From 2bd9cd80e6bc1a41f52dfb8cbd2f75b332a29b96 Mon Sep 17 00:00:00 2001
From: teravest <ejteravest@gmail.com>
Date: Fri, 14 Feb 2014 15:37:04 -0700
Subject: [PATCH 01/16] separatating barcode edits

---
 python_code/data_access/qiime_data_access.py | 20 +++++
 www/wwwadmin/edit_barcode.psp                | 79 ++++++++++++++++++++
 www/wwwadmin/header.psp                      | 16 +++-
 3 files changed, 112 insertions(+), 3 deletions(-)
 create mode 100644 www/wwwadmin/edit_barcode.psp

diff --git a/python_code/data_access/qiime_data_access.py b/python_code/data_access/qiime_data_access.py
index 2c638321..77ebf169 100755
--- a/python_code/data_access/qiime_data_access.py
+++ b/python_code/data_access/qiime_data_access.py
@@ -2999,3 +2999,23 @@ def getProjectNames(self):
         projnames = [row[0] for row in result]
         return projnames
 
+    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()
+        try:
+            barcode_details = {
+                'create_date' : row[0],
+                'status' : row[1],
+                'sample_postmark_date' : row[2],
+                'biomass_remaining' : row[3],
+                'sequencing_status' : row[4],
+                'obsolete' : row[5]
+                }
+        except TypeError :
+            #no results mean barcode doesn't exist 
+            return {}
+        return barcode_details
\ No newline at end of file
diff --git a/www/wwwadmin/edit_barcode.psp b/www/wwwadmin/edit_barcode.psp
new file mode 100644
index 00000000..6e7d136b
--- /dev/null
+++ b/www/wwwadmin/edit_barcode.psp
@@ -0,0 +1,79 @@
+<script src="../americangut/js/jquery.ui.timepicker.js"></script>
+
+<%@ include file="common_vars.psp" %>
+
+<form action="fusebox.psp" method="post" name="submit_data" id="submit_data">
+    <input type="hidden" name="page" value="select_task.psp"/>
+    <input type="hidden" name="message" value="Barcode was updated successfully."/>
+</form>
+
+<%
+qiime_data_access = data_access = data_access_factory(ServerConfig.data_access_type)
+if 'submit_flag' in form:
+	if form['submit_flag'] == '1':
+		# Submit and redirect to fusebox
+		qiime_data_access.updateBarcode(form['barcode'], form['status'], 
+			form['scan_date'], form['sample_postmark_date'], 
+			form['biomass_remaining'], form['sequencing_status'], 
+			form['obsolete'])
+		req.write('<script>document.submit_data.submit();</script>')
+# End if
+%>
+
+<form method="post" name="edit_barcode" id="edit_barcode" action="fusebox.psp?page=edit_barcode.psp">
+	<input type="hidden" name="submit_flag" id="submit_flag" value="0"/>
+	<table>
+		<tr>
+			<td>Barcode</td>
+			<td>
+				<input type="text" name="barcode" id="barcode" />
+			</td>
+		</tr>
+	</table>
+</form>
+
+<% 
+
+if 'barcode' in form:
+	barcode = form['barcode']
+	if len(barcode) != 9:
+		req.write('Barcode does not exist')
+	else:
+		details = qiime_data_access.getBarcodeDetails(barcode)
+		if len(details) == 0:
+			req.write('Barcode does not exist')
+		else: 
+			date_created = details['create_date']
+			status = details['status']
+			sample_postmark_date = details['sample_postmark_date']
+			biomass_remaining = details['biomass_remaining']
+			obsolete = details['obsolete']
+			#Indent
+			%>
+			<form>
+			<table>
+			<tr>
+			<td>Date Created</td>
+			<td> value="<%=date_created%>"/></td>
+			</tr>
+			<tr>
+			<td>Status</td>
+			<td input type="text" name="status" id="status" value="<%=status%>"/></td>
+			</tr>
+			<tr>
+			<tdSample Postmark Date</td>
+			<td input type="text" name="sample_postmark_date" id="sample_postmark_date" value="<%=sample_postmark_date%>"/></td>
+			</tr>
+			<tr>
+			<td>Biomass Remaining (Y or N)</td>
+			<td input type="text" maxlength="1" name="biomass_remaining" id="biomass_remaining" value="<%=biomass_remaining%>"/></td>
+			</tr>
+			<tr>
+			<td>Obsolete (Y or N)</td>
+			<td input type="text" maxlength="1" name="obsolete" id="obsolete" value="<%=obsolete%>"/></td>
+			</tr>
+			</table>
+			</form>
+<%
+#END Indent
+%>
\ No newline at end of file
diff --git a/www/wwwadmin/header.psp b/www/wwwadmin/header.psp
index 3300ab09..2fffa4ee 100644
--- a/www/wwwadmin/header.psp
+++ b/www/wwwadmin/header.psp
@@ -72,6 +72,11 @@ else:
             <input type="hidden" name="page_title" value="Manage Fast UniFrac limits">
         </form>
 
