Release v2.0.1

See release note

README.md

@@ -1,19 +1,19 @@
 # tRFtarget
 ![tRFtarget](static/img/tRFtarget.png)
 
-**tRFtarget** (http://trftarget.net/) integrates **computational predicted** and **experimental validated** binding interactions between transfer RNA-derived fragments (tRFs) and target transcripts for multiple organisms.
+**tRFtarget** (http://trftarget.net/) is a comprehensive platform consolidating both **computationally predicted** and **experimentally validated** binding interactions between transfer RNA-derived fragments (tRFs) and target transcripts across multiple organisms.
 
 Users can:
 
-* Search or browse predicted tRF targets
-* Run our pipeline [tRFtarget-pipeline](https://github.com/ZWang-Lab/tRFtarget-pipeline) to get targets of tRFs or other small non-coding RNAs (such as miRNAs) locally or via our web service in [http://trftarget.net/online_targets](http://trftarget.net/online_targets)
-* Browse experimental evidences of the predicted tRF-RNA interactions based on manually curated publications
+* Search or browse predicted tRF targets.
+* Run our pipeline [tRFtarget-pipeline](https://github.com/ZWang-Lab/tRFtarget-pipeline) to get targets of tRFs or other small non-coding RNAs (such as miRNAs) locally or via our web service in [http://trftarget.net/online_targets](http://trftarget.net/online_targets).
+* Browse experimental evidences of the predicted tRF-RNA interactions based on manually curated publications.
 
 ## Citation
 
 If you use tRFtarget or tRFtarget pipeline, please cite:
 
-Ningshan Li, Nayang Shan, Lingeng Lu, Zuoheng Wang. tRFtarget: a database for transfer RNA-derived fragment targets. *Nucleic Acids Research*, 2020, gkaa831. https://doi.org/10.1093/nar/gkaa831.
+Ningshan Li, Nayang Shan, Lingeng Lu, Zuoheng Wang. tRFtarget: a database for transfer RNA-derived fragment targets. *Nucleic Acids Research*, Volume 49, Issue D1, 8 January 2021, Pages D254–D260. https://doi.org/10.1093/nar/gkaa831.
 
 ## Contact Us
 Users are welcome to send feedbacks, suggestions or comments on the tRFtarget database, and report tRF target experiments that are not included in the database through [Issues](https://github.com/ZWang-Lab/tRFtarget/issues).

datatables.py

@@ -13,15 +13,15 @@
 import peewee as pw
 from operator import attrgetter, and_
 from functools import reduce
+import os
 
 
 
 # number of binding site records displayed in result page
 n_result = 5e4
 
 
-MYSQLDB = pw.MySQLDatabase('trftarget', user='root', password='12345678',
-                           host='127.0.0.1', port=3306, autoconnect=False)
+MYSQLDB = pw.MySQLDatabase(os.environ.get("MYSQL_DATABASE"), user=os.environ.get("MYSQL_USER"), password=os.environ.get("MYSQL_PASSWORD"), host=os.environ.get("MYSQL_HOST"), port=int(os.environ.get("MYSQL_PORT")), autoconnect=False)
 
 
 # 定义MySQL data types (ref http://docs.peewee-orm.com/en/latest/peewee/models.html?highlight=table%20generation#field-types-table)

jobs.py

@@ -43,7 +43,7 @@
 
 
 # folder for saving and serving files for online service
-cache_folder = r'/media/volume/sdb/service_cache'
+cache_folder = os.environ.get("CACHE_FOLDER")
 
 
 

redis_fun.py

@@ -21,6 +21,7 @@
 
 
 import redis
+import os
 
 
 
@@ -43,7 +44,7 @@
 '''
 
 
-POOL = redis.ConnectionPool(host='localhost', port=6379, db=0)
+POOL = redis.ConnectionPool(host=os.environ.get("REDIS_HOST"), port=int(os.environ.get("REDIS_PORT")), db=int(os.environ.get("REDIS_DB")))
 
 
 

tRFapp.py

@@ -970,5 +970,5 @@ def team():
 
 
 if __name__ == '__main__':
-    # use intenal IP
-    app.run(host= '10.0.107.211', port=80)
+    # use internal IP
+    app.run(host=os.environ.get("INTERNAL_IP"), port=80)

templates/statistics.html

@@ -219,9 +219,9 @@ <h3 id="target-gene-number" style="margin-top: 10px; margin-bottom: 15px">Number
                           <tr>
                               <th scope="row" class="table-light text-center"><em>Homo sapiens</em></th>
                               <td class="table-secondary text-end">20,367</td>
-                              <td class="table-light text-end">17,673</td>
+                              <td class="table-light text-end">17,669</td>
                               <td class="table-secondary text-end">52</td>
-                              <td class="table-light text-end">38,092</td>
+                              <td class="table-light text-end">38,088</td>
                           </tr>
                           <tr>
                               <th scope="row" class="table-light text-center"><em>Mus musculus</em></th>
@@ -282,9 +282,9 @@ <h3 id="target-gene-number" style="margin-top: 10px; margin-bottom: 15px">Number
                           <tr>
                               <th scope="row" class="table-light text-center">Total</th>
                               <td class="table-secondary text-end">161,387</td>
-                              <td class="table-light text-end">35,631</td>
+                              <td class="table-light text-end">35,627</td>
                               <td class="table-secondary text-end">2,332</td>
-                              <td class="table-light text-end">199,350</td>
+                              <td class="table-light text-end">199,346</td>
                           </tr>
                       </tbody>
                   </table>