diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 4559a37e3e4c1ccc658982348c355a4eea464342..3a727c0dcd1170c5bb8775bdd96d811ff9a9957f 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -84,6 +84,13 @@ build conveyor: PACKAGE_PATH: "apps/cli/executables/pexable/conveyor" extends: .build-package +build data annotator: + interruptible: true + stage: build-packages + variables: + PACKAGE_PATH: "apps/cli/executables/pexable/data_annotator" + extends: .build-package + build deliver: interruptible: true stage: build-packages @@ -308,6 +315,13 @@ push conveyor: PIP_NAME: "conveyor" extends: .push-packages +push data-annotator: + stage: push-packages + variables: + PACKAGE_NAME: "data_annotator" + PIP_NAME: "data-annotator" + extends: .push-packages + push deliver: stage: push-packages variables: diff --git a/apps/cli/executables/pexable/data_annotator/LICENSE b/apps/cli/executables/pexable/data_annotator/LICENSE new file mode 100644 index 0000000000000000000000000000000000000000..bc08fe2e41e331fcf35fe07812c5f68f637f79ae --- /dev/null +++ b/apps/cli/executables/pexable/data_annotator/LICENSE @@ -0,0 +1,619 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/> + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. diff --git a/apps/cli/executables/pexable/data_annotator/README.md b/apps/cli/executables/pexable/data_annotator/README.md new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/apps/cli/executables/pexable/data_annotator/data_annotator/__init__.py b/apps/cli/executables/pexable/data_annotator/data_annotator/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..eb2c882f38f6033dd6c10291beb41509ecb8ae73 --- /dev/null +++ b/apps/cli/executables/pexable/data_annotator/data_annotator/__init__.py @@ -0,0 +1,21 @@ +# +# Copyright (C) 2021 Associated Universities, Inc. Washington DC, USA. +# +# This file is part of NRAO Workspaces. +# +# Workspaces is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# Workspaces is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with Workspaces. If not, see <https://www.gnu.org/licenses/>. +""" +Workspaces metrics reporter for users outside of SSA. +""" +__version__ = "2.8.2rc1" diff --git a/apps/cli/executables/pexable/data_annotator/data_annotator/annotator.py b/apps/cli/executables/pexable/data_annotator/data_annotator/annotator.py new file mode 100644 index 0000000000000000000000000000000000000000..09687592962df95d604e3dc8eb8803f1650bc67f --- /dev/null +++ b/apps/cli/executables/pexable/data_annotator/data_annotator/annotator.py @@ -0,0 +1,169 @@ +# +# Copyright (C) 2021 Associated Universities, Inc. Washington DC, USA. +# +# This file is part of NRAO Workspaces. +# +# Workspaces is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# Workspaces is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with Workspaces. If not, see <https://www.gnu.org/licenses/>. + +import argparse +from .queries import retrieve_problem_severities, retrieve_problem_types, get_exec_blocks, \ + get_all_spls_from_exec_blocks, create_comments, delete_comments, modify_comments +from .connections import MDDBConnector + + +def parser() -> argparse.ArgumentParser: + """ + Initialize argument parser for command-line arguments + + :return: Argument parser + """ + parser = argparse.ArgumentParser( + description="Workspaces data annotator", formatter_class=argparse.RawTextHelpFormatter + ) + + # Create a group to capture the action to be done; require that users select exactly one of this group + action_group = parser.add_mutually_exclusive_group(required=True) + action_group.add_argument( + "-c", + "--create", + action='store_true', + help="Create a comment for one or more datasets. Cannot be used with -d/--delete or -m/--modify.", + ) + action_group.add_argument( + "-m", + "--modify", + action='store_true', + help="Modify a comment for one or more datasets. Cannot be used with -d/--delete or -c/--create.", + ) + action_group.add_argument( + "-d", + "--delete", + action='store_true', + help="Delete a comment for one or more datasets. Cannot be used with -c/--create or -m/--modify.", + ) + + # Create a group to capture the data that will be searched by when querying the database; require at least one + search_group = parser.add_argument_group() + search_group.add_argument( + "--project_code", + action="store", + help="A string representing the project code to search by.", + ) + search_group.add_argument( + "--date-range", + nargs=2, + action="store", + help="Two