+        <form action="fusebox.psp" method="post" name="edit_barcode" id="edit_barcode">
+            <input type="hidden" name="page" value="edit_barcode.psp">
+            <input type="hidden" name="page_title" value="Edit Barcode">
+        </form>
+
         <!-- American Gut Utilities -->
 
         <form action="fusebox.psp" method="post" name="ag_search" id="ag_search">
@@ -150,14 +155,19 @@ else:
             <li><a href="" onclick="document.ag_edit_participant.submit(); return false;">Edit Participant</a></li>
             <li><a href="" onclick="document.ag_new_kit.submit(); return false;">Add New Kit</a></li>
             <li><a href="" onclick="document.ag_edit_kit.submit(); return false;">Edit Existing Kit</a></li>
-            <li><a href="" onclick="document.ag_new_barcode.submit(); return false;">Add New Barcode</a></li>
-            <li><a href="" onclick="document.ag_edit_barcode.submit(); return false;">Edit Existing Barcode</a></li>
+            <li><a href="" onclick="document.ag_new_barcode.submit(); return false;">Add New American Gut Barcode</a></li>
+            <li><a href="" onclick="document.ag_edit_barcode.submit(); return false;">Edit Existing American Gut Barcode</a></li>
             <!--<li><a href="" onclick="document.ag_reassign_barcode.submit(); return false;">Reassign Barcode</a></li>-->
-            <li><a href="" onclick="document.barcode_util.submit(); return false;">Scan Barcode</a></li>
             <li><a href="" onclick="document.update_geocode.submit(); return false;">Update Geocode</a></li>
             <li><a href="" onclick="document.ag_add_bruce_wayne.submit(); return false;">Add Bruce Wayne<img src="img/bruce.png"/></a></li>
         </ul>
 
+        <h3>General Project Utilities</h3>
+        <ul class="mainmenu">
+            <li><a href="" onclick="document.barcode_util.submit(); return false;">Scan Barcode</a></li>
+            <li><a href="" onclick="document.edit_barcode.submit(); return false;">Edit Barcode</a></li>
+        </ul>
+
         <h3>Legacy Web App Utilities</h3>
 
         <ul class="mainmenu">

From 7d4f3fa0c691ce3fae9713fbc121d42e7572e1b0 Mon Sep 17 00:00:00 2001
From: teravest <ejteravest@gmail.com>
Date: Fri, 14 Feb 2014 16:21:13 -0700
Subject: [PATCH 02/16] fixed indent

---
 www/wwwadmin/edit_barcode.psp | 77 ++++++++++++++++++-----------------
 1 file changed, 40 insertions(+), 37 deletions(-)

diff --git a/www/wwwadmin/edit_barcode.psp b/www/wwwadmin/edit_barcode.psp
index 6e7d136b..b1484182 100644
--- a/www/wwwadmin/edit_barcode.psp
+++ b/www/wwwadmin/edit_barcode.psp
@@ -33,47 +33,50 @@ if 'submit_flag' in form:
 </form>
 
 <% 
-
+barcode = ''
 if 'barcode' in form:
 	barcode = form['barcode']
 	if len(barcode) != 9:
 		req.write('Barcode does not exist')
 	else:
 		details = qiime_data_access.getBarcodeDetails(barcode)
-		if len(details) == 0:
-			req.write('Barcode does not exist')
-		else: 
-			date_created = details['create_date']
-			status = details['status']
-			sample_postmark_date = details['sample_postmark_date']
-			biomass_remaining = details['biomass_remaining']
-			obsolete = details['obsolete']
-			#Indent
-			%>
-			<form>
-			<table>
-			<tr>
-			<td>Date Created</td>
-			<td> value="<%=date_created%>"/></td>
-			</tr>
-			<tr>
-			<td>Status</td>
-			<td input type="text" name="status" id="status" value="<%=status%>"/></td>
-			</tr>
-			<tr>
-			<tdSample Postmark Date</td>
-			<td input type="text" name="sample_postmark_date" id="sample_postmark_date" value="<%=sample_postmark_date%>"/></td>
-			</tr>
-			<tr>
-			<td>Biomass Remaining (Y or N)</td>
-			<td input type="text" maxlength="1" name="biomass_remaining" id="biomass_remaining" value="<%=biomass_remaining%>"/></td>
-			</tr>
-			<tr>
-			<td>Obsolete (Y or N)</td>
-			<td input type="text" maxlength="1" name="obsolete" id="obsolete" value="<%=obsolete%>"/></td>
-			</tr>
-			</table>
-			</form>
+	if len(details) == 0:
+		req.write('Barcode does not exist')
+	else: 
+		date_created = details['create_date']
+		status = '' if details['status'] is None else details['status']
+		sample_postmark_date = '' if details['sample_postmark_date'] is None \
+			else details['sample_postmark_date']
+		biomass_remaining = '' if details['biomass_remaining'] is None \
+			else details['barcode']
+		obsolete = '' if details['obsolete'] is None else details['obsolete']
+		#Indent
+%>
+<form>
+<table>
+<tr>
+<td>Date Created</td>
+<td> <%=date_created%> </td>
+</tr>
+<tr>
+<td>Status</td>
+<td><input type="text" name="status" id="status" value="<%=status%>"/></td>
+</tr>
+<tr>
+<td>Sample Postmark Date</td>
+<td><input type="text" name="sample_postmark_date" id="sample_postmark_date" value="<%=sample_postmark_date%>"/></td>
+</tr>
+<tr>
+<td>Biomass Remaining (Y or N)</td>
+<td><input type="text" maxlength="1" name="biomass_remaining" id="biomass_remaining" value="<%=biomass_remaining%>"/></td>
+</tr>
+<tr>
+<td>Obsolete (Y or N)</td>
+<td><input type="text" maxlength="1" name="obsolete" id="obsolete" value="<%=obsolete%>"/></td>
+</tr>
+</table>
+</form>
+
 <%
-#END Indent
-%>
\ No newline at end of file
+#End Indent
+%>

