From b9f6b8470eb5d8014a1b6841bc63fb77e2adc79f Mon Sep 17 00:00:00 2001
From: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
Date: Tue, 5 Mar 2024 16:18:10 +0200
Subject: [PATCH 1/5] Truncate logging for sssom

This PR enables truncated logging when log levels is WARNING or lower.
---
 poetry.lock          | 1012 ++++++++++++++++++++----------------------
 src/sssom/cli.py     |   13 +-
 src/sssom/logging.py |   55 +++
 3 files changed, 558 insertions(+), 522 deletions(-)
 create mode 100644 src/sssom/logging.py

diff --git a/poetry.lock b/poetry.lock
index 4dd5a6f1..fec7e224 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.7.0 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
@@ -63,42 +63,45 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
 
 [[package]]
 name = "beautifulsoup4"
-version = "4.12.2"
+version = "4.12.3"
 description = "Screen-scraping library"
 optional = false
 python-versions = ">=3.6.0"
 files = [
-    {file = "beautifulsoup4-4.12.2-py3-none-any.whl", hash = "sha256:bd2520ca0d9d7d12694a53d44ac482d181b4ec1888909b035a3dbf40d0f57d4a"},
-    {file = "beautifulsoup4-4.12.2.tar.gz", hash = "sha256:492bbc69dca35d12daac71c4db1bfff0c876c00ef4a2ffacce226d4638eb72da"},
+    {file = "beautifulsoup4-4.12.3-py3-none-any.whl", hash = "sha256:b80878c9f40111313e55da8ba20bdba06d8fa3969fc68304167741bbf9e082ed"},
+    {file = "beautifulsoup4-4.12.3.tar.gz", hash = "sha256:74e3d1928edc070d21748185c46e3fb33490f22f52a3addee9aee0f4f7781051"},
 ]
 
 [package.dependencies]
 soupsieve = ">1.2"
 
 [package.extras]
+cchardet = ["cchardet"]
+chardet = ["chardet"]
+charset-normalizer = ["charset-normalizer"]
 html5lib = ["html5lib"]
 lxml = ["lxml"]
 
 [[package]]
 name = "cachetools"
-version = "5.3.2"
+version = "5.3.3"
 description = "Extensible memoizing collections and decorators"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "cachetools-5.3.2-py3-none-any.whl", hash = "sha256:861f35a13a451f94e301ce2bec7cac63e881232ccce7ed67fab9b5df4d3beaa1"},
-    {file = "cachetools-5.3.2.tar.gz", hash = "sha256:086ee420196f7b2ab9ca2db2520aca326318b68fe5ba8bc4d49cca91add450f2"},
+    {file = "cachetools-5.3.3-py3-none-any.whl", hash = "sha256:0abad1021d3f8325b2fc1d2e9c8b9c9d57b04c3932657a72465447332c24d945"},
+    {file = "cachetools-5.3.3.tar.gz", hash = "sha256:ba29e2dfa0b8b556606f097407ed1aa62080ee108ab0dc5ec9d6a723a007d105"},
 ]
 
 [[package]]
 name = "certifi"
-version = "2023.11.17"
+version = "2024.2.2"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2023.11.17-py3-none-any.whl", hash = "sha256:e036ab49d5b79556f99cfc2d9320b34cfbe5be05c5871b51de9329f0603b0474"},
-    {file = "certifi-2023.11.17.tar.gz", hash = "sha256:9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1"},
+    {file = "certifi-2024.2.2-py3-none-any.whl", hash = "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1"},
+    {file = "certifi-2024.2.2.tar.gz", hash = "sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f"},
 ]
 
 [[package]]
@@ -238,13 +241,13 @@ files = [
 
 [[package]]
 name = "curies"
-version = "0.7.4"
+version = "0.7.7"
 description = "Idiomatic conversion between URIs and compact URIs (CURIEs)."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "curies-0.7.4-py3-none-any.whl", hash = "sha256:478f1818345988933d8bc6060f80a985401331f856ff8cf9bd98fa00d178ad39"},
-    {file = "curies-0.7.4.tar.gz", hash = "sha256:d3aaf16644b26ac2605ff83c565ec7df0ba0b5f7425516047666e609ec5fb718"},
+    {file = "curies-0.7.7-py3-none-any.whl", hash = "sha256:609de3e8cdf39f410e8f4d9f06eb7df379465860f4fb441bf0e79672430f8e2a"},
+    {file = "curies-0.7.7.tar.gz", hash = "sha256:a8d674029f906fb9c3564eafa0862ce96725932bd801fa751e076265b111cb34"},
 ]
 
