From 0959d53c19d1e679d52524e23e27114943832dd7 Mon Sep 17 00:00:00 2001 From: Lianet Sepulveda Torres Date: Tue, 30 Jan 2024 10:27:38 -0500 Subject: [PATCH 01/30] printing a message for testing the image in kubernetes --- document_indexer_service/document_indexer_service.py | 1 + 1 file changed, 1 insertion(+) diff --git a/document_indexer_service/document_indexer_service.py b/document_indexer_service/document_indexer_service.py index d3cb5a8..73434e6 100644 --- a/document_indexer_service/document_indexer_service.py +++ b/document_indexer_service/document_indexer_service.py @@ -81,6 +81,7 @@ def main(): ] logger.info(f"Indexing {len(xml_files)} documents.") + logger.info(f"Testing a new image in Kubernetes!!!!") # Split the list of files in batch if xml_files: while xml_files: From e19c8a50ddcad761f4aac41ea6875ae21892eb4f Mon Sep 17 00:00:00 2001 From: Lianet Sepulveda Torres Date: Tue, 30 Jan 2024 16:30:29 -0500 Subject: [PATCH 02/30] testing a workflow for processing a batch in kubernetes --- ht_utils/sample_data/sample_data_ht_ids.txt | 4 ++++ run_retriever_processor_kubernetes.sh | 17 +++++++++++++++++ 2 files changed, 21 insertions(+) create mode 100644 ht_utils/sample_data/sample_data_ht_ids.txt create mode 100755 run_retriever_processor_kubernetes.sh diff --git a/ht_utils/sample_data/sample_data_ht_ids.txt b/ht_utils/sample_data/sample_data_ht_ids.txt new file mode 100644 index 0000000..8bf8c47 --- /dev/null +++ b/ht_utils/sample_data/sample_data_ht_ids.txt @@ -0,0 +1,4 @@ +umn.31951002065930r +umn.31951d031321278 +nyp.33433044165144 +mdp.39015019232449 \ No newline at end of file diff --git a/run_retriever_processor_kubernetes.sh b/run_retriever_processor_kubernetes.sh new file mode 100755 index 0000000..eadecda --- /dev/null +++ b/run_retriever_processor_kubernetes.sh @@ -0,0 +1,17 @@ +#!/usr/bin/env bash +# TODO ADD ALL_ITEMS parameter +#if [ $source_resource=='local' ]; then + # You should use the sample_data_creator.sh script to generate the local folder with the documents you want to process +for line in $(cat "$PWD/ht_utils/sample_data/sample_data_ht_ids.txt") + do + ht_id="$line" + echo "🔁 Processing record $ht_id" + python document_retriever_service/full_text_search_retriever_service.py --query ht_id:"$ht_id" --document_repository pairtree + # docker compose exec document_retriever python document_retriever_service/full_text_search_retriever_service.py --query ht_id:"$ht_id" + done +#else # This option should work in Kubernetes, not use it locally if you do not have a local folder like a pairtree repository +# echo "🔁 Processing all the record included in Catalog image" +# docker compose exec document_retriever python document_retriever_service/full_text_search_retriever_service.py --query "*:*" --document_repository pairtree +#fi + +echo "🎉 Done!" \ No newline at end of file From 4667948c448e4a970383a83e5ed52ac7ff1b90ad Mon Sep 17 00:00:00 2001 From: Lianet Sepulveda Torres Date: Wed, 31 Jan 2024 17:16:31 -0500 Subject: [PATCH 03/30] modify document generator to process a batch of documents --- .../full_text_search_retriever_service.py | 162 +- filter_ids.txt | 20000 ++++++++++++++++ run_retriever_processor_kubernetes.sh | 12 +- 3 files changed, 20116 insertions(+), 58 deletions(-) create mode 100644 filter_ids.txt diff --git a/document_retriever_service/full_text_search_retriever_service.py b/document_retriever_service/full_text_search_retriever_service.py index 1ac7e96..d7c9c14 100644 --- a/document_retriever_service/full_text_search_retriever_service.py +++ b/document_retriever_service/full_text_search_retriever_service.py @@ -29,45 +29,60 @@ def __init__(self, catalogApi=None, document_generator=None): self.document_generator = document_generator - def generate_full_text_entry(self, query, start, rows, all_items, document_repository): + def generate_full_text_entry(self, query, start, rows, all_items, document_repository, chunk=None): + + # TODO: Split the logic of retrieve_documents and generate_full_text_entry. The function that generates the entry + # should receive the ht_id to process and their metadata. + # The logic to retrieve from Catalog (all fields or only the first one) should be in the retrieve_documents function + # Right now the logic is too complex because if I want to retrieve all the items of a record, then in the query I should I the id + # but if I want to retrieve an specific item (ht_id), then I should use the ht_id field in the query + # This is not intuitive and it is not clear + # An issue of the current implementation is that we are processing the first element of the record and not the + # ht_id passed as a parameter + for results in self.retrieve_documents(query, start, rows): for record in results: + """ if all_items: # Process all the records of a Catalog total_items = len(record.get("ht_id")) else: # Process the first item of the Catalog record total_items = 1 - - for i in range(0, total_items): - item_id = record.get("ht_id")[i] - logger.info(f"Item ID {item_id}") - - logger.info(f"Processing document {item_id}") - - # Instantiate each document - ht_document = HtDocument(document_id=item_id, document_repository=document_repository) - - logger.info(f"Checking path {ht_document.source_path}") - - # TODO: Temporal local for testing using a sample of files - # Checking if the file exist, otherwise go to the next - if os.path.isfile(f"{ht_document.source_path}.zip"): - - logger.info(f"Processing item {ht_document.document_id}") - - try: - entry = self.document_generator.make_full_text_search_document( - ht_document, record - ) - # yield entry - except Exception as e: - logger.error(f"Document {item_id} failed {e}") + """ + for i in range(0, len(record.get("ht_id"))): + current_ht_id = record.get("ht_id")[i] + if current_ht_id in chunk: + item_id = record.get("ht_id")[i] + logger.info(f"Item ID {item_id}") + + logger.info(f"Processing document {item_id}") + + # Instantiate each document + ht_document = HtDocument(document_id=item_id, document_repository=document_repository) + + logger.info(f"Checking path {ht_document.source_path}") + + # TODO: Temporal local for testing using a sample of files + # Checking if the file exist, otherwise go to the next + if os.path.isfile(f"{ht_document.source_path}.zip"): + + logger.info(f"Processing item {ht_document.document_id}") + + try: + entry = self.document_generator.make_full_text_search_document( + ht_document, record + ) + # yield entry + except Exception as e: + logger.error(f"Document {item_id} failed {e}") + continue + + yield entry, ht_document.file_name, ht_document.namespace + else: + logger.info(f"{ht_document.document_id} does not exist") continue - - yield entry, ht_document.file_name, ht_document.namespace else: - logger.info(f"{ht_document.document_id} does not exist") continue @@ -134,6 +149,13 @@ def main(): default=None ) + parser.add_argument( + "--list_ids_path", + help="Path of the TXT files with the list of id to generate", + required=False, + default=None + ) + args = parser.parse_args() document_generator = DocumentGenerator(db_conn) @@ -157,29 +179,65 @@ def main(): count = 0 query = args.query start = 0 - rows = 50 - - for ( - entry, - file_name, - namespace, - ) in document_indexer_service.generate_full_text_entry( - query, - start, - rows, - all_items=args.all_items, - document_repository=args.document_repository - ): - count = count + 1 - solr_str = create_solr_string(entry) - logger.info(f"Creating XML file to index") - with open( - f"/{os.path.join(document_local_path, document_local_folder)}/{namespace}{file_name}_solr_full_text.xml", - "w", - ) as f: - f.write(solr_str) - - logger.info(count) + rows = 100 + + if args.list_ids_path: + # If a document with the list of id to process is received as a parameter, then create batch of queries + with open(args.list_ids_path) as f: + list_ids = f.read().splitlines() + + while list_ids: + chunk, list_ids = list_ids[:100], list_ids[100:] + values = "\" OR \"".join(chunk) + values = '"'.join(("", values, "")) + query = f"ht_id:({values})" + # query = f"ht_id:({' OR '.join(chunk)})" + + for ( + entry, + file_name, + namespace, + ) in document_indexer_service.generate_full_text_entry( + query, + start, + rows, + all_items=args.all_items, + document_repository=args.document_repository, + chunk=chunk + ): + count = count + 1 + solr_str = create_solr_string(entry) + logger.info(f"Creating XML file to index") + with open( + f"/{os.path.join(document_local_path, document_local_folder)}/{namespace}{file_name}_solr_full_text.xml", + "w", + ) as f: + f.write(solr_str) + + logger.info(count) + + else: + for ( + entry, + file_name, + namespace, + ) in document_indexer_service.generate_full_text_entry( + query, + start, + rows, + all_items=args.all_items, + document_repository=args.document_repository + ): + count = count + 1 + solr_str = create_solr_string(entry) + logger.info(f"Creating XML file to index") + with open( + f"/{os.path.join(document_local_path, document_local_folder)}/{namespace}{file_name}_solr_full_text.xml", + "w", + ) as f: + f.write(solr_str) + + logger.info(count) if __name__ == "__main__": diff --git a/filter_ids.txt b/filter_ids.txt new file mode 100644 index 0000000..8be3808 --- /dev/null +++ b/filter_ids.txt @@ -0,0 +1,20000 @@ +mdp.39015012203793 +mdp.39015032424023 +mdp.39015023851986 +mdp.39015048939568 +mdp.39015006431624 +mdp.39015004517044 +mdp.39015013483931 +uc1.31822034555870 +uc1.31822006452601 +uiug.30112054665838 +hvd.32044019333236 +mdp.39015095243468 +uiug.30112104413122 +mdp.39015021320224 +mdp.35128001481421 +pst.000019952659 +nyp.33433019157191 +uc1.b3773565 +mdp.35128001942943 +iau.31858054425222 +osu.32435000226480 +pst.000014273346 +uc1.31210016909671 +mdp.35128001719663 +mdp.39015000808108 +hvd.32044090523549 +mdp.39015049312773 +mdp.39015012767102 +mdp.39015013038495 +mdp.39015004519438 +mdp.39015007153920 +mdp.39015000481013 +mdp.39015007665089 +mdp.39015051889882 +mdp.39015006417888 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a/run_retriever_processor_kubernetes.sh b/run_retriever_processor_kubernetes.sh index eadecda..44ddcf4 100755 --- a/run_retriever_processor_kubernetes.sh +++ b/run_retriever_processor_kubernetes.sh @@ -2,13 +2,13 @@ # TODO ADD ALL_ITEMS parameter #if [ $source_resource=='local' ]; then # You should use the sample_data_creator.sh script to generate the local folder with the documents you want to process -for line in $(cat "$PWD/ht_utils/sample_data/sample_data_ht_ids.txt") - do - ht_id="$line" - echo "🔁 Processing record $ht_id" - python document_retriever_service/full_text_search_retriever_service.py --query ht_id:"$ht_id" --document_repository pairtree +#for line in $(cat "$PWD/filter_ids.txt") +# do +# ht_id="$line" +# echo "🔁 Processing record $ht_id" +python document_retriever_service/full_text_search_retriever_service.py --list_ids_path "$PWD/filter_ids.txt" --document_repository pairtree # docker compose exec document_retriever python document_retriever_service/full_text_search_retriever_service.py --query ht_id:"$ht_id" - done +# done #else # This option should work in Kubernetes, not use it locally if you do not have a local folder like a pairtree repository # echo "🔁 Processing all the record included in Catalog image" # docker compose exec document_retriever python document_retriever_service/full_text_search_retriever_service.py --query "*:*" --document_repository pairtree From 079b4efda126b87bc3583339c57f69100cc82f05 Mon Sep 17 00:00:00 2001 From: Lianet Sepulveda Torres Date: Thu, 1 Feb 2024 08:00:50 -0500 Subject: [PATCH 04/30] create a process to control the list of ids already processed --- .../full_text_search_retriever_service.py | 18 +- .../ht_status_retriever_service.py | 11 + document_retriever_status.txt | 8096 +++++++++++++++++ 3 files changed, 8121 insertions(+), 4 deletions(-) create mode 100644 document_retriever_service/ht_status_retriever_service.py create mode 100644 document_retriever_status.txt diff --git a/document_retriever_service/full_text_search_retriever_service.py b/document_retriever_service/full_text_search_retriever_service.py index d7c9c14..ab995ad 100644 --- a/document_retriever_service/full_text_search_retriever_service.py +++ b/document_retriever_service/full_text_search_retriever_service.py @@ -5,6 +5,7 @@ import argparse from ht_utils.ht_logger import get_ht_logger +from ht_status_retriever_service import get_non_processed_ids logger = get_ht_logger(name=__name__) @@ -78,7 +79,7 @@ def generate_full_text_entry(self, query, start, rows, all_items, document_repos logger.error(f"Document {item_id} failed {e}") continue - yield entry, ht_document.file_name, ht_document.namespace + yield entry, ht_document.file_name, ht_document.namespace, item_id else: logger.info(f"{ht_document.document_id} does not exist") continue @@ -181,22 +182,28 @@ def main(): start = 0 rows = 100 + status_file = os.path.join(parentdir, "document_retriever_status.txt") + if args.list_ids_path: # If a document with the list of id to process is received as a parameter, then create batch of queries with open(args.list_ids_path) as f: list_ids = f.read().splitlines() - while list_ids: - chunk, list_ids = list_ids[:100], list_ids[100:] + ids2process = get_non_processed_ids(status_file, list_ids) + + logger.info(f"Total of items to process {len(ids2process)}") + + while ids2process: + chunk, ids2process = ids2process[:100], ids2process[100:] values = "\" OR \"".join(chunk) values = '"'.join(("", values, "")) query = f"ht_id:({values})" - # query = f"ht_id:({' OR '.join(chunk)})" for ( entry, file_name, namespace, + item_id ) in document_indexer_service.generate_full_text_entry( query, start, @@ -214,6 +221,9 @@ def main(): ) as f: f.write(solr_str) + with open(status_file, "a+") as file: + file.write(item_id + "\n") + logger.info(count) else: diff --git a/document_retriever_service/ht_status_retriever_service.py b/document_retriever_service/ht_status_retriever_service.py new file mode 100644 index 0000000..1d956ca --- /dev/null +++ b/document_retriever_service/ht_status_retriever_service.py @@ -0,0 +1,11 @@ +from ht_utils.ht_logger import get_ht_logger + +logger = get_ht_logger(name=__name__) + + +def get_non_processed_ids(status_file, list_ids): + with open(status_file, "r") as f: + processed_ids = f.read().splitlines() + logger.info(f"Total of items have been processed before {len(processed_ids)}") + items2process = list(set(list_ids) - set(processed_ids)) + return items2process diff --git a/document_retriever_status.txt b/document_retriever_status.txt new file mode 100644 index 0000000..d4912e9 --- /dev/null +++ b/document_retriever_status.txt @@ -0,0 +1,8096 @@ +mdp.39015007122842 +wu.89033912585 +mdp.39015047292985 +uva.x004774957 +uc1.31822022761670 +mdp.39015029984211 +mdp.39015043770166 +mdp.39015029201228 +mdp.49015001401406 +uc1.31822020604492 +mdp.39015061463231 +mdp.39015103935428 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No newline at end of file From 76f64d3a56da955592769563b9906effd16879fc Mon Sep 17 00:00:00 2001 From: Lianet Sepulveda Torres Date: Thu, 1 Feb 2024 09:06:58 -0500 Subject: [PATCH 05/30] create status file in tmp folder --- .../full_text_search_retriever_service.py | 11 ++++++++--- .../ht_status_retriever_service.py | 2 +- 2 files changed, 9 insertions(+), 4 deletions(-) diff --git a/document_retriever_service/full_text_search_retriever_service.py b/document_retriever_service/full_text_search_retriever_service.py index ab995ad..cd92949 100644 --- a/document_retriever_service/full_text_search_retriever_service.py +++ b/document_retriever_service/full_text_search_retriever_service.py @@ -189,10 +189,15 @@ def main(): with open(args.list_ids_path) as f: list_ids = f.read().splitlines() - ids2process = get_non_processed_ids(status_file, list_ids) + ids2process, processed_ids = get_non_processed_ids(status_file, list_ids) logger.info(f"Total of items to process {len(ids2process)}") + tmp_file_status = open(os.path.join(document_local_path, "document_retriever_status.txt"), "w+") + for doc in processed_ids: + tmp_file_status.write(doc + "\n") + tmp_file_status.close() + while ids2process: chunk, ids2process = ids2process[:100], ids2process[100:] values = "\" OR \"".join(chunk) @@ -221,9 +226,9 @@ def main(): ) as f: f.write(solr_str) - with open(status_file, "a+") as file: + with open(os.path.join(document_local_path, 'document_retriever_status.txt'), "a+") as file: file.write(item_id + "\n") - + logger.info(count) else: diff --git a/document_retriever_service/ht_status_retriever_service.py b/document_retriever_service/ht_status_retriever_service.py index 1d956ca..a7d893f 100644 --- a/document_retriever_service/ht_status_retriever_service.py +++ b/document_retriever_service/ht_status_retriever_service.py @@ -8,4 +8,4 @@ def get_non_processed_ids(status_file, list_ids): processed_ids = f.read().splitlines() logger.info(f"Total of items have been processed before {len(processed_ids)}") items2process = list(set(list_ids) - set(processed_ids)) - return items2process + return items2process, processed_ids From 912d129a78aee1b74c74b96b35fc089f7670f821 Mon Sep 17 00:00:00 2001 From: Lianet Sepulveda Torres Date: Thu, 8 Feb 2024 15:24:59 -0500 Subject: [PATCH 06/30] reduced the time the index is waiting for indexing documents --- document_indexer_service/document_indexer_service.