From a32ffb278c756f656b1003f293a2246fe55c07ff Mon Sep 17 00:00:00 2001
From: teravest <ejteravest@gmail.com>
Date: Wed, 19 Feb 2014 09:32:18 -0700
Subject: [PATCH 03/16] updates to barcode_util

---
 python_code/data_access/ag_data_access.py    |   4 +-
 python_code/data_access/qiime_data_access.py |  13 +--
 www/wwwadmin/barcode_util.psp                |  37 ++++++-
 www/wwwadmin/edit_barcode.psp                | 107 +++++++++++++------
 www/wwwadmin/style/qiime.css                 |   4 +
 5 files changed, 119 insertions(+), 46 deletions(-)

diff --git a/python_code/data_access/ag_data_access.py b/python_code/data_access/ag_data_access.py
index 1bcbe738..2def2356 100755
--- a/python_code/data_access/ag_data_access.py
+++ b/python_code/data_access/ag_data_access.py
@@ -164,7 +164,9 @@ def getAGBarcodeDetails(self, barcode):
             'sample_date': barcode_details[6],
             'sample_time': barcode_details[7],
             'participant_name': barcode_details[8],
-            'notes': barcode_details[9]
+            'notes': barcode_details[9],
+            'refunded' : barcode_details[10],
+            'withdrawn' : barcode_details[11]
         }
 
         return row_dict
diff --git a/python_code/data_access/qiime_data_access.py b/python_code/data_access/qiime_data_access.py
index 77ebf169..cb7efaaf 100755
--- a/python_code/data_access/qiime_data_access.py
+++ b/python_code/data_access/qiime_data_access.py
@@ -2962,11 +2962,11 @@ 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.
@@ -3010,10 +3010,11 @@ def getBarcodeDetails(self, barcode):
             barcode_details = {
                 'create_date' : row[0],
                 'status' : row[1],
-                'sample_postmark_date' : row[2],
-                'biomass_remaining' : row[3],
-                'sequencing_status' : row[4],
-                'obsolete' : row[5]
+                'scan_date' : row[2],
+                'sample_postmark_date' : row[3],
+                'biomass_remaining' : row[4],
+                'sequencing_status' : row[5],
+                'obsolete' : row[6]
                 }
         except TypeError :
             #no results mean barcode doesn't exist 
diff --git a/www/wwwadmin/barcode_util.psp b/www/wwwadmin/barcode_util.psp
index c60efd0a..2a759fa8 100644
--- a/www/wwwadmin/barcode_util.psp
+++ b/www/wwwadmin/barcode_util.psp
@@ -24,7 +24,10 @@ if prev_barcode:
         # else: scan_date = form['scan_date']
 
         data_access.updateBarcodeStatus('Received', form['postmark_date'],
-                                        form['scan_date'], prev_barcode)
+                                        form['scan_date'], prev_barcode,
+                                        form['biomass_remaining'],
+                                        form['sequencing_status'], 
+                                        form['obsolete_status'])
     
         sent_date = form['sent_date']
 
