outpack-query-parser 0.3.0

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outpack

Rust implementation of outpack.

Usage

This crate provides an outpack command which can be used to create and operate on Outpack repositories.

The command can be built with cargo build, after which it can be found in target/debug/outpack. Alternatively it can be started directly by using cargo run.

Initializing a new repository

outpack init --use-file-store <path>

Query CLI usage

outpack query --root <path> <query>

API Server

The outpack command includes an API server which can be used to expose the repository over an HTTP interface.

outpack start-server --root <path>

Usage of docker image

docker run --name outpack_server -v /full/path/to/root:/outpack -p 8000:8000 -d mrcide/outpack_server:main

Schema

The outpack schema is imported into this package by running ./scripts/import_schema, and needs to be kept manually up to date by re-running that script as needed.

Tests

Run all tests with cargo test.

API

GET /

{
   "status": "succcess",
   "data": {
        "schema_version": "0.0.1"
   },
   "errors": null
}

GET /checksum

Returns hash of all current packet ids, ordered alphanumerically and concatenated. This will use the hashing algorithm specified in the outpack config, unless a query parameter specifying an alternative is passed: e.g. /checksum?alg=md5.

{
   "status": "succcess",
   "data": "md5:117723186364b4b409081b1bd347d406"
   "errors": null
}

GET /metadata/list

{
    "status": "success",
    "errors": null,
    "data": [
        {
            "packet": "20220812-155808-c873e405",
            "time": "2022-08-12 15:58:08",
            "hash": "sha256:df6edb3d6cd50f5aec9308a357111592cde480f45a5f46341877af21ae30d93e"
        },
        {
            "packet": "20220812-155808-d5747caf",
            "time": "2022-08-12 15:58:08",
            "hash": "sha256:edc70ef51e69f2cde8238142af29a9419bb27c94b320b87e88f617dfc977a46b"
        },
        {
            "packet": "20220812-155808-dbd3ce81",
            "time": "2022-08-12 15:58:08",
            "hash": "sha256:a7da8c3464a2da4722b9d15daa98eb13f4f8c1949c6d00100428b2e9d0668f29"
        },
        {
            "packet": "20220812-155808-e21bc5fc",
            "time": "2022-08-12 15:58:08",
            "hash": "sha256:df1b91aaf3393483515ac61596aa35117891eacc533a55ec2f4759d0036514f9"
        }
    ]
}

GET /packit/metadata

Returns a list of (truncated) packet metadata. Accepts an optional query parameter known_since specifying a Unix epoch time from which to return results. This will filter packets by the time property of the location metadata, i.e. the point at which they were inserted into the index. e.g. /packit/metadata?known_since=1683117048.

{
    "status": "success",
    "errors": null,
    "data": [
        {
            "id": "20220812-155808-c873e405",
            "name": "depends",
            "custom": { "orderly": { "display": "Report with dependencies" }}
            "parameters": null
        },
        {
            "id": "20220812-155808-d5747caf",
            "name": "params",
            "custom": { "orderly": { "display": "Report with parameters" }},
            "parameters": { "alpha": 1 }
        }
    ]
}

GET /metadata/<id>/json

{
  "status": "success",
  "errors": null,
  "data": {
    "custom": null,
    "depends": [],
    "files": [
      {
        "hash": "sha256:e9aa9f2212aba6fba4464212800a2927afa02eda688cf13131652da307e3d7c1",
        "path": "orderly.yml",
        "size": 955
      },
      {
        "hash": "sha256:11a2cd93493defa673b198d5be7a180cef7b133baaacc046923e1e2da77c6f75",
        "path": "modified_update.R",
        "size": 1133
      },
      {
        "hash": "sha256:c4d4c95af9da912f2f20c65a0502c7da19a5712767a39e07a2dd1ea7fcb615b0",
        "path": "R/util.R",
        "size": 2757
      }
    ],
    "id": "20170818-164043-7cdcde4b",
    "name": "modup-201707",
    "parameters": null,
    "schema_version": "0.0.1",
    "script": [
      "modified_update.R"
    ],
    "session": {
      "packages": [
        {
          "attached": true,
          "package": "RcppRoll",
          "version": "0.2.2"
        },
        {
          "attached": false,
          "package": "Rcpp",
          "version": "0.12.12"
        },
        {
          "attached": false,
          "package": "ids",
          "version": "1.0.1"
        }
      ],
      "platform": {
        "os": "Debian GNU/Linux 9 (stretch)",
        "system": "x86_64, linux-gnu",
        "version": "R version 3.4.0 (2017-04-21)"
      }
    },
    "time": {
      "end": 1503074545.8687,
      "start": 1503074545.8687
    }
  }
}

GET /metadata/<id>/text

Returns the same as GET /metadata/<id>/json but just the data as plain text.

GET /file/<hash>

Downloads the file with the provided hash. 404 if it doesn't exist.

POST /packets/missing

Body

{
    "ids": ["20220812-155808-c873e405","20220812-155808-d5747caf"],
    "unpacked": false
}

Given a list of ids, returns those that are missing in the current root. If unpacked is true returns missing unpacked packets, otherwise just looks at missing metadata.

Response

{
  "status": "success",
  "errors": null,
  "data": ["20220812-155808-c873e405", "20220812-155808-d5747caf"]
}

POST /files/missing

Body

{
  "hashes": [
    "sha256:b189579a9326f585d308304bd9e03326be5d395ac71b31df359ab8bac408d248",
    "sha256:a189579a9326f585d308304bd9e03326be5d395ac71b31df359ab8bac408d247"
  ]
}

Given a list of file hashes, returns those that are missing in the current root.

Response

{
  "status": "success",
  "errors": null,
  "data": ["sha256:a189579a9326f585d308304bd9e03326be5d395ac71b31df359ab8bac408d24"]
}

POST /file/

Upload a file with the given hash. Returns a 400 if the hash does not match the file contents. This method is idempotent; if the file already exists it will not do anything.

Body

The file contents should be written directly to the request body.

Response

{
  "status": "success",
  "errors": null,
  "data": null
}

POST /packet/

Upload packet metadata with the given hash. Returns a 400 if the hash does not match the contents. This method is idempotent; if the file already exists it will not do anything.

Body

The metadata should be written directly to the request body.

Response

{
  "status": "success",
  "errors": null,
  "data": null
}

Python bindings

This crate provides Python bindings for its query parser. The bindings can be installed using pip install ..

Local development

hatch run python  # Start a Python interpreter with the bindings installed
hatch run test    # Run the bindings test-suite
hatch run develop # Rebuild the bindings. Necessary whenever changes to Rust code is made.

License

MIT © Imperial College of Science, Technology and Medicine