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/document_indexer_service/document_indexer_service.py b/document_indexer_service/document_indexer_service.py index 73434e6..74358e9 100644 --- a/document_indexer_service/document_indexer_service.py +++ b/document_indexer_service/document_indexer_service.py @@ -99,10 +99,10 @@ def main(): except Exception as e: logger.info(f"{document_local_path} does not exit {e}") - sleep(30) # Wait until the folder is created + sleep(3) # Wait until the folder is created logger.info(f"Processing ended, sleeping for 5 minutes") - sleep(30) + sleep(3) if __name__ == "__main__": From e11e1ef065682a2cc0b33368ad38e12c2f97bc5d Mon Sep 17 00:00:00 2001 From: Lianet Sepulveda Torres Date: Thu, 8 Feb 2024 15:25:36 -0500 Subject: [PATCH 07/30] clean up status file --- document_retriever_status.txt | 8096 --------------------------------- 1 file changed, 8096 deletions(-) diff --git a/document_retriever_status.txt b/document_retriever_status.txt index d4912e9..e69de29 100644 --- a/document_retriever_status.txt +++ b/document_retriever_status.txt @@ -1,8096 +0,0 @@ -mdp.39015007122842 -wu.89033912585 -mdp.39015047292985 -uva.x004774957 -uc1.31822022761670 -mdp.39015029984211 -mdp.39015043770166 -mdp.39015029201228 -mdp.49015001401406 -uc1.31822020604492 -mdp.39015061463231 -mdp.39015103935428 -uc1.31822033816679 -uva.x004308835 -mdp.39015047899326 -uva.x002498507 -mdp.39015025148720 -mdp.39015021633170 -mdp.39015048297322 -mdp.49015001450247 -uc1.b4413063 -mdp.39015049066353 -mdp.39015047704559 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-ucm.5311799947 -uc1.31822002204857 -coo.31924005055912 -coo.31924068406267 -coo.31924064022381 -coo.31924004256156 -wu.89058492067 -coo.31924003570557 -coo.31924109347983 -coo.31924101588113 -coo.31924088913573 -coo.31924005026442 -coo.31924004287086 -coo.31924004787895 -coo.31924004756775 -coo.31924005009802 -coo.31924059155667 -coo.31924068318595 -coo.31924003897661 -coo.31924090210125 -coo.31924003240219 -coo.31924098125978 -coo.31924001702517 -uc1.31822003604337 -coo.31924004300079 -coo.31924067466148 -coo.31924003850009 -coo.31924063313823 -coo.31924004764688 -coo.31924004004267 -coo.31924083629612 -coo.31924063436558 -coo.31924001140163 -coo.31924083629802 -coo.31924083624555 -coo.31924088872803 -coo.31924068659733 -coo.31924097805331 -mdp.39015086561076 -mdp.39076001792436 -umn.31951001862567n -coo.31924001524192 -uc1.31822035232305 -hvd.hc11dn -wu.89031245723 -umn.31951001823154v -uc1.b4279951 -uc1.31822006689376 -wu.89119928794 -chi.087020837 -ien.35556031410038 -ien.35556031410137 -ien.35556019599612 -ien.35556018941856 -ien.35556022368666 -ien.35556031843816 -ien.35556023519259 -ien.35558000505111 -ien.35556021039037 -uiug.30112106562868 -uiug.30112004093370 -uiug.30112101587316 -uiug.30112105058470 -uiug.30112105081423 -uiug.30112106677948 -uiug.30112101891973 -uiug.30112068353272 -uiug.30112104075939 -uiug.30112007643130 -uiug.30112105105164 -uiug.30112019293148 -uiug.30112075639416 -uva.x030491106 -uiug.30112002645726 -uiug.30112075698933 -uiug.30112105180167 -uiug.30112104121816 -uiug.30112105136680 -mdp.35112200695932 -mdp.35112101801852 -uiug.30112105115411 -uiug.30112059871621 -uiug.30112041251247 -uiug.30112105058611 -uiug.30112106557587 -uiug.30112105193756 -uiug.30112106614008 -uiug.30112105086182 \ No newline at end of file From 042eeaac9a17015b44879267f6c2269424dafb1f Mon Sep 17 00:00:00 2001 From: Lianet Sepulveda Torres Date: Thu, 22 Feb 2024 16:57:30 -0500 Subject: [PATCH 08/30] re-structuring the logic to generate full-text search document --- catalog_metadata/__init__.py | 0 catalog_metadata/catalog_metadata.py | 106 +++++++ catalog_metadata/catalog_metadata_test.py | 118 ++++++++ catalog_metadata/data/catalog.json | 114 ++++++++ document_generator/document_generator.py | 262 +++--------------- document_generator/document_generator_test.py | 122 +------- document_generator/mysql_data_extractor.py | 103 +++++++ .../document_retriever_service.py | 3 - ht_document/ht_document.py | 10 +- ht_document/ht_document_test.py | 6 +- ht_utils/ht_mysql.py | 44 ++- .../indexer_config.py => indexer_config.py | 0 12 files changed, 512 insertions(+), 376 deletions(-) create mode 100644 catalog_metadata/__init__.py create mode 100644 catalog_metadata/catalog_metadata.py create mode 100644 catalog_metadata/catalog_metadata_test.py create mode 100644 catalog_metadata/data/catalog.json create mode 100644 document_generator/mysql_data_extractor.py delete mode 100644 document_retriever_service/document_retriever_service.py rename document_generator/indexer_config.py => indexer_config.py (100%) diff --git a/catalog_metadata/__init__.py b/catalog_metadata/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/catalog_metadata/catalog_metadata.py b/catalog_metadata/catalog_metadata.py new file mode 100644 index 0000000..8a6400c --- /dev/null +++ b/catalog_metadata/catalog_metadata.py @@ -0,0 +1,106 @@ +import json + +from indexer_config import IDENTICAL_CATALOG_METADATA, RENAMED_CATALOG_METADATA + + +class CatalogRecordMetadata: + """This class is used to retrieve the metadata of a specific item in the Catalog""" + + def __init__(self, record: dict): + self.metadata = self.get_metadata(record) + + def get_metadata(self, record: dict) -> dict: + + metadata = {} + + metadata.update(CatalogRecordMetadata.get_catalog_identical_fields(record)) + metadata.update(CatalogRecordMetadata.rename_catalog_fields(record)) + + # Create bothPublishDate field + if record.get("date") and record.get("enumPublishDate"): + metadata.update({"bothPublishDate": record.get("enumPublishDate")}) + + return metadata + + @staticmethod + def get_catalog_identical_fields(metadata: dict) -> dict: + entry = {} + for field in IDENTICAL_CATALOG_METADATA: + value = metadata.get(field) + if value: + entry[field] = value + return entry + + @staticmethod + def rename_catalog_fields(metadata: dict) -> dict: + entry = {} + for new_field in RENAMED_CATALOG_METADATA.keys(): + catalog_field = RENAMED_CATALOG_METADATA[new_field] + entry[new_field] = metadata.get(catalog_field) + return entry + + +class CatalogItemMetadata: + """This class is used to retrieve the metadata of a specific item in the Catalog""" + + def __init__(self, record: dict, ht_id: str, record_metadata: CatalogRecordMetadata = None): + + self.ht_id = ht_id + metadata = self.get_metadata(record) + + # Merge both dictionaries + self.metadata = {**record_metadata.metadata, **metadata} + + @staticmethod + def get_volume_enumcron(ht_id_display: str = None): + # TODO REVIEW THIS METHOD + enumcron = ht_id_display[0].split("|")[2] + return enumcron + + def get_metadata(self, record: dict) -> dict: + + metadata = {} + volume_enumcron = CatalogItemMetadata.get_volume_enumcron(record.get("ht_id_display")) + + metadata.update({"volume_enumcron": volume_enumcron}) + + doc_json = [ + item + for item in json.loads(record.get("ht_json")) + if (_v := item.get("enum_pubdate") and self.ht_id == item.get("htid")) + ] + + if len(doc_json) > 0: + metadata.update(CatalogItemMetadata.get_data_ht_json_obj(doc_json[0])) + + if len(volume_enumcron) > 1: + metadata["volume_enumcron"] = volume_enumcron + metadata["htsource"] = CatalogItemMetadata.get_item_htsource( + self.ht_id, record.get("htsource"), record.get("ht_id") + ) + + metadata["vol_id"] = self.ht_id + return metadata + + @staticmethod + def get_data_ht_json_obj(ht_json: dict = None) -> dict: + catalog_json_data = {"enumPublishDate": ht_json.get("enum_pubdate")} + return catalog_json_data + + @staticmethod + def get_item_htsource( + id: str = None, catalog_htsource: list = None, catalog_htid: list = None + ) -> str: + """ + In catalog it could be a list of sources, should obtain the source of an specific item + :param id: Catalod ht_id field + :param catalog_htsource: catalog item source + :param catalog_htid: catalog item ht_id + :return: + """ + item_position = catalog_htid.index(id) + try: + htsource = catalog_htsource[item_position] + except IndexError: + htsource = catalog_htsource[0] + return htsource diff --git a/catalog_metadata/catalog_metadata_test.py b/catalog_metadata/catalog_metadata_test.py new file mode 100644 index 0000000..0b8463a --- /dev/null +++ b/catalog_metadata/catalog_metadata_test.py @@ -0,0 +1,118 @@ +import inspect +import json +import os + +import pytest + +from catalog_metadata.catalog_metadata import CatalogItemMetadata, CatalogRecordMetadata + +current = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe()))) + + +@pytest.fixture() +def get_record_data(): + with open(os.path.join(current, "data/catalog.json"), "r", ) as file: + data = json.load(file) + + return data + + +@pytest.fixture() +def get_catalog_record_metadata(get_record_data): + return CatalogRecordMetadata(get_record_data) + + +@pytest.fixture() +def get_item_metadata(get_record_data: dict, get_catalog_record_metadata: CatalogRecordMetadata): + return CatalogItemMetadata(get_record_data, "mdp.39015078560292", get_catalog_record_metadata) + + +class TestCatalogMetadata: + + def test_catalog_record_metadata_class(self, get_catalog_record_metadata): + + assert 'ht_id' not in get_catalog_record_metadata.metadata.keys() + assert 'htsource' in get_catalog_record_metadata.metadata.keys() + assert 'vol_id' not in get_catalog_record_metadata.metadata.keys() + + def test_catalog_item_metadata_class(self, get_item_metadata): + + assert get_item_metadata.ht_id == "mdp.39015078560292" + assert "mdp.39015078560292" == get_item_metadata.metadata.get('vol_id') + assert "title" in get_item_metadata.metadata.keys() + + def test_get_item_htsource(self): + htsource = CatalogItemMetadata.get_item_htsource( + "mdp.39015061418433", # it is in solr core 7 + ["University of Michigan", "Indiana University"], + ["mdp.39015061418433", "inu.30000108625017"], + ) + assert htsource == "University of Michigan" + + htsource = CatalogItemMetadata.get_item_htsource( + "inu.30000108625017", # it is in solr core 7 + ["University of Michigan", "Indiana University"], + ["mdp.39015061418433", "inu.30000108625017"], + ) + assert htsource == "Indiana University" + + def test_get_item_htsource_sharinghtsource(self): + htsource = CatalogItemMetadata.get_item_htsource( + "inu.30000108625017", # it is in solr core 7 + ["University of Michigan"], + ["mdp.39015061418433", "inu.30000108625017"], + ) + assert htsource == "University of Michigan" + + def test_get_volume_enumcron_empty(self): + # TODO: Check if is correct the generation of volume_enumcrom (line 417: + # https://github.com/hathitrust/slip-lib/blob/master/Document/Doc/vSolrMetadataAPI/Schema_LS_11.pm) + """ + Some documents do not have the field volume_enumcrom, that is because it is an empty string in the second position. + Is that correct + :return: + """ + volume_enumcrom = "" + ht_id_display = [ + "mdp.39015078560292|20220910||1860|1860-1869|||RÄ\x81binsan KrÅ«so kÄ\x81 itihÄ\x81sa. " + "The adventures of Robinson Crusoe, translated [into Hindi] by BadrÄ« LÄ\x81la, from a Bengali version ..." + ] + assert volume_enumcrom == ht_id_display[0].split("|")[2] + + def test_missed_enumPublishDate(self, get_item_metadata): + ht_json = ('[{"htid":"nyp.33433069877805","newly_open":null,' + '"ingest":"20220501","rights":["pdus",null],"heldby":["nypl"],"collection_code":"nyp",' + '"enumcron":"v. 1","dig_source":"google"}]') + + doc_json = [] + for record in json.loads(ht_json): + if ( + _v := record.get("enum_pubdate") and "nyp.33433069877805" == record.get("htid") + ): + doc_json.append(record) + + if len(doc_json) > 0: + entry = get_item_metadata.get_data_ht_json_obj(doc_json[0]) + + assert "enumPublishDate" not in entry.keys() + + def test_extract_enumPublishDate(self, get_item_metadata): + ht_json = ('[{"htid":"mdp.39015082023097","newly_open":null,"ingest":"20230114",' + '"rights":["pdus",null],"heldby":["cornell","emory","harvard","stanford","uiowa","umich","umn"],' + '"collection_code":"miu","enumcron":"1958","enum_pubdate":"1958","enum_pubdate_range":"1950-1959",' + '"dig_source":"google"},{"htid":"mdp.39015082023246","newly_open":null,"ingest":"20230114",' + '"rights":["pdus",null],"heldby":["cornell","emory","harvard","stanford","uiowa","umich","umn"],' + '"collection_code":"miu","enumcron":"1959","enum_pubdate":"1959","enum_pubdate_range":"1950-1959",' + '"dig_source":"google"}]') + + doc_json = [] + for record in json.loads(ht_json): + if ( + _v := record.get("enum_pubdate") + and "mdp.39015082023097" == record.get("htid") + ): + doc_json.append(record) + + if len(doc_json) > 0: + entry = get_item_metadata.get_data_ht_json_obj(doc_json[0]) + assert "enumPublishDate" in entry.keys() diff --git a/catalog_metadata/data/catalog.json b/catalog_metadata/data/catalog.json new file mode 100644 index 0000000..b78272f --- /dev/null +++ b/catalog_metadata/data/catalog.json @@ -0,0 +1,114 @@ +{ + "id": "001417961", + "id_int": 1417961, + "format": [ + "Book" + ], + "oclc": [ + "23549320" + ], + "oclc_search": [ + "23549320" + ], + "sdrnum": [ + "sdr-miu.990014179610106381" + ], + "mainauthor": [ + "Defoe, Daniel, 1661?-1731." + ], + "mainauthor_just_name": [ + "Defoe, Daniel," + ], + "author": [ + "Defoe, Daniel, 1661?-1731.", + "Badarīnātha, pandit," + ], + "authorStr": [ + "Defoe, Daniel, 1661?-1731.", + "Badarīnātha, pandit," + ], + "author2": [ + "Badarīnātha, pandit," + ], + "author_top": [ + "Defoe, Daniel, 1661?-1731.", + "translated [into Hindi] by Badrī Lāla, from a Bengali version ...", + "Badarīnātha, pandit, tr." + ], + "author_sortkey": "defoe, daniel 1661 1731", + "title": [ + "Rābinsan Krūso kā itihāsa. The adventures of Robinson Crusoe" + ], + "title_a": [ + "Rābinsan Krūso kā itihāsa" + ], + "title_ab": [ + "Rābinsan Krūso kā itihāsa. The adventures of Robinson Crusoe" + ], + "title_c": [ + "translated [into Hindi] by Badrī Lāla, from a Bengali version ..." + ], + "title_top": [ + "Rābinsan Krūso kā itihāsa. The adventures of Robinson Crusoe," + ], + "title_rest": [ + "Robinson Crusoe." + ], + "title_display": "Rābinsan Krūso kā itihāsa. The adventures of Robinson Crusoe, translated [into Hindi] by Badrī Lāla, from a Bengali version ...", + "titleSort": "Rābinsan Krūso kā itihāsa. The adventures of Robinson Crusoe", + "title_sortkey": "rābinsan krūso kā itihāsa the adventures of robinson crusoe", + "countryOfPubStr": [ + "India" + ], + "place_of_publication": [ + "India" + ], + "publishDate": [ + "1860" + ], + "publishDateRange": [ + "1860", + "1860-1869" + ], + "display_date": "1860", + "language": [ + "Hindi", + "English" + ], + "language008": "hin", + "ht_availability": [ + "Full text" + ], + "ht_availability_intl": [ + "Full text" + ], + "ht_count": 1, + "ht_id": [ + "mdp.39015078560292" + ], + "ht_id_display": [ + "mdp.39015078560292|20220910||1860|1860-1869|||Rābinsan Krūso kā itihāsa. The adventures of Robinson Crusoe, translated [into Hindi] by Badrī Lāla, from a Bengali version ..." + ], + "ht_id_update": [ + 20220910 + ], + "ht_rightscode": [ + "pd" + ], + "htsource": [ + "University of Michigan" + ], + "ht_json": "[{\"htid\":\"mdp.39015078560292\",\"newly_open\":null,\"ingest\":\"20220910\",\"rights\":[\"pd\",null],\"heldby\":[\"umich\"],\"collection_code\":\"miu\",\"enum_pubdate\":\"1860\",\"enum_pubdate_range\":\"1860-1869\",\"dig_source\":\"lit-dlps-dc\"}]", + "ht_searchonly": false, + "ht_searchonly_intl": false, + "language008_full": "Hindi", + "print_holdings": [ + "umich" + ], + "deleted": false, + "time_of_index": "2024-02-03T05:11:08.372Z", + "fullrecord": "00967nam a22002651 4500001417961MiAaHDL20220910000000.0m d cr bn ---auaua890828s1860 ii |||||||||||||||||hin|d(MiU)990014179610106381sdr-miu.990014179610106381(MiU)MIU01000000000000001417961-goog(OCoLC)23549320(SAZTEC)097201870(CaOTULAS)176405114(MiU)Aleph001417961SAZTEChinengbenDefoe, Daniel,1661?-1731.Rābinsan Krūso kā itihāsa.The adventures of Robinson Crusoe,translated [into Hindi] by Badrī Lāla, from a Bengali version ...Benares,1860455 p. incl. front., illus. plates.20 cm.Title from Catalogue of Hindi books in the British museum.Mode of access: Internet.Badarīnātha, pandit,tr.Robinson Crusoe.3901507856029200141796119890828000000.020220910000000.020220910060531.02022-09-10T14:33:44Z2020-04-22T17:30:02ZSDR-MIUALMAprepare.pl-004-008BKsdr-miu.990014179610106381MiUSDRMIUmdp.39015078560292MIU990014179610106381MIUMIU20220910lit-dlps-dcmdp.390150785602921860pdbibnon-US bib date1 < 1899", + "country_of_pub_facet": [ + "India" + ] +} \ No newline at end of file diff --git a/document_generator/document_generator.py b/document_generator/document_generator.py index 69a9c96..4a5806c 100644 --- a/document_generator/document_generator.py +++ b/document_generator/document_generator.py @@ -1,133 +1,30 @@ import argparse -import json +import zipfile +from catalog_metadata.catalog_metadata import CatalogItemMetadata +from ht_utils.ht_mysql import HtMysql from ht_utils.ht_logger import get_ht_logger - -logger = get_ht_logger(name=__name__) - -import zipfile -from xml.sax.saxutils import quoteattr - -from typing import Dict, List -from document_generator.indexer_config import ( - IDENTICAL_CATALOG_METADATA, - RENAMED_CATALOG_METADATA, - MAX_ITEM_IDS, -) -from lxml import etree -from io import BytesIO - -from ht_utils.ht_mysql import query_mysql -from document_generator.mets_file_extractor import MetsAttributeExtractor from ht_utils.text_processor import string_preparation +from document_generator.mysql_data_extractor import MysqlMetadataExtractor -from ht_document.ht_document import HtDocument - - -class DocumentGenerator: - def __init__(self, db_conn, catalogApi=None): - self.db_conn = db_conn - self.catalogApi = catalogApi - - def get_record_metadata(self, query: str = None) -> Dict: - """ - API call to query Catalog Solr index - :param query: input query - :return dictionary with the API result - - """ - response = self.catalogApi.get_documents(query) - - return { - "status": response.status_code, - "description": response.headers, - "content": json.loads(response.content.decode("utf-8")), - } - - @staticmethod - def make_solr_query(doc_id): - query = f"ht_id:{doc_id}" - return query - - @staticmethod - def get_catalog_identical_fields(metadata: Dict) -> Dict: - entry = {} - for field in IDENTICAL_CATALOG_METADATA: - value = metadata.get(field) - if value: - entry[field] = value - return entry - - @staticmethod - def rename_catalog_fields(metadata: Dict) -> Dict: - entry = {} - for new_field in RENAMED_CATALOG_METADATA.keys(): - catalog_field = RENAMED_CATALOG_METADATA[new_field] - entry[new_field] = metadata.get(catalog_field) - return entry - - @staticmethod - def get_volume_enumcron(ht_id_display: str = None): - enumcron = ht_id_display[0].split("|")[2] - return enumcron - - @staticmethod - def get_data_ht_json_obj(ht_json: Dict = None): - catalog_json_data = {"enumPublishDate": ht_json.get("enum_pubdate")} - return catalog_json_data - - @staticmethod - def get_item_htsource( - id: str = None, catalog_htsource: List = None, catalog_htid: List = None - ): - """ - In catalog it could be a list of sources, should obtain the source of an specific item - :param id: Catalod ht_id field - :param catalog_htsource: catalog item source - :param catalog_htid: catalog item ht_id - :return: - """ - item_position = catalog_htid.index(id) - try: - htsource = catalog_htsource[item_position] - except IndexError as e: - htsource = catalog_htsource[0] - return htsource +import xml.sax.saxutils - @staticmethod - def retrieve_fields_from_Catalog_index(doc_id: str, metadata: Dict) -> Dict: - entry = {} +import lxml.etree +import io - entry.update(DocumentGenerator.get_catalog_identical_fields(metadata)) - entry.update(DocumentGenerator.rename_catalog_fields(metadata)) +import document_generator.mets_file_extractor +import ht_document.ht_document - volume_enumcron = DocumentGenerator.get_volume_enumcron( - metadata.get("ht_id_display") - ) - - doc_json = [ - record - for record in json.loads(metadata.get("ht_json")) - if (v := record.get("enum_pubdate") and doc_id == record.get("htid")) - ] - - if len(doc_json) > 0: - entry.update(DocumentGenerator.get_data_ht_json_obj(doc_json[0])) - - if len(volume_enumcron) > 1: - entry["volume_enumcron"] = volume_enumcron - entry["htsource"] = DocumentGenerator.get_item_htsource( - doc_id, metadata.get("htsource"), metadata.get("ht_id") - ) +logger = get_ht_logger(name=__name__) - if entry.get("date") and entry.get("enumPublishDate"): - entry.update({"bothPublishDate": entry.get("enumPublishDate")}) - entry["vol_id"] = doc_id - return entry +class DocumentGenerator: + def __init__(self, db_conn: HtMysql, catalog_api=None): + self.mysql_data_extractor = MysqlMetadataExtractor(db_conn) + self.catalogApi = catalog_api @staticmethod - def create_ocr_field(document_zip_path) -> Dict: + def create_ocr_field(document_zip_path: str) -> dict: # TODO: As part of this function we could extract the following attributes # numPages, numChars, charsPerPage. In the future, these attributes could be use to measure query performance logger.info(f"Reading {document_zip_path}.zip file") @@ -135,97 +32,11 @@ def create_ocr_field(document_zip_path) -> Dict: return {"ocr": full_text} @staticmethod - def create_allfields_field(fullrecord_field: str) -> Dict: + def create_allfields_field(fullrecord_field: str) -> dict: # TODO Create a different class to manage the XML files allfields = DocumentGenerator.get_allfields_field(fullrecord_field) return {"allfields": allfields} - # TODO I could have a class to retrieve data from MySql - def add_large_coll_id_field(self, doc_id): - """ - Get the list of coll_ids for the given id that are large so those - coll_ids can be added as fields of the Solr doc. - - So, if sync-i found an id to have, erroneously, a *small* coll_id - field in its Solr doc and queued it for re-indexing, this routine - would create a Solr doc not containing that coll_id among its - fields. - """ - - query_coll_item = ( - f'SELECT MColl_ID FROM mb_coll_item WHERE extern_item_id="{doc_id}"' - ) - - query_large_coll = ( - f"SELECT MColl_ID FROM mb_collection WHERE num_items>{MAX_ITEM_IDS}" - ) - - coll_id_entry = query_mysql(self.db_conn, query=query_coll_item) - coll_id_large_entry = query_mysql(self.db_conn, query=query_large_coll) - - return coll_id_entry, coll_id_large_entry - - # TODO probably I do not need the functions below to retrieve the fields from MySql - # I can directly call query_mysql, less lines of code - def add_right_field(self, doc_id) -> Dict: - namespace, id = doc_id.split(".") - query = ( - f'SELECT * FROM rights_current WHERE namespace="{namespace}" AND id="{id}"' - ) - slip_rights_entry = query_mysql(self.db_conn, query=query) - return slip_rights_entry - - def add_ht_heldby_field(self, doc_id) -> Dict: - query = ( - f'SELECT member_id FROM holdings_htitem_htmember WHERE volume_id="{doc_id}"' - ) - - ht_heldby_entry = query_mysql(self.db_conn, query=query) - # ht_heldby is a list of institutions - return ht_heldby_entry - - def add_add_heldby_brlm_field(self, doc_id) -> Dict: - query = f'SELECT member_id FROM holdings_htitem_htmember WHERE volume_id="{doc_id}" AND access_count > 0' - - ht_heldby_entry = query_mysql(self.db_conn, query=query) - return ht_heldby_entry - - def retrieve_mysql_data(self, doc_id): - entry = {} - logger.info((f"Retrieving data from MySql {doc_id}")) - doc_rights = self.add_right_field(doc_id) - - # Only one element - if len(doc_rights) == 1: - entry.update({"rights": doc_rights[0].get("attr")}) - - # It is a list of members, if the query result is empty the field does not appear in Solr index - ht_heldby = self.add_ht_heldby_field(doc_id) - if len(ht_heldby) > 0: - list_members = [member_id.get("member_id") for member_id in ht_heldby] - entry.update({"ht_heldby": list_members}) - - # It is a list of members, if the query result is empty the field does not appear in Solr index - heldby_brlm = self.add_add_heldby_brlm_field(doc_id) - if len(heldby_brlm) > 0: - list_brl_members = [member_id.get("member_id") for member_id in heldby_brlm] - entry.update({"ht_heldby_brlm": list_brl_members}) - - # It is a list of coll_id, if the query result is empty, the value of this field in Solr index will be [0] - coll_id_result, large_coll_id_result = self.add_large_coll_id_field(doc_id) - if len(coll_id_result) > 0: - list_coll_ids = [coll_id.get("MColl_ID") for coll_id in coll_id_result] - list_large_coll_id = [ - coll_id.get("MColl_ID") for coll_id in large_coll_id_result - ] - - entry.update( - {"coll_id": list(set(list_coll_ids) & set(list_large_coll_id))} - ) - else: - entry.update({"coll_id": [0]}) - return entry - @staticmethod def get_full_text_field(zip_doc_path: str): """ @@ -260,9 +71,9 @@ def get_allfields_field(catalog_xml: str = None) -> str: allfields = "" - xml_string_like_file = BytesIO(catalog_xml.encode(encoding="utf-8")) + xml_string_like_file = io.BytesIO(catalog_xml.encode(encoding="utf-8")) - for event, element in etree.iterparse( + for event, element in lxml.etree.iterparse( xml_string_like_file, events=("start", "end"), ): @@ -281,44 +92,39 @@ def get_allfields_field(catalog_xml: str = None) -> str: except ValueError as e: logger.info(f"Element tag is not an integer value {e}") pass - return quoteattr(allfields) + return xml.sax.saxutils.quoteattr(allfields) - # TODO Check exception if doc_id is None - def make_full_text_search_document( - self, ht_document: HtDocument, doc_metadata: Dict - ) -> Dict: + def make_full_text_search_document(self, ht_document: ht_document.ht_document.HtDocument, + doc_metadata: CatalogItemMetadata) -> dict: + # TODO Check exception if doc_id is None """ - Receive the ht_id and create the HtDocument entry + Receive the HtDocument object and the metadata from the Catalog API and generate the full text search entry :param ht_document: - :param doc_id: :param doc_metadata: - :return: + :return: a dictionary with the full text search entry """ entry = {"id": ht_document.document_id} - # Add Catalog fields to full-text document - entry.update( - DocumentGenerator.retrieve_fields_from_Catalog_index( - ht_document.document_id, doc_metadata - ) - ) - # Generate ocr field entry.update(DocumentGenerator.create_ocr_field(ht_document.source_path)) - logger.info(doc_metadata) - # Generate allfields field + # Generate allfields field from fullrecord field + # This field is in Catalog object, we process it here and after that we delete because it is not + # necessary to be in Solr index entry.update( - DocumentGenerator.create_allfields_field(doc_metadata.get("fullrecord")) + DocumentGenerator.create_allfields_field(doc_metadata.metadata.get("fullrecord")) ) - logger.info(entry) + doc_metadata.metadata.pop("fullrecord") + + # Add Catalog fields to full-text document + entry.update(doc_metadata.metadata) # Retrieve data from MariaDB - entry.update(self.retrieve_mysql_data(ht_document.document_id)) + entry.update(self.mysql_data_extractor.retrieve_mysql_data(ht_document.document_id)) # Extract fields from METS file - mets_obj = MetsAttributeExtractor(f"{ht_document.source_path}.mets.xml") + mets_obj = document_generator.mets_file_extractor.MetsAttributeExtractor(f"{ht_document.source_path}.mets.xml") mets_entry = mets_obj.create_mets_entry() diff --git a/document_generator/document_generator_test.py b/document_generator/document_generator_test.py index f044995..35fc1ba 100644 --- a/document_generator/document_generator_test.py +++ b/document_generator/document_generator_test.py @@ -1,22 +1,17 @@ +import inspect import os -from pathlib import Path - import sys -import inspect -import json +from pathlib import Path +from xml.sax.saxutils import quoteattr import pytest -import pytest_cov - from _pytest.outcomes import Failed from document_generator.document_generator import DocumentGenerator -from xml.sax.saxutils import quoteattr -from ht_indexer_api.ht_indexer_api import HTSolrAPI -currentdir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe()))) -parentdir = os.path.dirname(currentdir) -sys.path.insert(0, parentdir) +current = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe()))) +parent = os.path.dirname(current) +sys.path.insert(0, parent) @pytest.fixture() @@ -35,49 +30,15 @@ def get_allfield_string(): ) -@pytest.fixture() -def get_document_generator(): - db_conn = None - solr_api = HTSolrAPI(url="http://solr-sdr-catalog:9033/solr/#/catalog/") - - document_generator = DocumentGenerator(db_conn, solr_api) - - return document_generator - - class TestDocumentGenerator: - def test_get_item_htsource(self): - htsource = DocumentGenerator.get_item_htsource( - "mdp.39015061418433", # it is in solr core 7 - ["University of Michigan", "Indiana University"], - ["mdp.39015061418433", "inu.30000108625017"], - ) - assert htsource == "University of Michigan" - - htsource = DocumentGenerator.get_item_htsource( - "inu.30000108625017", # it is in solr core 7 - ["University of Michigan", "Indiana University"], - ["mdp.39015061418433", "inu.30000108625017"], - ) - assert htsource == "Indiana University" - - def test_get_item_htsource_sharinghtsource(self): - htsource = DocumentGenerator.get_item_htsource( - "inu.30000108625017", # it is in solr core 7 - ["University of Michigan"], - ["mdp.39015061418433", "inu.30000108625017"], - ) - assert htsource == "University of Michigan" def test_not_exist_zip_file_full_text_field(self): try: - with pytest.raises(Exception) as e: + with pytest.raises(Exception): DocumentGenerator.get_full_text_field("data/test.zip") - except Failed as e: + except Failed: pass - # assert e.type == TypeError - def test_full_text_field(self): zip_path = f"{Path(__file__).parents[1]}/data/document_generator/mb.39015078560292_test.zip" full_text = DocumentGenerator.get_full_text_field(zip_path) @@ -88,70 +49,3 @@ def test_create_allfields_field(self, get_fullrecord_xml, get_allfield_string): allfield = DocumentGenerator.get_allfields_field(get_fullrecord_xml) assert len(allfield.strip()) == len(get_allfield_string.strip()) assert allfield.strip() == get_allfield_string.strip() - - def test_get_volume_enumcron_empty(self): - # TODO: Check if is correct the generation of volume_enumcrom (line 417: https://github.com/hathitrust/slip-lib/blob/master/Document/Doc/vSolrMetadataAPI/Schema_LS_11.pm) - """ - Some documents do not have the field volume_enumcrom, that is because it is an empty string in the second position. - Is that correct - :return: - """ - volume_enumcrom = "" - ht_id_display = [ - "mdp.39015078560292|20220910||1860|1860-1869|||RÄ\x81binsan KrÅ«so kÄ\x81 itihÄ\x81sa. The adventures of Robinson Crusoe, translated [into Hindi] by BadrÄ« LÄ\x81la, from a Bengali version ..." - ] - assert volume_enumcrom == ht_id_display[0].split("|")[2] - - def test_get_records(self, get_document_generator): - query = "ht_id:nyp.33433082046503" - doc_metadata = get_document_generator.get_record_metadata(query) - - assert "nyp.33433082046503" in doc_metadata.get("content").get("response").get( - "docs" - )[0].get("ht_id") - - def test_create_entry(self, get_document_generator): - """ - Test the function that creates the entry with fields retrieved from Catalog index - :return: - """ - - query = "ht_id:nyp.33433082046503" - doc_metadata = get_document_generator.get_record_metadata(query) - - assert "nyp.33433082046503" in doc_metadata.get("content").get("response").get( - "docs" - )[0].get("ht_id") - - def test_missed_enumPublishDate(self, get_document_generator): - ht_json = '[{"htid":"nyp.33433069877805","newly_open":null,"ingest":"20220501","rights":["pdus",null],"heldby":["nypl"],"collection_code":"nyp","enumcron":"v. 1","dig_source":"google"}]' - - doc_json = [ - record - for record in json.loads(ht_json) - if ( - v := record.get("enum_pubdate") - and "nyp.33433069877805" == record.get("htid") - ) - ] - - if len(doc_json) > 0: - entry = get_document_generator.get_data_ht_json_obj(doc_json[0]) - - assert "enumPublishDate" not in entry.keys() - - def test_extract_enumPublishDate(self, get_document_generator): - ht_json = '[{"htid":"mdp.39015082023097","newly_open":null,"ingest":"20230114","rights":["pdus",null],"heldby":["cornell","emory","harvard","stanford","uiowa","umich","umn"],"collection_code":"miu","enumcron":"1958","enum_pubdate":"1958","enum_pubdate_range":"1950-1959","dig_source":"google"},{"htid":"mdp.39015082023246","newly_open":null,"ingest":"20230114","rights":["pdus",null],"heldby":["cornell","emory","harvard","stanford","uiowa","umich","umn"],"collection_code":"miu","enumcron":"1959","enum_pubdate":"1959","enum_pubdate_range":"1950-1959","dig_source":"google"}]' - - doc_json = [ - record - for record in json.loads(ht_json) - if ( - v := record.get("enum_pubdate") - and "mdp.39015082023097" == record.get("htid") - ) - ] - - if len(doc_json) > 0: - entry = get_document_generator.get_data_ht_json_obj(doc_json[0]) - assert "enumPublishDate" in entry.keys() diff --git a/document_generator/mysql_data_extractor.py b/document_generator/mysql_data_extractor.py new file mode 100644 index 0000000..14e8aa8 --- /dev/null +++ b/document_generator/mysql_data_extractor.py @@ -0,0 +1,103 @@ +from ht_utils.ht_mysql import HtMysql +from ht_utils.ht_logger import get_ht_logger +import indexer_config + +logger = get_ht_logger(name=__name__) + + +class MysqlMetadataExtractor: + def __init__(self, db_conn: HtMysql): + self.mysql_obj = db_conn + + def get_results_query(self, query: str) -> list: + + results = self.mysql_obj.query_mysql(query=query) + + list_docs = [] + for row in results: + doc = {} + for name, value in zip(self.mysql_obj.cursor.description, row): + doc.update({name[0]: value}) + list_docs.append(doc) + + return list_docs + + def add_large_coll_id_field(self, doc_id: str) -> [dict, dict]: + """ + Get the list of coll_ids for the given id that are large so those + coll_ids can be added as fields of the Solr doc. + + So, if sync-i found an id to have, erroneously, a *small* coll_id + field in its Solr doc and queued it for re-indexing, this routine + would create a Solr doc not containing that coll_id among its + fields. + """ + + query_coll_item = ( + f'SELECT MColl_ID FROM mb_coll_item WHERE extern_item_id="{doc_id}"' + ) + + query_large_coll = ( + f"SELECT MColl_ID FROM mb_collection WHERE num_items>{indexer_config.MAX_ITEM_IDS}" + ) + + coll_id_entry = self.mysql_obj.query_mysql(query_coll_item) + coll_id_large_entry = self.mysql_obj.query_mysql(query_large_coll) + + return coll_id_entry, coll_id_large_entry + + def add_right_field(self, doc_id) -> list[tuple]: + namespace, _id = doc_id.split(".") + query = ( + f'SELECT * FROM rights_current WHERE namespace="{namespace}" AND id="{_id}"' + ) + return self.mysql_obj.query_mysql(query) + + def add_ht_heldby_field(self, doc_id) -> list[tuple]: + query = ( + f'SELECT member_id FROM holdings_htitem_htmember WHERE volume_id="{doc_id}"' + ) + # ht_heldby is a list of institutions + return self.mysql_obj.query_mysql(query) + + def add_add_heldby_brlm_field(self, doc_id) -> list[tuple]: + query = f'SELECT member_id FROM holdings_htitem_htmember WHERE volume_id="{doc_id}" AND access_count > 0' + + return self.mysql_obj.query_mysql(query) + + def retrieve_mysql_data(self, doc_id): + entry = {} + logger.info(f"Retrieving data from MySql {doc_id}") + + doc_rights = self.add_right_field(doc_id) + + # Only one element + if len(doc_rights) == 1: + entry.update({"rights": doc_rights[0].get("attr")}) + + # It is a list of members, if the query result is empty the field does not appear in Solr index + ht_heldby = self.add_ht_heldby_field(doc_id) + if len(ht_heldby) > 0: + list_members = [member_id.get("member_id") for member_id in ht_heldby] + entry.update({"ht_heldby": list_members}) + + # It is a list of members, if the query result is empty the field does not appear in Solr index + heldby_brlm = self.add_add_heldby_brlm_field(doc_id) + if len(heldby_brlm) > 0: + list_brl_members = [member_id.get("member_id") for member_id in heldby_brlm] + entry.update({"ht_heldby_brlm": list_brl_members}) + + # It is a list of coll_id, if the query result is empty, the value of this field in Solr index will be [0] + coll_id_result, large_coll_id_result = self.add_large_coll_id_field(doc_id) + if len(coll_id_result) > 0: + list_coll_ids = [coll_id.get("MColl_ID") for coll_id in coll_id_result] + list_large_coll_id = [ + coll_id.get("MColl_ID") for coll_id in large_coll_id_result + ] + + entry.update( + {"coll_id": list(set(list_coll_ids) & set(list_large_coll_id))} + ) + else: + entry.update({"coll_id": [0]}) + return entry diff --git a/document_retriever_service/document_retriever_service.py b/document_retriever_service/document_retriever_service.py