diff --git a/README.md b/README.md index 72ee940..efa2982 100644 --- a/README.md +++ b/README.md @@ -37,12 +37,6 @@ Both the OIT Legacy Data Warehouse and the Experts Data Warehouse are Oracle databases. See [experts\_dw on GitHub](https://github.com/UMNLibraries/experts_dw) for supported versions of the required Oracle InstanctClient library. -#### LDAP - -Experts ETL uses LDAP to search for some student researcher information. See the -[python-ldap build prerequisites](https://www.python-ldap.org/en/python-ldap-3.3.0/installing.html#build-prerequisites) -for the required system libraries to install in your local environment. - ### pyenv, venv, and poetry To install and manage Python versions we use @@ -90,9 +84,6 @@ via environment variables: * `EXPERTS_DB_PASS` * `EXPERTS_DB_HOSTNAME` * `EXPERTS_DB_SERVICE_NAME` -* UMN LDAP - * `UMN_LDAP_DOMAIN` - * `UMN_LDAP_PORT` Some tests are integration tests that connect to these external services, so these variables must be set for testing. One option is to set these diff --git a/env.dist b/env.dist index 419d1d4..c666d16 100644 --- a/env.dist +++ b/env.dist @@ -17,6 +17,3 @@ EXPERTS_ETL_FROM_EMAIL_ADDRESS="expert@some.host" EXPERTS_ETL_TICKET_EMAIL_ADDRESS="some.ticketing.system.address@umn.edu" EXPERTS_ETL_ERROR_EMAIL_ADDRESS="error.notification.address@umn.edu" - -UMN_LDAP_DOMAIN="umn.ldap.domain" -UMN_LDAP_PORT="umn_ldap_port_number" diff --git a/experts_etl/demographics.py b/experts_etl/demographics.py index f3fa45a..5e84318 100644 --- a/experts_etl/demographics.py +++ b/experts_etl/demographics.py @@ -7,7 +7,7 @@ def latest_demographics_for_emplid(session, emplid): session.query(PureEligibleDemogChngHst) .filter( PureEligibleDemogChngHst.emplid == emplid, - PureEligibleDemogChngHst.timestamp == subqry + PureEligibleDemogChngHst.timestamp == subqry.scalar_subquery() ) .one_or_none() ) diff --git a/experts_etl/oit_to_edw/person.py b/experts_etl/oit_to_edw/person.py index fe6d3db..3e15393 100644 --- a/experts_etl/oit_to_edw/person.py +++ b/experts_etl/oit_to_edw/person.py @@ -6,8 +6,8 @@ from sqlalchemy import and_, func, text from experts_dw import db +from experts_dw.rawsql import update_pure_sync_person_data, insert_pure_sync_person_data, update_pure_sync_user_data, insert_pure_sync_user_data, update_pure_sync_staff_org_association, insert_pure_sync_staff_org_association, delete_obsolete_primary_jobs from experts_dw.models import PureEligiblePersonNew, PureEligiblePersonChngHst, PureEligibleDemogNew, PureEligibleDemogChngHst, Person, PureSyncPersonDataScratch, PureSyncStaffOrgAssociationScratch, PureSyncUserDataScratch -from experts_dw.sqlapi import sqlapi from experts_etl import loggers from experts_etl.demographics import latest_demographics_for_emplid, latest_not_null_internet_id_for_emplid from experts_etl.umn_data_error import record_person_no_job_data_error @@ -25,9 +25,6 @@ def run( transaction_record_limit=transaction_record_limit, experts_etl_logger=None ): - # This connection API in general needs work. Including this here for the sake of consistency - # with other ETL module.run() functions. - sqlapi.setengine(db.engine(db_name)) if experts_etl_logger is None: experts_etl_logger = loggers.experts_etl_logger() @@ -58,24 +55,36 @@ def run( session.commit() load_count = 0 - update_targets_from_scratch() + # We now use cx_oracle_connection() to prepare our target tables + with db.cx_oracle_connection() as connection: + update_targets_from_scratch(connection, experts_etl_logger) session.commit() experts_etl_logger.info('ending: oit -> edw', extra={'pure_sync_job': 'person'}) -def update_targets_from_scratch(): - with sqlapi.transaction(): - sqlapi.update_pure_sync_person_data() - sqlapi.insert_pure_sync_person_data() +def