Add logging for qiita pushing

README.rst

@@ -1,7 +1,10 @@
 Knight Lab administrative portal
 ================================
 
-This is the internal Knight Lab administration portal for creating, tracking, and processing general barcodes and the American Gut.
+This is the internal Knight Lab administration portal for creating, tracking,
+and processing general barcodes and the American Gut.
+This codebase assumes that https://github.com/biocore/american-gut-web.git has
+already been installed.
 
 
 Installation instructions

knimin/handlers/barcode_util.py

@@ -14,6 +14,15 @@
 from knimin.handlers.access_decorators import set_access
 from knimin.lib.configuration import config
 
+import logging
+
+handler = logging.StreamHandler()
+fmt_str = '%(asctime)s %(name)-12s %(levelname)-8s %(message)s'
+handler.setFormatter(logging.Formatter(fmt_str))
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.DEBUG)
+logger.addHandler(handler)
+
 
 def get_qiita_client():
     if config.debug:
@@ -218,45 +227,65 @@ class PushQiitaHandler(BaseHandler):
 
     @concurrent.run_on_executor
     def _push_to_qiita(self, study_id, samples):
-        # TODO: add a mutex or block to ensure a single call process at a time
-        cats = self.qclient.get('/api/v1/study/%s/samples/info' % study_id)
-        cats = cats['categories']
+        logger.debug('Entering PushQiitaHandler._push_to_qiita()')
 
+        try:
+            cats = self.qclient.get('/api/v1/study/%s/samples/info' % study_id)
+        except Exception as e:
+            logger.debug("GETing failed: " + e.msg)
+
+        cats = cats['categories']
         samples = align_with_qiita_categories(samples, cats)
         data = json_encode(samples)
 
-        return self.qclient.http_patch('/api/v1/study/%s/samples' % study_id,
-                                       data=data)
+        logger.debug('PATCHing Qiita Database')
+        try:
+            self.qclient.http_patch('/api/v1/study/%s/samples' % study_id,
+                                    data=data)
+        except Exception as e:
+            logger.debug("PATCHing failed: " + e.msg)
+
+        logger.debug('Leaving PushQiitaHandler._push_to_qiita()')
 
     @authenticated
     def get(self):
+        dat = {}
+
         barcodes = db.get_unsent_barcodes_from_qiita_buffer()
         status = db.get_send_qiita_buffer_status()
         dat = {'status': status, "barcodes": barcodes}
+
         self.write(json_encode(dat))
         self.finish()
 
     @authenticated
     @gen.coroutine
     def post(self):
         barcodes = db.get_unsent_barcodes_from_qiita_buffer()
+        logger.debug(barcodes)
+
         if not barcodes:
+            logger.debug('No barcodes were present in the buffer')
             return
 
         # certainly not a perfect mutex, however tornado is single threaded
         status = db.get_send_qiita_buffer_status()
         if status in ['Failed!', 'Pushing...']:
+            logger.debug(status)
+            logger.debug('Leaving(2) PushQiitaHandler.post()')
             return
 
         db.set_send_qiita_buffer_status("Pushing...")
 
+        logger.debug('Pushing to Qiita')
         try:
             yield self._push_to_qiita(self.study_id, barcodes)
         except:  # noqa
+            logger.debug('Push failed')
             db.set_send_qiita_buffer_status("Failed!")
-        else:
-            db.mark_barcodes_sent_to_qiita(barcodes)
-            db.set_send_qiita_buffer_status("Idle")
+
+        db.mark_barcodes_sent_to_qiita(barcodes)
+        db.set_send_qiita_buffer_status("Idle")
 
 
 @set_access(['Scan Barcodes'])

knimin/lib/data_access.py

@@ -28,6 +28,15 @@
 from geocoder import geocode, Location
 from string_converter import converter
 
+import logging
+
+handler = logging.StreamHandler()
+fmt_str = '%(asctime)s %(name)-12s %(levelname)-8s %(message)s'
+handler.setFormatter(logging.Formatter(fmt_str))
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.DEBUG)
+logger.addHandler(handler)
+
 
 class IncorrectEmailError(Exception):
     pass
@@ -1454,7 +1463,10 @@ def mark_barcodes_sent_to_qiita(self, barcodes):
             sql = """UPDATE project_qiita_buffer
                      SET pushed_to_qiita = 'Y'
                      WHERE barcode IN %s"""
-            self._con.execute(sql, [tuple(barcodes)])
+            try:
+                self._con.execute(sql, [tuple(barcodes)])
+            except Exception as e:
+                logger.debug(e.pgcode)
 
     def add_barcodes_to_kit(self, ag_kit_id, num_barcodes=1):
         """Attaches barcodes to an existing american gut kit