Update Barcode Scanner

database/procedures/ag_get_barcode_details.sql

@@ -12,7 +12,8 @@ begin
                 cast(akb.ag_kit_id as varchar2(100)), 
                 akb.barcode, 
                 akb.site_sampled, akb.environment_sampled, akb.sample_date, 
-                akb.sample_time, akb.participant_name, akb.notes
+                akb.sample_time, akb.participant_name, akb.notes, akb.refunded, akb.withdrawn,
+                akb.moldy, akb.other, akb.other_text, akb.date_of_last_email ,akb.overloaded, al.name
         from    ag_kit_barcodes akb
                 inner join ag_kit ak
                 on akb.ag_kit_id = ak.ag_kit_id
@@ -29,5 +30,3 @@ execute ag_get_barcode_details('000001029', :user_data_);
 print user_data_;
 */
 
-
-

database/procedures/get_barcode_details.sql

@@ -0,0 +1,18 @@
+create or replace procedure get_barcode_details 
+(
+  barcode_ in varchar2 
+, results_ out types.ref_cursor
+) as 
+begin
+  open results_ for
+  select create_date_time, status, scan_date, sample_postmark_date, biomass_remaining, sequencing_status, obsolete
+  from barcode
+  where barcode = barcode_;
+end get_barcode_details;
+
+
+/* 
+variable user_data_ REFCURSOR;
+execute get_barcode_details('000001029', :user_data_);
+print user_data_;
+*/

database/procedures/get_barcode_statuses.sql

@@ -0,0 +1,16 @@
+create or replace procedure get_barcode_statuses(
+  statuses_ out types.ref_cursor
+)as 
+begin
+  open statuses_ for 
+  select status from barcode_status;
+
+end get_barcode_statuses;
+
+
+
+/*
+variable results REFCURSOR;
+execute get_barcode_statuses(:results);
+print results;
+*/

database/procedures/get_project_group.sql

@@ -0,0 +1,16 @@
+create or replace procedure get_project_group 
+(
+  project_name in varchar2 ,
+  group_name_ out types.ref_cursor
+) as 
+begin
+open group_name_ for
+select g.group_name from project_groups g inner join project p on g.group_id = p.group_id 
+where p.project = project_name;
+end get_project_group;
+
+
+/*variable x REFCURSOR;
+execute get_project_group('Handout Kits', :x);
+print x;
+*/

database/procedures/get_sequencing_statuses.sql

@@ -0,0 +1,14 @@
+create or replace procedure get_sequencing_statuses(
+seq_statuses_ out types.ref_cursor
+)as 
+
+begin
+  open seq_statuses_ for 
+  select sequencing_status from BARCODE_SEQUENCING_STATUS;
+
+end get_sequencing_statuses;
+
+/*variable sequencing_statuses_ REFCURSOR;
+execute get_sequencing_statuses(:sequencing_statuses_);
+print sequencing_statuses_;
+*/

python_code/data_access/ag_data_access.py

@@ -154,19 +154,30 @@ def getAGBarcodeDetails(self, barcode):
         results = con.cursor()
         con.cursor().callproc('ag_get_barcode_details', [barcode, results])
         barcode_details = results.fetchone()
-        row_dict = {
-            'email': barcode_details[0],
-            'ag_kit_barcode_id': barcode_details[1],
-            'ag_kit_id': barcode_details[2],
-            'barcode': barcode_details[3],
-            'site_sampled': barcode_details[4],
-            'environment_sampled': barcode_details[5],
-            'sample_date': barcode_details[6],
-            'sample_time': barcode_details[7],
-            'participant_name': barcode_details[8],
-            'notes': barcode_details[9]
-        }
-
+        if barcode_details is not None:
+            row_dict = {
+                'email': barcode_details[0],
+                'ag_kit_barcode_id': barcode_details[1],
+                'ag_kit_id': barcode_details[2],
+                'barcode': barcode_details[3],
+                'site_sampled': barcode_details[4],
+                'environment_sampled': barcode_details[5],
+                'sample_date': barcode_details[6],
+                'sample_time': barcode_details[7],
+                'participant_name': barcode_details[8],
+                'notes': barcode_details[9],
+                'refunded' : barcode_details[10],
+                'withdrawn' : barcode_details[11],
+                'moldy' : barcode_details[12],
+                'other' : barcode_details[13],
+                'other_text' : barcode_details[14],
+                'date_of_last_email' : barcode_details[15],
+                'overloaded' : barcode_details[16],
+                'kit_name' : barcode_details[17]
+            }
+        else:
+            #no results so return an empty dict 
+            row_dict = {}
         return row_dict
 
     def getAGKitDetails(self, supplied_kit_id):
@@ -241,9 +252,14 @@ def addAGBarcode(self, ag_kit_id, barcode):
         con = self.getMetadataDatabaseConnection()
         con.cursor().callproc('ag_insert_barcode', [ag_kit_id, barcode])
 
