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Interactive ChRIS REPL Shell","maintainers":[{"name":"jbernal0019","email":"jbernal0019@yahoo.es"},{"name":"jennydaman","email":"npm@sl.jennin.xyz"},{"name":"debio","email":"rudolph.pienaar@gmail.com"}],"readme":"# ChELL: ChELL Executes Layered Logic\n\n**The Interactive Shell for ChRIS**\n\nChELL is a command-line shell that presents a ChRIS distributed-computing platform as a familiar Unix filesystem. If you know `bash` or `zsh`, you already know most of ChELL.\n\n## Installation\n\n```bash\nnpm install -g @fnndsc/chell\n```\n\nRequires Node.js ≥ 20.12. This installs the `chell` command — see [Getting Started](#getting-started) to connect to a CUBE.\n\n## The Concept\n\nChRIS stores data, analysis tools, and results behind a REST API. ChELL maps all of that onto paths:\n\n- your data lives under `/home/<user>/`\n- every registered plugin and Pipeline is a virtual executable in `/bin`\n- system configuration is readable at `/etc`\n- PACS query results surface under `/net/pacs/queries/`\n\nYou navigate with `cd`, inspect with `ls`, read files with `cat`, and run analyses by invoking plugin names — the same muscle memory you use on any Unix system.\n\nPACS retrieval can also establish the input of a new analysis directly:\n\n```bash\npacs query AccessionNumber:12345678\npacs pull /net/pacs/queries/.../Study_... --new-feed \"Brain MRI\"\n```\n\n`--new-feed` waits for the complete selected series set, creates one feed rooted\nat `pl-dircopy`, and prints the feed ID, root job ID, and feed path. Without the\nflag, `pacs pull` only retrieves data into CUBE storage.\n\nOptional analysis attachment is available with `--plugin <selector>` or\n`--pipeline <selector>`. Both require `--new-feed`, attach to that new root, and\nforward arguments after `--` through the selected command's existing invocation\nsemantics. See\n[PACS Query / Retrieve / Resolve](docs/pacsqr.adoc#planned-analysis-attachment)\nfor the complete behavioral contract.\n\n---\n\n## The Virtual Filesystem\n\nThe ChELL filesystem has two kinds of paths:\n\n- **CFS (CubeFS)** — real ChRIS storage: files you upload, feed outputs, symlink files. Readable, writable, persistent.\n- **VFS (Virtual)** — synthesised on the fly from API resources: plugins, config, PACS results. Read-only views, no stored bytes.\n\n| Path | Type | What you see |\n|------|:----:|-------------|\n| `/home/<user>/` | CFS | Your uploaded files and directories |\n| `/home/<user>/feeds/` | CFS | Your analysis feeds and their output trees |\n| `/PIPELINES/` | CFS | Shared pipeline output data |\n| `/PUBLIC/` | CFS | Publicly accessible files |\n| `/SERVICES/` | CFS | Service-level data |\n| `/SHARED/` | CFS | Cross-user shared data |\n| `*.chrislink` | CFS | Symbolic links to other ChRIS paths |\n| `/bin` | VFS | Every plugin and Pipeline registered in this CUBE |\n| `/usr/bin` | VFS | Built-in shell commands (`id`, `whoami`, `whereami`, …) |\n| `/etc/` | VFS | Config: compute environments, groups, users, CUBE info |\n| `/net/pacs/queries/` | VFS | PACS query result sets |\n| `/proc/jobs/` | VFS | Job monitoring — live status of all plugin instances |\n\n```bash\ncd /etc\ncat compute.yaml          # inspect available compute environments\ncat group                 # list groups and their current CUBE users\n\ncd /bin\nls pl-mri*                # browse MRI-related plugins\n\ncd /home/chris/feeds\nls -l                     # see your analysis feeds\n```\n\n### Symlinks (`.chrislink` files)\n\nChRIS uses `.chrislink` files as symbolic links. `ls -l` renders them as `l` entries; `cd` and `cat` follow them transparently. The link target is resolved through the VFS dispatcher — it can point anywhere in the virtual tree.\n\n---\n\n## Running Plugins\n\nBecause plugins live in `/bin` as virtual executables, you invoke them **directly by name** — exactly like running a local binary. ChELL uses your **current working directory** to determine context automatically, so you never need to supply a `--previous_id` by hand.