refscan 0.1.2__tar.gz → 0.1.4__tar.gz

{refscan-0.1.2 → refscan-0.1.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: refscan
-Version: 0.1.2
+Version: 0.1.4
 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

{refscan-0.1.2 → refscan-0.1.4}/pyproject.toml

@@ -2,7 +2,7 @@
 
 [tool.poetry]
 name = "refscan"
-version = "v0.1.2"
+version = "v0.1.4"
 description = "Command-line program that scans the NMDC MongoDB database for referential integrity violations"
 authors = []
 readme = "README.md"

{refscan-0.1.2 → refscan-0.1.4}/refscan/lib/helpers.py

@@ -3,6 +3,7 @@ from functools import cache
 
 from pymongo import MongoClient, timeout
 from linkml_runtime import SchemaView
+from rich.console import Console
 from rich.progress import (
     Progress,
     TextColumn,
@@ -121,3 +122,15 @@ def init_progress_bar() -> Progress:
 def get_lowercase_key(key_value_pair: tuple) -> str:
     r"""Returns the key from a `(key, value)` tuple, in lowercase."""
     return key_value_pair[0].lower()
+
+
+def print_section_header(console: Console, text: str) -> None:
+    r"""
+    Helper function that prints a vertically-padded,
+    labeled, horizontal rule to the specified console.
+
+    Reference: https://rich.readthedocs.io/en/stable/console.html#rules
+    """
+    console.print("")
+    console.rule(f"[bold]{text}[/bold]")
+    console.print("")

{refscan-0.1.2 → refscan-0.1.4}/refscan/refscan.py

@@ -4,6 +4,7 @@ from typing_extensions import Annotated
 
 import typer
 import linkml_runtime
+from rich import padding
 
 from refscan.lib.Finder import Finder
 from refscan.lib.constants import DATABASE_CLASS_NAME, console
@@ -13,6 +14,7 @@ from refscan.lib.helpers import (
     derive_schema_class_name_from_document,
     init_progress_bar,
     get_lowercase_key,
+    print_section_header,
 )
 from refscan.lib.Reference import Reference
 from refscan.lib.ReferenceList import ReferenceList
@@ -108,7 +110,8 @@ def scan(
     console.print(f"refscan version: {app_version}")
     console.print(f"Schema version: {schema_view.schema.version}")
 
-    console.rule("[bold]Identifying references")
+    # Show a header on the console, to tell the user which stage of execution we're entering.
+    print_section_header(console, text="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
@@ -174,7 +177,7 @@ def scan(
                                                   target_class_name=name_of_eligible_target_class)
                             references.append(reference)
 
-    console.print(f"Slot-to-ID references described by schema: {len(references)}")
+    console.print(f"References described by schema: {len(references)}")
 
     # Create a reference report in TSV format.
     console.print(f"Writing reference report: {reference_report_file_path}")
@@ -184,7 +187,7 @@ def scan(
     if verbose:
         console.print(references.as_table())
 
-    console.rule("[bold]Scanning for violations")
+    print_section_header(console, text="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()
@@ -319,7 +322,7 @@ def scan(
     # Close the connection to the MongoDB server.
     mongo_client.close()
 
-    console.rule("[bold]Results summary")
+    print_section_header(console, text="Summarizing results")
 
     # Create a violation report in TSV format — for all collections combined.
     all_violations = ViolationList()