-    def updateAGBarcode(self, barcode, ag_kit_id, site_sampled, environment_sampled, sample_date, sample_time, participant_name, notes):
+    def updateAGBarcode(self, barcode, ag_kit_id, site_sampled, 
+                        environment_sampled, sample_date, sample_time, 
+                        participant_name, notes, refunded='N', withdrawn='N'):
         con = self.getMetadataDatabaseConnection()
-        con.cursor().callproc('ag_update_barcode', [barcode, ag_kit_id, site_sampled, environment_sampled, sample_date, sample_time, participant_name, notes])
+        con.cursor().callproc('ag_update_barcode', [barcode, ag_kit_id, 
+                              site_sampled, environment_sampled, sample_date, 
+                              sample_time, participant_name, notes, refunded,
+                              withdrawn])
 
     def addAGHumanParticipant(self, ag_login_id, participant_name):
         con = self.getMetadataDatabaseConnection()

python_code/data_access/qiime_data_access.py

@@ -2963,11 +2963,14 @@ def updateSeqOtuCounts(self, sequence_prep_id, num_sequences, num_otus, otu_perc
             print 'Exception caught: %s.\nThe error is: %s' % (type(e), e)
             return False  
 
-    def updateBarcodeStatus(self, status, postmark, scan_date, barcode):
+    def updateBarcodeStatus(self, status, postmark, scan_date, barcode, 
+                            biomass_remaining, sequencing_status, obsolete):
         """ Updates a barcode's status
         """
         con = self.getMetadataDatabaseConnection()
-        con.cursor().callproc('update_barcode_status', [status, postmark, scan_date, barcode])
+        con.cursor().callproc('update_barcode_status', [status, postmark, 
+                               scan_date, barcode, biomass_remaining, 
+                               sequencing_status, obsolete])
 
     def getBarcodeProjType(self, barcode):
         """ Get the project type of the barcode.
@@ -2999,4 +3002,57 @@ def getProjectNames(self):
         con.cursor().callproc('get_project_names', [result])
         projnames = [row[0] for row in result]
         return projnames
+
+    def getSequencingStatuses(self):
+        """Returns a list of sequencings statuses
+        """
+        con = self.getMetadataDatabaseConnection()
+        result = con.cursor()
+        con.cursor().callproc('get_sequencing_statuses', [result])
+        seq_statuses = [row[0] for row in result]
+        return seq_statuses
+
+    def getBarcodeStatuses(self):
+        """Returns a list of barcode statuses
+        """
+        con = self.getMetadataDatabaseConnection()
+        result = con.cursor()
+        con.cursor().callproc('get_barcode_statuses', [result])
+        bar_statuses = [row[0] for row in result]
+        return bar_statuses
+
+    def getProjectGroup(self, project_name):
+        """Returns a project group name
 
+        project_name is the name of the project from the table project
+        """
+        con = self.getMetadataDatabaseConnection()
+        result = con.cursor()
+        con.cursor().callproc('get_project_group', [project_name,result])
+        group = result.fetchone()
+        if group:
+            return group[0]
+        else:
+            return None
+
+    def getBarcodeDetails(self, barcode):
+        """returns a dictionary of barcode deatails
+        """
+        con = self.getMetadataDatabaseConnection()
+        results = con.cursor()
+        con.cursor().callproc('get_barcode_details',[barcode, results])
+        row = results.fetchone()
+        if row is not None:
+            barcode_details = {
+                'create_date' : row[0],
+                'status' : row[1],
+                'scan_date' : row[2],
+                'sample_postmark_date' : row[3],
+                'biomass_remaining' : row[4],
+                'sequencing_status' : row[5],
+                'obsolete' : row[6]
+                }
+        else:
+            #no results mean barcode doesn't exist 
+            barcode_details = {}
+        return barcode_details

