refscan 0.1.0__tar.gz → 0.1.2__tar.gz

refscan-0.1.2/PKG-INFO

@@ -0,0 +1,256 @@
+Metadata-Version: 2.1
+Name: refscan
+Version: 0.1.2
+Summary: Command-line program that scans the NMDC MongoDB database for referential integrity violations
+Home-page: https://github.com/microbiomedata/refscan
+Keywords: mongodb,mongo,relationships,reference,database,data,referential integrity,scan
+Requires-Python: >=3.10,<4.0
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Dist: linkml-runtime (>=1.7.5,<2.0.0)
+Requires-Dist: pymongo (>=4.7.1,<5.0.0)
+Requires-Dist: rich (>=13.7.1,<14.0.0)
+Requires-Dist: typer (>=0.12.3,<0.13.0)
+Project-URL: Documentation, https://github.com/microbiomedata/refscan
+Project-URL: Repository, https://github.com/microbiomedata/refscan
+Description-Content-Type: text/markdown
+
+# 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
+```
+
+## How it works
+
+`refscan` does its job in two stages:
+1. It uses the LinkML schema to determine "what to scan;" i.e. all of the document-to-document references
+   that _can_ exist in a database that conforms to the schema.
+   > **Example:** The schema might say that, if a document exists in a collection named `cars`, that document must have
+   > a field named `owner` that contains the `id` of a document in a collection named `persons`.
+2. It scans the MongoDB database to check the integrity of all of the references that _do_ exist.
+   > **Example:** For each document in the collection named `cars`, `refscan` checks whether the value in its `owner`
+   > field matches the `id` of some document in the collection named `persons`.
+
+## Limitations
+
+`refscan` was designed under the assumption that **each document 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 of which the document represents an instance**.
+`refscan` relies on that `type` field when determining the name of the class of which a document represents an
+instance; which it does in order to determine "which fields" of that document can contain a reference.
+
+## Usage
+
+### Installation
+
+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`.
+
+### Running
+
+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.          │
+│    --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>
+
+### Updating
+
+You can update the tool to [the latest version available on PyPI](https://pypi.org/project/refscan/) by running:
+
+```shell
+pipx upgrade refscan
+```
+
+### Uninstallation
+
+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) publish packages to PyPI.
+
+- `pyproject.toml`: Configuration file for Poetry and other tools (was generated via `$ poetry init`)
+- `poetry.lock`: List of dependencies, direct and indirect (was generated via `$ poetry update`)
+
+### 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
+```
+
+## 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.
+
+The GitHub Actions workflow will automatically 
+
+### 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.
+

refscan-0.1.2/README.md

@@ -0,0 +1,236 @@
+# 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
+```
+
+## How it works
+
+`refscan` does its job in two stages:
+1. It uses the LinkML schema to determine "what to scan;" i.e. all of the document-to-document references
+   that _can_ exist in a database that conforms to the schema.
+   > **Example:** The schema might say that, if a document exists in a collection named `cars`, that document must have
+   > a field named `owner` that contains the `id` of a document in a collection named `persons`.
+2. It scans the MongoDB database to check the integrity of all of the references that _do_ exist.
+   > **Example:** For each document in the collection named `cars`, `refscan` checks whether the value in its `owner`
+   > field matches the `id` of some document in the collection named `persons`.
+
+## Limitations
+
+`refscan` was designed under the assumption that **each document 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 of which the document represents an instance**.
+`refscan` relies on that `type` field when determining the name of the class of which a document represents an
+instance; which it does in order to determine "which fields" of that document can contain a reference.
+
+## Usage
+
+### Installation
+
+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`.
+
+### Running
+
+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.          │
+│    --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>
+
+### Updating
+
+You can update the tool to [the latest version available on PyPI](https://pypi.org/project/refscan/) by running:
+
+```shell
+pipx upgrade refscan
+```
+
+### Uninstallation
+
+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) publish packages to PyPI.
+
+- `pyproject.toml`: Configuration file for Poetry and other tools (was generated via `$ poetry init`)
+- `poetry.lock`: List of dependencies, direct and indirect (was generated via `$ poetry update`)
+
+### 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
+```
+
+## 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.
+
+The GitHub Actions workflow will automatically 
+
+### 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.

{refscan-0.1.0 → refscan-0.1.2}/pyproject.toml

@@ -2,7 +2,7 @@
 
 [tool.poetry]
 name = "refscan"
-version = "v0.1.0"
+version = "v0.1.2"
 description = "Command-line program that scans the NMDC MongoDB database for referential integrity violations"
 authors = []
 readme = "README.md"

refscan-0.1.2/refscan/__init__.py

@@ -0,0 +1,18 @@
+from importlib.metadata import metadata, PackageMetadata, PackageNotFoundError
+
+
+def get_package_metadata(key: str) -> str:
+    r"""
+    Returns metadata about the installed package.
+
+    References:
+    - https://docs.python.org/3/library/importlib.metadata.html#distribution-metadata
+    - https://github.com/python-poetry/poetry/issues/273#issuecomment-570999678
+    """
+    metadata_value = ""
+    try:
+        package_metadata: PackageMetadata = metadata("refscan")
+        metadata_value = package_metadata.get(key)
+    except PackageNotFoundError:
+        pass
+    return metadata_value

{refscan-0.1.0 → refscan-0.1.2}/refscan/refscan.py

@@ -18,6 +18,7 @@ from refscan.lib.Reference import Reference
 from refscan.lib.ReferenceList import ReferenceList
 from refscan.lib.Violation import Violation
 from refscan.lib.ViolationList import ViolationList
+from refscan import get_package_metadata
 
 app = typer.Typer(
     help="Scans the NMDC MongoDB database for referential integrity violations.",
@@ -25,6 +26,22 @@ app = typer.Typer(
     rich_markup_mode="markdown",  # enables use of Markdown in docstrings and CLI help
 )
 