@@ -133,7 +136,12 @@ try:
         ''' % barcode)
     else: 
         div_id = message = email_type = ""
-        if all(barcodeinfo[0:3]):
+
+        if (barcodeinfo[15] == "Y"):
+                #the barcode is obsolete
+                div_id = "obsolete"
+                message = "Barcode is Obsolete"
+        elif all(barcodeinfo[0:3]):
             # it has all sample details (sample time, date, site)
             if len(barcode_metadata) == 1:
                 # and we can successfully retrieve sample metadata
@@ -177,7 +185,18 @@ try:
           <input type="hidden" name="login_user"  value="{login_user}" />
           <input type="hidden" name="login_email" value="{login_email}" />
           <input type="hidden" name="email_type" value="{email_type}" />
+          <input type="hidden" name="sample_date" id="sample_date" value={sample_date}/>
+          <input type="hidden" name="sample_time" id="sample_time" value={sample_time}/>
+          <input type="hidden" name="sample_site" id="sample_site" value={sample_site}/>
           <ul>
+             <li>
+             Sample details: <br/>
+             <table>
+             <tr><td>Sample Date</td><td>{sample_date}</td></tr>
+             <tr><td>Sample Time</td><td>{sample_time}</td></tr>
+             <tr><td>Sample Site</td><td>{sample_site}</td></tr>
+             </table>
+             </li>
              <li>
                Sample issues: <br />
                   <input class="checkbox" type="checkbox" name="sample_issue" id="moldy" value="moldy" {moldy_checked}/> 
@@ -191,7 +210,7 @@ try:
                Other notes: <br />
                   <textarea name="other_text" onclick="this.select()">{other_text}</textarea>
              </li>
-        '''.format(div_id = div_id,
+              '''.format(div_id = div_id,
                    proj_type = proj_type,
                    barcode = barcode,
                    message = message,
@@ -206,7 +225,10 @@ try:
                    scan_date = barcodeinfo[9],
                    login_email = barcodeinfo[11],
                    login_user = barcodeinfo[12],
-                   email_type = email_type))
+                   email_type = email_type,
+                   sample_date = "" if barcodeinfo[1]==None else barcodeinfo[1],
+                   sample_time = "" if barcodeinfo[2]==None else barcodeinfo[2],
+                   sample_site = "" if barcodeinfo[0]==None else barcodeinfo[0]))
         # indent
 %>
              <li>
@@ -241,6 +263,13 @@ try:
                         </script>
                   (please follow the format mm/dd/yyyy. Example: 12/25/2012)
              </li>
+             <li>General Sample Information: <br>
+             <table>
+             <tr><td>Biomass Remaining (Y or N)</td><td><input type="text" name="biomass_remaining" id="biomass_remaining" value="<%=barcodeinfo[13] if barcodeinfo[13] else ''%>"/></td></tr>
+             <tr><td>Sequencing Status</td><td><input type="text" name="sequencing_status" id="sequencing_status" value="<%=barcodeinfo[14] if barcodeinfo[14] else ''%>"/></td></tr>
+             <tr><td>Obsolete (Y or N)</td><td><input type="text" name="obsolete_status" id="obsolete_status" value="<%=barcodeinfo[15] if barcodeinfo[15] else ''%>"/></td></tr>
+             </table>
+             </li>
              <li>
                Send an email notification (previously sent: <%=barcodeinfo[7]%>): <br />
                <table><tr>
diff --git a/www/wwwadmin/edit_barcode.psp b/www/wwwadmin/edit_barcode.psp
index b1484182..02743a66 100644
--- a/www/wwwadmin/edit_barcode.psp
+++ b/www/wwwadmin/edit_barcode.psp
@@ -9,52 +9,45 @@
 
 <%
 qiime_data_access = data_access = data_access_factory(ServerConfig.data_access_type)
-if 'submit_flag' in form:
-	if form['submit_flag'] == '1':
-		# Submit and redirect to fusebox
-		qiime_data_access.updateBarcode(form['barcode'], form['status'], 
-			form['scan_date'], form['sample_postmark_date'], 
-			form['biomass_remaining'], form['sequencing_status'], 
-			form['obsolete'])
-		req.write('<script>document.submit_data.submit();</script>')
-# End if
-%>
+if 'sample_postmark_date' in form:
+	# Submit and redirect to fusebox
+	qiime_data_access.updateBarcodeStatus(form['status'], 
+		form['sample_postmark_date'], form['scan_date'], form['barcode'],
+		form['biomass_remaining'], form['sequencing_status'], 
+		form['obsolete'])
+	qiime_data_access.setBarcodeProjType(form['project'], form['barcode'])
+	req.write('<script>document.submit_data.submit();</script>')
 
-<form method="post" name="edit_barcode" id="edit_barcode" action="fusebox.psp?page=edit_barcode.psp">
-	<input type="hidden" name="submit_flag" id="submit_flag" value="0"/>
-	<table>
-		<tr>
-			<td>Barcode</td>
-			<td>
-				<input type="text" name="barcode" id="barcode" />
-			</td>
-		</tr>
-	</table>
-</form>
 
