# refscan
`refscan` is a command-line tool people can use to scan the [NMDC](https://microbiomedata.org/) MongoDB database
for referential integrity violations.
```mermaid
%% This is the source code of a Mermaid diagram, which GitHub will render as a diagram.
%% Note: PyPI does not render Mermaid diagrams, and instead displays their source code.
%% Reference: https://github.com/pypi/warehouse/issues/13083
graph LR
schema[LinkML<br>schema]
database[(MongoDB<br>database)]
script[["refscan.py"]]
violations["List of<br>violations"]
references["List of<br>references"]:::dashed_border
schema --> script
database --> script
script -.-> references
script --> violations
classDef dashed_border stroke-dasharray: 5 5
```
## Table of contents
<!-- TOC -->
* [refscan](#refscan)
* [Table of contents](#table-of-contents)
* [How it works](#how-it-works)
* [Limitations](#limitations)
* [Usage](#usage)
* [Install](#install)
* [Run](#run)
* [The MongoDB connection string (`--mongo-uri`)](#the-mongodb-connection-string---mongo-uri)
* [The schema (`--schema`)](#the-schema---schema)
* [Output](#output)
* [Update](#update)
* [Uninstall](#uninstall)
* [Development](#development)
* [Clone repository](#clone-repository)
* [Create virtual environment](#create-virtual-environment)
* [Install dependencies](#install-dependencies)
* [Make changes](#make-changes)
* [Run tests](#run-tests)
* [Format code](#format-code)
* [Check format](#check-format)
* [Building and publishing](#building-and-publishing)
* [Build for production](#build-for-production)
* [Test the build process locally](#test-the-build-process-locally)
* [Appendix](#appendix)
* [refgraph](#refgraph)
<!-- TOC -->
## How it works
`refscan` does its job in two stages:
1. It uses the LinkML schema to determine where references _can_ exist in a MongoDB database that conforms to the schema.
> **Example:** The schema might say that, if a document in the `biosample_set` collection has a field named
> `associated_studies`, that field must contain a list of `id`s of documents in the `study_set` collection.
2. It scans the MongoDB database to check the integrity of all the references that _do_ exist.
> **Example:** For each document in the `biosample_set` collection that _has_ a field named `associated_studies`,
> for each value in that field, confirm there _is_ a document having that `id` in the `study_set` collection.
## Limitations
`refscan` was designed under the assumption that **every document** in **every collection described by the schema** has
a **field named `type`**, whose value is the [class_uri](https://linkml.io/linkml/code/metamodel.html#linkml_runtime.linkml_model.meta.ClassDefinition.class_uri) of the schema class the document represents an instance
of. `refscan` uses that `class_uri` value (in that `type` field) to determine the name of that schema class,
which it, in turn, uses to determine _which fields_ of that document can contain references.
## Usage
### Install
Assuming you have `pipx` installed, you can install the tool by running the following command:
```shell
pipx install refscan
```
> [`pipx`](https://pipx.pypa.io/stable/) is a tool people can use to
> [download and install](https://pipx.pypa.io/stable/#where-does-pipx-install-apps-from)
> Python scripts that are hosted on PyPI.
> You can [install `pipx`](https://pipx.pypa.io/stable/installation/) by running `$ python -m pip install pipx`.
### Run
You can display the tool's `--help` snippet by running:
```shell
refscan --help
```
At the time of this writing, the tool's `--help` snippet is:
```console
Usage: refscan [OPTIONS]
Scans the NMDC MongoDB database for referential integrity violations.
╭─ Options ──────────────────────────────────────────────────────────────────────────────╮
│ * --schema FILE Filesystem path at which the YAML file │
│ representing the schema is located. │
│ [default: None] │
│ [required] │
│ --database-name TEXT Name of the database. │
│ [default: nmdc] │
│ --mongo-uri TEXT Connection string for accessing the │
│ MongoDB server. If you have Docker │
│ installed, you can spin up a temporary │
│ MongoDB server at the default URI by │
│ running: $ docker run --rm --detach -p │
│ 27017:27017 mongo │
│ [env var: MONGO_URI] │
│ [default: mongodb://localhost:27017] │
│ --verbose Show verbose output. │
│ --skip-source-collection,--skip TEXT Name of collection you do not want to │
│ search for referring documents. Option │
│ can be used multiple times. │
│ [default: None] │
│ --reference-report FILE Filesystem path at which you want the │
│ program to generate its reference │
│ report. │
│ [default: references.tsv] │
│ --violation-report FILE Filesystem path at which you want the │
│ program to generate its violation │
│ report. │
│ [default: violations.tsv] │
│ --version Show version number and exit. │
│ --no-scan Generate a reference report, but do │
│ not scan the database for violations. │
│ --locate-misplaced-documents For each referenced document not found │
│ in any of the collections the schema │
│ allows, also search for it in all │
│ other collections. │
│ --help Show this message and exit. │
╰────────────────────────────────────────────────────────────────────────────────────────╯
```
> Note: The above snippet was captured from a terminal window whose width was 90 characters.