 [package.dependencies]
@@ -315,13 +318,12 @@ files = [
 
 [[package]]
 name = "editorconfig"
-version = "0.12.3"
+version = "0.12.4"
 description = "EditorConfig File Locator and Interpreter for Python"
 optional = false
 python-versions = "*"
 files = [
-    {file = "EditorConfig-0.12.3-py3-none-any.whl", hash = "sha256:6b0851425aa875b08b16789ee0eeadbd4ab59666e9ebe728e526314c4a2e52c1"},
-    {file = "EditorConfig-0.12.3.tar.gz", hash = "sha256:57f8ce78afcba15c8b18d46b5170848c88d56fd38f05c2ec60dbbfcb8996e89e"},
+    {file = "EditorConfig-0.12.4.tar.gz", hash = "sha256:24857fa1793917dd9ccf0c7810a07e05404ce9b823521c7dce22a4fb5d125f80"},
 ]
 
 [[package]]
@@ -373,76 +375,74 @@ dev = ["flake8", "markdown", "twine", "wheel"]
 
 [[package]]
 name = "greenlet"
-version = "2.0.1"
+version = "3.0.3"
 description = "Lightweight in-process concurrent programming"
 optional = false
-python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*"
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 ]
 
 [package.extras]
-docs = ["Sphinx", "docutils (<0.18)"]
-test = ["faulthandler", "objgraph", "psutil"]
+docs = ["Sphinx", "furo"]
+test = ["objgraph", "psutil"]
 
 [[package]]
 name = "hbreader"
@@ -498,13 +498,13 @@ testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs
 
 [[package]]
 name = "importlib-resources"
-version = "6.1.1"
+version = "6.1.2"
 description = "Read resources from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -512,7 +512,7 @@ zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
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+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)", "zipp (>=3.17)"]
 
 [[package]]
 name = "iniconfig"
@@ -558,12 +558,12 @@ i18n = ["Babel (>=2.7)"]
 
 [[package]]
 name = "jsbeautifier"
-version = "1.14.11"
+version = "1.15.1"
 description = "JavaScript unobfuscator and beautifier."
 optional = false
 python-versions = "*"
 files = [
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 ]
 
 [package.dependencies]
@@ -601,13 +601,13 @@ hbreader = "*"
 
 [[package]]
 name = "jsonschema"
-version = "4.20.0"
+version = "4.21.1"
 description = "An implementation of JSON Schema validation for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -639,13 +639,13 @@ referencing = ">=0.31.0"
 
 [[package]]
 name = "linkml-runtime"
-version = "1.6.3"
+version = "1.7.2"
 description = "Runtime environment for LinkML, the Linked open data modeling language"
 optional = false
-python-versions = ">=3.7.6,<4.0.0"
+python-versions = ">=3.8,<4.0"
 files = [
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 ]
 
 [package.dependencies]
@@ -707,71 +707,71 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 
 [[package]]
 name = "markupsafe"
-version = "2.1.3"
+version = "2.1.5"
 description = "Safely add untrusted strings to HTML/XML markup."
 optional = false
 python-versions = ">=3.7"
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 [[package]]
@@ -848,13 +848,13 @@ min-versions = ["babel (==2.9.0)", "click (==7.0)", "colorama (==0.4)", "ghp-imp
 
 [[package]]
 name = "mkdocs-material"
-version = "9.5.3"
+version = "9.5.12"
 description = "Documentation that simply works"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [[package]]
@@ -1046,8 +1046,8 @@ files = [
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 pytz = ">=2020.1"
@@ -1116,28 +1116,28 @@ files = [
 
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+version = "4.2.0"
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 python-versions = ">=3.8"
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 [[package]]
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 [[package]]
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 [package.dependencies]
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 typing-extensions = ">=4.6.1"
 
 [package.extras]
@@ -1204,116 +1197,90 @@ email = ["email-validator (>=2.0.0)"]
 
 [[package]]
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 [package.dependencies]
@@ -1336,13 +1303,13 @@ windows-terminal = ["colorama (>=0.4.6)"]
 
 [[package]]
 name = "pymdown-extensions"
-version = "10.7"
+version = "10.7.1"
 description = "Extension pack for Python Markdown."
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -1387,13 +1354,13 @@ testing = ["covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytes
 
 [[package]]
 name = "pytest"
-version = "7.4.4"
+version = "8.0.2"
 description = "pytest: simple powerful testing with Python"
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 [package.dependencies]
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 iniconfig = "*"
 packaging = "*"
-pluggy = ">=0.12,<2.0"
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 tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
 