deleted file mode 100644 index e00f614..0000000 --- a/document_retriever_service/document_retriever_service.py +++ /dev/null @@ -1,3 +0,0 @@ -class DocumentRetrieverService: - def retrieve_documents(self): - raise NotImplementedError("not method to retrieve documents") diff --git a/ht_document/ht_document.py b/ht_document/ht_document.py index 5026bf4..676869a 100644 --- a/ht_document/ht_document.py +++ b/ht_document/ht_document.py @@ -1,14 +1,14 @@ import os from typing import Text -from document_generator.indexer_config import ( - DOCUMENT_LOCAL_PATH, - TRANSLATE_TABLE, - LOCAL_DOCUMENT_FOLDER -) from pypairtree import pairtree from ht_utils.ht_logger import get_ht_logger +from indexer_config import ( + DOCUMENT_LOCAL_PATH, + TRANSLATE_TABLE, + LOCAL_DOCUMENT_FOLDER +) logger = get_ht_logger(name=__name__) diff --git a/ht_document/ht_document_test.py b/ht_document/ht_document_test.py index 41f0be9..9ce9964 100644 --- a/ht_document/ht_document_test.py +++ b/ht_document/ht_document_test.py @@ -1,7 +1,9 @@ +import os +from pathlib import Path + from pypairtree import pairtree + from ht_document.ht_document import HtDocument -from pathlib import Path -import os os.environ["SDR_DIR"] = f"{Path(__file__).parents[1]}/data/document_generator" diff --git a/ht_utils/ht_mysql.py b/ht_utils/ht_mysql.py index a1cb940..c047df3 100644 --- a/ht_utils/ht_mysql.py +++ b/ht_utils/ht_mysql.py @@ -1,37 +1,33 @@ import mysql.connector -from mysql.connector import Connect from ht_utils.ht_logger import get_ht_logger logger = get_ht_logger(name=__name__) -def create_mysql_conn( - host: str = None, user: str = None, password: str = None, database: str = None -): - db_conn = None - if all([host, user, password, database]): - db_conn = mysql.connector.connect( - host=host, user=user, password=password, database=database - ) +class HtMysql: - else: - logger.error("Please pass the valid host, user, password and database") - exit() + def __init__(self, host: str = None, user: str = None, password: str = None, database: str = None): + self.db_conn = HtMysql.create_mysql_conn(host=host, user=user, password=password, database=database) - return db_conn + @staticmethod + def create_mysql_conn(host: str = None, user: str = None, password: str = None, database: str = None): + if not all([host, user, password, database]): + logger.error("Please pass the valid host, user, password and database") + exit() + return mysql.connector.connect(host=host, user=user, password=password, database=database) + def query_mysql(self, query: str = None) -> list: + cursor = self.db_conn.cursor() + cursor.execute(query) -def query_mysql(db_conn: Connect = None, query: str = None): - cursor = db_conn.cursor() - cursor.execute(query) + results = cursor.fetchall() - results = cursor.fetchall() + list_docs = [] + for row in results: + doc = {} + for name, value in zip(cursor.description, row): + doc.update({name[0]: value}) + list_docs.append(doc) - list_docs = [] - for row in results: - doc = {} - for name, value in zip(cursor.description, row): - doc.update({name[0]: value}) - list_docs.append(doc) - return list_docs # [{name[0]: value} for row in results for name, value in zip(cursor.description, row)] + return list_docs # [{name[0]: value} for row in results for name, value in zip(cursor.description, row)] diff --git a/document_generator/indexer_config.py b/indexer_config.py similarity index 100% rename from document_generator/indexer_config.py rename to indexer_config.py From 102e58efab9d1ed4537a6915339c45b720235cde Mon Sep 17 00:00:00 2001 From: Lianet Sepulveda Torres Date: Thu, 22 Feb 2024 18:40:15 -0500 Subject: [PATCH 09/30] documenting the different use cases implemented in this repository --- README.md | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/README.md b/README.md index 300118c..d6c8f39 100644 --- a/README.md +++ b/README.md @@ -9,6 +9,39 @@ This application instantiates two solr servers, through docker containers. Catal documents and Full-text (solr-lss-dev) search index for indexing them. Both containers, must be running before load the API, so the docker-compose.yml file takes care of it. +## Use cases + +For all the use cases, the query look like: + +``` --query id:100673101 + --query ht_id:umn.31951d01828300z + --query *:* default query to retrieve all the documents in Catalog +``` + +1- Create a TXT file listing ht_id from Catalog index +`python ht_indexer/document_retriever_service/catalog_retriever_service.py --query id:100673101 +--output_file ~/tmp/ht_ids.txt` + +* By default, the file will be created in the folder the root of the project + +2- Generate full-text search documents for all the items in Catalog index +`python ht_indexer/document_retriever_service/full_text_search_retriever_service.py --query id:100673101 +--document_local_path ~/tmp` + +* The query parameter could be *:* to retrieve all the documents in Catalog index + +3- Generate full-text search documents given ht_id +`python ht_indexer/document_retriever_service/full_text_search_retriever_service.py --query ht_id:umn.31951d01828300z +--document_local_path ~/tmp` + +4- Retrieve files from pairtree-based repository +`python ~/ht_indexer/document_retriever_service/full_text_search_retriever_by_file.py +--list_ids_path /Users/lisepul/Documents/repositories/python/ht_indexer/filter_ids.txt` + +4- Index the documents in full-text search index +`python3 ~/ht_indexer/document_indexer_service/document_indexer_service.py --solr_indexing_api +http://localhost:8983/solr/#/core-x/ --document_local_path ~/tmp/indexing_data` + ## Setting up ht_indexer 1. Clone the repository in your working environment @@ -227,6 +260,10 @@ export PUBLIC_KEY=public_key_name Reference used for python implementation +Python Linter: +Ruff: https://astral.sh/ruff +Enhancing Python Code Quality: A Comprehensive Guide to Linting with +Ruff: https://dev.to/ken_mwaura1/enhancing-python-code-quality-a-comprehensive-guide-to-linting-with-ruff-3d6g Parser XML files https://lxml.de/tutorial.html#parsing-from-strings-and-files https://pymotw.com/3/xml.etree.ElementTree/parse.html From fde38a201d92db64149fb1c2d08a06983fa01c23 Mon Sep 17 00:00:00 2001 From: Lianet Sepulveda Torres Date: Thu, 22 Feb 2024 18:48:00 -0500 Subject: [PATCH 10/30] formatting change --- document_generator/mets_file_extractor_test.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/document_generator/mets_file_extractor_test.py b/document_generator/mets_file_extractor_test.py index 2b8b5e6..ad4da4a 100644 --- a/document_generator/mets_file_extractor_test.py +++ b/document_generator/mets_file_extractor_test.py @@ -16,9 +16,9 @@ def test_create_METS_map(self, metsAttrExtractorObj): mets_map = metsAttrExtractorObj.create_METS_map() assert ( - mets_map.get("488").get("features") == "CHAPTER_START, IMPLICIT_PAGE_NUMBER" + mets_map.get("488").get("features") == "CHAPTER_START, IMPLICIT_PAGE_NUMBER" ) - assert mets_map.get("488").get("pgnum") == None + assert mets_map.get("488").get("pgnum") is None assert mets_map.get("488").get("filename") == [ "IMG00000488", "HTML00000488", From 33b4aad074ada0e9e9c2b6a763426639313df85b Mon Sep 17 00:00:00 2001 From: Lianet Sepulveda Torres Date: Thu, 22 Feb 2024 19:16:47 -0500 Subject: [PATCH 11/30] remove non-used package --- ht_indexer_api/ht_indexer_api.py | 1 - 1 file changed, 1 deletion(-) diff --git a/ht_indexer_api/ht_indexer_api.py b/ht_indexer_api/ht_indexer_api.py index 3d104fc..bef90dc 100644 --- a/ht_indexer_api/ht_indexer_api.py +++ b/ht_indexer_api/ht_indexer_api.py @@ -1,4 +1,3 @@ -import glob from pathlib import Path from typing import Text From f503987a9304fb10c99b85443803a939d60cbb41 Mon Sep 17 00:00:00 2001 From: Lianet Sepulveda Torres Date: Thu, 22 Feb 2024 19:17:34 -0500 Subject: [PATCH 12/30] remove non-used package --- .../document_indexer_service.py | 17 +- .../document_indexer_service_test.py | 8 - .../catalog_retriever_service.py | 113 ++++--- .../full_text_search_retriever_service.py | 314 +++++++----------- ...full_text_search_retriever_service_test.py | 13 +- ht_indexer_api/ht_indexer_api_test.py | 5 +- 6 files changed, 193 insertions(+), 277 deletions(-) diff --git a/document_indexer_service/document_indexer_service.py b/document_indexer_service/document_indexer_service.py index 74358e9..6828710 100644 --- a/document_indexer_service/document_indexer_service.py +++ b/document_indexer_service/document_indexer_service.py @@ -1,25 +1,24 @@ # Read from a folder, index documents to solr and delete the content of the sercer -from time import sleep import argparse -import os import glob import inspect +import os import sys +from time import sleep from ht_utils.ht_logger import get_ht_logger +from ht_indexer_api.ht_indexer_api import HTSolrAPI logger = get_ht_logger(name=__name__) -currentdir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe()))) -parentdir = os.path.dirname(currentdir) -sys.path.insert(0, parentdir) +current = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe()))) +parent = os.path.dirname(current) +sys.path.insert(0, parent) CHUNK_SIZE = 500 DOCUMENT_LOCAL_PATH = "/tmp/indexing_data/" -from ht_indexer_api.ht_indexer_api import HTSolrAPI - class DocumentIndexerService: def __init__(self, solr_api_full_text=None): @@ -81,7 +80,7 @@ def main(): ] logger.info(f"Indexing {len(xml_files)} documents.") - logger.info(f"Testing a new image in Kubernetes!!!!") + logger.info("Testing a new image in Kubernetes!!!!") # Split the list of files in batch if xml_files: while xml_files: @@ -101,7 +100,7 @@ def main(): logger.info(f"{document_local_path} does not exit {e}") sleep(3) # Wait until the folder is created - logger.info(f"Processing ended, sleeping for 5 minutes") + logger.info("Processing ended, sleeping for 5 minutes") sleep(3) diff --git a/document_indexer_service/document_indexer_service_test.py b/document_indexer_service/document_indexer_service_test.py index 575ebd1..fab5094 100644 --- a/document_indexer_service/document_indexer_service_test.py +++ b/document_indexer_service/document_indexer_service_test.py @@ -1,11 +1,3 @@ -import pytest -import os -import inspect -import sys - -from document_indexer_service.document_indexer_service import DocumentIndexerService - - class TestFullTextRetrieverService: """ def test_retrieve_xml_fields_from_directory(self): diff --git a/document_retriever_service/catalog_retriever_service.py b/document_retriever_service/catalog_retriever_service.py index 1a8b0a5..302bffb 100644 --- a/document_retriever_service/catalog_retriever_service.py +++ b/document_retriever_service/catalog_retriever_service.py @@ -1,75 +1,77 @@ -# from document_retrieval_service.document_retrieval_service import DocumentRetrievalService -import json import argparse +import json -from document_retriever_service.document_retriever_service import ( - DocumentRetrieverService, -) -from ht_indexer_api.ht_indexer_api import HTSolrAPI +from catalog_metadata.catalog_metadata import CatalogRecordMetadata, CatalogItemMetadata +from ht_indexer_api.ht_indexer_api import HTSolrAPI from ht_utils.ht_logger import get_ht_logger logger = get_ht_logger(name=__name__) -class CatalogRetrieverService(DocumentRetrieverService): - def __init__(self, catalogApi=None): - super().__init__() +class CatalogRetrieverService: + def __init__(self, catalog_api=None): - self.catalogApi = catalogApi + self.catalog_api = catalog_api + + @staticmethod + def get_catalog_object(record: dict, item_id: str, + record_metadata: CatalogRecordMetadata) -> CatalogItemMetadata: + + catalog_item_metadata = CatalogItemMetadata(record, item_id, record_metadata) + return catalog_item_metadata def retrieve_documents(self, query, start, rows): - response = self.catalogApi.get_documents(query=query, start=start, rows=rows) + + """ + This method is used to retrieve the documents from the Catalog, then it will be used to return instances + of a CatalogMetadata + """ + + response = self.catalog_api.get_documents(query=query, start=start, rows=rows) output = response.json() try: total_records = output.get("response").get("numFound") logger.info(total_records) except Exception as e: - logger.error(f"Solr index {self.catalogApi} seems empty {e}") + logger.error(f"Solr index {self.catalog_api} seems empty {e}") exit() count_records = 0 while count_records < total_records: results = [] - response = self.catalogApi.get_documents( + response = self.catalog_api.get_documents( query=query, start=start, rows=rows ) output = json.loads(response.content.decode("utf-8")) + # TODO: Add a check to verify if the response is empty + for record in output.get("response").get("docs"): count_records = count_records + 1 - results.append(record) + + catalog_record_metadata = CatalogRecordMetadata(record) + if 'ht_id' in query: + # Process a specific item of a record + try: + item_id = query.split(':')[1] + except Exception as e: + logger.error(f"Query {query} does not have a valid format {e}") + exit() + results.append(CatalogRetrieverService.get_catalog_object(record, item_id, catalog_record_metadata)) + # This is the most efficient way to retrieve the items from Catalog + else: + # Process all the items of a record + for item_id in record.get('ht_id'): # Append list of CatalogMetadata object + results.append(CatalogRetrieverService.get_catalog_object(record, item_id, + catalog_record_metadata)) logger.info(f"Batch documents {count_records}") start += rows logger.info(f"Result lenght {len(results)}") yield results - def retrieve_list_ht_ids(self, query, start, rows, all_items: bool = False): - total_htid = 0 - for results in self.retrieve_documents(query, start, rows): - for record in results: - if all_items: - for item_id in record.get("ht_id"): - total_htid = total_htid + 1 - logger.info(f"Processing document {item_id}") - yield item_id - else: - try: - item_id = record.get("ht_id")[0] - except Exception as e: - logger.error( - f"The record {record.get('id')} does not have items." - ) - continue - total_htid = total_htid + 1 - logger.info(f"Processing document {item_id}") - yield item_id - continue - - logger.info(f"Total of items (ht_id) {total_htid}") - def main(): parser = argparse.ArgumentParser() @@ -79,13 +81,17 @@ def main(): required=True, default="http://localhost:8983/solr/#/core-x/", ) - parser.add_argument( - "--all_items", - help="If store, you will obtain all the items of record, otherwise you will retrieve only the first item", - action="store_true", - default=False, - ) + parser.add_argument("--query", help="Query used to retrieve documents", default='*:*' + ) + + parser.add_argument("--output_file", + help="Path of the file to load the list of ht_id.", + required=False, + default="../items_list.txt" + ) + + # Use case: Given a query, generate a list of ht_id from Catalog index args = parser.parse_args() solr_api_catalog = HTSolrAPI(url=args.solr_url) @@ -93,21 +99,18 @@ def main(): catalog_retrieval_service = CatalogRetrieverService(solr_api_catalog) count = 0 - # TODO How can I paralelize the process of retrieving documents from solr Catalog? - # Print ids - file_object = open("../items_list.txt", "w+") + # TODO Parallelize the process of retrieving documents from solr Catalog + file_object = open(args.output_file, "w+") - query = "*:*" start = 0 rows = 100 - for ht_id in catalog_retrieval_service.retrieve_list_ht_ids( - query, start, rows, all_items=args.all_items - ): - count = count + 1 - # list_ids.append(ht_id) - logger.info(f"Item id: {ht_id}") - file_object.write(f"{ht_id}\n") + for result in catalog_retrieval_service.retrieve_documents(args.query, start, rows): + for record in result: + item_id = record.ht_id + logger.info(f"Item id: {item_id}") + file_object.write(f"{item_id}\n") + count = count + 1 file_object.close() logger.info(count) diff --git a/document_retriever_service/full_text_search_retriever_service.py b/document_retriever_service/full_text_search_retriever_service.py index cd92949..faf1130 100644 --- a/document_retriever_service/full_text_search_retriever_service.py +++ b/document_retriever_service/full_text_search_retriever_service.py @@ -1,90 +1,104 @@ +import argparse +import inspect import os import sys -import inspect - -import argparse - -from ht_utils.ht_logger import get_ht_logger -from ht_status_retriever_service import get_non_processed_ids - -logger = get_ht_logger(name=__name__) - -currentdir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe()))) -parentdir = os.path.dirname(currentdir) -sys.path.insert(0, parentdir) - +import catalog_metadata.catalog_metadata as catalog_metadata from document_generator.document_generator import DocumentGenerator +from ht_utils.ht_logger import get_ht_logger from catalog_retriever_service import CatalogRetrieverService - -from ht_indexer_api.ht_indexer_api import HTSolrAPI - -from ht_utils.ht_mysql import create_mysql_conn +import ht_indexer_api.ht_indexer_api +import ht_utils.ht_mysql from ht_utils.text_processor import create_solr_string -from document_generator.indexer_config import DOCUMENT_LOCAL_PATH +from indexer_config import DOCUMENT_LOCAL_PATH from ht_document.ht_document import HtDocument +logger = get_ht_logger(name=__name__) + +current = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe()))) +parent = os.path.dirname(current) +sys.path.insert(0, parent) + class FullTextSearchRetrieverService(CatalogRetrieverService): - def __init__(self, catalogApi=None, document_generator=None): - super().