\n\n### Case 1 — Starting a new analysis from a data directory\n\n```bash\ncd /home/chris/uploads/SAG-anon\npl-fshack-v1.2.0 --inputFile brain.mgz --outputFile brain.nii\n```\n\nChELL detects you are **outside a feed**. It:\n1. Automatically runs `pl-dircopy` on the current directory to stage the data into a new feed\n2. Attaches your plugin to that dircopy instance as the next step\n\nA new feed is created for you — no boilerplate.\n\n### Case 2 — Continuing an existing analysis\n\n```bash\ncd /home/chris/feeds/feed_123/pl-fshack_456/data\npl-segmentation-v1.0.0 --threshold 0.5\n```\n\nChELL detects you are **inside a feed**. It extracts the plugin instance ID from the path (`456`) and uses it as `previous_id` automatically. The new plugin node is wired into the existing computation DAG.\n\n### Naming feeds and instances\n\nUse `--` to separate plugin parameters from feed-level context:\n\n```bash\npl-fshack-v1.2.0 --inputFile brain.mgz -- feed_title=\"Brain MRI Study\" instance_title=\"FreeSurfer recon\"\n```\n\nEverything before `--` goes to the plugin; everything after sets ChRIS metadata.\n\n### Inspecting a versioned plugin\n\nThe executable itself exposes help, parameters, and repository documentation:\n\n```bash\npl-fshack-v1.2.0 --help\npl-fshack-v1.2.0 --parameters\npl-fshack-v1.2.0 --readme\npl-fshack-v1.2.0 --readme --raw > pl-fshack-README.md\n```\n\nMarkdown READMEs are styled for terminal display, while reStructuredText is\npreserved as written. `--raw` returns only the original README content, making\nit safe for pipes and redirection. These forms behave the same in local and\nremote sessions.\n\n### Monitoring\n\n```bash\njob inspect <instance_id>\njobs list --feed <feed_id>\n```\n\n### Installing new plugins\n\n```bash\n# Search the public peer store\nstore search simplefs\n\n# Install (auto-discovers compute resources)\nstore install pl-simplefsapp\n\n# Install pinned to specific compute\nstore install pl-simplefsapp --compute ares,argentum\n```\n\n`store install` runs a three-phase resolution:\n1. Already in this CUBE → reports `[INFO] already registered`\n2. Found in peer store (cube.chrisproject.org) → imports via admin API\n3. Not found → Docker extraction and registration\n\nWhen registration needs escalation, ChELL reports the original failure and\nsuggests the explicit retry, for example `sudo store install pl-simplefsapp`.\n`sudo` prompts for administrator credentials with a hidden password and uses\nthe resulting CUBE identity only for that nested command. In a remote session\nthose prompts and their guidance stay on the originating client surface.\n\n---\n\n## Running Pipelines\n\nA **pipeline** is a registered template — a named, reusable graph of plugins with their parameter defaults wired together. Pipelines are static definitions; they do not run on their own.\n\nA **workflow** is a live instantiation of a pipeline, attached to a specific feed node. Creating a workflow is the act of \"running\" a pipeline: ChRIS schedules each plugin step in order, feeding outputs of one into the inputs of the next.\n\n```bash\n# Browse registered pipeline templates\npipeline list\npipeline info <name|id>\n\n# Inspect or draw a registered template\npipeline manifest <name|id|slug>\npipeline diagram <name|id>\n\n# Run by invoking its /bin name in the current context\nbrain-segmentation\nbrain-segmentation --segmentation.threshold 0.5\nbrain-segmentation --paramFile ~/experiments/run-1.yaml\n\n# Equivalent explicit form\npipeline run brain-segmentation --previous <instance_id>\n\n# Monitor all the jobs it spawns\njobs list --feed <feed_id>\n```\n\n`<pipeline> --manifest` is the direct alias for the complete registered\ninvocation YAML, including piping IDs, stored values, compute placement, resource\ncontrols, and topology. `cat /bin/<pipeline>` intentionally remains immediate:\nit prints only a cached executable summary pointing to the manifest command.\n\n`<pipeline> --diagram` is the direct drawing alias; add `--withargs` for stored\ndefaults or `--signalflow` for SignalFlow YAML. Pipeline parameters and execution\ncontrols use `--<node>.<field> <value>`, while `--paramFile <cfs-file>` reads one\nsparse overlay from durable CFS. ChELL resolves the current context automatically;\n`--previous <instance_id>` selects an explicit attachment point.