docs: add exclude include check feature tutorial

docs/source/pages/developers_guide/index.rst

@@ -1,6 +1,8 @@
 .. Copyright (c) 2023 - 2024, Oracle and/or its affiliates. All rights reserved.
 .. Licensed under the Universal Permissive License v 1.0 as shown at https://oss.oracle.com/licenses/upl/.
 
+.. _macaron-developer-guide:
+
 =========================
 Macaron Developer's Guide
 =========================

docs/source/pages/tutorials/detect_malicious_java_dep.rst

@@ -1,6 +1,8 @@
 .. Copyright (c) 2024 - 2024, Oracle and/or its affiliates. All rights reserved.
 .. Licensed under the Universal Permissive License v 1.0 as shown at https://oss.oracle.com/licenses/upl/.
 
+.. _detect-malicious-java-dep:
+
 ------------------------------------------------------------------------
 Detecting a malicious Java dependency uploaded manually to Maven Central
 ------------------------------------------------------------------------

docs/source/pages/tutorials/exclude_include_checks.rst

@@ -0,0 +1,174 @@
+.. Copyright (c) 2024 - 2024, Oracle and/or its affiliates. All rights reserved.
+.. Licensed under the Universal Permissive License v 1.0 as shown at https://oss.oracle.com/licenses/upl/.
+
+=====================================
+Exclude and include checks in Macaron
+=====================================
+
+.. note::
+
+    This feature is only available from Macaron 0.8.0
+
+This tutorial will show how you can configure Macaron to:
+
+* exclude checks that you don't want to run.
+* include only checks that you want to run.
+
+.. note::
+
+    By default, Macaron will run all of its checks.
+
+-------------
+Prerequisites
+-------------
+
+* You are expected to have gone through :ref:`this tutorial <detect-malicious-java-dep>`.
+* This tutorial requires a high-level understanding of checks in Macaron and how they depend on each other. Please see this :ref:`page <macaron-developer-guide>` for more information.
+
+------------------
+Motivating example
+------------------
+
+Let's say you want to run the analysis on Maven artifact ``io.micronaut/micronaut-core`` version ``4.3.10``.
+
+Normally, this is how you would run Macaron:
+
+.. code-block:: shell
+
+  ./run_macaron.sh analyze --package-url pkg:maven/io.micronaut/[email protected] --skip-deps
+
+However, there can be checks in Macaron that are not relevant for the ``io.micronaut/micronaut-core`` artifact.
+For example, the ``mcn_provenance_witness_level_one_1`` check (defined in :class:`ProvenanceWitnessL1Check <macaron.slsa_analyzer.checks.provenance_witness_l1_check.ProvenanceWitnessL1Check>`) is not relevant because ``micronaut-projects/micronaut-core`` generates and publishes :term:`SLSA` provenances and no :term:`Witness` provenances. Therefore, we could exclude this check from running by performing the following steps.
+
+1. In your current directory, create a ``defaults.ini`` configuration file with the following content.
+
+.. code-block:: ini
+
+    [analysis.checks]
+    exclude = mcn_provenance_witness_level_one_1
+    include = *
+
+In the ini configuration above:
+
+* The ``exclude`` option contains the check ID ``mcn_provenance_witness_level_one_1``. The check with this ID will be excluded.
+* The ``include`` option contains the `glob <https://docs.python.org/3/library/glob.html>`_ pattern ``*``. Checks with IDs matching this glob pattern will be included in the analysis. In this case, ``*`` matches all check IDs.
+
+With these two configuration options, all checks except for the excluded ``mcn_provenance_witness_level_one_1`` will run.
+
+2. Run Macaron analyze by providing the path to the custom ``defaults.ini`` configuration.
+
+.. code-block:: shell
+
+  ./run_macaron.sh --defaults-path ./defaults.ini analyze --package-url pkg:maven/io.micronaut/[email protected] --skip-deps
+
+This time, the check ``mcn_provenance_witness_level_one_1`` doesn't run. After the ``analyze`` command finishes, we can view the data that Macaron has gathered about the ``micronaut-projects/micronaut-core`` repository at ``v4.3.10`` in an HTML report. Note that the result of the excluded check is not recorded in the Macaron HTML reports, JSON reports, or the database).