__init__(catalogApi=catalogApi) - - self.document_generator = document_generator - - def generate_full_text_entry(self, query, start, rows, all_items, document_repository, chunk=None): - - # TODO: Split the logic of retrieve_documents and generate_full_text_entry. The function that generates the entry - # should receive the ht_id to process and their metadata. - # The logic to retrieve from Catalog (all fields or only the first one) should be in the retrieve_documents function - # Right now the logic is too complex because if I want to retrieve all the items of a record, then in the query I should I the id - # but if I want to retrieve an specific item (ht_id), then I should use the ht_id field in the query - # This is not intuitive and it is not clear - # An issue of the current implementation is that we are processing the first element of the record and not the - # ht_id passed as a parameter - - for results in self.retrieve_documents(query, start, rows): - for record in results: - """ - if all_items: - # Process all the records of a Catalog - total_items = len(record.get("ht_id")) - else: - # Process the first item of the Catalog record - total_items = 1 - """ - for i in range(0, len(record.get("ht_id"))): - current_ht_id = record.get("ht_id")[i] - if current_ht_id in chunk: - item_id = record.get("ht_id")[i] - logger.info(f"Item ID {item_id}") - - logger.info(f"Processing document {item_id}") - - # Instantiate each document - ht_document = HtDocument(document_id=item_id, document_repository=document_repository) - - logger.info(f"Checking path {ht_document.source_path}") - - # TODO: Temporal local for testing using a sample of files - # Checking if the file exist, otherwise go to the next - if os.path.isfile(f"{ht_document.source_path}.zip"): - - logger.info(f"Processing item {ht_document.document_id}") - - try: - entry = self.document_generator.make_full_text_search_document( - ht_document, record - ) - # yield entry - except Exception as e: - logger.error(f"Document {item_id} failed {e}") - continue - - yield entry, ht_document.file_name, ht_document.namespace, item_id - else: - logger.info(f"{ht_document.document_id} does not exist") - continue - else: - continue + """ + This class is responsible to retrieve the documents from the Catalog and generate the full text search entry + There are three main use cases: + 1- Retrieve all the items of a record in the Catalog - the query will contain the id of the record + 2- Retrieve a specific item of a record in the Catalog - the query will contain the ht_id of the item + 3- Retrieve all the items of all the records in the Catalog - the query will be *:* + By default, the query is None, then an error will be raised if the query is not provided + """ + + def __init__(self, catalog_api=None, + document_generator_obj: DocumentGenerator = None, + document_local_path: str = None, document_local_folder: str = None + ): + super().__init__(catalog_api) + self.document_generator = document_generator_obj + + # TODO: Define the queue to publish the documents + self.document_local_path = document_local_path + self.document_local_folder = document_local_folder + + # Create the directory to load the xml files if it does not exit + try: + if self.document_local_path: + document_local_path = os.path.abspath(self.document_local_path) + os.makedirs(os.path.join(document_local_path, document_local_folder)) + except FileExistsError: + pass + + def publish_document(self, file_name: str = None, content: str = None): + """ + Right now, the entry is saved in a file and, but it could be published in a queue + + """ + file_path = f"{os.path.join(self.document_local_path, self.document_local_folder)}/{file_name}" + with open(file_path, "w") as f: + f.write(content) + logger.info(f"File {file_name} created in {file_path}") + + def full_text_search_retriever_service(self, query, start, rows, document_repository): + """ + This method is used to retrieve the documents from the Catalog and generate the full text search entry + """ + count = 0 + for result in self.retrieve_documents(query, start, rows): + for record in result: + + item_id = record.ht_id + logger.info(f"Processing document {item_id}") + + try: + self.generate_full_text_entry(item_id, record, document_repository) + except Exception as e: + logger.error(f"Document {item_id} failed {e}") + continue + count += len(result) + logger.info(f"Total of processed items {count}") + + def generate_full_text_entry(self, item_id: str, record: catalog_metadata.CatalogItemMetadata, + document_repository: str): + + logger.info(f"Generating document {item_id}") + + # Instantiate each document + ht_document = HtDocument(document_id=item_id, document_repository=document_repository) + + logger.info(f"Checking path {ht_document.source_path}") + + # TODO: Temporal local for testing using a sample of files + # Checking if the file exist, otherwise go to the next + if os.path.isfile(f"{ht_document.source_path}.zip"): + logger.info(f"Processing item {ht_document.document_id}") + try: + entry = self.document_generator.make_full_text_search_document(ht_document, record) + except Exception as e: + raise e + self.publish_document(file_name=f"{ht_document.namespace}{ht_document.file_name}_solr_full_text.xml", + content=create_solr_string(entry)) + else: + logger.info(f"{ht_document.document_id} does not exist") def main(): @@ -97,7 +111,7 @@ def main(): logger.error("Error: `SOLR_URL` environment variable required") sys.exit(1) - solr_api_catalog = HTSolrAPI(url=solr_url) + solr_api_catalog = ht_indexer_api.ht_indexer_api.HTSolrAPI(url=solr_url) # MySql connection try: @@ -118,141 +132,53 @@ def main(): logger.error("Error: `MYSQL_PASS` environment variable required") sys.exit(1) - db_conn = create_mysql_conn( + ht_mysql = ht_utils.ht_mysql.HtMysql( host=mysql_host, user=mysql_user, password=mysql_pass, - database=os.environ.get("MYSQL_DATABASE", "ht"), + database=os.environ.get("MYSQL_DATABASE", "ht") ) + logger.info("Access by default to `ht` Mysql database") - # By default, only the first item of each record is process - # If ALL_ITEMS=True, then all the items per record will be processed - parser.add_argument( - "--all_items", - help="If store, you will obtain all the items of record, otherwise you will retrieve only the first item", - action="store_true", - default=False, - ) + parser.add_argument("--query", help="Query used to retrieve documents", default=None + ) - parser.add_argument( - "--query", help="Query used to retrieve documents", default="*:*" - ) - parser.add_argument( - "--document_repository", help="Could be pairtree or local", default="local" - ) + parser.add_argument("--document_repository", + help="Could be pairtree or local", default="local" + ) # Path to the folder where the documents are stored. This parameter is useful for runing the script locally - parser.add_argument( - "--document_local_path", - help="Path of the folder where the documents (.xml file to index) are stored.", - required=False, - default=None - ) - - parser.add_argument( - "--list_ids_path", - help="Path of the TXT files with the list of id to generate", - required=False, - default=None - ) + parser.add_argument("--document_local_path", + help="Path of the folder where the documents (.xml file to index) are stored.", + required=False, + default=None + ) args = parser.parse_args() - document_generator = DocumentGenerator(db_conn) - - document_indexer_service = FullTextSearchRetrieverService( - solr_api_catalog, document_generator - ) + document_generator = DocumentGenerator(ht_mysql) document_local_folder = "indexing_data" document_local_path = DOCUMENT_LOCAL_PATH - # Create the directory to load the xml files if it does not exit + document_indexer_service = FullTextSearchRetrieverService(solr_api_catalog, document_generator, document_local_path, + document_local_folder + ) - try: - if args.document_local_path: - document_local_path = os.path.abspath(args.document_local_path) - os.makedirs(os.path.join(document_local_path, document_local_folder)) - except FileExistsError: - pass - - count = 0 - query = args.query + if args.query is None: + logger.error("Error: `query` parameter required") + sys.exit(1) + + # TODO: Add start and rows to a configuration file start = 0 rows = 100 - status_file = os.path.join(parentdir, "document_retriever_status.txt") - - if args.list_ids_path: - # If a document with the list of id to process is received as a parameter, then create batch of queries - with open(args.list_ids_path) as f: - list_ids = f.read().splitlines() - - ids2process, processed_ids = get_non_processed_ids(status_file, list_ids) - - logger.info(f"Total of items to process {len(ids2process)}") - - tmp_file_status = open(os.path.join(document_local_path, "document_retriever_status.txt"), "w+") - for doc in processed_ids: - tmp_file_status.write(doc + "\n") - tmp_file_status.close() - - while ids2process: - chunk, ids2process = ids2process[:100], ids2process[100:] - values = "\" OR \"".join(chunk) - values = '"'.join(("", values, "")) - query = f"ht_id:({values})" - - for ( - entry, - file_name, - namespace, - item_id - ) in document_indexer_service.generate_full_text_entry( - query, - start, - rows, - all_items=args.all_items, - document_repository=args.document_repository, - chunk=chunk - ): - count = count + 1 - solr_str = create_solr_string(entry) - logger.info(f"Creating XML file to index") - with open( - f"/{os.path.join(document_local_path, document_local_folder)}/{namespace}{file_name}_solr_full_text.xml", - "w", - ) as f: - f.write(solr_str) - - with open(os.path.join(document_local_path, 'document_retriever_status.txt'), "a+") as file: - file.write(item_id + "\n") - - logger.info(count) - - else: - for ( - entry, - file_name, - namespace, - ) in document_indexer_service.generate_full_text_entry( - query, - start, - rows, - all_items=args.all_items, - document_repository=args.document_repository - ): - count = count + 1 - solr_str = create_solr_string(entry) - logger.info(f"Creating XML file to index") - with open( - f"/{os.path.join(document_local_path, document_local_folder)}/{namespace}{file_name}_solr_full_text.xml", - "w", - ) as f: - f.write(solr_str) - - logger.info(count) + document_indexer_service.full_text_search_retriever_service( + args.query, + start, + rows, + document_repository=args.document_repository) if __name__ == "__main__": diff --git a/document_retriever_service/full_text_search_retriever_service_test.py b/document_retriever_service/full_text_search_retriever_service_test.py index 0965847..6abcca0 100644 --- a/document_retriever_service/full_text_search_retriever_service_test.py +++ b/document_retriever_service/full_text_search_retriever_service_test.py @@ -1,14 +1,9 @@ -import pytest -import os -import inspect -import sys - -currentdir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe()))) -parentdir = os.path.dirname(currentdir) -sys.path.insert(0, parentdir) +class TestFullTextRetrieverService: + def test_publish_document(self): + # TODO Use the json file to index the document without the need to connect to the Catalog + pass -class TestFullTextRetrieverService: """ def test_create_directory_to_load_xml_fields(self): document_local_path = "indexing_data" diff --git a/ht_indexer_api/ht_indexer_api_test.py b/ht_indexer_api/ht_indexer_api_test.py index 3d8e76b..7afb1e1 100644 --- a/ht_indexer_api/ht_indexer_api_test.py +++ b/ht_indexer_api/ht_indexer_api_test.py @@ -1,6 +1,7 @@ -import pytest -from pathlib import Path import os +from pathlib import Path + +import pytest from ht_indexer_api.ht_indexer_api import HTSolrAPI From d53dd202b9bf13bbd6736e7e07f8a90eabebc143 Mon Sep 17 00:00:00 2001 From: Lianet Sepulveda Torres Date: Thu, 22 Feb 2024 19:18:46 -0500 Subject: [PATCH 13/30] code optimization --- ht_utils/convert_solr_schema2csv.py | 2 +- ht_utils/ht_logger.py | 3 ++- ht_utils/ht_pairtree.py | 8 ++++---- ht_utils/text_processor.py | 6 +++--- indexer_config.py | 3 ++- 5 files changed, 12 insertions(+), 10 deletions(-) diff --git a/ht_utils/convert_solr_schema2csv.py b/ht_utils/convert_solr_schema2csv.py index 26d85ff..6a7cf94 100644 --- a/ht_utils/convert_solr_schema2csv.py +++ b/ht_utils/convert_solr_schema2csv.py @@ -23,7 +23,7 @@ {"origen": f"copyField by {field.attrib['source']}"} ) -schema_fields_list = list(schema_fields_dic.values()) +schema_fields_list = dict(schema_fields_dic.values()) df = pd.DataFrame.from_dict(schema_fields_list, orient="columns") df.to_csv(sep="\t", path_or_buf="full_text_fields.csv", encoding="utf-8") diff --git a/ht_utils/ht_logger.py b/ht_utils/ht_logger.py index 40f3e89..fca90c3 100644 --- a/ht_utils/ht_logger.py +++ b/ht_utils/ht_logger.py @@ -1,4 +1,5 @@ -import logging, sys +import logging +import sys def get_ht_logger(name=__name__, log_level=logging.INFO): diff --git a/ht_utils/ht_pairtree.py b/ht_utils/ht_pairtree.py index 4362345..391917c 100644 --- a/ht_utils/ht_pairtree.py +++ b/ht_utils/ht_pairtree.py @@ -8,22 +8,22 @@ def download_document_file( - source_path: str = None, target_path: str = None, extension: str = "zip" + source_path: str = None, target_path: str = None, extension: str = "zip" ): try: public_key = os.environ["PUBLIC_KEY"] except KeyError: - print(f"Please define the environment variable PUBLIC_KEY") + print("Please define the environment variable PUBLIC_KEY") sys.exit(1) try: user = os.environ["USER"] except KeyError: - logger.info(f"Please define the environment variable USER") + logger.info("Please define the environment variable USER") sys.exit(1) try: host = os.environ["HOST"] except KeyError: - logger.info(f"Please define the environment variable HOST") + logger.info("Please define the environment variable HOST") sys.exit(1) # Copy the file from remote path diff --git a/ht_utils/text_processor.py b/ht_utils/text_processor.py index 79240e3..1dc6705 100644 --- a/ht_utils/text_processor.py +++ b/ht_utils/text_processor.py @@ -1,8 +1,8 @@ -from io import BytesIO - import re -from xml.sax.saxutils import quoteattr +from io import BytesIO from typing import Dict, List +from xml.sax.saxutils import quoteattr + from ht_utils.ht_logger import get_ht_logger table = str.maketrans( diff --git a/indexer_config.py b/indexer_config.py index 6c5c849..631eaf6 100644 --- a/indexer_config.py +++ b/indexer_config.py @@ -7,7 +7,7 @@ DOCUMENT_LOCAL_PATH = "/tmp/" # Variables to manage IO operations, local folder with files -LOCAL_DOCUMENT_FOLDER = f"{Path(__file__).parents[2]}/sdr1/obj" +LOCAL_DOCUMENT_FOLDER = f"{Path(__file__).parents[1]}/sdr1/obj" TRANSLATE_TABLE = str.maketrans({"=": r"\=", ",": r"\,"}) @@ -72,4 +72,5 @@ "countryOfPubStr", "genre", "era", + "fullrecord" ] From 9abdb83fb04549cd446c33accafab7022d76e218 Mon Sep 17 00:00:00 2001 From: Lianet Sepulveda Torres Date: Thu, 22 Feb 2024 19:19:30 -0500 Subject: [PATCH 14/30] update dependencies --- poetry.lock | 1348 ++++++++++++++++++++++++------------------------ pyproject.toml | 1 + 2 files changed, 668 insertions(+), 681 deletions(-) diff --git a/poetry.lock b/poetry.lock index 01725b6..c3e7078 100644 --- a/poetry.lock +++ b/poetry.lock @@ -7,19 +7,19 @@ description = "Reusable constraint types to use with typing.Annotated" optional = false python-versions = ">=3.8" files = [ - {file = "annotated_types-0.6.0-py3-none-any.whl", hash = "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43"}, - {file = "annotated_types-0.6.0.tar.gz", hash = "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"}, + { file = "annotated_types-0.6.0-py3-none-any.whl", hash = "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43" }, + { file = "annotated_types-0.6.0.tar.gz", hash = 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[package.dependencies] @@ -1235,4 +1221,4 @@ standard = ["colorama (>=0.4)", "httptools (>=0.5.0)", "python-dotenv (>=0.13)", [metadata] lock-version = "2.0" python-versions = "^3.11" -content-hash = "482e973446be52b2b842e208e515fca5db0e4b07fa37eec6c5a92885b9790825" +content-hash = "25e4313ce2d4819ce5e3f8bc89a7404398cd4dc0fa9a2771f48ff576ae76ced9" diff --git a/pyproject.toml b/pyproject.toml index 115f1a7..fdc42e8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -35,6 +35,7 @@ nest-asyncio = "^1.5.6" #pytest = "^7.4.0" #nest-asyncio = "^1.5.6" python-dotenv = "^1.0.0" +ruff = "^0.2.2" [build-system] requires = ["poetry-core>=1.5.1"] From b8d73727ceab469df63363611459abaf87672e0f Mon Sep 17 00:00:00 2001 From: Lianet Sepulveda Torres Date: Thu, 22 Feb 2024 19:20:49 -0500 Subject: [PATCH 15/30] including use case for processing documents in batch (kubernetes) --- .../full_text_search_retriever_by_file.py | 198 ++++++++++++++++++ 1 file changed, 198 insertions(+) create mode 100644 document_retriever_service/full_text_search_retriever_by_file.py diff --git a/document_retriever_service/full_text_search_retriever_by_file.py b/document_retriever_service/full_text_search_retriever_by_file.py new file mode 100644 index 0000000..33fb870 --- /dev/null +++ b/document_retriever_service/full_text_search_retriever_by_file.py @@ -0,0 +1,198 @@ +""" +This script is used to generate the full text search entries for a list of ht_id defined in a TXT file +""" +import argparse +import inspect +import json +import os +import sys + +from catalog_metadata.catalog_metadata import CatalogRecordMetadata +from document_generator.document_generator import DocumentGenerator +from document_retriever_service.catalog_retriever_service import CatalogRetrieverService +from document_retriever_service.full_text_search_retriever_service import FullTextSearchRetrieverService +from document_retriever_service.ht_status_retriever_service import get_non_processed_ids +from ht_document.ht_document import logger +from ht_indexer_api.ht_indexer_api import HTSolrAPI +import ht_utils.ht_mysql +from indexer_config import DOCUMENT_LOCAL_PATH + +current = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe()))) +parent = os.path.dirname(current) +sys.path.insert(0, parent) + + +class FullTextSearchRetrieverServiceByFile(FullTextSearchRetrieverService): + + def __init__(self, catalog_api: HTSolrAPI, + document_generator_obj: DocumentGenerator = None, + document_local_path: str = None, document_local_folder: str = None + ): + FullTextSearchRetrieverService.