 [package.extras]
@@ -1422,13 +1389,13 @@ pytest = ">=2.8.1"
 
 [[package]]
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 [package.dependencies]
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 [[package]]
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+version = "2024.1"
 description = "World timezone definitions, modern and historical"
 optional = false
 python-versions = "*"
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 [[package]]
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 [[package]]
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-version = "0.32.1"
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 [[package]]
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-version = "0.16.2"
+version = "0.18.0"
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@@ -1839,19 +1806,19 @@ test = ["asv", "gmpy2", "mpmath", "pytest", "pytest-cov", "pytest-xdist", "sciki
 
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 ]
 
 [package.extras]
diff --git a/src/sssom/cli.py b/src/sssom/cli.py
index 5beb4828..e77184b4 100644
--- a/src/sssom/cli.py
+++ b/src/sssom/cli.py
@@ -32,6 +32,7 @@
     SchemaValidationType,
     _get_sssom_schema_object,
 )
+from sssom.logging import SSSOMLogger
 
 from . import __version__
 from .cliques import split_into_cliques, summarize_cliques
@@ -61,6 +62,7 @@
 )
 from .writers import WRITER_FUNCTIONS, write_table
 
+_logging.setLoggerClass(SSSOMLogger)
 logging = _logging.getLogger(__name__)
 
 SSSOM_SV_OBJECT = _get_sssom_schema_object()
@@ -159,6 +161,7 @@ def convert(input: str, output: TextIO, output_format: str):
         sssom convert my.sssom.tsv --output-format rdfxml --output my.sssom.owl
     """  # noqa: DAR101
     convert_file(input_path=input, output=output, output_format=output_format)
+    _log_summary()
 
 
 # Input and metadata would be files (file paths). Check if exists.
@@ -399,6 +402,7 @@ def diff(inputs: Tuple[str, str], output: TextIO):
         f"Diff between {input1} and {input2}. See comment column for information."
     )
     write_table(msdf, output)
+    _log_summary()
 
 
 @main.command()
@@ -632,6 +636,12 @@ def sort(input: str, output: TextIO, by_columns: bool, by_rows: bool):
 #     write_table(msdf=filtered_msdf, file=output)
 
 
+def _log_summary():
+    logger = _logging.getLogger()
+    if isinstance(logger, SSSOMLogger):
+        logger.print_summary()
+
+
 def dynamically_generate_sssom_options(options) -> Callable[[Any], Any]:
     """Dynamically generate click options.
 
@@ -729,7 +739,8 @@ def remove(input: str, output: TextIO, remove_map: str):
     "--merge-inverted/--no-merge-inverted",
     default=True,
     is_flag=True,
-    help="If True (default), add inverted mappings to the input mapping set, else, just return inverted mappings as a separate mapping set.",
+    help="If True (default), add inverted mappings to the input mapping set, "
+    "else, just return inverted mappings as a separate mapping set.",
 )
 @click.option("--inverse-map", help="Path to file that contains the inverse predicate dictionary.")
 def invert(
diff --git a/src/sssom/logging.py b/src/sssom/logging.py
new file mode 100644
index 00000000..0e65ad52
--- /dev/null
+++ b/src/sssom/logging.py
@@ -0,0 +1,55 @@
+"""Logging utilities for sssom-py."""
+
+import logging
+from logging import NOTSET, WARNING, Logger
+
+
+class SSSOMLogger(Logger):
+    """Custom logger for SSSOM."""
+
+    def __init__(self, name, level=NOTSET, truncate_log_messages=20):
+        """Construct SSSOM logger, including truncate_log_messages parameter to truncate messages."""
+        super().__init__(name, level)
+        self.count_logs = {}
+        self.truncate_log_messages = truncate_log_messages
+
+    def _log(self, level, msg, args, exc_info=None, extra=None, stack_info=False, stacklevel=1):
+        # You can check the current log level here and modify the message or add extra information.
+
+        log_id = extra.get("log_id") if extra else None
+        if log_id:
+            self._count_up(log_id)
+            log_type_printed_count = self.count_logs[log_id]
+        else:
+            log_type_printed_count = 0
+
+        block_logging = False
+
+        if level >= self.level:
+            # Add custom behavior based on the log level
+            if level <= WARNING and log_type_printed_count > self.truncate_log_messages:
+                # If the loglevel is WARNING or less (DEBUG, INFO) and we have already recorded more than
+                # the configured truncate_log_messages limit
+                block_logging = True
+
+        # Call the original _log method to actually log the message
+        if not block_logging:
+            super()._log(level, msg, args, exc_info, extra, stack_info, stacklevel)
+
+    def _count_up(self, log_id):
+        if log_id in self.count_logs:
+            self.count_logs[log_id] = self.count_logs[log_id] + 1
+        else:
+            self.count_logs[log_id] = 1
+
+    def print_summary(self):
+        """Log a warning if any errors were truncated."""
+        outstring = "Summary of errors logged.+\n"
+        truncated = False
+        for log_id in self.count_logs:
+            truncated = True
+            outstring += f"{log_id}: {self.count_logs[log_id]} errors\n"
+        if self.level <= WARNING and truncated:
+            outstring += f"Some errors which were logged more than {self.truncate_log_messages} times were truncated."
+        if truncated:
+            logging.warning(outstring)

