https://github.com/gersteinlab/papers.gersteinlab.org
https://github.com/gersteinlab/papers.gersteinlab.org
Last synced: 2 months ago
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- Host: GitHub
- URL: https://github.com/gersteinlab/papers.gersteinlab.org
- Owner: gersteinlab
- Created: 2015-10-23T16:46:48.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2020-09-29T13:58:18.000Z (over 4 years ago)
- Last Synced: 2024-03-26T12:26:40.745Z (about 1 year ago)
- Language: Go
- Size: 1.34 MB
- Stars: 2
- Watchers: 20
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# papers.gersteinlab.org
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](http://info.gersteinlab.org/Papers_Page_Code) and [private wiki](http://wiki.gersteinlab.org/labinfo/Papers_Page_Documentation)
## Contents
Contains the following directories from lectures.gersteinlab.org
* /var/www
* /var/www/cgi-bin
* /var/www/html/papers/update
## Papers 2.0 (under development @ dev.papers)
### What's New
* 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
### How to Execute
#### Quick update
* Rebuild batch script, which executes STEP 1 to 4
* **Executable: http://dev.papers.gersteinlab.org/cgi-bin/rebuild.py**
#### Step-by-step update
* 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