__init__(self, catalog_api, document_generator_obj, + document_local_path, + document_local_folder) + + def retrieve_documents(self, query, start, rows): + + """ + This method is used to retrieve the documents from the Catalog, then it will be used to return instances + of a CatalogMetadata + """ + + # Get list ids from query parameter + if 'ht_id' in query and ' OR ' in query: + list_ids = [i.strip("\)").strip('\"') for i in query.split(':(')[1].split(' OR ')] + else: + logger.info(f"Query {query} does not have a valid format for this use case") + exit() + + response = self.catalog_api.get_documents(query=query, start=start, rows=rows) + output = response.json() + + try: + total_records = output.get("response").get("numFound") + logger.info(total_records) + except Exception as e: + logger.error(f"Solr index {self.catalog_api} seems empty {e}") + exit() + count_records = 0 + while count_records < total_records: + results = [] + response = self.catalog_api.get_documents( + query=query, start=start, rows=rows + ) + + output = json.loads(response.content.decode("utf-8")) + + # TODO: Add a check to verify if the response is empty + + for record in output.get("response").get("docs"): + count_records = count_records + 1 + + catalog_record_metadata = CatalogRecordMetadata(record) + + for item_id in record.get('ht_id'): # Append list of CatalogMetadata object + if item_id in list_ids: + results.append(CatalogRetrieverService.get_catalog_object(record, item_id, + catalog_record_metadata)) + + logger.info(f"Batch documents {count_records}") + start += rows + logger.info(f"Result length {len(results)}") + yield results + + +def main(): + parser = argparse.ArgumentParser() + + # Catalog Solr server + try: + solr_url = os.environ["SOLR_URL"] + except KeyError: + logger.error("Error: `SOLR_URL` environment variable required") + sys.exit(1) + + # MySql connection + try: + mysql_host = os.environ["MYSQL_HOST"] + except KeyError: + logger.error("Error: `MYSQL_HOST` environment variable required") + sys.exit(1) + + try: + mysql_user = os.environ["MYSQL_USER"] + except KeyError: + logger.error("Error: `MYSQL_USER` environment variable required") + sys.exit(1) + + try: + mysql_pass = os.environ["MYSQL_PASS"] + except KeyError: + logger.error("Error: `MYSQL_PASS` environment variable required") + sys.exit(1) + + ht_mysql = ht_utils.ht_mysql.HtMysql( + host=mysql_host, + user=mysql_user, + password=mysql_pass, + database=os.environ.get("MYSQL_DATABASE", "ht") + ) + + logger.info("Access by default to `ht` Mysql database") + + parser.add_argument( + "--document_repository", help="Could be pairtree or local", default="local" + ) + + # Path to the folder where the documents are stored. This parameter is useful for runing the script locally + parser.add_argument( + "--document_local_path", + help="Path of the folder where the documents (.xml file to index) are stored.", + required=False, + default=None + ) + + parser.add_argument( + "--list_ids_path", + help="Path of the TXT files with the list of id to generate", + required=False, + default=None + ) + + args = parser.parse_args() + + # Create the CatalogRetrieverService object + # catalog_retriever_service = CatalogRetrieverService(solr_api_catalog) + + document_generator = DocumentGenerator(ht_mysql) + + document_local_folder = "indexing_data" + document_local_path = DOCUMENT_LOCAL_PATH + + solr_api_catalog = HTSolrAPI(url=solr_url) + + document_indexer_service = FullTextSearchRetrieverServiceByFile(solr_api_catalog, + document_generator, + document_local_path, + document_local_folder) + + # TODO: Add start and rows to a configuration file + start = 0 + rows = 100 + + # TODO: Review the logic of the status file + status_file = os.path.join(parent, "document_retriever_status.txt") + + if args.list_ids_path: + # If a document with the list of id to process is received as a parameter, then create batch of queries + with open(args.list_ids_path) as f: + list_ids = f.read().splitlines() + + ids2process, processed_ids = get_non_processed_ids(status_file, list_ids) + + logger.info(f"Total of items to process {len(ids2process)}") + + tmp_file_status = open(os.path.join(document_local_path, "document_retriever_status.txt"), "w+") + for doc in processed_ids: + tmp_file_status.write(doc + "\n") + tmp_file_status.close() + + while ids2process: + chunk, ids2process = ids2process[:5], ids2process[5:] + values = "\" OR \"".join(chunk) + values = '"'.join(("", values, "")) + query = f"ht_id:({values})" + + # Create queries that contain a list of ht_id + document_indexer_service.full_text_search_retriever_service( + query, + start, + rows, + document_repository=args.document_repository) + else: + logger.info("Provide the file with the list of ids to process is a required parameter") + exit() + + +if __name__ == "__main__": + main() From 39ef80c2d715a9be31232db567e9ffbda700fbf7 Mon Sep 17 00:00:00 2001 From: Lianet Sepulveda Torres Date: Thu, 22 Feb 2024 20:27:58 -0500 Subject: [PATCH 16/30] update the script for generating batch of documents in Kubernetes --- run_retriever_processor_kubernetes.sh | 17 +++-------------- 1 file changed, 3 insertions(+), 14 deletions(-) diff --git a/run_retriever_processor_kubernetes.sh b/run_retriever_processor_kubernetes.sh index 44ddcf4..2cb9018 100755 --- a/run_retriever_processor_kubernetes.sh +++ b/run_retriever_processor_kubernetes.sh @@ -1,17 +1,6 @@ #!/usr/bin/env bash -# TODO ADD ALL_ITEMS parameter -#if [ $source_resource=='local' ]; then - # You should use the sample_data_creator.sh script to generate the local folder with the documents you want to process -#for line in $(cat "$PWD/filter_ids.txt") -# do -# ht_id="$line" -# echo "🔁 Processing record $ht_id" -python document_retriever_service/full_text_search_retriever_service.py --list_ids_path "$PWD/filter_ids.txt" --document_repository pairtree - # docker compose exec document_retriever python document_retriever_service/full_text_search_retriever_service.py --query ht_id:"$ht_id" -# done -#else # This option should work in Kubernetes, not use it locally if you do not have a local folder like a pairtree repository -# echo "🔁 Processing all the record included in Catalog image" -# docker compose exec document_retriever python document_retriever_service/full_text_search_retriever_service.py --query "*:*" --document_repository pairtree -#fi + +# This script is used to run the retriever processor in a kubernetes environment and having a TXT file with the list of IDs to be processed. +python document_retriever_service/full_text_search_retriever_by_file.py --list_ids_path "$PWD/filter_ids.txt" --document_repository pairtree echo "🎉 Done!" \ No newline at end of file From 0d87e2ae9f6992d8b94a2ec75e4664174cda391c Mon Sep 17 00:00:00 2001 From: Lianet Sepulveda Torres Date: Fri, 23 Feb 2024 10:53:57 -0500 Subject: [PATCH 17/30] add steps to test indexer service locally --- README.md | 19 +++++++++++++++++++ docker-compose.yml | 2 +- ht_utils/text_processor.py | 8 ++------ 3 files changed, 22 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index d6c8f39..48c0879 100644 --- a/README.md +++ b/README.md @@ -222,6 +222,25 @@ On mac, * `` poetry export -f requirements.txt --output requirements.txt `` * Use `` poetry update `` if you change your .toml file and want to generate a new version the .lock file +## How to test locally indexer service + +In your workdir: + +Step 1. Create /sdr1/obj directory +`mkdir ../sdr1/obj` + +Step 2. Retrieve from pairtree repository data for testing +`scp $HT_SSH_HOST:/sdr1/obj/umn/pairtree_root/31/95/1d/03/01/41/20/v/31951d03014120v/31951d03014120v{.zip,mets.xml} ../sdr1/obj` + +Step 3. Create the image +`docker build -t document_generator . docker compose up document_retriever -d` + +Step 4. export MYSQL_USER= +export MYSQL_PASS= + +Step 5. Generate document +`docker exec document_retriever python document_retriever_service/full_text_search_retriever_service.py --query ht_id:mb.39015078560292 --document_local_path /Users/lisepul/Documents/repositories/python/tmp --document_repository local` + ## DockerFile explanations **What is the best python Docker image to use?** diff --git a/docker-compose.yml b/docker-compose.yml index 364312e..02ec69d 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -11,7 +11,7 @@ services: - "8081:8081" environment: - SOLR_URL=http://solr-sdr-catalog:9033/solr/#/catalog/ - - MYSQL_HOST=mudslide.umdl.umich.edu + - MYSQL_HOST=macc-ht-mysql-ro.umdl.umich.edu - MYSQL_USER=${MYSQL_USER} - MYSQL_PASS=${MYSQL_PASS} - MYSQL_DATABASE=ht diff --git a/ht_utils/text_processor.py b/ht_utils/text_processor.py index 1dc6705..4dbca2c 100644 --- a/ht_utils/text_processor.py +++ b/ht_utils/text_processor.py @@ -33,12 +33,8 @@ def string_preparation(doc_content: BytesIO) -> str: # Convert byte to str str_content = str(doc_content.decode()) except Exception as e: - try: - str_content = str(doc_content.decode(encoding="latin1")) - logger.info(f"File encode compatible with latin1 {e}") - except Exception as e: - logger.info(f"There are especial characters on the file {e}") - raise Exception + logger.info(f"File encode incompatible with UTF-8 {e}") + raise Exception # Remove line breaks str_content = str_content.replace("\n", " ") From c18583dd0c85a113c31241a279a1c7badcf3ec73 Mon Sep 17 00:00:00 2001 From: Lianet Sepulveda Torres Date: Thu, 7 Mar 2024 18:37:27 -0500 Subject: [PATCH 18/30] documenting enumcrom generation --- catalog_metadata/catalog_metadata_test.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/catalog_metadata/catalog_metadata_test.py b/catalog_metadata/catalog_metadata_test.py index 0b8463a..1da6a4c 100644 --- a/catalog_metadata/catalog_metadata_test.py +++ b/catalog_metadata/catalog_metadata_test.py @@ -65,11 +65,10 @@ def test_get_item_htsource_sharinghtsource(self): assert htsource == "University of Michigan" def test_get_volume_enumcron_empty(self): - # TODO: Check if is correct the generation of volume_enumcrom (line 417: - # https://github.com/hathitrust/slip-lib/blob/master/Document/Doc/vSolrMetadataAPI/Schema_LS_11.pm) """ Some documents do not have the field volume_enumcrom, that is because it is an empty string in the second position. - Is that correct + See here https://github.com/hathitrust/hathitrust_catalog_indexer/blob/main/indexers/common_ht.rb#L50 how this + field is generated. :return: """ volume_enumcrom = "" From 6093ed24d27313785091cec1f61ba0ed5267fab8 Mon Sep 17 00:00:00 2001 From: Lianet Sepulveda Torres Date: Thu, 7 Mar 2024 18:39:06 -0500 Subject: [PATCH 19/30] add db-image to access MySQL --- docker-compose.yml | 34 +++++++++++++++++++++++++++++----- 1 file changed, 29 insertions(+), 5 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index 02ec69d..894aeef 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -1,4 +1,5 @@ version: "3" + services: document_retriever: container_name: document_retriever @@ -6,23 +7,45 @@ services: volumes: - ../tmp:/tmp:rm - ../sdr1/obj:/sdr1/obj - #- ../sample_data/sdr1/obj:/sample_data ports: - "8081:8081" environment: - SOLR_URL=http://solr-sdr-catalog:9033/solr/#/catalog/ - - MYSQL_HOST=macc-ht-mysql-ro.umdl.umich.edu - - MYSQL_USER=${MYSQL_USER} - - MYSQL_PASS=${MYSQL_PASS} - - MYSQL_DATABASE=ht - SDR_DIR=/sdr1/obj depends_on: solr-sdr-catalog: condition: service_healthy solr-lss-dev: condition: service_healthy + mysql-sdr: + condition: service_healthy tty: true stdin_open: true + mysql-sdr: + image: ghcr.io/hathitrust/db-image + volumes: + - mysql_sdr_data:/var/lib/mysql + restart: always + ports: + - "3307:3306" + environment: + - MYSQL_HOST=mysql-sdr + - MYSQL_USER=mdp-lib + - MYSQL_PASS=mdp-lib + - MYSQL_DATABASE=ht + - MYSQL_RANDOM_ROOT_PASSWORD=1 + healthcheck: + interval: 30s + retries: 3 + test: + [ + "CMD", + "healthcheck.sh", + "--su-mysql", + "--connect", + "--innodb_initialized" + ] + timeout: 30s solr-lss-dev: image: ghcr.io/hathitrust/full-text-search-embedded_zoo:example-8.11 container_name: solr-lss-dev @@ -76,4 +99,5 @@ services: stdin_open: true volumes: solr_data: + mysql_sdr_data: From 3a18a5847856ac7908127dcf44ab637148d2d21a Mon Sep 17 00:00:00 2001 From: Lianet Sepulveda Torres Date: Thu, 7 Mar 2024 18:39:37 -0500 Subject: [PATCH 20/30] create new methods to generate some fields --- document_generator/mysql_data_extractor.py | 42 ++++++++++++++-------- 1 file changed, 27 insertions(+), 15 deletions(-) diff --git a/document_generator/mysql_data_extractor.py b/document_generator/mysql_data_extractor.py index 14e8aa8..5e55035 100644 --- a/document_generator/mysql_data_extractor.py +++ b/document_generator/mysql_data_extractor.py @@ -5,6 +5,28 @@ logger = get_ht_logger(name=__name__) +def create_coll_id_field(coll_id_result, large_coll_id_result) -> dict: + if len(coll_id_result) > 0: + list_coll_ids = [coll_id.get("MColl_ID") for coll_id in coll_id_result] + list_large_coll_id = [ + coll_id.get("MColl_ID") for coll_id in large_coll_id_result + ] + + return {"coll_id": list(set(list_coll_ids) & set(list_large_coll_id))} + else: + return {"coll_id": [0]} + + +def create_ht_heldby_brlm_field(heldby_brlm) -> dict: + list_brl_members = [member_id.get("member_id") for member_id in heldby_brlm] + return {"ht_heldby_brlm": list_brl_members} + + +def create_ht_heldby_field(heldby_brlm) -> dict: + list_brl_members = [member_id.get("member_id") for member_id in heldby_brlm] + return {"ht_heldby": list_brl_members} + + class MysqlMetadataExtractor: def __init__(self, db_conn: HtMysql): self.mysql_obj = db_conn @@ -78,26 +100,16 @@ def retrieve_mysql_data(self, doc_id): # It is a list of members, if the query result is empty the field does not appear in Solr index ht_heldby = self.add_ht_heldby_field(doc_id) if len(ht_heldby) > 0: - list_members = [member_id.get("member_id") for member_id in ht_heldby] - entry.update({"ht_heldby": list_members}) + entry.update(create_ht_heldby_field(ht_heldby)) # It is a list of members, if the query result is empty the field does not appear in Solr index heldby_brlm = self.add_add_heldby_brlm_field(doc_id) + if len(heldby_brlm) > 0: - list_brl_members = [member_id.get("member_id") for member_id in heldby_brlm] - entry.update({"ht_heldby_brlm": list_brl_members}) + entry.update(create_ht_heldby_brlm_field(heldby_brlm)) # It is a list of coll_id, if the query result is empty, the value of this field in Solr index will be [0] coll_id_result, large_coll_id_result = self.add_large_coll_id_field(doc_id) - if len(coll_id_result) > 0: - list_coll_ids = [coll_id.get("MColl_ID") for coll_id in coll_id_result] - list_large_coll_id = [ - coll_id.get("MColl_ID") for coll_id in large_coll_id_result - ] - - entry.update( - {"coll_id": list(set(list_coll_ids) & set(list_large_coll_id))} - ) - else: - entry.update({"coll_id": [0]}) + entry.update(create_coll_id_field(coll_id_result, large_coll_id_result)) + return entry From a756d4d8c30ff474b0528f11cd1a4a878ebbd18c Mon Sep 17 00:00:00 2001 From: Lianet Sepulveda Torres Date: Thu, 7 Mar 2024 18:42:23 -0500 Subject: [PATCH 21/30] remove remandeir comments --- document_indexer_service/document_indexer_service.py | 1 - 1 file changed, 1 deletion(-) diff --git a/document_indexer_service/document_indexer_service.py b/document_indexer_service/document_indexer_service.py index 6828710..4df1f81 100644 --- a/document_indexer_service/document_indexer_service.py +++ b/document_indexer_service/document_indexer_service.py @@ -80,7 +80,6 @@ def main(): ] logger.info(f"Indexing {len(xml_files)} documents.") - logger.info("Testing a new image in Kubernetes!!!!") # Split the list of files in batch if xml_files: while xml_files: From 8f153ef3652880c3693cfed7aaa01c1a471fb290 Mon Sep 17 00:00:00 2001 From: Lianet Sepulveda Torres Date: Thu, 7 Mar 2024 18:44:05 -0500 Subject: [PATCH 22/30] create a class to managing arguments --- .../full_text_search_retriever_by_file.py | 95 +++------------- .../full_text_search_retriever_service.py | 87 +++------------ .../retriever_arguments.py | 104 ++++++++++++++++++ 3 files changed, 130 insertions(+), 156 deletions(-) create mode 100644 document_retriever_service/retriever_arguments.py diff --git a/document_retriever_service/full_text_search_retriever_by_file.py b/document_retriever_service/full_text_search_retriever_by_file.py index 33fb870..3273946 100644 --- a/document_retriever_service/full_text_search_retriever_by_file.py +++ b/document_retriever_service/full_text_search_retriever_by_file.py @@ -12,10 +12,9 @@ from document_retriever_service.catalog_retriever_service import CatalogRetrieverService from document_retriever_service.full_text_search_retriever_service import FullTextSearchRetrieverService from document_retriever_service.ht_status_retriever_service import get_non_processed_ids +from document_retriever_service.retriever_arguments import RetrieverServiceArgumentsByFile from ht_document.ht_document import logger from ht_indexer_api.ht_indexer_api import HTSolrAPI -import ht_utils.ht_mysql -from indexer_config import DOCUMENT_LOCAL_PATH current = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe()))) parent = os.path.dirname(current) @@ -84,95 +83,27 @@ def retrieve_documents(self, query, start, rows): def main(): parser = argparse.ArgumentParser() + init_args_obj = RetrieverServiceArgumentsByFile(parser) - # Catalog Solr server - try: - solr_url = os.environ["SOLR_URL"] - except KeyError: - logger.error("Error: `SOLR_URL` environment variable required") - sys.exit(1) - - # MySql connection - try: - mysql_host = os.environ["MYSQL_HOST"] - except KeyError: - logger.error("Error: `MYSQL_HOST` environment variable required") - sys.exit(1) - - try: - mysql_user = os.environ["MYSQL_USER"] - except KeyError: - logger.error("Error: `MYSQL_USER` environment variable required") - sys.exit(1) - - try: - mysql_pass = os.environ["MYSQL_PASS"] - except KeyError: - logger.error("Error: `MYSQL_PASS` environment variable required") - sys.exit(1) - - ht_mysql = ht_utils.ht_mysql.HtMysql( - host=mysql_host, - user=mysql_user, - password=mysql_pass, - database=os.environ.get("MYSQL_DATABASE", "ht") - ) - - logger.info("Access by default to `ht` Mysql database") - - parser.add_argument( - "--document_repository", help="Could be pairtree or local", default="local" - ) - - # Path to the folder where the documents are stored. This parameter is useful for runing the script locally - parser.add_argument( - "--document_local_path", - help="Path