#### The MongoDB connection string (`--mongo-uri`)
As documented in the `--help` snippet above, you can provide the MongoDB connection string to the tool via either
(a) the `--mongo-uri` option; or (b) an environment variable named `MONGO_URI`. The latter can come in handy
when the MongoDB connection string contains information you don't want to appear in your shell history,
such as a password.
Here's how you could create that environment variable:
```shell
export MONGO_URI='mongodb://username:password@localhost:27017'
```
#### The schema (`--schema`)
As documented in the `--help` snippet above, you can provide the path to a YAML-formatted LinkML schema file to the tool
via the `--schema` option.
<details>
<summary>
Show/hide tips for getting a schema file
</summary>
---
If you have `curl` installed, you can download a YAML file from GitHub by running the following command (after replacing
the `{...}` placeholders and customizing the path):
```shell
# Download the raw content of https://github.com/{user_or_org}/{repo}/blob/{branch}/path/to/schema.yaml
curl -o schema.yaml https://raw.githubusercontent.com/{user_or_org}/{repo}/{branch}/path/to/schema.yaml
```
For example:
```shell
# Download the raw content of https://github.com/microbiomedata/berkeley-schema-fy24/blob/main/nmdc_schema/nmdc_materialized_patterns.yaml
curl -o schema.yaml https://raw.githubusercontent.com/microbiomedata/berkeley-schema-fy24/main/nmdc_schema/nmdc_materialized_patterns.yaml
```
---
</details>
#### Output
While `refscan` is running, it will display console output indicating what it's currently doing.
Once the scan is complete, the reference report (TSV file) and violation report (TSV file) will be available
in the current directory (or in custom directories, if any were specified via CLI options).
### Update
You can update the tool to [the latest version available on PyPI](https://pypi.org/project/refscan/) by running:
```shell
pipx upgrade refscan
```
### Uninstall
You can uninstall the tool from your computer by running:
```shell
pipx uninstall refscan
```
## Development
We use [Poetry](https://python-poetry.org/) to both (a) manage dependencies and (b) build distributable packages that can be published to PyPI.
- `pyproject.toml`: Configuration file for Poetry and other tools (was initialized via `$ poetry init`)
- `poetry.lock`: List of dependencies, both direct and [indirect/transitive](https://en.wikipedia.org/wiki/Transitive_dependency)
### Clone repository
```shell
git clone https://github.com/microbiomedata/refscan.git
cd refscan
```
### Create virtual environment
Create a Poetry virtual environment and attach to its shell:
```shell
poetry shell
```
> You can see information about the Poetry virtual environment by running: `$ poetry env info`
> You can detach from the Poetry virtual environment's shell by running: `$ exit`
From now on, I'll refer to the Poetry virtual environment's shell as the "Poetry shell."
### Install dependencies
At the Poetry shell, install the project's dependencies:
```shell
poetry install
```
### Make changes
Edit the tool's source code and documentation however you want.
While editing the tool's source code, you can run the tool as you normally would in order to test things out.
```shell
refscan --help
```
### Run tests
We use [pytest](https://docs.pytest.org/en/8.2.x/) as the testing framework for `refscan`.
Tests are defined in the `tests` directory.
You can run the tests by running the following command from the root directory of the repository:
```shell
poetry run pytest
```
### Format code
We use [`black`](https://black.readthedocs.io/en/stable/) as the code formatter for `refscan`.
We do not use it with its default options. Instead, we include an option that allows lines to be 120 characters
instead of the default 88 characters. That option is defined in the `[tool.black]` section of `pyproject.toml`.
You can format all the Python code in the repository by running this command
from the root directory of the repository:
```shell
poetry run black .
```
#### Check format
You can _check_ the format of the Python code by including the `--check` option, like this:
```shell
poetry run black --check .
