Implement ensembl-py logging

.github/workflows/mkdocs_docs_generation.yaml → .github/workflows/mkdocs_docs_generation.yml

@@ -1,3 +1,17 @@
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 name: Documentation_deploy_mkdocs
 run-name: ${{ github.actor }} triggered mkdocs generation
 on:

docs/gen_ref_pages.py

@@ -4,8 +4,10 @@
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
+#
 # http://www.apache.org/licenses/LICENSE-2.0
 #
+#
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

docs/index.md

@@ -1,6 +1,6 @@
 # [Ensembl GenomIO](https://github.com/Ensembl/ensembl-genomio)
 
-*Ensembl-genomIO Base Library Documentation*
+*Ensembl GenomIO Base Library Documentation*
 
 A repository dedicated to pipelines used to turn basic genomic data into formatted 
 Ensembl core databases. Also allow users to dump core databases into various formats.

mkdocs.yml

@@ -13,10 +13,13 @@
 # limitations under the License.
 
 site_name: Ensembl-GenomIO
+site_url: "https://ensembl.github.io/ensembl-genomio"
+repo_url: "https://github.com/Ensembl/ensembl-genomio"
+repo_name: "Ensembl-GenomIO"
+copyright: Copyright © [2016-2023] EMBL-European Bioinformatics Institute
 
 theme:
   name: "material"
-  logo: img/logo.png
 
 plugins:
 - search

pipelines/nextflow/modules/download/download_asm_data.nf

@@ -36,6 +36,6 @@ process DOWNLOAD_ASM_DATA {
 
     shell:
         '''
-        assembly_download --accession !{meta.accession} --asm_download_dir ./
+        assembly_download --accession !{meta.accession} --download_dir ./ --verbose
         '''
 }

pipelines/nextflow/modules/events/dump_events.nf

@@ -33,6 +33,7 @@ process DUMP_EVENTS {
             --user '${server.user}' \
             --password '${server.password}' \
             --database '${db.database}' \
-            --output_file "events.txt"
+            --output_file "events.txt" \
+            --verbose
         """
 }

pipelines/nextflow/modules/genome_metadata/dump_genome_meta.nf

@@ -33,6 +33,7 @@ process DUMP_GENOME_META {
             --user '${server.user}' \
             --password '${server.password}' \
             --database '${db.database}' \
+            --verbose \
             > genome.json
         """
 }

pipelines/nextflow/modules/genome_metadata/compare_genome_stats.nf → pipelines/nextflow/modules/genome_stats/compare_genome_stats.nf

@@ -27,6 +27,6 @@ process COMPARE_GENOME_STATS {
 
     script:
         """
-        genome_stats_compare --ncbi $ncbi_stats --core $core_stats > diff_stats.json
+        genome_stats_compare --ncbi $ncbi_stats --core $core_stats --verbose > diff_stats.json
         """
 }

pipelines/nextflow/modules/manifest/check_integrity_db.nf

@@ -29,6 +29,6 @@ process CHECK_INTEGRITY {
     script:
         brc_mode = params.brc_mode ? '--brc_mode' : ''
         """
-        manifest_check_integrity --manifest_file ${manifest_dir}/manifest.json $brc_mode
+        manifest_check_integrity --manifest_file ${manifest_dir}/manifest.json $brc_mode --verbose
         """
 }

pipelines/nextflow/modules/patch_build/load_events.nf

@@ -29,6 +29,7 @@ process LOAD_EVENTS {
     --password $server.password \\
     --database $server.database \\
     --input_file $events \\
-    --update
+    --update \\
+    --verbose
     """
 }

pipelines/nextflow/subworkflows/dump_metadata/main.nf

@@ -16,11 +16,10 @@
 include { DUMP_SEQ_REGIONS } from '../../modules/seq_region/dump_seq_regions.nf'
 include { DUMP_EVENTS } from '../../modules/events/dump_events.nf'
 include { DUMP_GENOME_META } from '../../modules/genome_metadata/dump_genome_meta.nf'
-include { DUMP_GENOME_STATS } from '../../modules/genome_metadata/dump_genome_stats.nf'
-include { COMPARE_GENOME_STATS } from '../../modules/genome_metadata/compare_genome_stats.nf'
+include { DUMP_GENOME_STATS } from '../../modules/genome_stats/dump_genome_stats.nf'
+include { COMPARE_GENOME_STATS } from '../../modules/genome_stats/compare_genome_stats.nf'
 include { DUMP_NCBI_STATS } from '../../modules/genome_metadata/dump_ncbi_stats.nf'
 include { CHECK_JSON_SCHEMA } from '../../modules/schema/check_json_schema_db.nf'
-
 include { COLLECT_FILES } from '../../modules/files/collect_files_db.nf'
 include { MANIFEST } from '../../modules/files/collect_files_db.nf'
 include { PUBLISH_DIR } from '../../modules/files/collect_files_db.nf'

pyproject.toml

@@ -48,7 +48,7 @@ dependencies = [
     "bcbio-gff == 0.7.0",
     "biopython == 1.81",
     "ensembl-hive @ git+https://github.com/Ensembl/ensembl-hive.git",
-    "ensembl-py @ git+https://github.com/Ensembl/ensembl-py.git",  # minimum v1.2.0
+    "ensembl-py @ git+https://github.com/Ensembl/ensembl-py.git",  # minimum v1.2.1
     "jsonschema >= 4.6.0",
     "importlib_resources",  # not needed from Python 3.9+
     "intervaltree >= 3.1.0",
@@ -83,6 +83,7 @@ doc = [
 [project.urls]
 homepage = "https://www.ensembl.org"
 repository = "https://github.com/Ensembl/ensembl-genomio"
+documentation = "https://ensembl.github.io/ensembl-genomio"
 
