Restore missing symlink to python in docker image (SCP-4547)

[jlchang]

Minor updates to Dockerfile and requirements.txt to fix broken ingest docker image:

• Restore missing symlink to python
• Update pymongo for python 3.10 breaking change (references: PEP-0353 and bpo-40943)

This docker image update may be more easily evaluated by checking that portal core integration tests pass. For those who wish to test at this stage, the following instructions are for manual testing:

To test, follow README instructions for Testing in Docker locally Steps 1,2 & 4

Once in the docker container, set up to bypass the mongo database requirement:
export BYPASS_MONGO_WRITES='yes'

Test ingest of cluster and metadata files should succeed (despite unregistered study-id and study-file-id provided):

1. python ingest_pipeline.py --study-id 5d276a50421aa9117c982845 --study-file-id 5dd5ae25421aa910a723a337 ingest_cell_metadata --cell-metadata-file ../tests/data/annotation/metadata/convention/valid_no_array_v2.0.0.txt --study-accession SCP123 --ingest-cell-metadata
2. python ingest_pipeline.py --study-id 5d276a50421aa9117c982845 --study-file-id 5dd5ae25421aa910a723a337 ingest_cluster --cluster-file ../tests/data/cluster_example.txt --ingest-cluster --name cluster1 --domain-ranges "{'x':[-1, 1], 'y':[-1, 1], 'z':[-1, 1]}"

Test ingest of expression matrix file will fail (due to unregistered study-id and study-file-id provided) with:

ValueError: Study ID is not registered with a study. Please provide a valid study ID.
Due to lack of database bypass mechanism for expression matrix ingests.

for reference, expression matrix ingest command:
python ingest_pipeline.py --study-id 5d276a50421aa9117c982845 --study-file-id 5dd5ae25421aa910a723a337 ingest_expression --taxon-name 'Homo sapiens' --taxon-common-name human --ncbi-taxid 9606 --matrix-file ../tests/data/dense_matrix_19_genes_1000_cells.txt --matrix-file-type dense

Expression matrix validity can be tested by pointing a portal core instance to an ingest docker image with a docker build from this PR (eg. gcr.io/broad-singlecellportal-staging/scp-ingest-jlc_fix_image:e42abd1) and running the test_create_default_testing_study integration test:
bin/run_tests.sh -l -t test/integration/study_creation_test.rb
The above test would also validate metadata and cluster ingest.

[eweitz]

Code looks good!