```
## Building and publishing
### Build for production
Whenever someone publishes a [GitHub Release](https://github.com/microbiomedata/refscan/releases) in this repository,
a [GitHub Actions workflow](.github/workflows/build-and-publish-package-to-pypi.yml)
will automatically build a package and publish it to [PyPI](https://pypi.org/project/refscan/).
That package will have a version identifier that matches the name of the Git tag associated with the Release.
### Test the build process locally
In case you want to test the build process locally, you can do so by running:
```shell
poetry build
```
> That will create both a
> [source distribution](https://setuptools.pypa.io/en/latest/deprecated/distutils/sourcedist.html#creating-a-source-distribution)
> file (whose name ends with `.tar.gz`) and a
> [wheel](https://packaging.python.org/en/latest/specifications/binary-distribution-format/#binary-distribution-format)
> file (whose name ends with `.whl`) in the `dist` directory.
## Appendix
### refgraph
When `pipx` installs `refscan`, it also installs a program called `refgraph`. `refgraph` is a program you can use to
generate a web-based, interactive graph (network diagram) of the relationships that can exist between documents in a
database that conforms to a given schema. It can present the relationships in terms of either database collections
or schema classes.
You can learn more about `refgraph` by running:
```shell
refgraph --help
```
> Note: `refgraph` is still in early development and its features and CLI are subject to change.
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"description": "# refscan\n\n`refscan` is a command-line tool people can use to scan the [NMDC](https://microbiomedata.org/) MongoDB database\nfor referential integrity violations.\n\n```mermaid\n%% This is the source code of a Mermaid diagram, which GitHub will render as a diagram.\n%% Note: PyPI does not render Mermaid diagrams, and instead displays their source code.\n%% Reference: https://github.com/pypi/warehouse/issues/13083\ngraph LR\n schema[LinkML<br>schema]\n database[(MongoDB<br>database)]\n script[[\"refscan.py\"]]\n violations[\"List of<br>violations\"]\n references[\"List of<br>references\"]:::dashed_border\n schema --> script\n database --> script\n script -.-> references\n script --> violations\n \n classDef dashed_border stroke-dasharray: 5 5\n```\n\n## Table of contents\n\n<!-- TOC -->\n* [refscan](#refscan)\n * [Table of contents](#table-of-contents)\n * [How it works](#how-it-works)\n * [Limitations](#limitations)\n * [Usage](#usage)\n * [Install](#install)\n * [Run](#run)\n * [The MongoDB connection string (`--mongo-uri`)](#the-mongodb-connection-string---mongo-uri)\n * [The schema (`--schema`)](#the-schema---schema)\n * [Output](#output)\n * [Update](#update)\n * [Uninstall](#uninstall)\n * [Development](#development)\n * [Clone repository](#clone-repository)\n * [Create virtual environment](#create-virtual-environment)\n * [Install dependencies](#install-dependencies)\n * [Make changes](#make-changes)\n * [Run tests](#run-tests)\n * [Format code](#format-code)\n * [Check format](#check-format)\n * [Building and publishing](#building-and-publishing)\n * [Build for production](#build-for-production)\n * [Test the build process locally](#test-the-build-process-locally)\n * [Appendix](#appendix)\n * [refgraph](#refgraph)\n<!-- TOC -->\n\n## How it works\n\n`refscan` does its job in two stages:\n1. It uses the LinkML schema to determine where references _can_ exist in a MongoDB database that conforms to the schema.\n > **Example:** The schema might say that, if a document in the `biosample_set` collection has a field named\n > `associated_studies`, that field must contain a list of `id`s of documents in the `study_set` collection.\n2. It scans the MongoDB database to check the integrity of all the references that _do_ exist.\n > **Example:** For each document in the `biosample_set` collection that _has_ a field named `associated_studies`,\n > for each value in that field, confirm there _is_ a document having that `id` in the `study_set` collection.\n\n## Limitations\n\n`refscan` was designed under the assumption that **every document** in **every collection described by the schema** has\na **field named `type`**, whose value is the [class_uri](https://linkml.io/linkml/code/metamodel.html#linkml_runtime.linkml_model.meta.ClassDefinition.class_uri) of the schema class the document represents an instance\nof. `refscan` uses that `class_uri` value (in that `type` field) to determine the name of that schema class,\nwhich it, in turn, uses to determine _which fields_ of that document can contain references.