diff --git a/python/nistoar/doi/datacite.py b/python/nistoar/doi/datacite.py
@@ -7,7 +7,8 @@
 DataCite services.  
 """
 import re
-from collections import OrderedDict, Mapping
+from collections import OrderedDict
+from collections.abc import Mapping
 from copy import deepcopy
 from io import StringIO
 import requests

diff --git a/python/nistoar/id/persist.py b/python/nistoar/id/persist.py
@@ -4,7 +4,8 @@
 locking to prevent two processes from acquiring the same ID.
 """
 import os, logging, json
-from collections import Mapping
+from collections import OrderedDict
+from collections.abc import Mapping
 from copy import deepcopy
 from .minter import IDRegistry, IDMinter, NoidMinter, NIST_ARK_NAAN
 import pynoid as noid, filelock

diff --git a/python/nistoar/nerdm/convert/latest.py b/python/nistoar/nerdm/convert/latest.py
@@ -2,7 +2,8 @@
 Module for converting a NERDm record to the latest schema versions.  
 """
 import re
-from collections import OrderedDict, Mapping
+from collections import OrderedDict
+from collections.abc import Mapping
 from copy import deepcopy
 from urllib.parse import urlparse
 

diff --git a/python/nistoar/nerdm/convert/pod.py b/python/nistoar/nerdm/convert/pod.py
@@ -2,7 +2,8 @@
 Classes and functions for converting from and to the NERDm schema
 """
 import os, json, re
-from collections import OrderedDict, Mapping
+from collections import OrderedDict
+from collections.abc import Mapping
 
 from ... import jq
 from ...doi import resolve, is_DOI

diff --git a/python/nistoar/nerdm/convert/rmm.py b/python/nistoar/nerdm/convert/rmm.py
@@ -17,7 +17,8 @@
                        as a version-specific ID.
 """
 import re
-from collections import OrderedDict, Mapping
+from collections import OrderedDict
+from collections.abc import Mapping
 from urllib.parse import urljoin
 from copy import deepcopy
 

diff --git a/python/nistoar/nerdm/validate.py b/python/nistoar/nerdm/validate.py
@@ -1,7 +1,8 @@
 """
 tools for validating NERDm metadata
 """
-from collections import Mapping
+from collections import OrderedDict
+from collections.abc import Mapping
 
 import ejsonschema as ejs
 from ejsonschema import ValidationError, RefResolutionError

diff --git a/python/nistoar/rmm/mongo/nerdm.py b/python/nistoar/rmm/mongo/nerdm.py
@@ -3,7 +3,8 @@
 """
 # import pandas as pd
 import json, os, sys, warnings
-from collections import Mapping
+from collections import OrderedDict
+from collections.abc import Mapping
 
 from .loader import (Loader, RecordIngestError, JSONEncodingError,
                      UpdateWarning, LoadLog)

diff --git a/python/tests/nistoar/doi/resolving/test_crossref.py b/python/tests/nistoar/doi/resolving/test_crossref.py
@@ -1,6 +1,6 @@
 import os, sys, pdb, shutil, logging, json
 import unittest as test
-from collections import Mapping
+from collections.abc import Mapping
 # from nistoar.tests import *
 
 import nistoar.doi.resolving.crossref as res

diff --git a/python/tests/nistoar/doi/resolving/test_datacite.py b/python/tests/nistoar/doi/resolving/test_datacite.py
@@ -1,6 +1,6 @@
 import os, sys, pdb, shutil, logging, json
 import unittest as test
-from collections import Mapping
+from collections.abc import Mapping
 # from nistoar.tests import *
 
 import nistoar.doi.resolving.datacite as res

diff --git a/python/tests/nistoar/doi/sim_datacite_srv.py b/python/tests/nistoar/doi/sim_datacite_srv.py
@@ -1,7 +1,8 @@
 import json, os, sys, re, hashlib, json, logging, random
 from datetime import datetime
 from wsgiref.headers import Headers
-from collections import OrderedDict, Mapping
+from collections import OrderedDict
+from collections.abc import Mapping
 from copy import deepcopy
 from urllib.parse import parse_qs
 

diff --git a/python/tests/nistoar/nerdm/test_validate.py b/python/tests/nistoar/nerdm/test_validate.py
@@ -1,5 +1,5 @@
 import unittest, pdb, os, json
-from collections import Mapping
+from collections.abc import Mapping
 
 import ejsonschema as ejs