of the folder where the documents (.xml file to index) are stored.", - required=False, - default=None - ) - - parser.add_argument( - "--list_ids_path", - help="Path of the TXT files with the list of id to generate", - required=False, - default=None - ) - - args = parser.parse_args() - - # Create the CatalogRetrieverService object - # catalog_retriever_service = CatalogRetrieverService(solr_api_catalog) - - document_generator = DocumentGenerator(ht_mysql) - - document_local_folder = "indexing_data" - document_local_path = DOCUMENT_LOCAL_PATH - - solr_api_catalog = HTSolrAPI(url=solr_url) - - document_indexer_service = FullTextSearchRetrieverServiceByFile(solr_api_catalog, - document_generator, - document_local_path, - document_local_folder) - - # TODO: Add start and rows to a configuration file - start = 0 - rows = 100 + document_indexer_service = FullTextSearchRetrieverServiceByFile(init_args_obj.solr_api_catalog, + init_args_obj.document_generator, + init_args_obj.document_local_path, + init_args_obj.document_local_folder) # TODO: Review the logic of the status file status_file = os.path.join(parent, "document_retriever_status.txt") - if args.list_ids_path: + if init_args_obj.list_ids_path: # If a document with the list of id to process is received as a parameter, then create batch of queries - with open(args.list_ids_path) as f: + with open(init_args_obj.list_ids_path) as f: list_ids = f.read().splitlines() ids2process, processed_ids = get_non_processed_ids(status_file, list_ids) logger.info(f"Total of items to process {len(ids2process)}") - tmp_file_status = open(os.path.join(document_local_path, "document_retriever_status.txt"), "w+") + tmp_file_status = open(os.path.join(init_args_obj.document_local_path, "document_retriever_status.txt"), + "w+") for doc in processed_ids: tmp_file_status.write(doc + "\n") tmp_file_status.close() @@ -186,9 +117,9 @@ def main(): # Create queries that contain a list of ht_id document_indexer_service.full_text_search_retriever_service( query, - start, - rows, - document_repository=args.document_repository) + init_args_obj.start, + init_args_obj.rows, + document_repository=init_args_obj.document_repository) else: logger.info("Provide the file with the list of ids to process is a required parameter") exit() diff --git a/document_retriever_service/full_text_search_retriever_service.py b/document_retriever_service/full_text_search_retriever_service.py index faf1130..76bf611 100644 --- a/document_retriever_service/full_text_search_retriever_service.py +++ b/document_retriever_service/full_text_search_retriever_service.py @@ -6,11 +6,9 @@ from document_generator.document_generator import DocumentGenerator from ht_utils.ht_logger import get_ht_logger from catalog_retriever_service import CatalogRetrieverService -import ht_indexer_api.ht_indexer_api -import ht_utils.ht_mysql from ht_utils.text_processor import create_solr_string -from indexer_config import DOCUMENT_LOCAL_PATH from ht_document.ht_document import HtDocument +from document_retriever_service.retriever_arguments import RetrieverServiceArguments logger = get_ht_logger(name=__name__) @@ -19,7 +17,7 @@ sys.path.insert(0, parent) -class FullTextSearchRetrieverService(CatalogRetrieverService): +class FullTextSearchRetrieverService(CatalogRetrieverService, RetrieverServiceArguments): """ This class is responsible to retrieve the documents from the Catalog and generate the full text search entry There are three main use cases: @@ -103,82 +101,23 @@ def generate_full_text_entry(self, item_id: str, record: catalog_metadata.Catalo def main(): parser = argparse.ArgumentParser() + init_args_obj = RetrieverServiceArguments(parser) - # Catalog Solr server - try: - solr_url = os.environ["SOLR_URL"] - except KeyError: - logger.error("Error: `SOLR_URL` environment variable required") - sys.exit(1) - - solr_api_catalog = ht_indexer_api.ht_indexer_api.HTSolrAPI(url=solr_url) - - # MySql connection - try: - mysql_host = os.environ["MYSQL_HOST"] - except KeyError: - logger.error("Error: `MYSQL_HOST` environment variable required") - sys.exit(1) - - try: - mysql_user = os.environ["MYSQL_USER"] - except KeyError: - logger.error("Error: `MYSQL_USER` environment variable required") - sys.exit(1) - - try: - mysql_pass = os.environ["MYSQL_PASS"] - except KeyError: - logger.error("Error: `MYSQL_PASS` environment variable required") - sys.exit(1) - - ht_mysql = ht_utils.ht_mysql.HtMysql( - host=mysql_host, - user=mysql_user, - password=mysql_pass, - database=os.environ.get("MYSQL_DATABASE", "ht") - ) - - logger.info("Access by default to `ht` Mysql database") - - parser.add_argument("--query", help="Query used to retrieve documents", default=None - ) - - parser.add_argument("--document_repository", - help="Could be pairtree or local", default="local" - ) - - # Path to the folder where the documents are stored. This parameter is useful for runing the script locally - parser.add_argument("--document_local_path", - help="Path of the folder where the documents (.xml file to index) are stored.", - required=False, - default=None - ) - - args = parser.parse_args() - - document_generator = DocumentGenerator(ht_mysql) - - document_local_folder = "indexing_data" - document_local_path = DOCUMENT_LOCAL_PATH - - document_indexer_service = FullTextSearchRetrieverService(solr_api_catalog, document_generator, document_local_path, - document_local_folder - ) - - if args.query is None: + if init_args_obj.query is None: logger.error("Error: `query` parameter required") sys.exit(1) - # TODO: Add start and rows to a configuration file - start = 0 - rows = 100 + document_indexer_service = FullTextSearchRetrieverService(init_args_obj.solr_api_catalog, + init_args_obj.document_generator, + init_args_obj.document_local_path, + init_args_obj.document_local_folder + ) document_indexer_service.full_text_search_retriever_service( - args.query, - start, - rows, - document_repository=args.document_repository) + init_args_obj.query, + init_args_obj.start, + init_args_obj.rows, + document_repository=init_args_obj.document_repository) if __name__ == "__main__": diff --git a/document_retriever_service/retriever_arguments.py b/document_retriever_service/retriever_arguments.py new file mode 100644 index 0000000..8519937 --- /dev/null +++ b/document_retriever_service/retriever_arguments.py @@ -0,0 +1,104 @@ +import os +import sys +import inspect +from ht_utils.ht_logger import get_ht_logger +from document_generator.document_generator import DocumentGenerator +from indexer_config import DOCUMENT_LOCAL_PATH +import ht_utils.ht_mysql +import ht_indexer_api.ht_indexer_api + +logger = get_ht_logger(name=__name__) + +current = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe()))) +parent = os.path.dirname(current) +sys.path.insert(0, parent) + + +def get_solr_api(): + # Catalog Solr server + try: + solr_url = os.environ["SOLR_URL"] + except KeyError: + logger.error("Error: `SOLR_URL` environment variable required") + sys.exit(1) + + return ht_indexer_api.ht_indexer_api.HTSolrAPI(url=solr_url) + + +def get_mysql_conn(): + # MySql connection + try: + mysql_host = os.environ["MYSQL_HOST"] + except KeyError: + logger.error("Error: `MYSQL_HOST` environment variable required") + sys.exit(1) + + try: + mysql_user = os.environ["MYSQL_USER"] + except KeyError: + logger.error("Error: `MYSQL_USER` environment variable required") + sys.exit(1) + + try: + mysql_pass = os.environ["MYSQL_PASS"] + except KeyError: + logger.error("Error: `MYSQL_PASS` environment variable required") + sys.exit(1) + + ht_mysql = ht_utils.ht_mysql.HtMysql( + host=mysql_host, + user=mysql_user, + password=mysql_pass, + database=os.environ.get("MYSQL_DATABASE", "ht") + ) + + logger.info("Access by default to `ht` Mysql database") + + return ht_mysql + + +class RetrieverServiceArguments: + def __init__(self, parser): + parser.add_argument("--query", help="Query used to retrieve documents", default=None + ) + + parser.add_argument("--document_repository", + help="Could be pairtree or local", default="local" + ) + + # Path to the folder where the documents are stored. This parameter is useful for runing the script locally + parser.add_argument("--document_local_path", + help="Path of the folder where the documents (.xml file to index) are stored.", + required=False, + default=None + ) + + self.args = parser.parse_args() + + self.document_local_folder = "indexing_data" + self.document_local_path = DOCUMENT_LOCAL_PATH + self.document_repository = self.args.document_repository + + self.query = self.args.query + + # TODO: Add start and rows to a configuration file + self.start = 0 + self.rows = 100 + + self.document_generator = DocumentGenerator(get_mysql_conn()) + self.solr_api_catalog = get_solr_api() + + +class RetrieverServiceArgumentsByFile(RetrieverServiceArguments): + def __init__(self, parser): + parser.add_argument( + "--list_ids_path", + help="Path of the TXT files with the list of id to generate", + required=False, + default=None + ) + + super().__init__(parser) + + # args = self.parser.parse_args() + self.list_ids_path = 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[[package]] name = "typing-extensions" -version = "4.9.0" +version = "4.10.0" description = "Backported and Experimental Type Hints for Python 3.8+" optional = false python-versions = ">=3.8" files = [ - { file = "typing_extensions-4.9.0-py3-none-any.whl", hash = "sha256:af72aea155e91adfc61c3ae9e0e342dbc0cba726d6cba4b6c72c1f34e47291cd" }, - { file = "typing_extensions-4.9.0.tar.gz", hash = "sha256:23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783" }, + {file = "typing_extensions-4.10.0-py3-none-any.whl", hash = "sha256:69b1a937c3a517342112fb4c6df7e72fc39a38e7891a5730ed4985b5214b5475"}, + {file = "typing_extensions-4.10.0.tar.gz", hash = "sha256:b0abd7c89e8fb96f98db18d86106ff1d90ab692004eb746cf6eda2682f91b3cb"}, ] [[package]] @@ -1179,8 +1099,8 @@ description = "Provider of IANA time zone data" optional = false python-versions = ">=2" files = [ - { file = "tzdata-2024.1-py2.py3-none-any.whl", hash = "sha256:9068bc196136463f5245e51efda838afa15aaeca9903f49050dfa2679db4d252" }, - 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{ file = "uvicorn-0.23.2-py3-none-any.whl", hash = "sha256:1f9be6558f01239d4fdf22ef8126c39cb1ad0addf76c40e760549d2c2f43ab53" }, - { file = "uvicorn-0.23.2.tar.gz", hash = "sha256:4d3cc12d7727ba72b64d12d3cc7743124074c0a69f7b201512fc50c3e3f1569a" }, + {file = "uvicorn-0.23.2-py3-none-any.whl", hash = "sha256:1f9be6558f01239d4fdf22ef8126c39cb1ad0addf76c40e760549d2c2f43ab53"}, + {file = "uvicorn-0.23.2.tar.gz", hash = "sha256:4d3cc12d7727ba72b64d12d3cc7743124074c0a69f7b201512fc50c3e3f1569a"}, ] [package.dependencies] @@ -1221,4 +1141,4 @@ standard = ["colorama (>=0.4)", "httptools (>=0.5.0)", "python-dotenv (>=0.13)", [metadata] lock-version = "2.0" python-versions = "^3.11" -content-hash = "25e4313ce2d4819ce5e3f8bc89a7404398cd4dc0fa9a2771f48ff576ae76ced9" +content-hash = "3e708513887fecfb5f8d219ad35f6f15c3eca9faa3fd0225537feb2dc0b489aa" diff --git a/pyproject.toml b/pyproject.toml index fdc42e8..f204c3e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -17,7 +17,6 @@ mysql-client = "^0.0.1" mysql-connector-python = "^8.1.0" mysql = "^0.0.3" pypairtree = "^1.1.0" -black = "^23.7.0" pydocstyle = "^6.3.0" pytest-cov = "^4.1.0" cryptography = "^41.0.3" From d65dd9c7c75f725338b4ad72f10ad680f36565d4 Mon Sep 17 00:00:00 2001 From: Lianet Sepulveda Torres Date: Fri, 8 Mar 2024 08:43:07 -0500 Subject: [PATCH 24/30] typos --- document_generator/mysql_data_extractor.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/document_generator/mysql_data_extractor.py b/document_generator/mysql_data_extractor.py index 5e55035..0f2c4c3 100644 --- a/document_generator/mysql_data_extractor.py +++ b/document_generator/mysql_data_extractor.py @@ -68,7 +68,7 @@ def add_large_coll_id_field(self, doc_id: str) -> [dict, dict]: return coll_id_entry, coll_id_large_entry - def add_right_field(self, doc_id) -> list[tuple]: + def add_rights_field(self, doc_id) -> list[tuple]: namespace, _id = doc_id.split(".") query = ( f'SELECT * FROM rights_current WHERE namespace="{namespace}" AND id="{_id}"' @@ -82,7 +82,7 @@ def add_ht_heldby_field(self, doc_id) -> list[tuple]: # ht_heldby is a list of institutions return self.mysql_obj.query_mysql(query) - def add_add_heldby_brlm_field(self, doc_id) -> list[tuple]: + def add_heldby_brlm_field(self, doc_id) -> list[tuple]: query = f'SELECT member_id FROM holdings_htitem_htmember WHERE volume_id="{doc_id}" AND access_count > 0' return self.mysql_obj.query_mysql(query) @@ -91,7 +91,7 @@ def retrieve_mysql_data(self, doc_id): entry = {} logger.info(f"Retrieving data from MySql {doc_id}") - doc_rights = self.add_right_field(doc_id) + doc_rights = self.add_rights_field(doc_id) # Only one element if len(doc_rights) == 1: @@ -103,7 +103,7 @@ def retrieve_mysql_data(self, doc_id): entry.update(create_ht_heldby_field(ht_heldby)) # It is a list of members, if the query result is empty the field does not appear in Solr index - heldby_brlm = self.add_add_heldby_brlm_field(doc_id) + heldby_brlm = self.add_heldby_brlm_field(doc_id) if len(heldby_brlm) > 0: entry.update(create_ht_heldby_brlm_field(heldby_brlm)) From 80a846ee87c1086f9c192ce77342df7f1111a78c Mon Sep 17 00:00:00 2001 From: Lianet Sepulveda Torres Date: Wed, 13 Mar 2024 13:06:15 -0400 Subject: [PATCH 25/30] start the docker on bash console --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 346bcc2..6e6cf4c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -60,6 +60,6 @@ WORKDIR /app COPY . . -CMD ["python3"] +CMD ["tail", "-f", "/dev/null"] USER appuser From 109d969fd30d4f6d478c48bd5b16744a6b6349f3 Mon Sep 17 00:00:00 2001 From: Lianet Sepulveda Torres Date: Wed, 13 Mar 2024 13:06:50 -0400 Subject: [PATCH 26/30] fixed mysql healthcheck --- docker-compose.yml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index 894aeef..046a288 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -27,7 +27,7 @@ services: - mysql_sdr_data:/var/lib/mysql restart: always ports: - - "3307:3306" + - "3306:3306" environment: - MYSQL_HOST=mysql-sdr - MYSQL_USER=mdp-lib @@ -42,8 +42,7 @@ services: "CMD", "healthcheck.sh", "--su-mysql", - "--connect", - "--innodb_initialized" + "--connect" ] timeout: 30s solr-lss-dev: From 2a914e1d536da2aac2a0cc2b244118ce3a977624 Mon Sep 17 00:00:00 2001 From: Lianet Sepulveda Torres Date: Wed, 13 Mar 2024 13:08:19 -0400 Subject: [PATCH 27/30] record is an instance variable for CatalogMetadata --- catalog_metadata/catalog_metadata.py | 87 ++++++------ catalog_metadata/catalog_metadata_test.py | 132 ++++++++++-------- .../catalog_retriever_service.py | 9 +- .../full_text_search_retriever_by_file.py | 3 +- 4 files changed, 119 insertions(+), 112 deletions(-) diff --git a/catalog_metadata/catalog_metadata.py b/catalog_metadata/catalog_metadata.py index 8a6400c..e0c6eac 100644 --- a/catalog_metadata/catalog_metadata.py +++ b/catalog_metadata/catalog_metadata.py @@ -7,100 +7,99 @@ class CatalogRecordMetadata: """This class is used to retrieve the metadata of a specific item in the Catalog""" def __init__(self, record: dict): - self.metadata = self.get_metadata(record) + self.record = record + self.metadata = self.get_metadata() - def get_metadata(self, record: dict) -> dict: + def get_metadata(self) -> dict: + """Create a dictionary with the fulltext fields extracted from catalog metadata""" metadata = {} - metadata.update(CatalogRecordMetadata.get_catalog_identical_fields(record)) - metadata.update(CatalogRecordMetadata.rename_catalog_fields(record)) + metadata.update(self.get_catalog_identical_fields()) + metadata.update(self.rename_catalog_fields()) # Create bothPublishDate field - if record.get("date") and record.get("enumPublishDate"): - metadata.update({"bothPublishDate": record.get("enumPublishDate")}) + if self.record.get("date") and self.record.get("enumPublishDate"): + metadata.update({"bothPublishDate": self.record.get("enumPublishDate")}) return metadata - @staticmethod - def get_catalog_identical_fields(metadata: dict) -> dict: + def get_catalog_identical_fields(self) -> dict: + + """Retrieve the fields that have identical names in the catalog and fulltext documents.""" entry = {} for field in IDENTICAL_CATALOG_METADATA: - value = metadata.get(field) + value = self.record.get(field) if value: entry[field] = value return entry - @staticmethod - def rename_catalog_fields(metadata: dict) -> dict: + def rename_catalog_fields(self) -> dict: + """Rename the fields from the catalog to the ones used in the fulltext documents.""" entry = {} for new_field in RENAMED_CATALOG_METADATA.keys(): catalog_field = RENAMED_CATALOG_METADATA[new_field] - entry[new_field] = metadata.get(catalog_field) + entry[new_field] = self.record.get(catalog_field) return entry class CatalogItemMetadata: """This class is used to retrieve the metadata of a specific item in the Catalog""" - def __init__(self, record: dict, ht_id: str, record_metadata: CatalogRecordMetadata = None): + def __init__(self, ht_id: str, record_metadata: CatalogRecordMetadata = None): + self.record_metadata = record_metadata self.ht_id = ht_id - metadata = self.get_metadata(record) + metadata = self.get_metadata() # Merge both dictionaries - self.metadata = {**record_metadata.metadata, **metadata} + self.metadata = {**self.record_metadata.metadata, **metadata} - @staticmethod - def get_volume_enumcron(ht_id_display: str = None): - # TODO REVIEW THIS METHOD - enumcron = ht_id_display[0].split("|")[2] - return enumcron + def get_volume_enumcron(self) -> list: + try: + return self.record_metadata.record.get("ht_id_display")[0].split("|")[2] + except IndexError: + return [] - def get_metadata(self, record: dict) -> dict: + def get_metadata(self) -> dict: metadata = {} - volume_enumcron = CatalogItemMetadata.get_volume_enumcron(record.get("ht_id_display")) - metadata.update({"volume_enumcron": volume_enumcron}) + volume_enumcron = self.get_volume_enumcron() - doc_json = [ - item - for item in json.loads(record.get("ht_json")) - if (_v := item.get("enum_pubdate") and self.ht_id == item.get("htid")) - ] + doc_json = self.get_data_ht_json_obj() if len(doc_json) > 0: - metadata.update(CatalogItemMetadata.get_data_ht_json_obj(doc_json[0])) + metadata["enumPublishDate"] = doc_json[0].get("ht_json") if len(volume_enumcron) > 1: metadata["volume_enumcron"] = volume_enumcron - metadata["htsource"] = CatalogItemMetadata.get_item_htsource( - self.ht_id, record.get("htsource"), record.get("ht_id") - ) + metadata["htsource"] = self.get_item_htsource() metadata["vol_id"] = self.ht_id return metadata - @staticmethod - def get_data_ht_json_obj(ht_json: dict = None) -> dict: - catalog_json_data = {"enumPublishDate": ht_json.get("enum_pubdate")} - return catalog_json_data + def get_data_ht_json_obj(self) -> list: + """Obtain the publication data of a specific item in the catalog.""" + doc_json = [ + item + for item in json.loads(self.record_metadata.record.get("ht_json")) + if (_v := item.get("enum_pubdate") and self.ht_id == item.get("htid")) + ] + + return doc_json - @staticmethod - def get_item_htsource( - id: str = None, catalog_htsource: list = None, catalog_htid: list = None - ) -> str: + def get_item_htsource(self) -> str: """ - In catalog it could be a list of sources, should obtain the source of an specific item + In catalog it could be a list of sources, should obtain the source of a specific item :param id: Catalod ht_id field :param catalog_htsource: catalog item source :param catalog_htid: catalog item ht_id :return: """ - item_position = catalog_htid.index(id) + item_position = self.record_metadata.record.get("ht_id").index(self.ht_id) try: - htsource = catalog_htsource[item_position] + htsource = self.record_metadata.record.get("htsource")[item_position] except IndexError: - htsource = catalog_htsource[0] + htsource = self.record_metadata.record.get("htsource")[0] return htsource diff --git a/catalog_metadata/catalog_metadata_test.py b/catalog_metadata/catalog_metadata_test.py index 1da6a4c..e36cd6c 100644 --- a/catalog_metadata/catalog_metadata_test.py +++ b/catalog_metadata/catalog_metadata_test.py @@ -1,6 +1,7 @@ import inspect import json import os +from copy import deepcopy import pytest @@ -9,6 +10,7 @@ current = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe()))) +# Retrieve JSON file to create a dictionary with a catalog record @pytest.fixture() def get_record_data(): with open(os.path.join(current, "data/catalog.json"), "r", ) as file: @@ -17,101 +19,109 @@ def get_record_data(): return data +# Use the catalog record to create a CatalogRecordMetadata object @pytest.fixture() def get_catalog_record_metadata(get_record_data): return CatalogRecordMetadata(get_record_data) +# Create a CatalogItemMetadata object with the catalog record and the ht_id of the item @pytest.fixture() def get_item_metadata(get_record_data: dict, get_catalog_record_metadata: CatalogRecordMetadata): - return CatalogItemMetadata(get_record_data, "mdp.39015078560292", get_catalog_record_metadata) + return CatalogItemMetadata("mdp.39015078560292", get_catalog_record_metadata) + + +# Update some fields of the catalog record to test some functions that retrieve specific fields +@pytest.fixture() +def update_catalog_record_metadata(get_record_data): + new_record_data = deepcopy(get_record_data) + new_record_data["htsource"] = ["University of Michigan", "Indiana University"] + new_record_data["ht_id"].append("inu.30000108625017") + return new_record_data + + +# Create a CatalogRecordMetadata object with the updated catalog record +@pytest.fixture() +def get_update_catalog_record_metadata(update_catalog_record_metadata): + return CatalogRecordMetadata(update_catalog_record_metadata) + + +# Create a CatalogItemMetadata object with the updated catalog record and the ht_id of the item +@pytest.fixture() +def get_item_metadata_second_position(update_catalog_record_metadata: dict, + get_update_catalog_record_metadata: CatalogRecordMetadata): + """Fake data updating the input document to test the second position of the htsource field""" + + return CatalogItemMetadata("inu.30000108625017", + get_update_catalog_record_metadata) + + +@pytest.fixture() +def get_catalog_record_without_enum_pubdate(get_record_data): + updating_record = deepcopy(get_record_data) + updating_record[ + "ht_json"] = '[{"htid":"nyp.33433069877805","newly_open":null,"ingest":"20220501","rights":["pdus",null],"heldby":["nypl"],"collection_code":"nyp","enumcron":"v. 1","dig_source":"google"}]' + updating_record["ht_id"] = ["nyp.33433069877805"] + return updating_record + + +@pytest.fixture() +def get_catalog_record_metadata_without_enum_pubdate(get_catalog_record_without_enum_pubdate): + return CatalogRecordMetadata(get_catalog_record_without_enum_pubdate) + + +@pytest.fixture() +def get_item_metadata_without_enum_pubdate(get_catalog_record_without_enum_pubdate: dict, + get_catalog_record_metadata_without_enum_pubdate: CatalogRecordMetadata): + """Fake data updating the input document to test the second position of the htsource field""" + + return CatalogItemMetadata("nyp.33433069877805", + get_catalog_record_metadata_without_enum_pubdate) class TestCatalogMetadata: def test_catalog_record_metadata_class(self, get_catalog_record_metadata): - assert 'ht_id' not in get_catalog_record_metadata.metadata.keys() assert 'htsource' in get_catalog_record_metadata.metadata.keys() assert 'vol_id' not in get_catalog_record_metadata.metadata.keys() def test_catalog_item_metadata_class(self, get_item_metadata): - assert get_item_metadata.ht_id == "mdp.39015078560292" assert "mdp.39015078560292" == get_item_metadata.metadata.get('vol_id') assert "title" in get_item_metadata.metadata.keys() - def test_get_item_htsource(self): - htsource = CatalogItemMetadata.get_item_htsource( - "mdp.39015061418433", # it is in solr core 7 - ["University of Michigan", "Indiana University"], - ["mdp.39015061418433", "inu.30000108625017"], - ) + def test_get_item_htsource(self, get_item_metadata): + htsource = get_item_metadata.get_item_htsource() assert htsource == "University of Michigan" - htsource = CatalogItemMetadata.get_item_htsource( - "inu.30000108625017", # it is in solr core 7 - ["University of Michigan", "Indiana University"], - ["mdp.39015061418433", "inu.30000108625017"], - ) + def test_get_item_htsource_second_position(self, get_item_metadata_second_position): + htsource = get_item_metadata_second_position.get_item_htsource() assert htsource == "Indiana University" - def test_get_item_htsource_sharinghtsource(self): - htsource = CatalogItemMetadata.get_item_htsource( - "inu.30000108625017", # it is in solr core 7 - ["University of Michigan"], - ["mdp.39015061418433", "inu.30000108625017"], - ) + def test_get_item_htsource_sharinghtsource(self, get_item_metadata): + htsource = get_item_metadata.get_item_htsource() assert htsource == "University of Michigan" def test_get_volume_enumcron_empty(self): """ - Some documents do not have the field volume_enumcrom, that is because it is an empty string in the second position. + Some documents do not have the field volume_enumcrom, that is because it is an empty string in the second + position. See here https://github.com/hathitrust/hathitrust_catalog_indexer/blob/main/indexers/common_ht.rb#L50 how this field is generated. :return: """ + volume_enumcrom = "" ht_id_display = [ - "mdp.39015078560292|20220910||1860|1860-1869|||RÄ\x81binsan KrÅ«so kÄ\x81 itihÄ\x81sa. " - "The adventures of Robinson Crusoe, translated [into Hindi] by BadrÄ« LÄ\x81la, from a Bengali version ..." - ] + "mdp.39015078560292|20220910||1860|1860-1869|||Rābinsan Krūso kā itihāsa. The adventures of Robinson " + "Crusoe, translated [into Hindi] by Badrī Lāla, from a Bengali version ..."] assert volume_enumcrom == ht_id_display[0].split("|")[2] - def test_missed_enumPublishDate(self, get_item_metadata): - ht_json = ('[{"htid":"nyp.33433069877805","newly_open":null,' - '"ingest":"20220501","rights":["pdus",null],"heldby":["nypl"],"collection_code":"nyp",' - '"enumcron":"v. 1","dig_source":"google"}]') - - doc_json = [] - for record in json.loads(ht_json): - if ( - _v := record.get("enum_pubdate") and "nyp.33433069877805" == record.get("htid") - ): - doc_json.append(record) - - if len(doc_json) > 0: - entry = get_item_metadata.get_data_ht_json_obj(doc_json[0]) - - assert "enumPublishDate" not in entry.keys() - - def test_extract_enumPublishDate(self, get_item_metadata): - ht_json = ('[{"htid":"mdp.39015082023097","newly_open":null,"ingest":"20230114",' - '"rights":["pdus",null],"heldby":["cornell","emory","harvard","stanford","uiowa","umich","umn"],' - '"collection_code":"miu","enumcron":"1958","enum_pubdate":"1958","enum_pubdate_range":"1950-1959",' - '"dig_source":"google"},{"htid":"mdp.39015082023246","newly_open":null,"ingest":"20230114",' - '"rights":["pdus",null],"heldby":["cornell","emory","harvard","stanford","uiowa","umich","umn"],' - '"collection_code":"miu","enumcron":"1959","enum_pubdate":"1959","enum_pubdate_range":"1950-1959",' - '"dig_source":"google"}]') - - doc_json = [] - for record in json.loads(ht_json): - if ( - _v := record.get("enum_pubdate") - and "mdp.39015082023097" == record.get("htid") - ): - doc_json.append(record) - - if len(doc_json) > 0: - entry = get_item_metadata.get_data_ht_json_obj(doc_json[0]) - assert "enumPublishDate" in entry.keys() + def test_missed_enum_publish_date(self, get_item_metadata_without_enum_pubdate): + doc_json = get_item_metadata_without_enum_pubdate.get_data_ht_json_obj() + assert len(doc_json) == 0 + + def test_extract_enum_publish_date(self, get_item_metadata): + doc_json = get_item_metadata.get_data_ht_json_obj() + assert len(doc_json) == 1 diff --git a/document_retriever_service/catalog_retriever_service.py b/document_retriever_service/catalog_retriever_service.py index 302bffb..e164090 100644 --- a/document_retriever_service/catalog_retriever_service.py +++ b/document_retriever_service/catalog_retriever_service.py @@ -15,10 +15,10 @@ def __init__(self, catalog_api=None): self.catalog_api = catalog_api @staticmethod - def get_catalog_object(record: dict, item_id: str, + def get_catalog_object(item_id: str, record_metadata: CatalogRecordMetadata) -> CatalogItemMetadata: - catalog_item_metadata = CatalogItemMetadata(record, item_id, record_metadata) + catalog_item_metadata = CatalogItemMetadata(item_id, record_metadata) return catalog_item_metadata def retrieve_documents(self, query, start, rows): @@ -59,13 +59,12 @@ def retrieve_documents(self, query, start, rows): except Exception as e: logger.error(f"Query {query} does not have a valid format {e}") exit() - results.append(CatalogRetrieverService.get_catalog_object(record, item_id, catalog_record_metadata)) + results.append(CatalogRetrieverService.get_catalog_object(item_id, catalog_record_metadata)) # This is the most efficient way to retrieve the items from Catalog else: # Process all the items of a record for item_id in record.get('ht_id'): # Append list of CatalogMetadata object - results.append(CatalogRetrieverService.get_catalog_object(record, item_id, - catalog_record_metadata)) + results.append(CatalogRetrieverService.get_catalog_object(item_id, catalog_record_metadata)) logger.info(f"Batch documents {count_records}") start += rows diff --git a/document_retriever_service/full_text_search_retriever_by_file.py b/document_retriever_service/full_text_search_retriever_by_file.py index 3273946..f407830 100644 --- a/document_retriever_service/full_text_search_retriever_by_file.py +++ b/document_retriever_service/full_text_search_retriever_by_file.py @@ -72,8 +72,7 @@ def retrieve_documents(self, query, start, rows): for item_id in record.get('ht_id'): # Append list of CatalogMetadata object if item_id in list_ids: - results.append(CatalogRetrieverService.get_catalog_object(record, item_id, - catalog_record_metadata)) + results.append(CatalogRetrieverService.get_catalog_object(item_id, catalog_record_metadata)) logger.info(f"Batch documents {count_records}") start += rows From a72a07c41ad53f66ef3ed1f19aeadb4e67625984 Mon Sep 17 00:00:00 2001 From: Lianet Sepulveda Torres Date: Wed, 13 Mar 2024 13:08:59 -0400 Subject: [PATCH 28/30] simplified the functions to obtain vol_id --- document_generator/mysql_data_extractor.py | 38 +++++++++------------- 1 file changed, 15 insertions(+), 23 deletions(-) diff --git a/document_generator/mysql_data_extractor.py b/document_generator/mysql_data_extractor.py index 0f2c4c3..dbc30e2 100644 --- a/document_generator/mysql_data_extractor.py +++ b/document_generator/mysql_data_extractor.py @@ -5,24 +5,20 @@ logger = get_ht_logger(name=__name__) -def create_coll_id_field(coll_id_result, large_coll_id_result) -> dict: - if len(coll_id_result) > 0: - list_coll_ids = [coll_id.get("MColl_ID") for coll_id in coll_id_result] - list_large_coll_id = [ - coll_id.get("MColl_ID") for coll_id in large_coll_id_result - ] - - return {"coll_id": list(set(list_coll_ids) & set(list_large_coll_id))} +def create_coll_id_field(large_coll_id_result: dict) -> dict: + if len(large_coll_id_result) > 0: + # Obtain the list with the unique coll_id from the result + return {"coll_id": set(list(large_coll_id_result.get("MColl_ID").values()))} else: return {"coll_id": [0]} -def create_ht_heldby_brlm_field(heldby_brlm) -> dict: +def create_ht_heldby_brlm_field(heldby_brlm: dict) -> dict: list_brl_members = [member_id.get("member_id") for member_id in heldby_brlm] return {"ht_heldby_brlm": list_brl_members} -def create_ht_heldby_field(heldby_brlm) -> dict: +def create_ht_heldby_field(heldby_brlm: dict) -> dict: list_brl_members = [member_id.get("member_id") for member_id in heldby_brlm] return {"ht_heldby": list_brl_members} @@ -44,7 +40,7 @@ def get_results_query(self, query: str) -> list: return list_docs - def add_large_coll_id_field(self, doc_id: str) -> [dict, dict]: + def add_large_coll_id_field(self, doc_id: str) -> [dict]: """ Get the list of coll_ids for the given id that are large so those coll_ids can be added as fields of the Solr doc. @@ -55,18 +51,14 @@ def add_large_coll_id_field(self, doc_id: str) -> [dict, dict]: fields. """ - query_coll_item = ( - f'SELECT MColl_ID FROM mb_coll_item WHERE extern_item_id="{doc_id}"' - ) - - query_large_coll = ( - f"SELECT MColl_ID FROM mb_collection WHERE num_items>{indexer_config.MAX_ITEM_IDS}" - ) + query_item_in_large_coll = (f'SELECT mb_item.MColl_ID ' + f'FROM mb_coll_item mb_item, mb_collection mb_coll ' + f'WHERE mb_item.extern_item_id="{doc_id}" ' + f'AND mb_coll.num_items > {indexer_config.MAX_ITEM_IDS} ') - coll_id_entry = self.mysql_obj.query_mysql(query_coll_item) - coll_id_large_entry = self.mysql_obj.query_mysql(query_large_coll) + large_collection_id = self.mysql_obj.query_mysql(query_item_in_large_coll) - return coll_id_entry, coll_id_large_entry + return large_collection_id def add_rights_field(self, doc_id) -> list[tuple]: namespace, _id = doc_id.split(".") @@ -109,7 +101,7 @@ def retrieve_mysql_data(self, doc_id): entry.update(create_ht_heldby_brlm_field(heldby_brlm)) # It is a list of coll_id, if the query result is empty, the value of this field in Solr index will be [0] - coll_id_result, large_coll_id_result = self.add_large_coll_id_field(doc_id) - entry.update(create_coll_id_field(coll_id_result, large_coll_id_result)) + large_coll_id_result = self.add_large_coll_id_field(doc_id) + entry.update(create_coll_id_field(large_coll_id_result)) return entry From cfe9120da1f3bf6efcc082ce59d68001bfa665b2 Mon Sep 17 00:00:00 2001 From: Lianet Sepulveda Torres Date: Wed, 13 Mar 2024 13:09:38 -0400 Subject: [PATCH 29/30] create a class to remove duplicated code --- document_retriever_service/retriever_arguments.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/document_retriever_service/retriever_arguments.py b/document_retriever_service/retriever_arguments.py index 8519937..734a8a0 100644 --- a/document_retriever_service/retriever_arguments.py +++ b/document_retriever_service/retriever_arguments.py @@ -17,7 +17,7 @@ def get_solr_api(): # Catalog Solr server try: - solr_url = os.environ["SOLR_URL"] + solr_url = os.getenv("SOLR_URL") except KeyError: logger.error("Error: `SOLR_URL` environment variable required") sys.exit(1) @@ -28,19 +28,19 @@ def get_solr_api(): def get_mysql_conn(): # MySql connection try: - mysql_host = os.environ["MYSQL_HOST"] + mysql_host = os.getenv("MYSQL_HOST", "mysql-sdr") # os.environ["MYSQL_HOST"] except KeyError: logger.error("Error: `MYSQL_HOST` environment variable required") sys.exit(1) try: - mysql_user = os.environ["MYSQL_USER"] + mysql_user = os.getenv("MYSQL_USER", "mdp-lib") # os.environ["MYSQL_USER"] except KeyError: logger.error("Error: `MYSQL_USER` environment variable required") sys.exit(1) try: - mysql_pass = os.environ["MYSQL_PASS"] + mysql_pass = os.getenv("MYSQL_PASS", "mdp-lib") # os.environ["MYSQL_PASS"] except KeyError: logger.error("Error: `MYSQL_PASS` environment variable required") sys.exit(1) @@ -49,7 +49,7 @@ def get_mysql_conn(): host=mysql_host, user=mysql_user, password=mysql_pass, - database=os.environ.get("MYSQL_DATABASE", "ht") + database=os.getenv("MYSQL_DATABASE", "ht") ) logger.info("Access by default to `ht` Mysql database") From c59d84c97a6a8d354ca663a484b32af700f43129 Mon Sep 17 00:00:00 2001 From: Lianet Sepulveda Torres Date: Wed, 13 Mar 2024 13:10:17 -0400 Subject: [PATCH 30/30] Fixed an format issue --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 48c0879..b983754 100644 --- a/README.md +++ b/README.md @@ -233,7 +233,8 @@ Step 2. Retrieve from pairtree repository data for testing `scp $HT_SSH_HOST:/sdr1/obj/umn/pairtree_root/31/95/1d/03/01/41/20/v/31951d03014120v/31951d03014120v{.zip,mets.xml} ../sdr1/obj` Step 3. Create the image -`docker build -t document_generator . docker compose up document_retriever -d` +`docker build -t document_generator . +docker compose up document_retriever -d` Step 4. export MYSQL_USER= export MYSQL_PASS=