Merge pull request #376 from moka-guys/smartsheet_update

Smartsheet update

automate_demultiplex_config.py

@@ -8,7 +8,7 @@
 import os
 
 # Set debug mode
-testing = False
+testing = True
 
 # =====location of input/output files=====
 # root of folder that contains the apps, automate_demultiplexing_logfiles and

demultiplex.py

@@ -202,7 +202,7 @@ def __init__(self, now):
         # Requests info
         self.headers = config.smartsheet_request_headers
         self.url = config.smartsheet_request_url
-
+        
         # variables to hold checksums:
         self.sequencer_checksum = ""
         self.workstation_checksum = ""
@@ -527,33 +527,45 @@ def smartsheet_demultiplex_in_progress(self):
         ', "value": "Demultiplex"}, {"columnId": ' + self.ss_samples + ', "value": ' + str(self.sample_count) + '},{"columnId": ' + self.ss_status + \
         ', "value": "In Progress"},{"columnId": ' + self.ss_priority + ', "value": "Medium"},{"columnId": ' + self.ss_assigned + \
         ', "value": "aledjones@nhs.net"},{"columnId": ' + self.ss_received + ', "value": "' + str(self.smartsheet_started) + '"}],"toBottom":true}'
-
         # Create url for uploading a new row
         url = self.url + "/rows"
 
         # Add the row using POST
-        r = requests.post(url, headers=self.headers, data=payload)
-        # capture the output of the POST statement to capture the id of the row that has been updated.
-        # This can be used when updating the status to complete in function smartsheet_demultiplex_complete().
-        response = r.json()
-        # capture the value of the row id from the json response
-        self.rowid = response["result"]["id"]
-
-        # Use response.get("") instead of response[""] to avoid KeyError if "message" missing.
-        if response.get("message") == "SUCCESS":
-            # Report to system log file
-            self.logger("Smartsheet updated with initiation of demultiplexing for run " + self.runfolder, "smartsheet_pass")
+        #Add try statement to stop script from failing
+        try:
+            r = requests.post(url, headers=self.headers, data=payload)
+            # capture the output of the POST statement to capture the id of the row that has been updated.
+            # This can be used when updating the status to complete in function smartsheet_demultiplex_complete().
+            response = r.json()
+        except:
+            self.script_logfile.write("Unable to connect to SmartSheet API. Check payload and URL\n")
+            self.logger("Unable to connect to SmartSheet API for run " + self.runfolder, "Check payload and URL")
+            return False
         else:
-            # Record error message to script log file
-            self.script_logfile.write("smartsheet NOT updated at in progress step\n" + str(response))
-            # Record failure in system logs so that an error can be reported via slack.
-            # Failure to update smartsheet is not critical as it does not stop the run being processed.
-            self.logger("Smartsheet was NOT updated to say demultiplexing is in progress for run " + self.runfolder, "smartsheet_fail")
+            # capture the value of the row id from the json response
+            self.rowid = response["result"]["id"]
+            # Use response.get("") instead of response[""] to avoid KeyError if "message" missing.
+            if response.get("message") == "SUCCESS":
+                # Report to system log file
+                self.logger("Smartsheet updated with initiation of demultiplexing for run " + self.runfolder, "smartsheet_pass")
+            else:
+                # Record error message to script log file
+                self.script_logfile.write("smartsheet NOT updated at in progress step\n" + str(response))
+                # Record failure in system logs so that an error can be reported via slack.
+                # Failure to update smartsheet is not critical as it does not stop the run being processed.
+                self.logger("Smartsheet was NOT updated to say demultiplexing is in progress for run " + self.runfolder, "smartsheet_fail")
 
     def smartsheet_demultiplex_complete(self):
         """Update smartsheet to say demultiplexing is complete.
         Add the completed date and calculate the duration (in days) and if met TAT.
         """
+        try:
+            assert self.rowid
+        except AssertionError:
+            self.script_logfile.write("No rowid available to update API. RowID not added\n")
+            self.logger("No rowid available to update API " + self.runfolder, "RowID not added")
+            return
+
         # assign current timestamp to self.smartsheet_complete
         self.smartsheet_complete = '{:%Y-%m-%d}'.format(datetime.datetime.now())
 

upload_and_setoff_workflows.py

@@ -297,7 +297,7 @@ def quarterback(self):
             # if not TSO500 will return None
             if TSO500_sample_list:
                 # tar runfolder
-                self.tar_runfolder()
+                #self.tar_runfolder()
                 # set list of samplenames as list of processed samples - this will allow the project to be named properly.
                 # set tar folder path in place of the list of fastqs to upload
                 self.list_of_processed_samples, self.fastq_string = TSO500_sample_list, self.runfolder_obj.runfolder_tarball_path + " " + self.runfolder_obj.runfolder_samplesheet_path
@@ -2146,26 +2146,29 @@ def smartsheet_workflows_commands_sent(self):
 
         # create url for uploading a new row
         url = self.smartsheet_url + "/rows"
-
-        # add the row using POST
-        r = requests.post(url, headers=self.headers, data=payload)
-
-        # capture the row id
-        response = r.json()
-
+        try:
+            # add the row using POST
+            r = requests.post(url, headers=self.headers, data=payload)
+            # capture the row id
+            response = r.json()
+        except:
+            self.script_logfile.write("Unable to connect to API. Check payload and URL\n")
+            self.logger("Unable to connect to smartsheet API for run " + self.runfolder + ". Check payload and url")
+            return False
+        else:
         # check the result of the update attempt
-        for line_key in response:
-            if line_key == "message":
-                if response[line_key] == "SUCCESS":
-                    self.loggers.script.info(
-                        "smartsheet_pass 'smartsheet updated to say in progress'"
-                    )
-                else:
-                    self.loggers.script.error(
-                        "smartsheet_fail 'run started NOT added to smartsheet for run {}'".format(
-                            self.runfolder_obj.runfolder_name
+            for line_key in response:
+                if line_key == "message":
+                    if response[line_key] == "SUCCESS":
+                        self.loggers.script.info(
+                            "smartsheet_pass 'smartsheet updated to say in progress'"
+                        )
+                    else:
+                        self.loggers.script.error(
+                            "smartsheet_fail 'run started NOT added to smartsheet for run {}'".format(
+                                self.runfolder_obj.runfolder_name
+                            )
                         )
-                    )
 
     def write_opms_queries_custom_panel(self, list_of_processed_samples):
         """