-<% 
-barcode = ''
 if 'barcode' in form:
 	barcode = form['barcode']
 	if len(barcode) != 9:
 		req.write('Barcode does not exist')
 	else:
 		details = qiime_data_access.getBarcodeDetails(barcode)
-	if len(details) == 0:
-		req.write('Barcode does not exist')
-	else: 
-		date_created = details['create_date']
-		status = '' if details['status'] is None else details['status']
-		sample_postmark_date = '' if details['sample_postmark_date'] is None \
-			else details['sample_postmark_date']
-		biomass_remaining = '' if details['biomass_remaining'] is None \
-			else details['barcode']
-		obsolete = '' if details['obsolete'] is None else details['obsolete']
-		#Indent
+		if len(details) == 0:
+			req.write('Barcode does not exist')
+		else: 
+			date_created = details['create_date']
+			status = '' if details['status'] is None else details['status']
+			scan_date = '' if details['scan_date'] is None else \
+				details['scan_date']
+			sample_postmark_date = '' if details['sample_postmark_date'] is None \
+				else details['sample_postmark_date']
+			sequencing_status = '' if details['sequencing_status'] is None\
+				else details['sequencing_status']
+			biomass_remaining = '' if details['biomass_remaining'] is None \
+				else details['biomass_remaining']
+			obsolete = '' if details['obsolete'] is None else details['obsolete']
+			#Indent
 %>
-<form>
+<form action="fusebox.psp?page=edit_barcode.psp" method="post" name"edit_barcode_submit"=>
 <table>
 <tr>
+<td>Barcode</td>
+<td> <%=barcode%> </td>
+</tr>
+<tr>
 <td>Date Created</td>
 <td> <%=date_created%> </td>
 </tr>
@@ -63,20 +56,64 @@ if 'barcode' in form:
 <td><input type="text" name="status" id="status" value="<%=status%>"/></td>
 </tr>
 <tr>
+<td> Scan Date </td>
+<td><input type="text" name="scan_date" id="scan_date" value="<%=scan_date%>"/></td>
+</tr>
+<tr>
 <td>Sample Postmark Date</td>
 <td><input type="text" name="sample_postmark_date" id="sample_postmark_date" value="<%=sample_postmark_date%>"/></td>
 </tr>
 <tr>
+<td>Sequencing Status</td>
+<td><input type="text" name="sequencing_status" id="sequencing_status" value="<%=sequencing_status%>"/></td>
+</tr>
+<tr>
 <td>Biomass Remaining (Y or N)</td>
 <td><input type="text" maxlength="1" name="biomass_remaining" id="biomass_remaining" value="<%=biomass_remaining%>"/></td>
 </tr>
 <tr>
 <td>Obsolete (Y or N)</td>
 <td><input type="text" maxlength="1" name="obsolete" id="obsolete" value="<%=obsolete%>"/></td>
+<tr><td>Project</td><td><select name="project" id="project" >
+<%
+			project_names = qiime_data_access.getProjectNames()
+			current_project = qiime_data_access.getBarcodeProjType(barcode)
+			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 Indent
+%>
+		</select></td></tr>
 </tr>
+<td><input type="submit" id="submit_flag" value="Submit"/></td>
 </table>
+<input type="hidden" name="barcode" id="barcode" value="<%=barcode%>"/>
+<input type="hidden" name="date_created" id="date_created" value="<%=date_created%>"/>
 </form>
 
 <%
 #End Indent
+else:
+	#indent
+%>
+
+<form method="post" name="edit_barcode" id="edit_barcode" action="fusebox.psp?page=edit_barcode.psp">
+	<input type="hidden" name="submit_flag" id="submit_flag" value="0"/>
+	<table>
+		<tr>
+			<td>Barcode</td>
+			<td>
+				<input type="text" name="barcode" id="barcode" />
+			</td>
+		</tr>
+		<tr>
+		<td></td><td> <input type="submit" value="Go" style="width:50px;"></td>
+		</tr>
+	</table>
+</form>
+
+<% 
+#end indent
 %>
diff --git a/www/wwwadmin/style/qiime.css b/www/wwwadmin/style/qiime.css
index cf7ba8e6..3fc9876e 100755
--- a/www/wwwadmin/style/qiime.css
+++ b/www/wwwadmin/style/qiime.css
@@ -318,6 +318,10 @@ h2.verification_text{
 	background-color: #f00;
 }
 
+#obsolete {
+	background-color: #f00;
+}
+
 div#barcode_form form ul li{
     list-style-type: square;
     font-weigth: bold;

From b6f3b05697040dd9c7795c782fca871eee8f7b39 Mon Sep 17 00:00:00 2001
From: teravest <ejteravest@gmail.com>
Date: Wed, 19 Feb 2014 11:00:28 -0700
Subject: [PATCH 04/16] working version before refactoring barcode_utils