\n\n---\n\n## Monitoring Jobs: `/proc/jobs/`\n\nBecause every plugin runs asynchronously in ChRIS, `/proc/jobs/` is where you come back to see what happened. It exposes all your visible feeds and their plugin instances as a navigable DAG — the same tree structure the computation actually ran in.\n\n```\n/proc/jobs/\n└── feed_123/\n    ├── status                        ← aggregate feed status\n    ├── title                         ← feed name\n    └── pl-dircopy_456/               ← root node (j = job type in ls -l)\n        ├── status                    ← finishedSuccessfully\n        ├── params\n        ├── log\n        └── pl-fshack_789/\n            ├── status                ← started\n            └── pl-segmentation_1011/\n                └── status            ← scheduled\n```\n\n```bash\nls -l /proc/jobs/feed_123            # see all nodes with colour-coded status\ncat /proc/jobs/feed_123/pl-fshack_789/status   # terminal cached; active refreshed\ncat /proc/jobs/feed_123/pl-fshack_789/log      # stdout/stderr\ncat /proc/jobs/feed_123/pl-fshack_789/params   # what it ran with\n\n# The whole feed as one DAG view\nfeed tree 123                         # collapsed, status-coloured tree (⋈ marks joins)\nfeed tree 123 --focus 789             # scope to one node's subtree\nfeed diagram --signalflow 123 | signalflow -   # emit the DAG; render with your own tools\npipeline diagram brain-segmentation  # shallow registered-pipeline template\nbrain-segmentation --diagram --withargs  # /bin alias with stored defaults\nbrain-segmentation --signalflow | signalflow - # direct SignalFlow alias\n\n# Search across all jobs\ntree /proc/jobs | grep 789           # find instance 789 and see its full lineage\n\n# Cancel a running job\nrm /proc/jobs/feed_123/pl-fshack_789\n\n# Cancel all jobs in a feed (requires -r)\nrm -r /proc/jobs/feed_123\n```\n\nStatus colours in `ls -l`: green = `finishedSuccessfully`, yellow = `started`/`running`, gray = `scheduled`/`cancelled`, red = `finishedWithError`.\n\nConnected startup indexes the visible feed list and warms job topology in the\nbackground. A daemon first restores its identity-scoped local checkpoint,\nvalidates that its feeds are still visible, and serves that usable topology\nwhile reconciling it with CUBE. Terminal statuses can be restored; active\nstatuses and logs remain live. Inspect freshness and feed scope with `proc stat`:\n\n```bash\nproc stat                 # feed scope, loaded jobs, sweep and checkpoint state\nproc stat feed_123        # cached detail for one feed\nproc retry                # resume a failed topology sweep at its failed page\nproc refresh              # rebuild all and start one replacement topology sweep\nproc refresh feed_123     # scope to one feed\n```\n\nIf startup prefetch is disabled, first access builds the index lazily. Run a\nfull `proc refresh` after activity from another client or the web GUI; CUBE is\nalways authoritative.\n\nSince `/proc` paths encode the instance ID, you can also **continue an analysis from any node** just by `cd`-ing into it:\n\n```bash\ncd /proc/jobs/feed_123/pl-dircopy_456\npl-fshack-v1.2.0 --inputFile brain.mgz   # attaches here, no --previous_id needed\n```\n\n---\n\n## Key Commands\n\n### Filesystem\n```bash\nls [-l] [-h] [-a]       # list directory\ncd <path>               # change directory (follows .chrislinks)\ncat <file>              # print file content\nedit <file>             # open in $EDITOR, save back to ChRIS\ncp / mv / rm            # copy, move, delete\nmkdir / touch           # create directory or empty file\nupload <local> <remote> # upload local file or directory tree\ndownload <remote> <local>\ntree                    # recursive listing\ndu                      # disk usage\n```\n\n### Resources\n```bash\nplugin list / search / inspect / run\nplugins list [--search <term>] [--all]\n<plugin>-v<version> --help / --parameters / --readme [--raw]\nfeed list / inspect\nfeeds list [--user <name>] [--all]\nfeed note <id>          # read feed note\nfeed note edit <id>     # edit feed note in $EDITOR\nfeed comments <id>      # list comments\npipeline list / info / manifest / run / source / diagram\nworkflow list / create\njob inspect <id>\ncompute list            # list compute environments\n```\n\n### Store\n```bash\nstore list              # browse peer store\nstore search <query>\nstore install <plugin>  # install with admin escalation if needed\nstore inspect           # show current peer store URL\nstore set <url>         # override peer store\n```\n\n### System\n```bash\nid                      # CUBE UID, projected primary GID, and memberships\nwhoami                  # current CUBE user\nwhereami                # current CUBE URL (use pwd for working directory)\nprompt list             # list prompt themes\nprompt default          # compact single-line prompt\nprompt p10k             # vivid two-line powerline prompt\nconnect --user <u> --password <p> <url>\nlogout\nproc stat               # show /proc feed scope, freshness, and checkpoint\nproc retry              # resume failed /proc reconciliation without starting over\nproc refresh            # rebuild /proc job cache and restart topology warm-up\nproc refresh feed_123   # scope rebuild to one feed\n```\n\nBoth prompt themes display the authenticated user's home directory as `~`, so\n`/home/chris/uploads` appears as `~/uploads`. The `default` and `p10k` themes\nshare a vivid truecolor palette; `p10k` adds background-filled powerline\nsegments, high-contrast Font Awesome icons, and optional status information.\nThe icons and separators require a Nerd Font. Use `prompt --show` to preview\nthe active prompt.\n\nThe p10k prompt orders PACS, CUBE URL, user, path, and `/proc` from left to\nright; the optional physical-mode indicator and command telemetry follow that\ncore sequence. A visible `/proc` segment distinguishes cold indexing, cached\nrefresh, and refresh failure; it disappears once the CUBE-authoritative index\nis current.\n\n---\n\n## Getting Started\n\n```bash\n# Start the shell, then connect interactively\nchell\n> connect --user chris --password chris1234 http://localhost:8000/api/v1/\n\n# Connect via flags\nchell -u chris -p chris1234 http://localhost:8000/api/v1/\n\n# Compact user@host form (password prompted if omitted)\nchell chris@localhost:8000/api/v1/\nchell -p chris1234 chris@localhost:8000/api/v1/\n```\n\n### Scripting\n\n```bash\n# Non-interactive: single command via -c\nchell -c \"ls -l /home/user/study\" > study_contents.txt\nchell -c \"store install pl-dircopy\"\n\n# Run a script file\nchell -f my_workflow.chell\n```\n\n---\n\n## Architecture\n\nChELL is the presentation layer of the \"Sandwich Model\":\n\n1. **ChELL** — REPL, builtins, tab completion, prompt\n2. **ChILI** — typed commands, views, CLI controllers\n3. **Salsa** — business logic, VFS dispatcher, intent layer\n4. **Cumin** — connection, context persistence, state\n5. **`@fnndsc/chrisapi`** — raw ChRIS REST client\n\n---\n\n## Further Reading\n\n| Document | Topic |\n|----------|-------|\n| [docs/vfs.adoc](docs/vfs.adoc) | VFS architecture — providers, dispatch, path resolution |\n| [docs/pluginrun.adoc](docs/pluginrun.adoc) | Plugin execution in depth — new feed vs continue feed |\n| [docs/plugin-run-summary.md](docs/plugin-run-summary.md) | Quick-reference summary of plugin run modes |\n| [docs/store.adoc](docs/store.adoc) | Store install — three-phase resolution, admin escalation |\n| [docs/login.adoc](docs/login.adoc) | Connection and authentication options |\n| [docs/execution.adoc](docs/execution.adoc) | Command execution, scripting, and pipeline mode |\n| [docs/commands.adoc](docs/commands.adoc) | Full command reference |\n| [docs/pacsqr.adoc](docs/pacsqr.adoc) | PACS query and retrieve |\n| [docs/physicalMode.adoc](docs/physicalMode.adoc) | Physical vs logical filesystem mode |\n| [docs/gotchas.adoc](docs/gotchas.adoc) | Known edge cases and workarounds |\n| [docs/architecture.adoc](docs/architecture.adoc) | Full architecture deep-dive |\n| [CONTEXT.md](CONTEXT.md) | Domain glossary — ChRIS concepts, permission model, resource contract |\n\n---\n\n## License\n\nPart of the [ChRIS Project](https://chrisproject.org).\n\n---\n*ChELL is part of the ChRIS Project.*\n\n---\n_-30-_\n","readmeFilename":"README.md"}