PubTrends

PubTrends is a scientific literature exploratory tool for analyzing topics of a research field and similar papers analysis. It runs a Pubmed or Semantic Scholar search and allows user to explore high-level structure of result papers.

Open Access Paper: https://doi.org/10.1145/3459930.3469501, poster is here.
Citation: Shpynov, O. and Nikolai, K., 2021, August. PubTrends: a scientific literature explorer. In Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (pp. 1-1).

Technical details

PubTrends is a web service, written in Python and Javascript. It uses Postgres to store information about scientific publications.

Libraries

Web service is built with Gunicorn and Flask. Asynchronous computations are supported with Celery tasks queue and Redis as message broker. We use Postgres to store information about papers: titles, abstracts, authors and citations information. Postgres built-in text search engine is used for full text search. Kotlin Postgres ORM is used to store papers in the database. Sqlite database is used to store technical user information including users roles and admin credentials for admin dashboard.

All the data manipulations are made with Pandas, Numpy and Scikit-Learn libraries. The service uses Python Nltk and Spacy libraries for text processing and analysis. Graph objects are processed with NetworkX library, papers embeddings are created with word2vec library from GenSim and in-house node2vec implementation based on word2vec. All the plots are created with Bokeh, Holoviews, Seaborn and Matplotlib libraries. Interactive Bokeh plots are used in web pages and Jupyter notebook experiments. Frontend uses Bootstrap, JQuery and Cytoscape-JS for graphs rendering.

Please refer to environment.yml for the full list of libraries used in the project.

Docker

Two Docker images are used for testing and deployment: biolabs/pubtrends-test and biolabs/pubtrends, respectively. We use Docker Hub to store built images. Service deployment is done with Docker compose, which launches Redis container, Celery container and Gunicorn container.

Please refer to docker-compose.yml for more information about deployment.

Testing and CI

Testing is done with Pytest and JUnit. Flake8 linter is used for quality assessment of Python code. Python tests are launched within Docker. Continuous integration is done with TeamCity using build chains.

Development Prerequisites

• JDK 8+
• Conda
• Python 3.6+
• Docker
• Postgres 15 (in Docker)
• Redis 5.0 (in Docker)

Configuration

1. Copy and modify config.properties to ~/.pubtrends/config.properties.
   Ensure that file contains correct information about the database(s) (url, port, DB name, username and password).

2. Conda environment pubtrends can be easily created for launching Jupyter Notebook and Web Service:

   conda env create -f environment.yml
   source activate pubtrends
   

3. Build base Docker image biolabs/pubtrends and nested image biolabs/pubtrends-test for testing.

   docker build -f resources/docker/main/Dockerfile -t biolabs/pubtrends --platform linux/amd64  .
   docker build  -f resources/docker/test/Dockerfile -t biolabs/pubtrends-test --platform linux/amd64 .
   

4. Init Postgres database.

   • Launch Docker image:

   docker run --rm --name pubtrends-postgres \
       -e POSTGRES_USER=biolabs -e POSTGRES_PASSWORD=mysecretpassword \
       -v ~/postgres/:/var/lib/postgresql/data \
       -e PGDATA=/var/lib/postgresql/data/pgdata \
       -p 5432:5432 \
       -d postgres:15
   

   • Create database (once database is created use -d pubtrends argument):

   psql -h localhost -p 5432 -U biolabs
   ALTER ROLE biolabs WITH LOGIN;
   CREATE DATABASE pubtrends OWNER biolabs;
   

   • Configure memory params in ~/postgres/pgdata/postgresql.conf.

   # Memory settings
   effective_cache_size = 8GB  # ~ 50 to 75% (can be set precisely by referring to “top” free+cached)
   shared_buffers = 2GB        # ~ 1/4 – 1/3 total system RAM
   work_mem = 1GB            # For sorting, ordering etc
   max_connections = 4  # Total mem is work_mem * connections
   maintenance_work_mem = 1GB  # Memory for indexes, etc
   
   # Write performance
   checkpoint_timeout = 10min
   checkpoint_completion_target = 0.8
   synchronous_commit = off
   

   You can check current settings by command SHOW ALL; in psql console.

5. Clone the JetBrains-Research/pubtrends-review repository to the working directory, and enable it in ~/.pubtrends/config.properties file.

   git clone [email protected]:JetBrains-Research/pubtrends-review.git
   

Kotlin/Java Build

Use the following command to test and build JAR package:

./gradlew clean test shadowJar

Papers downloading and processing

Postgresql should be configured and launched.

Pubmed

Launch crawler to download and keep up-to-date Pubmed database:

java -cp build/libs/pubtrends-dev.jar org.jetbrains.bio.pubtrends.pm.PubmedLoader --fillDatabase

Command line options supported:

• resetDatabase - clear current contents of the database (for development)
• fillDatabase - option to fill database with Pubmed data. Can be interrupted at any moment.
• lastId - force downloading from given id from articles pack pubmed20n{lastId+1}.xml.