\n\n## Usage\n\n### Install\n\nAssuming you have `pipx` installed, you can install the tool by running the following command:\n\n```shell\npipx install refscan\n```\n\n> [`pipx`](https://pipx.pypa.io/stable/) is a tool people can use to\n> [download and install](https://pipx.pypa.io/stable/#where-does-pipx-install-apps-from)\n> Python scripts that are hosted on PyPI.\n> You can [install `pipx`](https://pipx.pypa.io/stable/installation/) by running `$ python -m pip install pipx`.\n\n### Run\n\nYou can display the tool's `--help` snippet by running:\n\n```shell\nrefscan --help\n```\n\nAt the time of this writing, the tool's `--help` snippet is:\n\n```console\n Usage: refscan [OPTIONS]\n\n Scans the NMDC MongoDB database for referential integrity violations.\n\n\u256d\u2500 Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 * --schema FILE Filesystem path at which the YAML file \u2502\n\u2502 representing the schema is located. \u2502\n\u2502 [default: None] \u2502\n\u2502 [required] \u2502\n\u2502 --database-name TEXT Name of the database. \u2502\n\u2502 [default: nmdc] \u2502\n\u2502 --mongo-uri TEXT Connection string for accessing the \u2502\n\u2502 MongoDB server. If you have Docker \u2502\n\u2502 installed, you can spin up a temporary \u2502\n\u2502 MongoDB server at the default URI by \u2502\n\u2502 running: $ docker run --rm --detach -p \u2502\n\u2502 27017:27017 mongo \u2502\n\u2502 [env var: MONGO_URI] \u2502\n\u2502 [default: mongodb://localhost:27017] \u2502\n\u2502 --verbose Show verbose output. \u2502\n\u2502 --skip-source-collection,--skip TEXT Name of collection you do not want to \u2502\n\u2502 search for referring documents. Option \u2502\n\u2502 can be used multiple times. \u2502\n\u2502 [default: None] \u2502\n\u2502 --reference-report FILE Filesystem path at which you want the \u2502\n\u2502 program to generate its reference \u2502\n\u2502 report. \u2502\n\u2502 [default: references.tsv] \u2502\n\u2502 --violation-report FILE Filesystem path at which you want the \u2502\n\u2502 program to generate its violation \u2502\n\u2502 report. \u2502\n\u2502 [default: violations.tsv] \u2502\n\u2502 --version Show version number and exit. \u2502\n\u2502 --no-scan Generate a reference report, but do \u2502\n\u2502 not scan the database for violations. \u2502\n\u2502 --locate-misplaced-documents For each referenced document not found \u2502\n\u2502 in any of the collections the schema \u2502\n\u2502 allows, also search for it in all \u2502\n\u2502 other collections. \u2502\n\u2502 --help Show this message and exit. \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n```\n\n> Note: The above snippet was captured from a terminal window whose width was 90 characters.\n\n#### The MongoDB connection string (`--mongo-uri`)\n\nAs documented in the `--help` snippet above, you can provide the MongoDB connection string to the tool via either\n(a) the `--mongo-uri` option; or (b) an environment variable named `MONGO_URI`. The latter can come in handy\nwhen the MongoDB connection string contains information you don't want to appear in your shell history,\nsuch as a password.\n\nHere's how you could create that environment variable:\n\n```shell \nexport MONGO_URI='mongodb://username:password@localhost:27017'\n```\n\n#### The schema (`--schema`)\n\nAs documented in the `--help` snippet above, you can provide the path to a YAML-formatted LinkML schema file to the tool\nvia the `--schema` option.\n\n<details>\n\n<summary>\nShow/hide tips for getting a schema file\n</summary>\n\n---\n\nIf you have `curl` installed, you can download a YAML file from GitHub by running the following command (after replacing\nthe `{...}` placeholders and customizing the path):\n\n```shell\n# Download the raw content of https://github.com/{user_or_org}/{repo}/blob/{branch}/path/to/schema.yaml\ncurl -o schema.yaml https://raw.githubusercontent.com/{user_or_org}/{repo}/{branch}/path/to/schema.yaml\n```\n\nFor example:\n\n```shell\n# Download the raw content of https://github.com/microbiomedata/berkeley-schema-fy24/blob/main/nmdc_schema/nmdc_materialized_patterns.yaml\ncurl -o schema.yaml https://raw.githubusercontent.com/microbiomedata/berkeley-schema-fy24/main/nmdc_schema/nmdc_materialized_patterns.yaml\n```\n\n---\n</details>\n\n#### Output\n\nWhile `refscan` is running, it will display console output indicating what it's currently doing.