 [project.scripts]
 # Assembly

src/python/ensembl/brc4/runnable/core_server.py

@@ -17,6 +17,7 @@
 import argparse
 import re
 from typing import Dict, List, Any
+import logging
 
 import mysql.connector
 
@@ -55,7 +56,11 @@ def connect(self) -> None:
         )
 
     def set_database(self, db_name: str) -> None:
-        self._connector.database = db_name
+        try:
+            self._connector.database = db_name
+        except mysql.connector.errors.ProgrammingError:
+            logging.exception(f"Unknown database ! DB:'{db_name}' not located on host {self.host}")
+            raise
 
     def get_cursor(self):
         return self._connector.cursor()
@@ -90,6 +95,10 @@ def get_cores(
 
         dbs = self.get_all_cores()
 
+        # Check if there are databases returned from query to host
+        if not dbs:
+            logging.warning("No databases returned from query")
+
         if prefix:
             dbs = [db for db in dbs if db.startswith(f"{prefix}")]
         if dbname_re:

src/python/ensembl/io/genomio/assembly/download.py

@@ -36,7 +36,7 @@
 from typing import Dict
 
 from ensembl.utils.argparse import ArgumentParser
-
+from ensembl.utils.logging import init_logging
 
 _FILE_ENDS = {
     "assembly_report.txt": "report",
@@ -281,6 +281,10 @@ def main() -> None:
     parser.add_argument_dst_path(
         "--download_dir", default=Path.cwd(), help="Folder where the data will be downloaded"
     )
+    parser.add_log_arguments(add_log_file=True)
     args = parser.parse_args()
 
-    retrieve_assembly_data(**vars(args))
+    # Configure and initialise logging
+    init_logging(args.log_level, args.log_file, args.log_file_level)
+
+    retrieve_assembly_data(args.accession, args.download_dir)

src/python/ensembl/io/genomio/events/dump.py

@@ -17,9 +17,11 @@
 from datetime import datetime
 from pathlib import Path
 from typing import List, Dict, Optional, Set, Tuple
+import logging
 
 from ensembl.brc4.runnable.core_server import CoreServer
 from ensembl.utils.argparse import ArgumentParser
+from ensembl.utils.logging import init_logging
 
 
 BRC4_START_DATE = datetime(2020, 5, 1)
@@ -307,7 +309,7 @@ def get_history(self) -> List:
 
         events = []
         for session in sessions:
-            print(f"Mapping session {session['release']}")
+            logging.info(f"Mapping session {session['release']}")
             pairs = self.get_pairs(session["id"])
             session_events = self.make_events(pairs)
             for event in session_events:
@@ -327,7 +329,7 @@ def print_events(self, events: List[StableIdEvent], output_file: Path) -> None:
 
         """
         if not events:
-            print("No events to print")
+            logging.info("No events to print")
             return
         with output_file.open("w") as out_fh:
             for event in events:
@@ -379,7 +381,7 @@ def get_pairs(self, session_id: int) -> List[Pair]:
         for db in cursor:
             pair = Pair(old_id=db[0], new_id=db[1])
             pairs.append(pair)
-        print(f"{len(pairs)} stable id events")
+        logging.debug(f"{len(pairs)} stable id events")
         return pairs
 
     def make_events(self, pairs: List[Pair]) -> List:
@@ -423,7 +425,7 @@ def make_events(self, pairs: List[Pair]) -> List:
                 stats[name] += 1
 
         for stat, value in stats.items():
-            print(f"\t{stat} = {value}")
+            logging.info(f"\t{stat} = {value}")
 
         return events
 
@@ -525,8 +527,12 @@ def main() -> None:
     )
     parser.add_server_arguments(include_database=True)
     parser.add_argument_dst_path("--output_file", required=True, help="Output file")
+    parser.add_log_arguments(add_log_file=True)
     args = parser.parse_args()
 
+    # Configure and initialise logging
+    init_logging(args.log_level, args.log_file, args.log_file_level)
+
     # Start
     factory = CoreServer(host=args.host, port=args.port, user=args.user, password=args.password)
     factory.set_database(args.database)

src/python/ensembl/io/genomio/events/load.py

@@ -21,13 +21,15 @@
 from os import PathLike
 from pathlib import Path
 import re
+import logging
 from typing import Dict, Generator, List, Optional, Tuple
 
 from sqlalchemy.orm import Session
 
 from ensembl.database import DBConnection
 from ensembl.core.models import MappingSession, StableIdEvent
 from ensembl.utils.argparse import ArgumentParser
+from ensembl.utils.logging import init_logging
 