strings representing beginning and end date to search by.", + ) + search_group.add_argument( + "--fsid", + action="store", + help="A string representing the FSID to search by", + ) + search_group.add_argument( + "--configuration", + action="store", + help="A string representing the configuration to search by.", + ) + search_group.add_argument( + "--band", + action="store", + help="A string representing the band to search by.", + ) + + # Create a group to capture other data that is not required at the start of the program + optional_group = parser.add_argument_group() + optional_group.add_argument( + "--comment", + action="store", + help="A string representing the comment to add.", + ) + optional_group.add_argument( + "--old-comment", + action="store", + help="A string representing the old comment to search by. Only used with -m/--modify.", + ) + optional_group.add_argument( + "--problem-severity", + action="store", + help="Two strings representing beginning and end date to search by.", + ) + optional_group.add_argument( + "--problem-type", + action="store", + help="Two strings representing beginning and end date to search by.", + ) + + return parser + + +def prompt_for_input_from_db_list(db_list, prompt): + """ + Accepts a list of id and description pairs and a sentence prompt to give to a user, and returns the user's choice + from this list. + + :param db_list: a list of id and description tuples + :param prompt: a string representing a question to ask the user + :return: the user's choice from the passed iin options + """ + output_string = prompt + "\n" + for item in db_list: + output_string += str(item[0]) + '. ' + item[1] + '\n' + + return input(output_string) + + +def main(): + print("**********************************") + print("* WELCOME TO THE DATA ANNOTATOR! *") + print("**********************************") + + args = parser().parse_args() + try: + conn = MDDBConnector() + except Exception as e: + print(e) + + # Prompt for any missing data + if not args.problem_severity: + problem_severities = retrieve_problem_severities(conn) + prompt = "A problem severity is required. Input the number for the value you wish to assign and hit enter:" + args.problem_severity = prompt_for_input_from_db_list(problem_severities, prompt) + if not args.problem_type: + problem_types = retrieve_problem_types(conn) + prompt = "A problem type is required. Input the number for the value you wish to assign and hit enter:" + args.problem_type = prompt_for_input_from_db_list(problem_types, prompt) + if not args.comment: + prompt = "Please type your comment and hit enter:\n" + args.comment = input(prompt) + + # Find the initial execution blocks, use them to find all relevant science product locators and proceed + ebs = get_exec_blocks(args.project_code, args.date_range, args.fsid, args.band, args.configuration, conn) + all_spls = get_all_spls_from_exec_blocks(ebs, conn) + if args.create: + create_comments(all_spls, args.comment, args.problem_severity, args.problem_type, conn) + elif args.delete: + delete_comments(all_spls, args.comment, args.problem_severity, args.problem_type, conn) + elif args.modify: + if not args.old_comment: + prompt = "Please type the old comment you wish to modify:\n" + args.old_comment = input(prompt) + modify_comments(all_spls, args.comment, args.old_comment, args.problem_severity, args.problem_type, conn) + + conn.commit() + conn.close() + + +if __name__ == '__main__': + main() \ No newline at end of file diff --git a/apps/cli/executables/pexable/data_annotator/data_annotator/connections.py b/apps/cli/executables/pexable/data_annotator/data_annotator/connections.py new file mode 100644 index 0000000000000000000000000000000000000000..d056b7a4010422b02544638fe0124e0949ecaa21 --- /dev/null +++ b/apps/cli/executables/pexable/data_annotator/data_annotator/connections.py @@ -0,0 +1,54 @@ +import logging +import sys +import psycopg2 as pg +from pycapo import CapoConfig +from sqlalchemy.engine import Connection + +logger = logging.getLogger("data_annotator") +logger.setLevel(logging.INFO) +logger.addHandler(logging.StreamHandler(sys.stdout)) + + +class MDDBConnector: + """Use this connection to interrogate the archive""" + + def __init__(self): + self.connection = self._connect_to_db() + + @staticmethod + def _connect_to_db() -> Connection: + """ + Establish a DB connection + + :return: + """ + settings = CapoConfig().settings("metadataDatabase") + + host_slash_db = settings["jdbcUrl"][len("jdbc:postgresql://") :] + host, dbname = host_slash_db.split("/") + port = 5432 + if ":" in host: + host, port = host.split(":") + try: + conn = pg.connect( + host=host, + port=port, + database=dbname, + user=settings.jdbcUsername, + password=settings.jdbcPassword, + ) + return conn + except Exception as exc: + logger.error(f"Unable to connect to database: {exc}") + raise exc + + def cursor(self): + return self.connection.cursor() + + def close(self): + self.connection.close() + + def commit(self): + self.connection.commit() + + diff --git a/apps/cli/executables/pexable/data_annotator/data_annotator/queries.py b/apps/cli/executables/pexable/data_annotator/data_annotator/queries.py new file mode 100644 index 0000000000000000000000000000000000000000..ee48cb700041008d0de4e60fcd9d44578322cfe6 --- /dev/null +++ b/apps/cli/executables/pexable/data_annotator/data_annotator/queries.py @@ -0,0 +1,160 @@ + + +def retrieve_problem_types(connection): + """ + Retrieves all valid problem types from the database. + + :param connection: a MDDBConnector object to interface with the database + :return: a list of tuples representing problem type descriptions and their database ids + """ + cur = connection.cursor() + cur.execute("SELECT * FROM problem_types") + rows = cur.fetchall() + return rows + +def retrieve_problem_severities(connection): + """ + Retrieves all valid problem severities from the database. + + :param connection: a MDDBConnector object to interface with the database + :return: a list of tuples representing problem severity descriptions and their database ids + """ + cur = connection.cursor() + cur.execute("SELECT * FROM problem_severity_list") + rows = cur.fetchall() + return rows + +def get_exec_blocks(project_code, date_range, fsid, band, configuration, connection): + """ + Finds all execution blocks associated with a user's query by building and executing a SQL query + + :param project_code: a string corresponding to the project_code field in the database + :param date_range: a tuple corresponding to the starttime and endtime fields in the database + :param fsid: a string corresponding to the external name field in the database + :param band: a string corresponding to the band field in the database + :param configuration: a string corresponding to the configuration field in the database + :param connection: a MDDBConnector object to interface with the database + :return: a list of spls for all execution blocks, images, and calibrations related to the initial query + """ + # Format WHERE clauses with provided search pieces + project_code = f"project_code='{project_code}' AND " if project_code else '' + date_range = f"starttime>={date_range[0]} AND endtime<={date_range[1]} AND " if date_range else '' + fsid = f"external_name='{fsid}' AND " if fsid else '' + configuration = f"configuration='{configuration}' AND " if configuration else '' + band = f"band='{band}'" if band else '' + + search_command = f"SELECT execution_block_id, execution_blocks.science_product_locator FROM execution_blocks \ + INNER JOIN science_products ON execution_blocks.science_product_locator=science_products.science_product_locator \ + WHERE {project_code}{configuration}{date_range}{fsid}{band}" + + # Remove trailing ANDs, if necessary + if search_command[-4:] == 'AND ': + search_command = search_command[:-4] + + cur = connection.cursor() + cur.execute(search_command) + return cur.fetchall() + +def get_all_spls_from_exec_blocks(ebs, connection): + """ + Finds all science product locators associated with a list of execution blocks + + :param ebs: a list tuples representing execution blocks + :return: a list of spls for all execution blocks, images, and calibrations related to the initial query + """ + ebs_to_find = [] + spls_to_return = [] + for eb in ebs: + ebs_to_find.append(str(eb[0])) + spls_to_return.append(str(eb[1])) + + print("Finding all exec blocks, cals, and images fitting the passed in search terms...") + spl_query = f""" + with recursive + input_outputs as (select sppg2.science_product_locator as input_spl, sppg1.science_product_locator as output_spl + from science_products_product_groups sppg1 + join product_groups pg on pg.product_group_id = sppg1.product_group_id + join product_groups ppg on ppg.product_group_id = pg.parent_product_group_id + join science_products_product_groups