From b22d3ddc5f07d6449bf8199b0b3e3c010e96f1b1 Mon Sep 17 00:00:00 2001 From: Harris Tzovanakis Date: Fri, 27 Oct 2023 11:24:12 +0200 Subject: [PATCH] global: addition of annual-reports --- .DS_Store | Bin 0 -> 6148 bytes .flake8 | 3 + .github/workflows/pull-request.yaml | 1 + .github/workflows/push-main.yaml | 2 + .github/workflows/tests.yaml | 3 + .gitignore | 2 + .isort.cfg | 3 + .pre-commit-config.yaml | 11 +- matomo-api/.python-version => .python-version | 0 Library-Notification-Service/.python-version | 1 - annual-reports/Dockerfile | 21 + annual-reports/README.md | 24 + annual-reports/docker-compose.yml | 12 + annual-reports/poetry.lock | 1183 +++++++++++++++++ annual-reports/pyproject.toml | 31 + annual-reports/src/__init__.py | 0 annual-reports/src/api.py | 273 ++++ annual-reports/src/cli.py | 26 + annual-reports/src/models.py | 34 + .../cassettes/TestAPI.test_categories.yaml | 83 ++ .../cassettes/TestAPI.test_journals.yaml | 68 + .../cassettes/TestAPI.test_publications.yaml | 428 ++++++ annual-reports/tests/test_api.py | 222 ++++ 23 files changed, 2422 insertions(+), 9 deletions(-) create mode 100644 .DS_Store create mode 100644 .flake8 create mode 100644 .isort.cfg rename matomo-api/.python-version => .python-version (100%) delete mode 100644 Library-Notification-Service/.python-version create mode 100644 annual-reports/Dockerfile create mode 100644 annual-reports/README.md create mode 100644 annual-reports/docker-compose.yml create mode 100644 annual-reports/poetry.lock create mode 100644 annual-reports/pyproject.toml create mode 100644 annual-reports/src/__init__.py create mode 100644 annual-reports/src/api.py create mode 100644 annual-reports/src/cli.py create mode 100644 annual-reports/src/models.py create mode 100644 annual-reports/tests/cassettes/TestAPI.test_categories.yaml create mode 100644 annual-reports/tests/cassettes/TestAPI.test_journals.yaml create mode 100644 annual-reports/tests/cassettes/TestAPI.test_publications.yaml create mode 100644 annual-reports/tests/test_api.py diff --git a/.DS_Store b/.DS_Store new file mode 100644 index 0000000000000000000000000000000000000000..6757fe6f9a6f678d0e97fa90bc3f331be30b2f41 GIT binary patch literal 6148 zcmeHKQA+|r5S~>_MG7AZ>TRJ{BU3S@m&5E2bWsl#c85|&*R6PGK8SGd^@sW+{hnra z*Fvmbf(V(B*>84sW|#d|c5VScbjJNdfHD9SPzf_dY`zd0CtZ?^^$-d@hX*0-!w3d2 zT#9DLe`J8pZWBC+@Ha;MJU@l!m_Y1L;-McZALCyAVHm_owfZJ9+1%QC9;KAOaqrc{ zO}u0rcf8RR_0E+F{kiS=7r|iCD{q~sDDi@5FwzM@e}Ey^mqFB5la3lk{aEL^W}t}D zEALLHjaIE*k+o)fR*}7PSWFG-s{_mLQZC9gC?!96=E#715*$`@|3?9sSbAITllcCLM%c8RxMp3;RM5dUf(L-CF(6I3B{!bKT^=p hr5IzW6z`yFLBAve(Xp5sL=Oso2xuC(VFvz`fp<}sQ3C(~ literal 0 HcmV?d00001 diff --git a/.flake8 b/.flake8 new file mode 100644 index 0000000..f295e07 --- /dev/null +++ b/.flake8 @@ -0,0 +1,3 @@ +[flake8] +max-line-length = 88 +extend-ignore = E203, E704 diff --git a/.github/workflows/pull-request.yaml b/.github/workflows/pull-request.yaml index 8af9858..f5e1668 100644 --- a/.github/workflows/pull-request.yaml +++ b/.github/workflows/pull-request.yaml @@ -14,3 +14,4 @@ jobs: directory: - matomo-api - Library-Notification-Service + - annual-reports diff --git a/.github/workflows/push-main.yaml b/.github/workflows/push-main.yaml index 304943f..4616dc8 100644 --- a/.github/workflows/push-main.yaml +++ b/.github/workflows/push-main.yaml @@ -29,3 +29,5 @@ jobs: image-name: cern-sis/matomo-api - directory: Library-Notification-Service image-name: cern-sis/library-notifications-service + - directory: annual-reports + image-name: cern-sis/annual-reports diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml index 1634081..35a6b21 100644 --- a/.github/workflows/tests.yaml +++ b/.github/workflows/tests.yaml @@ -30,6 +30,9 @@ jobs: if [ ${{ inputs.directory }} == 'matomo-api' ]; then docker-compose -f matomo-api/docker-compose-tests.yaml up -d fi + if [ ${{ inputs.directory }} == 'annual-reports' ]; then + docker-compose -f annual-reports/docker-compose.yml up -d + fi - uses: actions/setup-python@v4 with: python-version: "3.11" diff --git a/.gitignore b/.gitignore index 68bc17f..dbce267 100644 --- a/.gitignore +++ b/.gitignore @@ -158,3 +158,5 @@ cython_debug/ # and can be added to the global gitignore or merged into this file. For a more nuclear # option (not recommended) you can uncomment the following to ignore the entire idea folder. #.idea/ + +.DS_Store diff --git a/.isort.cfg b/.isort.cfg new file mode 100644 index 0000000..faea09e --- /dev/null +++ b/.isort.cfg @@ -0,0 +1,3 @@ +[settings] +profile=black +known_third_party = api,backoff,cli,click,freezegun,models,psycopg2,pytest,requests,sqlalchemy,structlog diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 6b053b4..94a466f 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -8,15 +8,10 @@ repos: - id: check-added-large-files - id: flake8 - - repo: https://github.com/asottile/seed-isort-config - rev: v1.9.1 + - repo: https://github.com/pycqa/isort + rev: 5.12.0 hooks: - - id: seed-isort-config - - - repo: https://github.com/pre-commit/mirrors-isort - rev: v4.3.20 - hooks: - - id: isort + - id: isort - repo: https://github.com/python/black rev: stable diff --git a/matomo-api/.python-version b/.python-version similarity index 100% rename from matomo-api/.python-version rename to .python-version diff --git a/Library-Notification-Service/.python-version b/Library-Notification-Service/.python-version deleted file mode 100644 index 0c7d5f5..0000000 --- a/Library-Notification-Service/.python-version +++ /dev/null @@ -1 +0,0 @@ -3.11.4 diff --git a/annual-reports/Dockerfile b/annual-reports/Dockerfile new file mode 100644 index 0000000..495d8c0 --- /dev/null +++ b/annual-reports/Dockerfile @@ -0,0 +1,21 @@ +FROM python:3.8 + +WORKDIR /matomo + +ENV PATH="/root/.local/bin:${PATH}" +ENV PYTHONBUFFERED=0 \ + POETRY_VIRTUALENVS_CREATE=false + + +ARG POETRY_VERSION +ENV POETRY_VERSION="${POETRY_VERSION:-1.6.1}" +RUN curl -sSL https://install.python-poetry.org \ + | python3 - --git https://github.com/python-poetry/poetry.git#{$POETRY_VERSION} \ + && poetry --version + + +COPY poetry.lock pyproject.toml ./ +COPY src ./src + +RUN poetry install +CMD poetry run python src/cli.py diff --git a/annual-reports/README.md b/annual-reports/README.md new file mode 100644 index 0000000..1746df9 --- /dev/null +++ b/annual-reports/README.md @@ -0,0 +1,24 @@ +# Annual Reports + +## Installation +``` +poetry install +docker-compose up -d + +export DB_PASSWORD=annual +export DB_USER=annual +export DB_NAME=annual +export DB_HOST=localhost +export DB_PORT=5432 +``` + +## Run +### With specific years +``` +poetry run python src/cli.py -y 2022 -y 2023 +``` + +### For all years +``` +poetry run python src/cli.py +``` diff --git a/annual-reports/docker-compose.yml b/annual-reports/docker-compose.yml new file mode 100644 index 0000000..fba002c --- /dev/null +++ b/annual-reports/docker-compose.yml @@ -0,0 +1,12 @@ +version: '3.1' + +services: + db: + ports: + - "5432:5432" + image: postgres:14 + restart: always + environment: + POSTGRES_PASSWORD: annual + POSTGRES_USER: annual + POSTGRES_DB: annual diff --git a/annual-reports/poetry.lock b/annual-reports/poetry.lock new file mode 100644 index 0000000..7f228a2 --- /dev/null +++ b/annual-reports/poetry.lock @@ -0,0 +1,1183 @@ +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. + +[[package]] +name = "appnope" +version = "0.1.3" +description = "Disable App Nap on macOS >= 10.9" +optional = false +python-versions = "*" +files = [ + {file = "appnope-0.1.3-py2.py3-none-any.whl", hash = "sha256:265a455292d0bd8a72453494fa24df5a11eb18373a60c7c0430889f22548605e"}, + {file = "appnope-0.1.3.tar.gz", hash = "sha256:02bd91c4de869fbb1e1c50aafc4098827a7a54ab2f39d9dcba6c9547ed920e24"}, +] + +[[package]] +name = "asttokens" +version = "2.4.1" +description = "Annotate AST trees with source code positions" +optional = false +python-versions = "*" +files = [ + {file = "asttokens-2.4.1-py2.py3-none-any.whl", hash = "sha256:051ed49c3dcae8913ea7cd08e46a606dba30b79993209636c4875bc1d637bc24"}, + {file = "asttokens-2.4.1.tar.gz", hash = "sha256:b03869718ba9a6eb027e134bfdf69f38a236d681c83c160d510768af11254ba0"}, +] + +[package.dependencies] +six = ">=1.12.0" + +[package.extras] +astroid = ["astroid (>=1,<2)", "astroid (>=2,<4)"] +test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"] + +[[package]] +name = "backcall" +version = "0.2.0" +description = "Specifications for callback functions passed in to an API" +optional = false +python-versions = "*" +files = [ + {file = "backcall-0.2.0-py2.py3-none-any.whl", hash = "sha256:fbbce6a29f263178a1f7915c1940bde0ec2b2a967566fe1c65c1dfb7422bd255"}, + {file = "backcall-0.2.0.tar.gz", hash = "sha256:5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e"}, +] + +[[package]] +name = "backoff" +version = "2.2.1" +description = "Function decoration for backoff and retry" +optional = false +python-versions = ">=3.7,<4.0" +files = [ + {file = "backoff-2.2.1-py3-none-any.whl", hash = "sha256:63579f9a0628e06278f7e47b7d7d5b6ce20dc65c5e96a6f3ca99a6adca0396e8"}, + {file = "backoff-2.2.1.tar.gz", hash = "sha256:03f829f5bb1923180821643f8753b0502c3b682293992485b0eef2807afa5cba"}, +] + +[[package]] +name = "certifi" +version = "2023.7.22" +description = "Python package for providing Mozilla's CA Bundle." +optional = false +python-versions = ">=3.6" +files = [ + {file = "certifi-2023.7.22-py3-none-any.whl", hash = "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9"}, + {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"}, +] + +[[package]] +name = "charset-normalizer" +version = "3.2.0" +description = "The Real First Universal Charset Detector. 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+[tool.poetry] +name = "Annual Reports" +version = "0.1.0" +description = "" +authors = ["CERN SIS TS"] +packages = [ + { include = "*", from = "src" }, +] + +[tool.poetry.dependencies] +python = "^3.8" +requests = "^2.31.0" +click = "^8.1.7" +pytest = "^7.4.2" +pytest-vcr = "^1.0.2" +urllib3 = "1.26.7" +freezegun = "^1.2.2" +sqlalchemy = "^2.0.22" +sqlalchemy-utils = "^0.41.1" +structlog = "^23.2.0" +backoff = "^2.2.1" +psycopg2 = "^2.9.9" + +[tool.poetry.dev-dependencies] + +[tool.poetry.group.dev.dependencies] +ipdb = "^0.13.13" + +[build-system] +requires = ["poetry-core>=1.0.0"] +build-backend = "poetry.core.masonry.api" diff --git a/annual-reports/src/__init__.py b/annual-reports/src/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/annual-reports/src/api.py b/annual-reports/src/api.py new file mode 100644 index 0000000..cbabd48 --- /dev/null +++ b/annual-reports/src/api.py @@ -0,0 +1,273 @@ +import datetime +import os +import re + +import backoff +import requests +import structlog +from models import Base, Categories, Journals, Publications +from sqlalchemy import create_engine +from sqlalchemy.orm import Session + +# noqa: E501 +PUBLICATIONS_PER_YEAR = "https://cds.cern.ch/search?p=(980:ARTICLE+or+980:BOOK+or+980:PROCEEDINGS+or+690:'YELLOW+REPORT'+or+980:REPORT)+and+year:{year}+and+(affiliation:CERN+or+260:CERN+or+595:'For+annual+report')+not+595:'Not+for+annual+report'&of=xm&rg=1" # noqa: E501 +JOURNALS_PER_YEAR = "https://cds.cern.ch/search?ln=en&cc=Published+Articles&p=(affiliation:CERN+or+595:'For+annual+report')+and+year:{year}+not+980:ConferencePaper+not+980:BookChapter+not+595:'Not+for+annual+report'&action_search=Search&op1=a&m1=a&p1=&f1=&c=Published+Articles&c=&sf=&so=d&rm=&rg=2000&sc=0&of=tb&ot=773__p" # noqa: E501 +PUBLISHED_ARTICLES_PER_YEAR = "https://cds.cern.ch/search?ln=en&cc=Published+Articles&p=%28affiliation%3ACERN+or+595%3A%27For+annual+report%27%29+and+year%3A{year}+not+980%3AConferencePaper+not+980%3ABookChapter+not+595%3A%27Not+for+annual+report%27&action_search=Search&op1=a&m1=a&p1=&f1=&c=Published+Articles&c=&sf=&so=d&rm=&rg=1&sc=0&of=xm" # noqa: E501 +CONTRIBUTIONS_TO_CONFERENCE_PROCEEDINGS_PER_YEAR = "https://cds.cern.ch/search?wl=0&ln=en&cc=Published+Articles&p=980%3AARTICLE+and+%28affiliation%3ACERN+or+595%3A%27For+annual+report%27%29+and+year%3A{year}+and+980%3AConferencePaper+not+595%3A%27Not+for+annual+report%27&f=&action_search=Search&c=Published+Articles&c=&sf=author&so=a&rm=&rg=1&sc=1&of=xm" # noqa: E501 +REPORTS_BOOKS_AND_BOOK_CHAPTERS_PER_YEAR = "https://cds.cern.ch/search?ln=en&p=affiliation%3ACERN+or+260%3ACERN+and+260%3A{year}++and+%28980%3ABOOK+or+980%3APROCEEDINGS+or+690%3A%27YELLOW+REPORT%27+or+980%3ABookChapter+or+980%3AREPORT%29+not+595%3A%27Not+for+annual+report%27&action_search=Search&op1=a&m1=a&p1=&f1=&c=Articles+%26+Preprints&c=Books+%26+Proceedings&sf=&so=d&rm=&rg=1&sc=1&of=xm" # noqa: E501 +THESES_PER_YEAR = "https://cds.cern.ch/search?wl=0&ln=en&cc=CERN+Theses&p=502%3A%27{year}%27+and+502%3Aphd&f=&action_search=Search&c=CERN+Theses&c=&sf=&so=d&rm=&rg=1&sc=1&of=xm" # noqa: E501,E261 +SUBJECT_CATEGORIES_PER_YEAR = "https://cds.cern.ch/search?ln=en&cc=Published+Articles&p=(affiliation:CERN+or+595:'For+annual+report')+and+year:{year}+not+980:ConferencePaper+not+980:BookChapter+not+595:'Not+for+annual+report'&action_search=Search&op1=a&m1=a&p1=&f1=&c=Published+Articles&c=&sf=&so=d&rm=&rg=2000&sc=0&of=tb&ot=65017" # noqa: E501 + + +LOGGING = structlog.get_logger("Annual_Report_API") + + +def _backoff_handler(details): + LOGGING.info( + "Backing off {wait:0.1f} seconds after {tries} tries " + "calling function {target} with args {args} and kwargs " + "{kwargs}".format(**details) + ) + + +def get_number_of_records(url): + # Get the response from the URL + response = requests.get(url) + # Raise exception if HTTP error + response.raise_for_status() + match = re.search(r"Search-Engine-Total-Number-Of-Results: (\d+)", response.text) + # Return the number of records + if match: + return int(match.group(1)) + return None + + +@backoff.on_exception( + backoff.expo, + requests.exceptions.RequestException, + max_tries=5, + on_backoff=_backoff_handler, +) +def get_publications_per_year(year): + """ + Get the number of publications for each publication type for a given year. + + Parameters + ---------- + year : int + The year to get the number of publications for. + + Returns + ------- + dict + The number of publications for each publication type for the given year. + """ + publications_per_year = get_number_of_records( + PUBLICATIONS_PER_YEAR.format(year=year) + ) + published_articles_per_year = get_number_of_records( + PUBLISHED_ARTICLES_PER_YEAR.format(year=year) + ) + contributions_to_conference_proceedings_per_year = get_number_of_records( + CONTRIBUTIONS_TO_CONFERENCE_PROCEEDINGS_PER_YEAR.format(year=year) + ) + reports_books_and_book_chapters_per_year = get_number_of_records( + REPORTS_BOOKS_AND_BOOK_CHAPTERS_PER_YEAR.format(year=year) + ) + theses_per_year = get_number_of_records(THESES_PER_YEAR.format(year=year)) + + return { + "publications": publications_per_year, + "published_articles": published_articles_per_year, + "contributions_to_conference_proceedings": contributions_to_conference_proceedings_per_year, # noqa: E501,E261 + "reports_books_and_book_chapters": reports_books_and_book_chapters_per_year, + "theses": theses_per_year, + } + + +@backoff.on_exception( + backoff.expo, + requests.exceptions.RequestException, + max_tries=5, + on_backoff=_backoff_handler, +) +def get_journals_per_year(year): + """ + Get the number of publications for each journal for a given year. + + Parameters + ---------- + year : int + The year to get the number of publications for. + + Returns + ------- + dict + The number of publications for each journal for the given year. + """ + url = JOURNALS_PER_YEAR.format(year=year) + + response = requests.get(url) + + response.raise_for_status() + journals = response.text.split("\n") + + journal_to_count = {} + for journal in journals: + journal_name = journal + if journal_name in journal_to_count: + journal_to_count[journal_name] += 1 + else: + if journal_name: + journal_to_count[journal_name] = 1 + return journal_to_count + + +@backoff.on_exception( + backoff.expo, + requests.exceptions.RequestException, + max_tries=5, + on_backoff=_backoff_handler, +) +def get_subject_categories_per_year(year): + """ + Get the number of publications for each subject category for a given year. + + Parameters + ---------- + year : int + The year to get the number of categories for. + + Returns + ------- + dict + The number of categories for the given year. + """ + + url = SUBJECT_CATEGORIES_PER_YEAR.format(year=year) + + response = requests.get(url) + response.raise_for_status() + + categories = response.text.split("\n") + + categories_to_count = {} + + for category in categories: + if "SzGeCERN" not in category: + continue + + try: + category_name = category.split("$$a")[1].split("$$")[0] + except IndexError: + # Skip this category since it's malformed + continue + + if category_name in categories_to_count: + categories_to_count[category_name] += 1 + else: + categories_to_count[category_name] = 1 + + return categories_to_count + + +class AnnualReportsAPI: + def __init__( + self, + db_user: str = "", + db_password: str = "", + db_host: str = "", + db_name: str = "", + db_port: str = "", + years: list = None, + ) -> None: + self.db_user = db_user or os.environ.get("DB_USER") + self.db_password = db_password or os.environ.get("DB_PASSWORD") + self.db_host = db_host or os.environ.get("DB_HOST") + self.db_name = db_name or os.environ.get("DB_NAME") + self.db_port = db_port or os.environ.get("DB_PORT") + if not all( + [ + self.db_user, + self.db_password, + self.db_host, + self.db_name, + self.db_port, + ] + ): + raise ValueError("All the required attributes must be passed!") + self.years = years + if not self.years: + current_year = datetime.datetime.now().year + self.years = list(range(2004, current_year + 1)) + database_url = f"postgresql://{self.db_name}:{self.db_password}@{self.db_host}:{self.db_port}/{self.db_name}" # noqa: E501 + self.engine = create_engine(database_url) + + def create_tables(self): + Base.metadata.create_all(self.engine, checkfirst=True) + + def get_categories(self): + for year in self.years: + year = int(year) + LOGGING.info("Getting categories", year=year) + results = get_subject_categories_per_year(year) + with Session(self.engine) as session: + try: + LOGGING.info("Deleting categories", year=year) + session.query(Categories).filter_by(year=year).delete() + records = [ + Categories(year=year, category=key, count=value) + for key, value in results.items() + ] + LOGGING.info( + "Populate categories", count=len(records), categories=results + ) + session.add_all(records) + session.commit() + except Exception as e: + print("ERROR: " + str(e)) + LOGGING.exception("Populate categories") + else: + LOGGING.info("Populate categories success") + + def