deploy development software version to production site

[jcschaff]

We will move the current biosimulations site software to production site.

Punch list

• initial configuration changes so that dev site uses dev resources (mongodb, s3 buckets, hpc/slurm config)
  • clone the production mongo database and S3 buckets to the dev site.
  • switch the configuration of the dev site (in the deployment/secrets repos) to point to the dev configuration, not production. the https://patch.biosimulations.dev/projects site will reflect the recent snapshot from the production database and then any new dev content.
• make all inter-app links to 'current site' (so bio.dev pages link to bio.dev pages)
  • with the exception of patch.biosimulations.dev which still points back to .org
• HSDS improvements
  • update HSDS to latest version
  • if HPC job data push to HSDS endpoint fails, don't fail the job
  • if data not present in HSDS, but exists as a .h5 file in the files resource, then lazily load it into HSDS upon request.
• systematically test dev version for correctness for all actions.
• temporarily move manual and automated simulation/publishing activity to dev site
  • Lucian's scripting of new simulation runs and project creation should point to the dev site.

[jcschaff]

cloned production data to dev site, and dev site uses dev resources (mongodb, s3 buckets, hpc/slurm config)

production mongo database was cloned to dev site for each <> (Files, Metadata, Projects, projectSummary, Simulation Run Logs, Simulation Runs, Simulators, Specifications, Statistics). This time, dev collections were dropped right before.

mongosh> use biosimulations-prod
mongosh> db.getCollection("<<collection>>").aggregate([ { $merge: { into: { db: "biosimulations-dev", coll: "<<collection>>" }}} ])

all simulation files were cloned from production to dev site
gsutil -m rsync -r -d gs://files.biosimulations.org gs://files.biosimulations.dev

all HSDS files were cloned from production to dev site
gsutil -m rsync -r -d gs://biosim-hsds-prod gs://biosim-hsds-dev