From af379ce3569cc9988c8c367425743e6dc9e4b233 Mon Sep 17 00:00:00 2001
From: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
Date: Tue, 5 Mar 2024 16:21:36 +0200
Subject: [PATCH 2/5] Update parsers.py

---
 src/sssom/parsers.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/sssom/parsers.py b/src/sssom/parsers.py
index 94cfd005..6eeefb50 100644
--- a/src/sssom/parsers.py
+++ b/src/sssom/parsers.py
@@ -916,8 +916,7 @@ def _ensure_valid_mapping_from_dict(mdict: Dict[str, Any]):
         m = Mapping(**mdict)
     except ValueError as e:
         logging.warning(
-            f"One mapping in the mapping set is not well-formed, "
-            f"and therfore not included in the mapping set ({mdict}). Error: {e}"
+            f"{mdict} not well-formed: {e}"
         )
         return None
     else:

From 4bdd0e04e0d7ef0dbb66707cff6e49fd30a5ce12 Mon Sep 17 00:00:00 2001
From: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
Date: Tue, 5 Mar 2024 16:23:14 +0200
Subject: [PATCH 3/5] Update parsers.py

---
 src/sssom/parsers.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/sssom/parsers.py b/src/sssom/parsers.py
index 6eeefb50..a988c345 100644
--- a/src/sssom/parsers.py
+++ b/src/sssom/parsers.py
@@ -916,7 +916,8 @@ def _ensure_valid_mapping_from_dict(mdict: Dict[str, Any]):
         m = Mapping(**mdict)
     except ValueError as e:
         logging.warning(
-            f"{mdict} not well-formed: {e}"
+            f"{mdict} not well-formed: {e}",
+            extra={"log_id": "mapping-not-wellformed"}
         )
         return None
     else:

From 20fe9b2f3ae9f70e4b8cdc620a858cfee422726d Mon Sep 17 00:00:00 2001
From: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
Date: Tue, 5 Mar 2024 16:23:58 +0200
Subject: [PATCH 4/5] Update parsers.py

---
 src/sssom/parsers.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/src/sssom/parsers.py b/src/sssom/parsers.py
index a988c345..11820e20 100644
--- a/src/sssom/parsers.py
+++ b/src/sssom/parsers.py
@@ -915,10 +915,7 @@ def _ensure_valid_mapping_from_dict(mdict: Dict[str, Any]):
     try:
         m = Mapping(**mdict)
     except ValueError as e:
-        logging.warning(
-            f"{mdict} not well-formed: {e}",
-            extra={"log_id": "mapping-not-wellformed"}
-        )
+        logging.warning(f"{mdict} not well-formed: {e}", extra={"log_id": "mapping-not-wellformed"})
         return None
     else:
         return m

From 6a6715207453451eb2b74df471a3f3c546ef03c0 Mon Sep 17 00:00:00 2001
From: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
Date: Tue, 5 Mar 2024 16:31:30 +0200
Subject: [PATCH 5/5] Update parsers.py

---
 src/sssom/parsers.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/sssom/parsers.py b/src/sssom/parsers.py
index 11820e20..eebd3573 100644
--- a/src/sssom/parsers.py
+++ b/src/sssom/parsers.py
@@ -915,7 +915,9 @@ def _ensure_valid_mapping_from_dict(mdict: Dict[str, Any]):
     try:
         m = Mapping(**mdict)
     except ValueError as e:
-        logging.warning(f"{mdict} not well-formed: {e}", extra={"log_id": "mapping-not-wellformed"})
+        logging.warning(
+            msg=f"{mdict} not well-formed: {e}", extra={"log_id": "mapping-not-wellformed"}
+        )
         return None
     else:
         return m