Readiness
- Readiness
- Needs Token/License
- Smoke
- not_tested
- Artifacts
- not_applicable
- Production
- needs_phenix_download_password_or_licensed_cctbx_runtime
- Storage
- <5
- Strategy
- compiled/binary SIF or shared python312_slim + ext3 overlay
- Next
- Obtain/provide Phenix download credentials or an already-licensed Phenix/cctbx/MolProbity runtime/SIF exposing phenix.clashscore, phenix.cbetadev, phenix.rotalyze, phenix.ramalyze, phenix.omegalyze, mmtbx.mp_geo, molprobity.suitename, and prekin; then rerun clean direct + Slurm/API smoke before adapter promotion.
MolProbity upstream source identified as rlabduke/MolProbity; Phenix docs also describe MolProbity validation. No local checkout/revision captured and no install completed. Conda/micromamba search found no bioconda/conda-forge molprobity package. Staging dir empty (~256 KB); no Slurm smoke. Likely needs controlled upstream bootstrap/build with cctbx/probe/reduce, or prebuilt container. 2026-07-05 SOP triage: backend staging directory remains effectively empty and no command-line MolProbity bootstrap/container is available; likely needs cctbx/probe/reduce controlled build or a prebuilt command-line container. Reclassified from Smoke Pending to Production Blocked until runnable upstream packaging is available. 2026-07-10T17:43:52+08:00 SOP blocked implementation attempt: staged rlabduke/MolProbity source rev daee5253054c978010b782c840bd3e3ec24b1b4d plus rlabduke/probe rev 835c2c63dd14b8c30599900b07c2296925cc933c and rlabduke/reduce rev d723303c0ae7a9991a4f723b74f9bfa268d33e87 under /media/nik/seagate_nik/bio_server/tools/molprobity/source. Probe and Reduce compiled successfully, and Ubuntu php-cli 8.3.6 was installed, but official MolProbity cmdline tools clashscore/mp_geometry/residue-analysis/oneline-analysis failed on the bundled PDB at /media/nik/seagate_nik/bio_server/artifacts/molprobity/direct_20260710_174210 with missing config/config.php warnings and fatal legacy PHP syntax error in lib/model.php (curly brace offset access unsupported by PHP 8.3). Keep Production Blocked until a PHP 5.6-compatible command-line container/bootstrap or modernized MolProbity/cctbx/Phenix CLI is available. 2026-07-10T22:37:32+08:00 continuation recheck: previous Probe/Reduce build is not enough; MolProbity PHP command-line tooling still requires PHP 5.6-compatible bootstrap or a modern cctbx/Phenix MolProbity CLI. No SOP-valid Slurm smoke can run under current PHP 8.3 path. 2026-07-10T22:55:53+08:00 reclassification: kept in Production Blocked because the remaining issue is a local packaging/bootstrap problem rather than missing large assets or authenticated model access: MolProbity needs PHP 5.6-compatible command-line bootstrap/container or a modern cctbx/Phenix MolProbity CLI after Probe/Reduce were compiled but legacy PHP failed under PHP 8.3. 2026-07-10T23:20:12+08:00 SOP continuation: backend MolProbity source was patched in-place for PHP 8.3 CLI compatibility (legacy curly-brace string offsets in lib/model.php, lib/analyze.php, lib/eff_resol.php, lib/pdbstat.php), minimal config/config.php was created for CLI job data under /media/nik/seagate_nik/bio_server/artifacts/molprobity, cctbxGetPath was relaxed to use bundled MP_BIN_PATH when no cctbx build/bin exists, and bin/linux/scrublines was materialized from scrublines_64 because the shared filesystem rejected symlinks. Direct PHP lint now passes for required CLI libraries; Reduce runs and mp_geometry/residue-analysis emit real output on bundled 1ubq.pdb. However full MolProbity production smoke is not valid yet: clashscore/oneline remain incomplete/noisy, Java is missing for rotarama/dangle jar paths, no cctbx/Phenix runtime or SIF exists, and a default-jre-headless apt install attempt hung on backend network/apt and was stopped. Keep Production Blocked pending a complete Java+cctbx/Phenix/MolProbity container or successful JRE/runtime install followed by clean Slurm/API smoke. 2026-07-10T23:37:34+08:00 SOP continuation: staged portable Temurin JRE 17 without apt. Downloaded JRE tarball to /media/nik/seagate_nik/bio_server/envs/molprobity_jre17/temurin-jre.tar.gz; extracted functional runtime under /home/nik/bio_mega_scratch/molprobity_jre17 and copied usable runtime to /media/nik/seagate_nik/bio_server/tools/molprobity/jre17 despite shared-drive hardlink warnings. Verified java -version reports OpenJDK 17.0.19. Reran MolProbity CLI smoke with JRE on PATH at /media/nik/seagate_nik/bio_server/artifacts/molprobity/jre_cli_20260710_233634. reduce succeeded; residue-analysis produced 135 output lines and mp_geometry produced header output. However clashscore remained zero-byte and oneline-analysis exited 255 because required Phenix/cctbx executables are missing: phenix.clashscore, phenix.cbetadev, phenix.rotalyze, phenix.ramalyze, phenix.omegalyze, mmtbx.mp_geo, molprobity.suitename/prekin. Java is no longer the primary blocker; keep Production Blocked pending Phenix/cctbx/MolProbity CLI runtime or SIF. 2026-07-10T23:55:29+08:00 SOP reclassification: moved from Production Blocked to Needs Token/License. Backend has MolProbity source, Probe/Reduce, PHP 8.3 compatibility patches, and a staged portable JRE 17, but clean production validation requires the Phenix/cctbx validation command stack (phenix.clashscore, phenix.cbetadev, phenix.rotalyze, phenix.ramalyze, phenix.omegalyze, mmtbx.mp_geo, molprobity.suitename/prekin). Official Phenix download instructions require academic users to request a download password with institutional email and industrial users to obtain licensed access via the Phenix Industrial Consortium; therefore this is now an access-gated runtime blocker rather than a generic production-blocked implementation bug. Primary references checked: https://phenix-online.org/download, https://phenix-online.org/passreq/, https://www.phenix-online.org/documentation/reference/molprobity_tool.html, https://cctbx.github.io/mmtbx/mmtbx.validation.molprobity.html.