 
 @dataclass
@@ -64,7 +66,7 @@ def add_event(self, event: IdEvent) -> None:
 
 
 class EventCollection:
-    """ "Collection of events with loader/writer in various formats."""
+    """Collection of events with loader/writer in various formats."""
 
     def __init__(self) -> None:
         self.events: List[IdEvent] = []
@@ -143,7 +145,7 @@ def _parse_gene_diff_event(self, event_string: str) -> Generator[Tuple[str, str,
         splitter = f"({event_sep})"
         parts = re.split(splitter, event_string)
         if len(parts) != 3:
-            print(f"Wrong partition: from '{event_string}' to '{parts}'")
+            logging.warning(f"Wrong partition: from '{event_string}' to '{parts}'")
             return
         [from_ids, sep, to_ids] = parts
         event_name = event_symbol[sep]
@@ -165,7 +167,7 @@ def remap_to_ids(self, map_dict: Dict[str, str]):
             elif event.to_id in map_dict:
                 event.to_id = map_dict[event.to_id]
             else:
-                print(f"No map for to_id {event.to_id}")
+                logging.info(f"No map for to_id {event.to_id}")
                 no_map += 1
 
         if no_map:
@@ -174,7 +176,7 @@ def remap_to_ids(self, map_dict: Dict[str, str]):
     def write_events_to_file(self, output_file: PathLike) -> None:
         """Write the events to a file."""
         with Path(output_file).open("w") as out_fh:
-            print(f"Write {len(self.events)} events to {output_file}")
+            logging.info(f"Write {len(self.events)} events to {output_file}")
             for event in self.events:
                 out_fh.write(f"{event}\n")
 
@@ -194,7 +196,7 @@ def write_events_to_db(self, session: Session, update: bool = False) -> None:
         # Then, add the mapping, and the events for this mapping
         for release, mapping in mappings.items():
             if update:
-                print(f"Adding mapping for release {release} ({len(mapping.events)} events)")
+                logging.info(f"Adding mapping for release {release} ({len(mapping.events)} events)")
                 map_session = MappingSession(new_release=mapping.release, created=mapping.release_date)
                 session.add(map_session)
                 session.flush()
@@ -217,9 +219,9 @@ def write_events_to_db(self, session: Session, update: bool = False) -> None:
                     session.add(id_event)
                 session.commit()
             else:
-                print(f"Found mapping for release {release} ({len(mapping.events)} events)")
+                logging.info(f"Found mapping for release {release} ({len(mapping.events)} events)")
         if not update:
-            print("Run your command again with '--update' to add them")
+            logging.info("Run your command again with '--update' to add them")
 
 
 def main() -> None:
@@ -235,8 +237,12 @@ def main() -> None:
         ),
     )
     parser.add_argument("--update", action="store_true", help="Make changes to the database")
+    parser.add_log_arguments(add_log_file=True)
     args = parser.parse_args()
 
+    # Configure and initialise logging
+    init_logging(args.log_level, args.log_file, args.log_file_level)
+
     # Start
     dbc = DBConnection(args.url)
 

src/python/ensembl/io/genomio/genome_metadata/dump.py

@@ -18,13 +18,15 @@
 
 import json
 from typing import Any, Dict
+import logging
 
 from sqlalchemy import select
 from sqlalchemy.orm import Session
 
 from ensembl.core.models import Meta
 from ensembl.database import DBConnection
 from ensembl.utils.argparse import ArgumentParser
+from ensembl.utils.logging import init_logging
 
 
 def get_genome_metadata(session: Session) -> Dict[str, Any]:
@@ -130,13 +132,17 @@ def check_assembly_version(gmeta_out: Dict[str, Any]) -> None:
     # Check the version is an integer
     if version is not None and version.isdigit():
         assembly["version"] = int(version)
+        logging.info(f"Located version [v{int(version)}] info from meta data.")
     else:
         # Get the version from the assembly accession
         accession = assembly["accession"]
         parts = accession.split(".")
         if len(parts) == 2 and parts[1].isdigit():
             version = parts[1]
             assembly["version"] = int(version)
+            logging.info(
+                f'Asm version [v{version}] obtained from: assembly accession ({assembly["accession"]}).'
+            )
         else:
             raise ValueError(f"Assembly version is not an integer in {assembly}")
 
@@ -147,10 +153,14 @@ def main() -> None:
         description="Fetch the genome metadata from a core database and print it in JSON format."
     )
     parser.add_server_arguments(include_database=True)
+    parser.add_log_arguments(add_log_file=True)
     args = parser.parse_args()
 
     dbc = DBConnection(args.url)
 
+    # Configure and initialise logging
+    init_logging(args.log_level, args.log_file, args.log_file_level)
+
     with dbc.session_scope() as session:
         genome_meta = get_genome_metadata(session)
         genome_meta = filter_genome_meta(genome_meta)