get_journals(self): + for year in self.years: + year = int(year) + LOGGING.info("Getting journals", year=year) + results = get_journals_per_year(year) + with Session(self.engine) as session: + try: + LOGGING.info("Deleting journals", year=year) + session.query(Journals).filter_by(year=year).delete() + records = [ + Journals(year=year, journal=key, count=value) + for key, value in results.items() + ] + LOGGING.info( + "Populate journals", count=len(records), journals=results + ) + session.add_all(records) + session.commit() + except Exception as e: # noqa: F841 + LOGGING.exception("Populate journals") + else: + LOGGING.info("Populate journals success") + + def get_publications(self): + for year in self.years: + year = int(year) + LOGGING.info("Getting publications", year=year) + results = get_publications_per_year(year) + with Session(self.engine) as session: + try: + LOGGING.info("Deleting publications", year=year) + session.query(Publications).filter_by(year=year).delete() + LOGGING.info("Populate publications", publications=results) + records = Publications(year=year, **results) + session.add(records) + session.commit() + except Exception as e: + print("ERROR: " + str(e)) + LOGGING.exception("Populate publications") + else: + LOGGING.info("Populate publications success") diff --git a/annual-reports/src/cli.py b/annual-reports/src/cli.py new file mode 100644 index 0000000..7c21314 --- /dev/null +++ b/annual-reports/src/cli.py @@ -0,0 +1,26 @@ +import click +from api import AnnualReportsAPI + + +@click.command() +@click.option("--years", "-y", multiple=True, default=[]) +def fetch_annual_reports(years: list[int]): + annual_reports = AnnualReportsAPI(years=years) + + click.echo("Create tables if missing") + annual_reports.create_tables() + + click.echo("Fetching categories") + annual_reports.get_categories() + + click.echo("Fetching journals") + annual_reports.get_journals() + + click.echo("Fetching publications") + annual_reports.get_publications() + + click.echo("Done") + + +if __name__ == "__main__": + fetch_annual_reports() diff --git a/annual-reports/src/models.py b/annual-reports/src/models.py new file mode 100644 index 0000000..eea6061 --- /dev/null +++ b/annual-reports/src/models.py @@ -0,0 +1,34 @@ +from sqlalchemy import Column, Integer, String +from sqlalchemy.orm import declarative_base + +Base = declarative_base() + + +class Publications(Base): + __tablename__ = "annual_reports_publications" + + id = Column(Integer, primary_key=True) + publications = Column(Integer, nullable=False) + published_articles = Column(Integer, nullable=False) + contributions_to_conference_proceedings = Column(Integer, nullable=False) + reports_books_and_book_chapters = Column(Integer, nullable=False) + theses = Column(Integer, nullable=False) + year = Column(Integer, nullable=False) + + +class Categories(Base): + __tablename__ = "annual_reports_categories" + + id = Column(Integer, primary_key=True) + category = Column(String, nullable=False) + count = Column(Integer, nullable=False) + year = Column(Integer, nullable=False) + + +class Journals(Base): + __tablename__ = "annual_reports_journals" + + id = Column(Integer, primary_key=True) + journal = Column(String, nullable=False) + count = Column(Integer, nullable=False) + year = Column(Integer, nullable=False) diff --git a/annual-reports/tests/cassettes/TestAPI.test_categories.yaml b/annual-reports/tests/cassettes/TestAPI.test_categories.yaml new file mode 100644 index 0000000..06396cc --- /dev/null +++ b/annual-reports/tests/cassettes/TestAPI.test_categories.yaml @@ -0,0 +1,83 @@ +interactions: +- request: + body: null + headers: + Accept: + - '*/*' + Accept-Encoding: + - gzip, deflate + Connection: + - keep-alive + User-Agent: + - python-requests/2.31.0 + method: GET + uri: https://cds.cern.ch/search?ln=en&cc=Published+Articles&p=(affiliation:CERN+or+595:'For+annual+report')+and+year:2022+not+980:ConferencePaper+not+980:BookChapter+not+595:'Not+for+annual+report'&action_search=Search&op1=a&m1=a&p1=&f1=&c=Published+Articles&c=&sf=&so=d&rm=&rg=2000&sc=0&of=tb&ot=65017 + response: + body: + string: !!binary | + H4sIAAAAAAAAA61cS3PbNhC+91fo4Ks8JEjwccw4qpOZvGrn0CtLIZY6EqVIVKbury9gWxYJf0ss + gN5sZ79d7BOLBZgkEZWsRSZnhUzScnZ1Je7/vVU3i7svV1fNzW67P/Xr7mHWdMvZ82/qcPwtMaiy + LjOIete2aqMOTb87HJ+A9/qn5kHN7jSnF3AhZYHBx/6w268ej+v2Gfz0h263fTwD8/oC/Pjl/tvH + u4XGLbqHdafUQYt4JsxEVSHCD6rZ9KvZt4GIu2a5bvr1rpstfvxQbX+c5uBaIoX72q/UYXZ/+uvv + 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Content-Length: + - '1726' + Content-Type: + - text/xml + Date: + - Fri, 27 Oct 2023 09:56:53 GMT + Keep-Alive: + - timeout=15, max=100 + Server: + - Apache + Set-Cookie: + - INVENIOSESSIONstub=NO; path=/; HttpOnly + - INVENIOSESSION=695ef8278edc799c9856114d95d00572; path=/; HttpOnly + Vary: + - ETag,Cache-Control,Accept-Encoding + Via: + - 1.1 cds.cern.ch + status: + code: 200 + message: OK +version: 1 diff --git a/annual-reports/tests/test_api.py b/annual-reports/tests/test_api.py new file mode 100644 index 0000000..78e79f5 --- /dev/null +++ b/annual-reports/tests/test_api.py @@ -0,0 +1,222 @@ +import pytest +from api import AnnualReportsAPI +from models import Categories, Journals, Publications +from sqlalchemy.orm import Session + + +class TestAPI: + def setup_class(self): + self.annual_reports = AnnualReportsAPI( + years=[2022], + db_user="annual", + db_password="annual", + db_host="localhost", + db_port="5432", + db_name="annual", + ) + self.annual_reports.create_tables() + + @pytest.mark.vcr() + def test_publications(self): + with Session(self.annual_reports.engine) as session: + publications = session.query(Publications).all() + assert len(publications) == 0 + + self.annual_reports.get_publications() + + with Session(self.annual_reports.engine) as session: + publications = session.query(Publications).all() + assert len(publications) == 1 + assert publications[0].publications == 2127 + assert publications[0].published_articles == 982 + assert publications[0].contributions_to_conference_proceedings == 1118 + assert publications[0].reports_books_and_book_chapters == 26 + assert publications[0].theses == 275 + assert publications[0].year == 2022 + + with Session(self.annual_reports.engine) as session: + session.query(Publications).delete() + session.commit() + + @pytest.mark.vcr() + def test_categories(self): + with Session(self.annual_reports.engine) as session: + categories = session.query(Categories).all() + assert len(categories) == 0 + + self.annual_reports.get_categories() + + with Session(self.annual_reports.engine) as session: + categories = session.query(Categories).all() + assert len(categories) == 19 + + expected = { + "Computing and Computers": 16, + "Accelerators and Storage Rings": 38, + "Astrophysics and Astronomy": 16, + "Nuclear Physics - Experiment": 15, + "Health Physics and Radiation Effects": 1, + "Detectors and Experimental Techniques": 44, + "Quantum Technology": 7, + "Mathematical Physics and Mathematics": 5, + "Education and Outreach": 3, + "Physics in General": 6, + "Particle Physics - Experiment": 18, + "General Theoretical Physics": 2, + "Other Fields of Physics": 3, + "Particle Physics - Phenomenology": 22, + "General Relativity and Cosmology": 6, + "Particle Physics - Theory": 6, + "Particle Physics - Lattice": 2, + "Nuclear Physics - Theory": 6, + "Engineering": 1, + } + for category in categories: + assert category.category in expected + assert category.count == expected[category.category] + assert category.year == 2022 + + with Session(self.annual_reports.engine) as session: + session.query(Categories).delete() + session.commit() + + @pytest.mark.vcr() + def test_journals(self): + with Session(self.annual_reports.engine) as session: + journals = session.query(Journals).all() + assert len(journals) == 0 + + self.annual_reports.get_journals() + + with Session(self.annual_reports.engine) as session: + journals = session.query(Journals).all() + + assert len(journals) == 117 + + expected = { + "JISTaP": 1, + "IEEE Trans. Appl. Supercond.": 2, + "The Messenger": 1, + "IFAC-PapersOnLine": 1, + "Future Microbiology": 1, + "Frontiers in Medicine": 1, + "J. Radiol. Prot.": 1, + "EJNMMI Physics": 1, + "Nature Chem.": 1, + "Transport in Porous Media": 1, + "IEEE Access": 3, + "Materials": 1, + "Environ. Sci. Technol.": 2, + "IEEE Trans. Rad. Plasma Med. Sci.": 2, + "CEAS Space J.": 1, + "Environments": 1, + "IEEE Trans. Parallel Distrib. Syst.": 2, + "IEEE Systems J.": 1, + "J. Chem. Phys.": 1, + "J. Math. Industry": 1, + "Inverse Prob. Imaging": 1, + "Photon.": 2, + "Chin. Phys. C": 1, + "Polymers": 1, + "J. Comput. Appl. Math.": 1, + "Eur. Financ. Manag.": 1, + "MagnetoHydrodyn.": 1, + "Phys. Educ.": 1, + "Atmos. Chem. Phys.": 1, + "Phys. Status Solidi B": 1, + "ACM Transactions on Privacy and Security": 1, + "Comput. Phys. Commun.": 1, + "Crystals": 5, + "Acta Mater.": 1, + "ChemPhysChem": 1, + "Swiss Journal of Geosciences": 1, + "Front. Phys.": 4, + "Robotics": 1, + "Nucl. Instrum. Methods Phys. Res., A": 12, + "Phys. Rev. Accel. Beams": 9, + "IEEE Trans. Educ.": 1, + "J. Mach. Learn. Res.": 1, + "J. Integer Sequences": 1, + "Batteries": 1, + "Comp. Meth. Appl. Math.": 1, + "Pharmaceutics": 1, + "Fortschr. Phys.": 1, + "JHEP": 11, + "IEEE Trans. Plasma Sci.": 1, + "Phys. Part. Nucl. Lett.": 1, + "Advanced Materials Interfaces": 1, + "MDPI Physics": 2, + "Phys. Rev. D": 6, + "EPL": 1, + "Phys. Rev. C": 5, + "Appl. Opt.": 1, + "Nature Astron.": 1, + "JINST": 10, + "AIP Adv.": 1, + "JCAP": 1, + "Res. Notes AAS": 1, + "Appl. Sciences": 3, + "J. Appl. Phys.": 1, + "J. Phys. A": 1, + "Eur. Phys. J. A": 1, + "Astron. Astrophys.": 1, + "Instruments": 1, + "IEEE Trans. Quantum Eng.": 1, + "Radiat. Prot. Dosim.": 1, + "Bull. Russ. Acad. Sci. Phys.": 1, + "IEEE Sensors J.": 1, + "Int. J. Sci. Edu.": 1, + "Fire Safety J.": 1, + "Front. Chem.": 1, + "Environmental Science: Atmospheres": 1, + "Mach. Learn. Sci. Tech.": 2, + "Roy. Soc. Open Sci.": 1, + "EPJ Tech. Instrum.": 2, + "Eur. Phys. J. Plus": 4, + "J. Mater. Chem.": 1, + "Front. Big Data": 1, + "Sensors": 1, + "The Physics Educator": 1, + "Phys. Rev. B": 2, + "J. Vac. Sci. Technol. A": 1, + "Materials Advances": 1, + "Sci. Rep.": 3, + "PoS": 1, + "Supercond. Sci. Technol.": 4, + "Rev. Sci. Instrum.": 1, + "Nature": 1, + "Model. Simul. Eng.": 1, + "Comput. Softw. Big Sci.": 1, + "Appl. Radiat. Isot.": 2, + "Phys. Lett. B": 2, + "Phys. Rev. E": 2, + "Swiss Medical Weekly": 1, + "J. Radioanal. Nucl. Chem.": 1, + "Nucl. Phys. News": 2, + "Nature Commun.": 1, + "PTEP": 1, + "Phys. Rev. Res.": 1, + "Nucl. Instrum. Methods Phys. Res., B": 2, + "New J. Phys.": 1, + "J. Lightwave Technol.": 1, + "Opt. Lett.": 1, + "Symmetry": 1, + "Pramana - J. Phys.": 1, + "Few-Body Syst.": 1, + "IEEE Trans. Nucl. Sci.": 1, + "Eur. Phys. J. C": 2, + "J. Phys. D": 1, + "Phys. Rev. Lett.": 3, + "Astrophys. J. Lett.": 1, + "Phys. Plasmas": 1, + "IEEE Trans. Electron Devices": 1, + "Rad. Det. Tech. Meth.": 1, + } + for journal in journals: + assert journal.journal in expected + assert journal.count == expected[journal.journal] + assert journal.year == 2022 + + with Session(self.annual_reports.engine) as session: + session.query(Journals).delete() + session.commit()