update_targets_from_scratch(connection, experts_etl_logger): + try: + cur = connection.cursor() - sqlapi.update_pure_sync_user_data() - sqlapi.insert_pure_sync_user_data() + cur.execute(update_pure_sync_person_data) + cur.execute(insert_pure_sync_person_data) - sqlapi.update_pure_sync_staff_org_association() - sqlapi.insert_pure_sync_staff_org_association() + cur.execute(update_pure_sync_user_data) + cur.execute(insert_pure_sync_user_data) - sqlapi.delete_obsolete_primary_jobs() + cur.execute(update_pure_sync_staff_org_association) + cur.execute(insert_pure_sync_staff_org_association) + + cur.execute(delete_obsolete_primary_jobs) + + connection.commit() + except Exception as e: + connection.rollback() + formatted_exception = loggers.format_exception(e) + experts_etl_logger.error( + f'Exception encountered during updating pure_sync_data tables: {formatted_exception}' + ) def load_into_scratch(session, person_dict): pure_sync_person_data = PureSyncPersonDataScratch( diff --git a/experts_etl/umn_data_error.py b/experts_etl/umn_data_error.py index a8ed980..60d499c 100644 --- a/experts_etl/umn_data_error.py +++ b/experts_etl/umn_data_error.py @@ -1,10 +1,12 @@ from datetime import datetime from experts_dw import db +from experts_dw.rawsql import unreported_umn_data_errors, record_reporting_of_umn_data_errors, count_pure_eligible_persons_in_dept from experts_dw.models import UmnDataError -from experts_dw.sqlapi import sqlapi from experts_etl.exceptions import * from experts_etl import loggers +from sqlalchemy.sql import text + import os import csv from io import StringIO @@ -23,32 +25,50 @@ def run( from_address=None, ticket_address=None ): - # This connection API in general needs work. Including this here for the sake of consistency - # with other ETL module.run() functions. - sqlapi.setengine(db.engine(db_name)) if experts_etl_logger is None: experts_etl_logger = loggers.experts_etl_logger() experts_etl_logger.info('starting: error reporting', extra={'pure_sync_job': 'error_reporting'}) - if smtp_server is None: - smtp_server = smtplib.SMTP('localhost', 25) - if from_address is None: - from_address = os.environ.get('EXPERTS_ETL_FROM_EMAIL_ADDRESS') - if ticket_address is None: - ticket_address = os.environ.get('EXPERTS_ETL_TICKET_EMAIL_ADDRESS') - with sqlapi.transaction(): - report_via_email(smtp_server=smtp_server, from_address=from_address, ticket_address=ticket_address) - smtp_server.quit() + with db.cx_oracle_connection() as connection: + unreported_errors = get_unreported_errors(connection) + if len(unreported_errors) > 0: + if smtp_server is None: + smtp_server = smtplib.SMTP('localhost', 25) + if from_address is None: + from_address = os.environ.get('EXPERTS_ETL_FROM_EMAIL_ADDRESS') + if ticket_address is None: + ticket_address = os.environ.get('EXPERTS_ETL_TICKET_EMAIL_ADDRESS') + + message = generate_error_report_message(unreported_errors, from_address, ticket_address) + message_sent_successfully = False + try: + smtp_server.send_message(message) + message_sent_successfully = True + except Exception as e: + formatted_exception = loggers.format_exception(e) + experts_etl_logger.error( + f'Exception encountered during sending of error report message: {formatted_exception}' + ) + smtp_server.quit() + if message_sent_successfully: + record_reporting_of_errors(connection, experts_etl_logger) experts_etl_logger.info('ending: error reporting', extra={'pure_sync_job': 'error_reporting'}) -def report_via_email(smtp_server, from_address, ticket_address): - unreported_errors = list(sqlapi.unreported_umn_data_errors()) - if len(unreported_errors) == 0: - return +def get_unreported_errors(connection): + cursor = connection.cursor() + cursor.execute(unreported_umn_data_errors) + cursor.rowfactory = lambda *args: dict( + zip([col[0] for col in cursor.description], args) + ) + unreported_errors = cursor.fetchall() + cursor.close() + return unreported_errors +def generate_error_report_message(unreported_errors, from_address, ticket_address): + # Build and send e-mail with csv attachment of errors datetime_string = datetime.now().strftime('%Y-%m-%dT%H:%M:%S') message = MIMEMultipart() @@ -68,9 +88,19 @@ def report_via_email(smtp_server, from_address, ticket_address): part.add_header('Content-Disposition', f'attachment; filename="umn-data-errors-{datetime_string}.csv"') message.attach(part) - smtp_server.send_message(message) + return message - sqlapi.record_reporting_of_umn_data_errors() +def record_reporting_of_errors(connection, experts_etl_logger): + try: + cursor = connection.cursor() + cursor.execute(record_reporting_of_umn_data_errors) + connection.commit() + except Exception as e: + connection.rollback() + formatted_exception = loggers.format_exception(e) + experts_etl_logger.error( + f'Exception encountered during recording of data errors: {formatted_exception}' + ) def create_csv_report(unreported_errors): # Remove fields which may confuse people doing data entry: @@ -123,7 +153,8 @@ def record_unknown_dept_errors( um_campus_descr=None, ): if persons_in_dept is None: - persons_in_dept = sqlapi.count_pure_eligible_persons_in_dept(deptid=deptid) + # We are using a SQL Alchemy session to execute a count statement. A workaround from having to introduce new connection objects into the process. + persons_in_dept = session.execute(text(count_pure_eligible_persons_in_dept), {"deptid": deptid}).scalars().one_or_none() session.add( find_or_create_umn_data_error( diff --git a/poetry.lock b/poetry.lock index 8b7070a..5c601c2 100644 --- a/poetry.lock +++ b/poetry.lock @@ -38,7 +38,7 @@ python-versions = "*" [[package]] name = "charset-normalizer" -version = "2.0.7" +version = "2.0.12" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." category = "main" optional = false @@ -57,15 +57,15 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [[package]] name = "cx-oracle" -version = "8.0.1" +version = "8.3.0" description = "Python interface to Oracle" category = "main" optional = false -python-versions = ">=3.5" +python-versions = "*" [[package]] name = "docutils" -version = "0.17.1" +version = "0.18.1" description = "Docutils -- Python Documentation Utilities" category = "main" optional = false @@ -73,45 +73,37 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [[package]] name = "dotenv-switch" -version = "0.1.1" +version = "0.1.2" description = "Switch between sourcing .env files based on $APP_ENV environment variable" category = "main" optional = false -python-versions = "^3.6.3" -develop = false +python-versions = ">=3.6.3,<4.0.0" [package.dependencies] -python_dotenv = "^0.10.3" +python_dotenv = ">=0.19.2,<0.20.0" [package.source] -type = "git" -url = "git://github.com/UMNLibraries/dotenv_switch.git" -reference = "master" -resolved_reference = "dc55429f6394bdd8c36d57232c6dc32e7eba7fd2" - +type = "url" +url = "https://github.com/UMNLibraries/dotenv_switch/raw/master/dist/dotenv_switch-0.1.2.tar.gz" [[package]] name = "experts-dw" -version = "7.15.0" +version = "7.18.0" description = "Tools for working with the Experts@Minnesota Data Warehouse." category = "main" optional = false -python-versions = "^3.6.3" -develop = false +python-versions = ">=3.6.3,<4.0.0" [package.dependencies] -cx-oracle = "8.0.1" -Jinja2 = "^2.11" -pugsql = "^0.2.3" -sqlalchemy = "*" -sqlalchemy_mptt = "*" -sqlparse = "*" +cx-oracle = ">=8.0.1,<9.0.0" +Jinja2 = ">=2.11,<3.0" +pugsql = ">=0.2.3,<0.3.0" +sqlalchemy = ">=1.3,<2.0" +sqlalchemy_mptt = ">=0.2.5,<0.3.0" +sqlparse = ">=0.4.2,<0.5.0" [package.source] -type = "git" -url = "git://github.com/UMNLibraries/experts_dw.git" -reference = "7.15.0" -resolved_reference = "4b664eed5dca4ce8adb53ac723cf78370edac18f" - +type = "url" +url = "https://github.com/UMNLibraries/experts_dw/raw/main/dist/experts_dw-7.18.0.tar.gz" [[package]] name = "greenlet" version = "1.1.2" @@ -131,23 +123,6 @@ category = "main" optional = false python-versions = ">=3.5" -[[package]] -name = "importlib-metadata" -version = "4.8.1" -description = "Read metadata from Python packages" -category = "main" -optional = false -python-versions = ">=3.6" - -[package.dependencies] -typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""} -zipp = ">=0.5" - -[package.extras] -docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"] -perf = ["ipython"] -testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"] - [[package]] name = "iniconfig" version = "1.1.1" @@ -188,38 +163,43 @@ python-versions = ">=3.6" [[package]] name = "numpy" -version = "1.19.5" +version = "1.22.3" description = "NumPy is the fundamental package for array computing with Python." category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.8" [[package]] name = "packaging" -version = "21.0" +version = "21.3" description = "Core utilities for Python packages" category = "dev" optional = false python-versions = ">=3.6" [package.dependencies] -pyparsing = ">=2.0.2" +pyparsing = ">=2.0.2,<3.0.5 || >3.0.5" [[package]] name = "pandas" -version = "1.1.5" +version = "1.4.1" description = "Powerful data structures for data analysis, time series, and statistics" category = "main" optional = false -python-versions = ">=3.6.1" +python-versions = ">=3.8" [package.dependencies] -numpy = ">=1.15.4" -python-dateutil = ">=2.7.3" -pytz = ">=2017.2" +numpy = [ + {version = ">=1.18.5", markers = "platform_machine != \"aarch64\" and platform_machine != \"arm64\" and python_version < \"3.10\""}, + {version = ">=1.19.2", markers = "platform_machine == \"aarch64\" and python_version < \"3.10\""}, + {version = ">=1.20.0", markers = "platform_machine == \"arm64\" and python_version < \"3.10\""}, + {version = ">=1.21.0", markers = "python_version >= \"3.10\""}, +] +python-dateutil = ">=2.8.1" +pytz = ">=2020.1" [package.extras] -test = ["pytest (>=4.0.2)", "pytest-xdist", "hypothesis (>=3.58)"] +test = ["hypothesis (>=5.5.3)", "pytest (>=6.0)", "pytest-xdist (>=1.31)"] [[package]] name = "pluggy" @@ -229,82 +209,77 @@ category = "dev" optional = false python-versions = ">=3.6" -[package.dependencies] -importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""} - [package.extras] dev = ["pre-commit", "tox"] testing = ["pytest", "pytest-benchmark"] [[package]] name = "pugsql" -version = "0.2.3" +version = "0.2.4" description = "PugSQL is an anti-ORM that facilitates interacting with databases using SQL in files." category = "main" optional = false -python-versions = ">=3.5" +python-versions = ">=3.7" [package.dependencies] sqlalchemy = ">=1.3,<2.0" [[package]] name = "pureapi" -version = "4.2.0" +version = "4.3.3" description = "Tools for working with Elsevier's Pure API." category = "main" optional = false -python-versions = "^3.6.3" -develop = false +python-versions = ">=3.6.3,<4.0.0" [package.dependencies] -addict = "*" -attrs = "^19.3.0" -requests = "^2.20.0" -tenacity = "*" +addict = ">=2.4.0,<3.0.0" +attrs = ">=19.3.0,<20.0.0" +requests = ">=2.20.0,<3.0.0" +tenacity = ">=8.0.1,<9.0.0" [package.source] -type = "git" -url = "git://github.com/UMNLibraries/pureapi.git" -reference = "4.2.0" -resolved_reference = "4e711d4831578e5d9afef04654d2bbfe5cfa4524" - +type = "url" +url = "https://github.com/UMNLibraries/pureapi/raw/main/dist/pureapi-4.3.3.tar.gz" [[package]] name = "py" -version = "1.10.0" +version = "1.11.0" description = "library with cross-python path, ini-parsing, io, code, log facilities" category = "dev" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [[package]] name = "pyparsing" -version = "2.4.7" +version = "3.0.7" description = "Python parsing module" category = "dev" optional = false -python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" +python-versions = ">=3.6" + +[package.extras] +diagrams = ["jinja2", "railroad-diagrams"] [[package]] name = "pytest" -version = "6.2.5" +version = "7.1.1" description = "pytest: simple powerful testing with Python" category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""} attrs = ">=19.2.0" colorama = {version = "*", markers = "sys_platform == \"win32\""} -importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""} iniconfig = "*" packaging = "*" pluggy = ">=0.12,<2.0" py = ">=1.8.2" -toml = "*" +tomli = ">=1.0.0" [package.extras] -testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xmlschema"] +testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "xmlschema"] [[package]] name = "python-daemon" @@ -334,11 +309,11 @@ six = ">=1.5" [[package]] name = "python-dotenv" -version = "0.10.5" -description = "Add .env support to your django/flask apps in development and deployments" +version = "0.19.2" +description = "Read key-value pairs from a .env file and set them as environment variables" category = "main" optional = false -python-versions = "*" +python-versions = ">=3.5" [package.extras] cli = ["click (>=5.0)"] @@ -353,7 +328,7 @@ python-versions = ">=3.5" [[package]] name = "pytz" -version = "2021.3" +version = "2022.1" description = "World timezone definitions, modern and historical" category = "main" optional = false @@ -361,7 +336,7 @@ python-versions = "*" [[package]] name = "requests" -version = "2.26.0" +version = "2.27.1" description = "Python HTTP for Humans." category = "main" optional = false @@ -395,7 +370,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" [[package]] name = "sqlalchemy" -version = "1.4.26" +version = "1.4.32" description = "Database Abstraction Library" category = "main" optional = false @@ -403,7 +378,6 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" [package.dependencies] greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and (platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\")"} -importlib-metadata = {version = "*", markers = "python_version < \"3.8\""} [package.extras] aiomysql = ["greenlet (!=0.4.17)", "aiomysql"] @@ -457,50 +431,30 @@ python-versions = ">=3.6" doc = ["reno", "sphinx", "tornado (>=4.5)"] [[package]] -name = "toml" -version = "0.10.2" -description = "Python Library for Tom's Obvious, Minimal Language" +name = "tomli" +version = "2.0.1" +description = "A lil' TOML parser" category = "dev" optional = false -python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" - -[[package]] -name = "typing-extensions" -version = "3.10.0.2" -description = "Backported and Experimental Type Hints for Python 3.5+" -category = "main" -optional = false -python-versions = "*" +python-versions = ">=3.7" [[package]] name = "urllib3" -version = "1.26.7" +version = "1.26.9" description = "HTTP library with thread-safe connection pooling, file post, and more." category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4" [package.extras] -brotli = ["brotlipy (>=0.6.0)"] +brotli = ["brotlicffi (>=0.8.0)", "brotli (>=1.0.9)", "brotlipy (>=0.6.0)"] secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", 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