sppg2 + on sppg2.product_group_id = ppg.product_group_id), + all_inputs_outputs as (select * + from input_outputs + union all + select input_outputs.input_spl, all_inputs_outputs.output_spl + from input_outputs + join all_inputs_outputs on input_outputs.output_spl = all_inputs_outputs.input_spl) + select distinct all_inputs_outputs.output_spl + from all_inputs_outputs, execution_blocks eb + where + eb.science_product_locator = all_inputs_outputs.input_spl AND + eb.execution_block_id in ({",".join(ebs_to_find)}) + """ + + cur = connection.cursor() + cur.execute(spl_query) + rows = cur.fetchall() + for row in rows: + spls_to_return.append(row[0]) + + return spls_to_return + + +def create_comments(ebs, comment, problem_severity, problem_type, connection): + """ + Creates a list of data comments and inserts them into the database. + + :param ebs: a list execution block ids + :param comment: a string representing the comment to create + :param problem_severity: an integer representing the problem severity id + :param problem_type: an integer representing the problem type id + :param connection: a MDDBConnector object to interface with the database + """ + print("Creating comments...") + comments_to_add = [] + for eb in ebs: + comments_to_add.append((problem_type, eb, problem_severity, comment)) + + cur = connection.cursor() + cur.executemany("INSERT INTO science_product_comments VALUES(DEFAULT,%s,%s,%s,%s)", comments_to_add) + print(f"Created comments for {cur.rowcount} total rows...") + + +def delete_comments(ebs, comment, problem_severity, problem_type, connection): + """ + Finds a list of comments in the database and deletes them. + + :param ebs: a list execution block ids + :param comment: a string representing the comment to delete + :param problem_severity: an integer representing the problem severity id + :param problem_type: an integer representing the problem type id + :param connection: a MDDBConnector object to interface with the database + """ + print("Deleting comments...") + comments_to_add = [] + for eb in ebs: + comments_to_add.append((problem_type, eb, problem_severity, comment)) + + cur = connection.cursor() + cur.executemany(f"DELETE FROM science_product_comments WHERE problem_type_id=%s AND science_product_locator=%s AND severity=%s AND comment=%s", comments_to_add) + print(f"Deleted comments for {cur.rowcount} total rows...") + + +def modify_comments(ebs, new_comment, old_comment, problem_severity, problem_type, connection): + """ + Finds a list of comments in the database and modifies the values. + + :param ebs: a list execution block ids + :param new_comment: a string representing the comment to be inserted + :param old_comment: a string representing the comment to be replaced + :param problem_severity: an integer representing the problem severity id + :param problem_type: an integer representing the problem type id + :param connection: a MDDBConnector object to interface with the database + """ + print("Modifying comments...") + comments_to_add = [] + for eb in ebs: + comments_to_add.append((new_comment, problem_type, eb, problem_severity, old_comment)) + + cur = connection.cursor() + cur.executemany(f"UPDATE science_product_comments SET comment=%s WHERE problem_type_id=%s AND science_product_locator=%s AND severity=%s AND comment=%s", comments_to_add) + print(f"Modified comments for {cur.rowcount} total rows...") \ No newline at end of file diff --git a/apps/cli/executables/pexable/data_annotator/poetry.lock 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"Workspaces CLI tool for creating and deleting comments associated with data quality." +authors = ["DMS SSA <dms-ssa@nrao.edu>"] +license = "GPL3+" +readme = "README.md" + +[tool.poetry.dependencies] +python = "^3.10" +pycapo = "^0.3.1" +psycopg2-binary = "^2.9.6" +sqlalchemy = "1.4.49" + +[tool.poetry.group.test.dependencies] +pytest = "^7.3.1" + +[tool.poetry.scripts] +data_annotator = "data_annotator.annotator:main" + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" diff --git a/apps/cli/executables/pexable/data_annotator/test/test_nothing.py b/apps/cli/executables/pexable/data_annotator/test/test_nothing.py new file mode 100644 index 0000000000000000000000000000000000000000..3b79f3d7c6cde773aff5ea674837f99aaad06fe3 --- /dev/null +++ b/apps/cli/executables/pexable/data_annotator/test/test_nothing.py @@ -0,0 +1,2 @@ +def test_always_passes(): + assert True