---
 www/wwwadmin/ag_edit_barcode.psp |  5 ++---
 www/wwwadmin/barcode_util.psp    | 15 +++++++++++++++
 2 files changed, 17 insertions(+), 3 deletions(-)

diff --git a/www/wwwadmin/ag_edit_barcode.psp b/www/wwwadmin/ag_edit_barcode.psp
index da2962b0..b27ac248 100644
--- a/www/wwwadmin/ag_edit_barcode.psp
+++ b/www/wwwadmin/ag_edit_barcode.psp
@@ -29,14 +29,13 @@ if 'submit_flag' in form:
 </script>
 -->
 
-<form method="post" name="edit_barcode" id="edit_barcode" action="fusebox.psp?page=ag_edit_barcode.psp">
+<form method="post" name="ag_edit_barcode1" id="ag_edit_barcode1" action="fusebox.psp?page=ag_edit_barcode.psp">
 	<input type="hidden" name="submit_flag" id="submit_flag" value="0"/>
 	<table>
 		<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();">
+				<select name="barcode" id="barcode" onChange="document.ag_edit_barcode1.submit();">
 				<option value="">Please Select...</a>
 <%
 barcodes = ag_data_access.getAGBarcodes()
diff --git a/www/wwwadmin/barcode_util.psp b/www/wwwadmin/barcode_util.psp
index 2a759fa8..e37f5e3d 100644
--- a/www/wwwadmin/barcode_util.psp
+++ b/www/wwwadmin/barcode_util.psp
@@ -28,6 +28,7 @@ if prev_barcode:
                                         form['biomass_remaining'],
                                         form['sequencing_status'], 
                                         form['obsolete_status'])
+        data_access.setBarcodeProjType(form['project'], form['barcode'])
     
         sent_date = form['sent_date']
 
@@ -270,6 +271,20 @@ try:
              <tr><td>Obsolete (Y or N)</td><td><input type="text" name="obsolete_status" id="obsolete_status" value="<%=barcodeinfo[15] if barcodeinfo[15] else ''%>"/></td></tr>
              </table>
              </li>
+             <li>
+             <tr><td>Project</td><td><select name="project" id="project" >
+<%
+        project_names = data_access.getProjectNames()
+        current_project = data_access.getBarcodeProjType(barcode)
+        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 Indent
+%>
+            </select></td></tr>
+            </li>
              <li>
                Send an email notification (previously sent: <%=barcodeinfo[7]%>): <br />
                <table><tr>

From 8e7716f7d31e8db022da2be8b66879f8a6036b58 Mon Sep 17 00:00:00 2001
From: teravest <ejteravest@gmail.com>
Date: Wed, 19 Feb 2014 12:54:44 -0700
Subject: [PATCH 05/16] partial refactor of barcode scanner

---
 www/wwwadmin/barcode_util.psp | 126 +++++++++++++++++-----------------
 www/wwwadmin/edit_barcode.psp | 119 --------------------------------
 www/wwwadmin/header.psp       |   6 --
 3 files changed, 64 insertions(+), 187 deletions(-)
 delete mode 100644 www/wwwadmin/edit_barcode.psp

diff --git a/www/wwwadmin/barcode_util.psp b/www/wwwadmin/barcode_util.psp
index e37f5e3d..25a96544 100644
--- a/www/wwwadmin/barcode_util.psp
+++ b/www/wwwadmin/barcode_util.psp
@@ -15,20 +15,21 @@ from datetime import date
 current_date = date.today().strftime("%m/%d/%Y")
 
 prev_barcode = form.get('prev_barcode', None)
-
 if prev_barcode:
     try: # try to update barcode current status.
         # do not change scan_date if it's already in the database.
         # it's gotten from the html form, so use str representation of None.
         # if form['scan_date'] == 'None': scan_date = current_date
         # else: scan_date = form['scan_date']
-
+        biomass_remaining_value = form.get('biomass_remaining', [])
+        biomass_remaining = 'N'
+        if 'biomass_remaining_checked' in biomass_remaining_value: biomass_remaining = 'Y'
         data_access.updateBarcodeStatus('Received', form['postmark_date'],
                                         form['scan_date'], prev_barcode,
-                                        form['biomass_remaining'],
+                                        biomass_remaining,
                                         form['sequencing_status'], 
                                         form['obsolete_status'])
-        data_access.setBarcodeProjType(form['project'], form['barcode'])
+        data_access.setBarcodeProjType(form['project'], prev_barcode)
     
         sent_date = form['sent_date']
 