+
+.. code-block:: shell
+
+  open output/reports/maven/io_micronaut/micronaut-core/micronaut-core.html
+
+.. _fig_exclude_provenance_withness_level_one:
+
+
+.. figure:: ../../_static/images/exclude_provenance_withness_level_one.png
+   :alt: Check results for ``io.micronaut/micronaut-core`` version ``4.3.10`` with witness provenance check excluded
+   :align: center
+
+
+------------------------------------------------
+Configuring exclude/include checks in ini config
+------------------------------------------------
+
+You can configure the exclusion and inclusion of checks through the ``[analysis.checks]`` section in the ``defaults.ini`` file. These are the defaults values:
+
+.. code-block:: ini
+
+    [analysis.checks]
+    # By default, we don't exclude any checks.
+    exclude =
+    # By default, we run all checks available.
+    include = *
+
+The ``exclude`` and ``include`` options accept a list of strings (terminated by new lines). Each element in that list can either be:
+
+* An ID of a check
+* A glob pattern (similar to patterns used in `glob <https://docs.python.org/3/library/glob.html>`_). When a glob pattern is given, all check IDs that match it will be included in the corresponding ``exclude`` or ``include`` list.
+
+The two lists of ``exclude`` and ``include`` check IDs obtained from your configuration can be defined as:
+
+* ``EXPLICIT_EXCLUDE`` = checks excluded from the user configuration.
+* ``EXPLICIT_INCLUDE`` = checks included from the user configuration.
+
+Checks in Macaron depend on each other. Therefore, when you want to exclude/include a check, you must be aware of how that will affect its transitive children/parents:
+
+* If a check is excluded, all of the children which can be transitively reached from it will be excluded.
+* If a check is included, all of the parents which can be transitively reached from it will be included.
+
+We define the list of check IDs after extending to transitive parents/children as:
+
+* ``EFFECTIVE_INCLUDED`` = ``EXPLICIT_INCLUDE`` set plus transitive parents
+* ``EFFECTIVE_EXCLUDED`` = ``EXPLICIT_EXCLUDE`` set plus transitive children
+
+The final list of checks that will run can be defined as:
+
+* ``FINAL_INCLUDED`` = ``EFFECTIVE_INCLUDED`` minus ``EFFECTIVE_EXCLUDED``
+
+-------------
+More examples
+-------------
+
+^^^^^^^^^^^^^^^^^^^^^
+Not running any check
+^^^^^^^^^^^^^^^^^^^^^
+The following configurations will result in no check running and Macaron will return on error.
+
+.. code-block:: ini
+
+    [analysis.checks]
+    exclude = *
+    include = *
+
+.. code-block:: ini
+
+    [analysis.checks]
+    exclude =
+    include =
+
+^^^^^^^^^^^^^^^^^^^^^^
+Run a subset of checks
+^^^^^^^^^^^^^^^^^^^^^^
+
+.. code-block:: ini
+
+    [analysis.checks]
+    exclude =
+    include =
+        mcn_provenance_witness_level_one_1
+        mcn_trusted_builder_level_three_1
+
+This will result in ``mcn_provenance_witness_level_one_1``, ``mcn_trusted_builder_level_three_1``, and their transitive parents running.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+Disable a subset of checks
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. code-block:: ini
+
+    [analysis.checks]
+    exclude =
+        mcn_provenance_witness_level_one_1
+        mcn_trusted_builder_level_three_1
+    include = *
+
+This will result in ``mcn_provenance_witness_level_one_1``, ``mcn_trusted_builder_level_three_1``, and their transitive children not running.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Only run checks whose ID starts with ``mcn_build_*``
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. code-block:: ini
+
+    [analysis.checks]
+    exclude =
+    include =
+        mcn_build_*

docs/source/pages/tutorials/index.rst

@@ -19,3 +19,4 @@ For the full list of supported technologies, such as CI services, registries, an
 
    detect_malicious_java_dep
    commit_finder
+   exclude_include_checks