\n\n\n\nOnce the scan is complete, the reference report (TSV file) and violation report (TSV file) will be available\nin the current directory (or in custom directories, if any were specified via CLI options).\n\n### Update\n\nYou can update the tool to [the latest version available on PyPI](https://pypi.org/project/refscan/) by running:\n\n```shell\npipx upgrade refscan\n```\n\n### Uninstall\n\nYou can uninstall the tool from your computer by running:\n\n```shell\npipx uninstall refscan\n```\n\n## Development\n\nWe use [Poetry](https://python-poetry.org/) to both (a) manage dependencies and (b) build distributable packages that can be published to PyPI.\n\n- `pyproject.toml`: Configuration file for Poetry and other tools (was initialized via `$ poetry init`)\n- `poetry.lock`: List of dependencies, both direct and [indirect/transitive](https://en.wikipedia.org/wiki/Transitive_dependency)\n\n### Clone repository\n\n```shell\ngit clone https://github.com/microbiomedata/refscan.git\ncd refscan\n```\n\n### Create virtual environment\n\nCreate a Poetry virtual environment and attach to its shell:\n\n```shell\npoetry shell\n```\n\n> You can see information about the Poetry virtual environment by running: `$ poetry env info`\n\n> You can detach from the Poetry virtual environment's shell by running: `$ exit`\n\nFrom now on, I'll refer to the Poetry virtual environment's shell as the \"Poetry shell.\"\n\n### Install dependencies\n\nAt the Poetry shell, install the project's dependencies:\n\n```shell\npoetry install\n```\n\n### Make changes\n\nEdit the tool's source code and documentation however you want.\n\nWhile editing the tool's source code, you can run the tool as you normally would in order to test things out.\n\n```shell\nrefscan --help\n```\n\n### Run tests\n\nWe use [pytest](https://docs.pytest.org/en/8.2.x/) as the testing framework for `refscan`.\n\nTests are defined in the `tests` directory.\n\nYou can run the tests by running the following command from the root directory of the repository:\n\n```shell\npoetry run pytest\n```\n\n### Format code\n\nWe use [`black`](https://black.readthedocs.io/en/stable/) as the code formatter for `refscan`. \n\nWe do not use it with its default options. Instead, we include an option that allows lines to be 120 characters\ninstead of the default 88 characters. That option is defined in the `[tool.black]` section of `pyproject.toml`.\n\nYou can format all the Python code in the repository by running this command\nfrom the root directory of the repository:\n\n```shell\npoetry run black .\n```\n\n#### Check format\n\nYou can _check_ the format of the Python code by including the `--check` option, like this:\n\n```shell\npoetry run black --check .\n```\n\n## Building and publishing\n\n### Build for production\n\nWhenever someone publishes a [GitHub Release](https://github.com/microbiomedata/refscan/releases) in this repository,\na [GitHub Actions workflow](.github/workflows/build-and-publish-package-to-pypi.yml)\nwill automatically build a package and publish it to [PyPI](https://pypi.org/project/refscan/).\nThat package will have a version identifier that matches the name of the Git tag associated with the Release.\n\n### Test the build process locally\n\nIn case you want to test the build process locally, you can do so by running:\n\n```shell\npoetry build\n```\n\n> That will create both a\n> [source distribution](https://setuptools.pypa.io/en/latest/deprecated/distutils/sourcedist.html#creating-a-source-distribution)\n> file (whose name ends with `.tar.gz`) and a\n> [wheel](https://packaging.python.org/en/latest/specifications/binary-distribution-format/#binary-distribution-format)\n> file (whose name ends with `.whl`) in the `dist` directory.\n\n## Appendix\n\n### refgraph\n\nWhen `pipx` installs `refscan`, it also installs a program called `refgraph`. `refgraph` is a program you can use to\ngenerate a web-based, interactive graph (network diagram) of the relationships that can exist between documents in a\ndatabase that conforms to a given schema. It can present the relationships in terms of either database collections\nor schema classes.\n\nYou can learn more about `refgraph` by running:\n\n```shell\nrefgraph --help\n```\n\n> Note: `refgraph` is still in early development and its features and CLI are subject to change.\n\n",
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