@@ -136,13 +137,33 @@ try:
          </div>
         ''' % barcode)
     else: 
+        sample_site = '' if barcodeinfo[0] == None else barcodeinfo[0]
+        sample_date = '' if barcodeinfo[1] == None else barcodeinfo[1]
+        sample_time = '' if barcodeinfo[2] == None else barcodeinfo[2]
+        moldy = 'NA' if barcodeinfo[3] == None else barcodeinfo[3]
+        overloaded = 'NA' if barcodeinfo[4] == None else barcodeinfo[4]
+        other = 'NA' if barcodeinfo[5] == None else barcodeinfo[5]
+        other_text = '' if barcodeinfo[6] == None else barcodeinfo[6]
+        date_of_last_email = '' if barcodeinfo[7] == None else barcodeinfo[7]
+        status = '' if barcodeinfo[8] == None else barcodeinfo[8]
+        scan_date = 'NA' if barcodeinfo[9] == None else barcodeinfo[9]
+        sample_postmark_date = 'NA' if barcodeinfo[10] == None else barcodeinfo[10]
+        email = '' if barcodeinfo[11] == None else barcodeinfo[11]
+        name = '' if barcodeinfo[12] == None else barcodeinfo[12]
+        biomass_remaining = '' if barcodeinfo[13] == None else barcodeinfo[13]
+        sequencing_status = '' if barcodeinfo[14] == None else barcodeinfo[14]
+        obsolete = '' if barcodeinfo[15] == None else barcodeinfo[15]
+        biomass_check = 'checked' if biomass_remaining == 'Y' else ''
+        moldy_checked = "checked" if moldy in ('Y','y') else ""
+        overloaded_checked = "checked" if overloaded in ('Y','y') else ""
+        other_checked = "checked" if other in ('Y','y') else "",
         div_id = message = email_type = ""
 
         if (barcodeinfo[15] == "Y"):
                 #the barcode is obsolete
                 div_id = "obsolete"
                 message = "Barcode is Obsolete"
-        elif all(barcodeinfo[0:3]):
+        elif not (sample_date == sample_site == sample_time == ''):
             # it has all sample details (sample time, date, site)
             if len(barcode_metadata) == 1:
                 # and we can successfully retrieve sample metadata
@@ -164,16 +185,17 @@ try:
             div_id = "not_assigned"
             message = "Missing info"
             email_type = "0"
-
-        req.write('''
+        #indent
+%>
+        
         <div id="{div_id}" class="verification_color">
            <div class="verification_text_wrapper">
               <br />
                
                 <h2 class="verification_text">
-                 Project type: {proj_type} <br><br>
-                 Barcode: {barcode}<br><br>
-                {message}</h2>
+                 Project type: <%=proj_type%> <br><br>
+                 Barcode: <%=barcode%><br><br>
+                <%=message%></h2>
             </div>
         </div>
 
