Remove dependency on outdated GitPython

Only used to write commit hashes to MongoDB (but most are blank or ab62755)
Current version if reinstalled has bug gitpython-developers/GitPython#983 without upgrading

Author: kevinlul

Dockerfile

@@ -34,7 +34,7 @@ RUN curl -LO https://jbrowse.org/releases/JBrowse-${JBROWSE_VERSION}/JBrowse-${J
     rm JBrowse-${JBROWSE_VERSION}.zip && \
     cd /var/www/html/jbrowse && ./setup.sh
 RUN pip install --no-cache-dir numpy==1.11.2 pymongo==3.8.0 requests==2.22.0 && \
-    pip3 install --no-cache-dir numpy==1.17.2 pymongo==3.8.0 requests==2.20.0 Jinja2==2.10.1 GitPython==3.0.5
+    pip3 install --no-cache-dir numpy==1.17.2 pymongo==3.8.0 requests==2.20.0 Jinja2==2.10.1
 COPY config-template /var/www/html/config
 
 CMD service mongodb start && exec apache2-foreground

src/guide-finder/GuideAdd.py

@@ -8,7 +8,7 @@
 
 """
 
-import os, sys, json, cgi, git, datetime
+import os, sys, json, cgi, datetime
 from subprocess import Popen, PIPE, DEVNULL
 
 dir_path = os.path.dirname(os.path.abspath(__file__))
@@ -139,15 +139,6 @@ def combineSequence(self, rgen, guideSeq, pamSeq):
 
     def insertGuide(self):
         """ create a new record in the database for the guide """
-
-        # get the current git commit hash
-        try:
-            repo = git.Repo(search_parent_directories=True)
-            git_hash = repo.head.object.hexsha
-        except Exception as e:
-            # don't prevent guide from being added
-            git_hash = ''
-        # build the dict
         newGuideRecord = {
             'batchName': self.metadata['gene'],
             'status': 'Accepted',
@@ -164,7 +155,6 @@ def insertGuide(self):
             'ENSID': self.metadata['ENSID'],
             'guideLocation': self.guide['guideLocation'],
             'rgenID': self.metadata['rgenID'],
-            'commitHash': git_hash,
             'dateAdded': datetime.datetime.utcnow()
         }
         # TODO: think about how best to display the scores -> on primer end need to allow for possibility of no score