This is a GitHub repository for papers page scripts used to generate http://papers.gersteinlab.org/
For more information, please visit our lab's public wiki and private wiki
Contains the following directories from lectures.gersteinlab.org
- /var/www
- /var/www/cgi-bin
- /var/www/html/papers/update
- Papers 2.0 is now version controlled under GitHub: https://github.com/gersteinlab/papers.gersteinlab.org
- Dedicated development instance is available at dev.papers.gersteinlab.org
- Papers page under development is accessed via http://dev.papers.gersteinlab.org/
- Production server (lectures.gersteinlab.org) is synced with development via Git
- Rebuild batch script, which executes STEP 1 to 4
- Executable: http://dev.papers.gersteinlab.org/cgi-bin/rebuild.py
- STEP 1. Download Master Google spreadsheet as a CSV file
- Executable: http://dev.papers.gersteinlab.org/cgi-bin/1_gsheet2csv.py
- CSV output 1: http://dev.papers.gersteinlab.org/update/master_gsheet.csv
- CSV output 2: http://dev.papers.gersteinlab.org/update/subject_gsheet.csv
- STEP 2. Build a PubMed query and retrieve results as XML
- Executable: http://dev.papers.gersteinlab.org/cgi-bin/2_csv2xml.py
- XML output: http://dev.papers.gersteinlab.org/update/pubmed.xml
- STEP 3. Parse PubMed XML into TSV file
- Executable: http://dev.papers.gersteinlab.org/cgi-bin/3_xml2tsv.py
- TSV output: http://dev.papers.gersteinlab.org/update/pubmed.tsv
- STEP 4. Merge Master Google spreadsheet with PubMed data and create HTMLs
- Executable: http://dev.papers.gersteinlab.org/cgi-bin/4_update.py
- CSV output: http://dev.papers.gersteinlab.org/update/merged.csv