v3.1.0

Release Notes: v3.1.0

Highlights

New: projark ls — list vault contents

projark ls 982
projark ls 982 --json

Lists all data objects archived under a project as a tree with human-readable sizes, depositor name (from registered_by_name), and deposit date (formatted YYMMDD). Accepts the same project number formats as deposit/retrieve. No Helix, tmux, or sync-gate checks required. Does not send email. See projark ls. (#62, @kopardev)

New: parkit ls — list any HPC-DME collection

parkit ls /CCBR_Archive/GRIDFTP
parkit ls /CCBR_Archive/GRIDFTP/Project_CCBR-982 --json

Lists any HPC-DME collection path using the same shared backend as projark ls. Renders a full recursive hierarchy at any depth. See parkit ls. (#62, @kopardev)

Bug Fixes

• projark deposit — HTTP 400 errors fixed: _register_collection now sends all required HPC-DME metadata fields when creating collections. Project collections include project_title, project_description, origin, method, access, organism, summary_of_samples, project_start_date. Analysis/Rawdata sub-collections include project_start_date, method, number_of_cases. Rawdata datatype now correctly maps to HPC-DME collection_type value Analysis. (#53, @kopardev)

• Split-tar conflict detection: projark deposit tarname resolution now also checks for the first split-chunk suffix (*.tar_0001). Previously, a project whose tarball had been split on a prior deposit (ccbr982.tar_0001, ccbr982.tar_0002, …) was not detected as a conflict because the base name ccbr982.tar never exists as a data object in the vault. (#61, @kopardev)

• Temp file isolation: run_dm_cmd now executes each dm_* subprocess inside a per-call tempfile.TemporaryDirectory, so HPC-DME CLI response files (*.tmp) no longer accumulate in the user's working directory. This also prevents concurrent runs from overwriting each other's temp files. (#60, @kopardev)

Improvements

• projark deposit — configuration display: After the host/session preflight checks, the active (non-comment) lines from $HPC_DM_UTILS/hpcdme.properties are printed so users can verify their HPC-DME configuration before transfer begins. (#56, @kopardev)

• projark deposit — proxy check: Deposits abort with a descriptive error if hpc.server.proxy.url or hpc.server.proxy.port are active (uncommented) in hpcdme.properties. Per HPC-DME team guidance, proxy lines must be commented out. (#57, @kopardev)

• projark deposit — dot-file exclusion: Hidden files (names starting with .) are automatically excluded from dm_register_directory via a temp exclude file, preventing shell history and other hidden files from being registered to HPC-DME. (#58, @kopardev)

• projark deposit — pre-transfer conflict detection: Before calling dm_register_directory, staged files are checked against the destination vault. If a conflict is found, staged files are renamed by inserting a zero-padded counter before the first extension (e.g. ccbr1431.tar → ccbr1431_001.tar) using the lowest available counter. (#59, @kopardev)

• projark retrieve — batch existence check: The per-filename existence check now uses a single dm_query_dataobject call instead of N serial dm_get_dataobject calls. (#62, @kopardev)

• projark retrieve — split-tar advisory: After fetching the object listing, retrieve automatically detects split tar parts (*.tar_NNNN) in the collection and prints an advisory if --unsplit was not passed. (#62, @kopardev)