refscan 0.4.1__tar.gz → 0.4.3__tar.gz

{refscan-0.4.1 → refscan-0.4.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: refscan
-Version: 0.4.1
+Version: 0.4.3
 Summary: Command-line program that scans the NMDC MongoDB database for referential integrity violations
 Keywords: mongodb,mongo,relationships,reference,database,data,referential integrity,scan
 Requires-Dist: linkml-runtime>=1.7.5,<2
@@ -36,7 +36,7 @@ graph LR
     classDef dashed_border stroke-dasharray: 5 5
 ```
 
-In addition to using refscan to scan the NMDC MongoDB database for referential integrity violations,
+In addition to using `refscan` to scan the NMDC MongoDB database for referential integrity violations,
 people can use `refscan` to generate **graphs** (diagrams) depicting which collections' documents (or which classes'
 instances) can contain references to which _other_ collections' documents (or classes' instances) while still being
 schema compliant.
@@ -60,6 +60,7 @@ Here is a summary of how each of `refscan`'s main functions works under the hood
 ### Graph
 
 `refscan` does this in three stages:
+
 1. It uses the LinkML schema to determine where references _can_ exist in a MongoDB database that conforms to the schema.
 2. It formats that list of references into a data structure compatible with [`Cytoscape.js`](https://js.cytoscape.org/).
 3. It outputs an HTML document that uses `Cytoscape.js` to visualize that data structure as a graph.
@@ -261,6 +262,18 @@ You can uninstall the tool from your computer by running:
 pipx uninstall refscan
 ```
 
+### Container-based usage
+
+You can also run `refscan` via a container image hosted by the [GitHub Container Registry](https://github.com/microbiomedata/refscan/pkgs/container/refscan).
+
+```shell
+docker run --rm -it refscan --help
+```
+
+> Note: When running `refscan` via a container image, you can reference your host machine via the [special hostname](https://docs.docker.com/desktop/troubleshoot-and-support/faqs/general/#how-do-i-connect-from-a-container-to-a-service-on-the-host), "`host.docker.internal`".
+> 
+> In other words, `$ docker run refscan --mongo-uri mongodb://host.docker.internal:27017` does the same thing as `$ refscan --mongo-uri mongodb://localhost:27017`, except the first command runs `refscan` within a container while the second one runs it directly on your hose machine.
+
 ## Development
 
 We use [`uv`](https://docs.astral.sh/uv/) to both (a) manage dependencies and (b) build distributable packages that can be published to PyPI.

{refscan-0.4.1 → refscan-0.4.3}/README.md

@@ -21,7 +21,7 @@ graph LR
     classDef dashed_border stroke-dasharray: 5 5
 ```
 
-In addition to using refscan to scan the NMDC MongoDB database for referential integrity violations,
+In addition to using `refscan` to scan the NMDC MongoDB database for referential integrity violations,
 people can use `refscan` to generate **graphs** (diagrams) depicting which collections' documents (or which classes'
 instances) can contain references to which _other_ collections' documents (or classes' instances) while still being
 schema compliant.
@@ -45,6 +45,7 @@ Here is a summary of how each of `refscan`'s main functions works under the hood
 ### Graph
 
 `refscan` does this in three stages:
+
 1. It uses the LinkML schema to determine where references _can_ exist in a MongoDB database that conforms to the schema.
 2. It formats that list of references into a data structure compatible with [`Cytoscape.js`](https://js.cytoscape.org/).
 3. It outputs an HTML document that uses `Cytoscape.js` to visualize that data structure as a graph.
@@ -246,6 +247,18 @@ You can uninstall the tool from your computer by running:
 pipx uninstall refscan
 ```
 
+### Container-based usage
+
+You can also run `refscan` via a container image hosted by the [GitHub Container Registry](https://github.com/microbiomedata/refscan/pkgs/container/refscan).
+
+```shell
+docker run --rm -it refscan --help
+```
+
+> Note: When running `refscan` via a container image, you can reference your host machine via the [special hostname](https://docs.docker.com/desktop/troubleshoot-and-support/faqs/general/#how-do-i-connect-from-a-container-to-a-service-on-the-host), "`host.docker.internal`".
+> 
+> In other words, `$ docker run refscan --mongo-uri mongodb://host.docker.internal:27017` does the same thing as `$ refscan --mongo-uri mongodb://localhost:27017`, except the first command runs `refscan` within a container while the second one runs it directly on your hose machine.
+
 ## Development
 
 We use [`uv`](https://docs.astral.sh/uv/) to both (a) manage dependencies and (b) build distributable packages that can be published to PyPI.

{refscan-0.4.1 → refscan-0.4.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "refscan"
-version = "0.4.1"
+version = "0.4.3"
 description = "Command-line program that scans the NMDC MongoDB database for referential integrity violations"
 authors = []
 requires-python = ">= 3.9, < 4.0"

{refscan-0.4.1 → refscan-0.4.3}/refscan/scanner.py

@@ -322,6 +322,18 @@ def scan(
                 remaining_time_label="remaining",
             )
 
+            # If the console is not connected to a device capable of understanding escape characters
+            # (in which case, Rich won't try to display the progress bar), print a message indicating
+            # that we are starting to scan this collection.
+            #
+            # Note: This output can serve as a "sign of life" for a user, when, for example, refscan is
+            #       running in a Kubernetes CronJob where `tty` is `false` (i.e. `tty: false`).
+            #
+            # Reference: https://rich.readthedocs.io/en/stable/reference/console.html#rich.console.Console.is_terminal
+            #
+            if not console.is_terminal:
+                console.print(f"Scanning collection '{source_collection_name}' ({num_relevant_documents} documents).")
+
             # Advance the progress bar by 0 (this makes it so that, even if there are 0 relevant documents, the progress
             # bar does not continue incrementing its "elapsed time" even after a subsequent task has begun).
             progress.update(task_id, advance=0)