Updates - add the following line to crontab:

crontab -e
0 22 * * * java -cp pubtrends-<version>.jar org.jetbrains.bio.pubtrends.pm.PubmedLoader --fillDatabase | \
tee -a crontab_update.log

Semantic Scholar

Download Sample from Semantic Scholar or full archive. See Open Corpus.
The latest release can be found at: https://api.semanticscholar.org/api-docs/datasets#tag/Release-Data

curl https://api.semanticscholar.org/datasets/v1/release/

• Linux & Mac OS

  # Fail on errors
  set -euox pipefail 
  
  DATE="2022-05-01"
  PUBTRENDS_JAR=
  
  wget https://s3-us-west-2.amazonaws.com/ai2-s2-research-public/open-corpus/$DATE/manifest.txt
  echo "" > complete.txt
  N=$(cat manifest.txt | grep corpus | wc -l)
  cat manifest.txt | grep corpus | while read -r file; do 
     if [[ -z $(grep "$file" complete.txt) ]]; then
        echo "Processing $file / $N"
        wget https://s3-us-west-2.amazonaws.com/ai2-s2-research-public/open-corpus/$DATE/$file;
        java -cp $PUBTRENDS_JAR org.jetbrains.bio.pubtrends.ss.SemanticScholarLoader --fillDatabase $(pwd)/$file
        rm $file;
        echo "$file" >> complete.txt
     fi;
  done
  java -cp $PUBTRENDS_JAR org.jetbrains.bio.pubtrends.ss.SemanticScholarLoader --index --finish
  

• Windows 10 PowerShell

  $DATE = "2023-03-14
  $PUBTRENDS_JAR = 
  curl.exe -o .\manifest.txt https://s3-us-west-2.amazonaws.com/ai2-s2-research-public/open-corpus/$DATE/manifest.txt 
  echo "" > .\complete.txt
  foreach ($file in Get-Content .\manifest.txt) {
      $sel = Select-String -Path .\complete.txt -Pattern $file
      if ($sel -eq $null) {
         echo "Processing $file"
         curl.exe -o .\$file https://s3-us-west-2.amazonaws.com/ai2-s2-research-public/open-corpus/$DATE/$file
         java -cp $PUBTRENDS_JAR org.jetbrains.bio.pubtrends.ss.SemanticScholarLoader --fillDatabase .\$file
         del ./$file
         echo $file >> .\complete.txt
      }
  }
  java -cp $PUBTRENDS_JAR org.jetbrains.bio.pubtrends.ss.SemanticScholarLoader --index --finish
  

Development

Please ensure that you have database configured, up and running.
Then launch web-service or use jupyter notebook for development.

Web service

1. Create necessary folders with script init.sh.

2. Start Redis

   docker run -p 6379:6379 redis:5.0
   

3. Configure conda environment pubtrends

   conda env create -f environment.yml
   

   Enable environment by command source activate pubtrends.

4. Start Celery worker queue

   celery -A pysrc.celery.tasks worker -c 1 --loglevel=debug
   

5. Start flask server at http://localhost:5000/

   python -m pysrc.app.app
   

Jupyter notebook

Notebooks are located under the /notebooks folder. Please configure PYTHONPATH before using jupyter.

export PYTHONPATH=$PYTHONPATH:$(pwd)
jupyter notebook

Testing

1. Start Docker image with Postgres environment for tests (Kotlin and Python development)

   docker run --rm --platform linux/amd64 --name pubtrends-test \
   --publish=5432:5432 --volume=$(pwd):/pubtrends -i -t biolabs/pubtrends-test
   

   NOTE: don't forget to stop the container afterward.

2. Kotlin tests

   ./gradlew clean test
   

3. Python tests with code style check for development (including integration with Kotlin DB writers)

   source activate pubtrends; pytest pysrc
   

4. Python tests within Docker (ensure that ./build/libs/pubtrends-dev.jar file is present)

   docker run --rm --platform linux/amd64 --volume=$(pwd):/pubtrends -t biolabs/pubtrends-test /bin/bash -c \
   "/usr/lib/postgresql/15/bin/pg_ctl -D /home/user/postgres start; \
   cd /pubtrends; mkdir ~/.pubtrends; cp config.properties ~/.pubtrends; \
   source activate pubtrends; pytest pysrc"
   

Deployment

Deployment is done with docker-compose:

• Gunicorn serving main pubtrends Flask app
• Redis as a message proxy
• Celery workers queue

Please ensure that you have configured and prepared the database(s).

1. Modify file config.properties with information about the database(s). File from the project folder is used in this case.

2. Start Postgres server.

   docker run --rm --name pubtrends-postgres -p 5432:5432 \
       --shm-size=8g \
       -e POSTGRES_USER=biolabs -e POSTGRES_PASSWORD=mysecretpassword \
       -e POSTGRES_DB=pubtrends \
       -v ~/postgres/:/var/lib/postgresql/data \
       -e PGDATA=/var/lib/postgresql/data/pgdata \
       -d postgres:15 
   

   NOTE: stop Postgres docker image with timeout --time=300 to avoid DB recovery.\

   NOTE2: for speed reason we use materialize views, which are updated upon successful database update. In case of emergency stop, the view should be refreshed manually to ensure sort by citations works correctly:

   psql -h localhost -p 5432 -U biolabs -d pubtrends
   refresh materialized view matview_pmcitations;
   

3. Build ready for deployment package with script dist.sh.

   dist.sh build=build-number ga=google-analytics-id
   

4. Launch pubtrends with docker-compose.

   # start
   docker-compose up -d --build
   

   Use these commands to stop compose build and check logs:

   # stop
   docker-compose down
   # inpect logs
   docker-compose logs
   

   Pubtrends will be serving on port 8888.

5. Nginx is used to proxy all traffic to port 8888 and redirect http -> https with Let's encrypt certificates.

Maintenance

Use simple placeholder during maintenance.

cd pysrc/app; python -m http.server 8888

Release

• Update CHANGES.md
• Update version in dist.sh
• Launch dist.sh, pubtrends-XXX.tar.gz will be created in the dist directory.

Authors

See AUTHORS.md for a list of authors and contributors.

Materials

• Open Access Paper: https://doi.org/10.1145/3459930.3469501, poster here - 2021.
• Project overview presentation - summer 2019.
• Review generation presentation - fall 2019.
• Extractive summarization presentation - spring 2020.
• Paper "Automatic generation of reviews of scientific papers" - 2021.
• Icons by Feather