+app_version = get_package_metadata("Version")
+
+
+def display_app_version_and_exit(is_active: bool = False) -> None:
+    r"""
+    Displays the app's version number, then exists.
+
+    Note: The `is_active` flag will be `True` if the program was
+          invoked with the associated CLI option.
+
+    Reference: https://typer.tiangolo.com/tutorial/options/version/
+    """
+    if is_active:
+        console.print(f"[white]{app_version}[/white]")
+        raise typer.Exit()
+
 
 @app.command("scan")
 def scan(
@@ -47,6 +64,7 @@ def scan(
                  "`$ docker run --rm --detach -p 27017:27017 mongo`",
         )] = "mongodb://localhost:27017",
         verbose: Annotated[bool, typer.Option(
+            "--verbose",
             help="Show verbose output.",
         )] = False,
         # Reference: https://typer.tiangolo.com/tutorial/multiple-values/multiple-options/
@@ -71,6 +89,12 @@ def scan(
             resolve_path=True,
             help="Filesystem path at which you want the program to generate its violation report.",
         )] = "violations.tsv",
+        version: Annotated[Optional[bool], typer.Option(
+            "--version",
+            callback=display_app_version_and_exit,
+            is_eager=True,  # tells Typer to process this option first
+            help="Show version number and exit.",
+        )] = None,
 ):
     """
     Scans the NMDC MongoDB database for referential integrity violations.
@@ -80,9 +104,11 @@ def scan(
         console.print(f"Schema YAML file: {schema_file_path}")
     schema_view = linkml_runtime.SchemaView(schema_file_path)
 
-    # Show high-level information about the schema and LinkML runtime.
-    console.print(f"Schema version:         {schema_view.schema.version}")
-    console.print(f"LinkML runtime version: {linkml_runtime.__version__}")
+    # Show high-level information about the application and schema.
+    console.print(f"refscan version: {app_version}")
+    console.print(f"Schema version: {schema_view.schema.version}")
+
+    console.rule("[bold]Identifying references")
 
     # Make a more self-documenting alias for the CLI option that can be specified multiple times.
     names_of_source_collections_to_skip: list[str] = [] if skip_source_collection is None else skip_source_collection
@@ -158,6 +184,8 @@ def scan(
     if verbose:
         console.print(references.as_table())
 
+    console.rule("[bold]Scanning for violations")
+
     # Get a dictionary that maps source class names to the names of their fields that can contain references.
     reference_field_names_by_source_class_name = references.get_reference_field_names_by_source_class_name()
 
@@ -291,6 +319,8 @@ def scan(
     # Close the connection to the MongoDB server.
     mongo_client.close()
 
+    console.rule("[bold]Results summary")
+
     # Create a violation report in TSV format — for all collections combined.
     all_violations = ViolationList()
     for collection_name, violations in sorted(source_collections_and_their_violations.items(), key=get_lowercase_key):

refscan-0.1.0/PKG-INFO

@@ -1,68 +0,0 @@
-Metadata-Version: 2.1
-Name: refscan
-Version: 0.1.0
-Summary: Command-line program that scans the NMDC MongoDB database for referential integrity violations
-Home-page: https://github.com/microbiomedata/refscan
-Keywords: mongodb,mongo,relationships,reference,database,data,referential integrity,scan
-Requires-Python: >=3.10,<4.0
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Requires-Dist: linkml-runtime (>=1.7.5,<2.0.0)
-Requires-Dist: pymongo (>=4.7.1,<5.0.0)
-Requires-Dist: rich (>=13.7.1,<14.0.0)
-Requires-Dist: typer (>=0.12.3,<0.13.0)
-Project-URL: Documentation, https://github.com/microbiomedata/refscan
-Project-URL: Repository, https://github.com/microbiomedata/refscan
-Description-Content-Type: text/markdown
-
-# refscan
-
-`refscan` is a command-line tool people can use to scan the NMDC 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
-```
-
-## Assumptions
-
-`refscan` was designed under some assumptions about the schema and database, including:
-
-1. Each source document (i.e. document containing references) has a field named `type`, whose value (a string) is the [class_uri](https://linkml.io/linkml/code/metamodel.html#linkml_runtime.linkml_model.meta.ClassDefinition.class_uri) of the schema class of which the document represents an instance. For example, the `type` field of each document in the `study_set` collection has the value `"nmdc:Study"`. 
-
-## Development status
-
-`refscan` is in early development and its author does not recommend anyone use it for anything without reviewing its code first.
-
-## Tips
-
-`refscan` requires the user to specify the path to a schema in YAML format. 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
-```
-

refscan-0.1.0/README.md

@@ -1,48 +0,0 @@
-# refscan
-
-`refscan` is a command-line tool people can use to scan the NMDC 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
-```
-
-## Assumptions
-
-`refscan` was designed under some assumptions about the schema and database, including:
-
-1. Each source document (i.e. document containing references) has a field named `type`, whose value (a string) is the [class_uri](https://linkml.io/linkml/code/metamodel.html#linkml_runtime.linkml_model.meta.ClassDefinition.class_uri) of the schema class of which the document represents an instance. For example, the `type` field of each document in the `study_set` collection has the value `"nmdc:Study"`. 
-
-## Development status
-
-`refscan` is in early development and its author does not recommend anyone use it for anything without reviewing its code first.
-
-## Tips
-
-`refscan` requires the user to specify the path to a schema in YAML format. 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
-```