www/wwwadmin/ag_edit_barcode.psp

@@ -13,7 +13,7 @@ if 'submit_flag' in form:
 		# Submit and redirect to fusebox
 		ag_data_access.updateAGBarcode(form['barcode'], form['ag_kit_id'], form['site_sampled'], 
 			form['environment_sampled'], form['sample_date'], form['sample_time'], 
-			form['participant_name'], form['notes'])
+			form['participant_name'], form['notes'], form['refunded'], form['withdrawn'])
 		req.write('<script>document.submit_data.submit();</script>')
 # End if
 %>
@@ -35,7 +35,6 @@ if 'submit_flag' in form:
 		<tr>
 			<td>Barcode</td>
 			<td>
-				<!--<select name="barcode" id="barcode" class="hidden" onChange="document.edit_barcode.submit();">-->
 				<select name="barcode" id="barcode" onChange="document.edit_barcode.submit();">
 				<option value="">Please Select...</a>
 <%
@@ -72,7 +71,8 @@ if 'barcode' in form:
 	participant_name = '' if details['participant_name'] is \
         None else details['participant_name']
 	notes = '' if details['notes'] is None else details['notes']
-
+	refunded = 'N' if details['refunded'] is None else details['refunded']
+	withdrawn = 'N' if details['withdrawn'] is None else details['withdrawn']
 	# Indent
 %>
 
@@ -188,9 +188,39 @@ if 'barcode' in form:
 			<td>Notes</td>
 			<td><textarea name="notes" id="notes" style="width:350px;height:100px;"><%=notes%></textarea></td>
 		</tr>
+		<tr>
+        <td>Refunded</td><td><select name="refunded" id="refunded">
+<%
+        if refunded == 'N':
+          req.write('<option value="N" selected>No</option>')
+          req.write('<option value="Y">Yes</option>')
+        else:
+          req.write('<option value="N">No</option>')
+          req.write('<option value="Y" selected>Yes</option>')
+        #END Indent
+%>
+		</select>
+		</td></tr>
+		<tr>
+        <td>Withdrawn</td><td><select name="withdrawn" id="withdrawn">
+<%
+        if withdrawn == 'N':
+          req.write('<option value="N" selected>No</option>')
+          req.write('<option value="Y">Yes</option>')
+        else:
+          req.write('<option value="N">No</option>')
+          req.write('<option value="Y" selected>Yes</option>')
+        #END Indent
+%>
+		</select>
+		</td></tr>
+
+
+
 		<tr>
 			<td></td><td><input type="button" onClick="validateEditBarcode();" value="Submit"></td>
 		</tr>
+
 
 <%
 # End indent

www/wwwadmin/ag_edit_kit.psp

@@ -11,9 +11,6 @@ if 'submit_flag' in form:
 		# Submit and redirect to fusebox
 		ag_data_access.updateAGKit(form['ag_kit_id'], form['kit_id'], form['kit_password'], \
 			form['swabs_per_kit'], form['kit_verification_code'])
-		barcodes = form['barcodes'].split('-')
-		for barcode in barcodes:
-			data_access.setBarcodeProjType(form['project'], barcode)
 		req.write('<script>document.submit_data.submit();</script>')
 # End if
 %>
@@ -67,19 +64,6 @@ if 'ag_kit_id' in form:
 		<tr><td>Kit Password</td><td><input type="text" name="kit_password" id="kit_password" value="<%=details[2]%>"></td></tr>
 		<tr><td>Number of Swabs</td><td><input type="text" name="swabs_per_kit" id="swabs_per_kit" onkeypress='validateNumber(event)' value="<%=details[3]%>"></td></tr>
 		<tr><td>Kit Verification Code</td><td><input type="text" name="kit_verification_code" id="kit_verification_code" value="<%=details[4]%>"></td></tr>
-		<tr><td>Project</td><td><select name="project" id="project" >
-<%
-	if barcodes:
-		current_project = data_access.getBarcodeProjType(barcodes[0])
-		barcodesstring = '-'.join(barcodes)
-	for project in project_names:
-		if project == current_project:
-			req.write('<option value="{0}" selected>{0}</option>'.format(project))
-		else:
-			req.write('<option value="{0}">{0}</option>'.format(project))
-	#end
-%>
-		</select></td></tr>
 		<tr><td></td><td><input type="button" onclick="validateAGForm();" value="Submit"></td></tr>