@@ -181,60 +203,39 @@ try:
         <form action="fusebox.psp?page=barcode_util.psp" method="post"
          onsubmit="return confirm('Are you sure to submit and update database?')"
          onreset="return confirm('Are you sure to reset?')">
-          <input type="hidden" name="prev_barcode" value="{barcode}" />
-          <input type="hidden" name="sent_date" value="{sent}" />
-          <input type="hidden" name="login_user"  value="{login_user}" />
-          <input type="hidden" name="login_email" value="{login_email}" />
-          <input type="hidden" name="email_type" value="{email_type}" />
-          <input type="hidden" name="sample_date" id="sample_date" value={sample_date}/>
-          <input type="hidden" name="sample_time" id="sample_time" value={sample_time}/>
-          <input type="hidden" name="sample_site" id="sample_site" value={sample_site}/>
+          <input type="hidden" name="prev_barcode" value="<%=barcode%>" />
+          <input type="hidden" name="sent_date" value="<%=date_of_last_email%>" />
+          <input type="hidden" name="login_user"  value="<%=name%>" />
+          <input type="hidden" name="login_email" value="<%=email%>" />
+          <input type="hidden" name="email_type" value="<%=email_type%>" />
+          <input type="hidden" name="sample_date" id="sample_date" value="<%=sample_date%>"/>
+          <input type="hidden" name="sample_time" id="sample_time" value="<%=sample_time%>"/>
+          <input type="hidden" name="sample_site" id="sample_site" value="<%=sample_site%>"/>
           <ul>
              <li>
              Sample details: <br/>
              <table>
-             <tr><td>Sample Date</td><td>{sample_date}</td></tr>
-             <tr><td>Sample Time</td><td>{sample_time}</td></tr>
-             <tr><td>Sample Site</td><td>{sample_site}</td></tr>
+             <tr><td>Sample Date</td><td><%=sample_date%></td></tr>
+             <tr><td>Sample Time</td><td><%=sample_time%></td></tr>
+             <tr><td>Sample Site</td><td><%=sample_site%></td></tr>
              </table>
              </li>
              <li>
                Sample issues: <br />
-                  <input class="checkbox" type="checkbox" name="sample_issue" id="moldy" value="moldy" {moldy_checked}/> 
-                    <label for="moldy"> moldy (current: {moldy}) </label> <br />
-                  <input class="checkbox" type="checkbox" name="sample_issue" id="overloaded" value="overloaded" {overloaded_checked}/>
-                    <label for="overloaded"> overloaded (current: {overloaded}) </label> <br />
-                  <input class="checkbox" type="checkbox" name="sample_issue" id="other" value="other" {other_checked}/>
-                    <label for="other"> other (current: {other}) </label> <br />
+                  <input class="checkbox" type="checkbox" name="sample_issue" id="moldy" value="moldy" <%=moldy_checked%>/> 
+                    <label for="moldy"> moldy (current: <%=moldy%>) </label> <br />
+                  <input class="checkbox" type="checkbox" name="sample_issue" id="overloaded" value="overloaded" <%=overloaded_checked%>/>
+                    <label for="overloaded"> overloaded (current: <%=overloaded%>) </label> <br />
+                  <input class="checkbox" type="checkbox" name="sample_issue" id="other" value="other" <%=other_checked%>/>
+                    <label for="other"> other (current: <%=other%>) </label> <br />
              </li>
              <li>
                Other notes: <br />
-                  <textarea name="other_text" onclick="this.select()">{other_text}</textarea>
+                  <textarea name="other_text" onclick="this.select()"><%=other_text%></textarea>
              </li>
-              '''.format(div_id = div_id,
-                   proj_type = proj_type,
-                   barcode = barcode,
-                   message = message,
-                   moldy = 'NA' if barcodeinfo[3]==None else barcodeinfo[3],
-                   moldy_checked = "checked" if barcodeinfo[3] in ('Y','y') else "",
-                   overloaded = 'NA' if barcodeinfo[4]==None else barcodeinfo[4],
-                   overloaded_checked = "checked" if barcodeinfo[4] in ('Y','y') else "",
-                   other = 'NA' if barcodeinfo[5]==None else barcodeinfo[5],
-                   other_checked = "checked" if barcodeinfo[5] in ('Y','y') else "",
-                   other_text = "" if barcodeinfo[6]==None else barcodeinfo[6],
-                   sent = barcodeinfo[7],
-                   scan_date = barcodeinfo[9],
-                   login_email = barcodeinfo[11],
-                   login_user = barcodeinfo[12],
-                   email_type = email_type,
-                   sample_date = "" if barcodeinfo[1]==None else barcodeinfo[1],
-                   sample_time = "" if barcodeinfo[2]==None else barcodeinfo[2],
-                   sample_site = "" if barcodeinfo[0]==None else barcodeinfo[0]))
-        # indent
-%>
              <li>
-               Sample postmark date (current: <%=barcodeinfo[10] if barcodeinfo[10] else 'NA'%>) : <br />
-                  <input type="text" name="postmark_date" id="postmark_date" value="<%=barcodeinfo[10] if barcodeinfo[10] else ''%>" onclick="this.select()" /> <br />
+               Sample postmark date (current: <%=sample_postmark_date%>) : <br />
+                  <input type="text" name="postmark_date" id="postmark_date" value="<%=sample_postmark_date if sample_postmark_date != 'NA' else ''%>" onclick="this.select()" /> <br />
                         <script>
                           $(function() {
                             $( "#postmark_date" ).datepicker({
@@ -249,8 +250,8 @@ try:
                   (please follow the format mm/dd/yyyy. Example: 12/25/2012)
              </li>
              <li>
-               Scan date (current: <%=barcodeinfo[9] if barcodeinfo[9] else 'NA'%>): <br />
-               <input type="text" name="scan_date" id="scan_date" value="<%=barcodeinfo[9] if barcodeinfo[9] else ''%>" onclick="this.select()" /> <br />
+               Scan date (current: <%=scan_date%>): <br />
+               <input type="text" name="scan_date" id="scan_date" value="<%=scan_date if scan_date != 'NA' else ''%>" onclick="this.select()" /> <br />
                         <script>
                           $(function() {
                             $( "#scan_date" ).datepicker({
@@ -265,14 +266,15 @@ try:
                   (please follow the format mm/dd/yyyy. Example: 12/25/2012)
              </li>
              <li>General Sample Information: <br>
-             <table>
-             <tr><td>Biomass Remaining (Y or N)</td><td><input type="text" name="biomass_remaining" id="biomass_remaining" value="<%=barcodeinfo[13] if barcodeinfo[13] else ''%>"/></td></tr>
-             <tr><td>Sequencing Status</td><td><input type="text" name="sequencing_status" id="sequencing_status" value="<%=barcodeinfo[14] if barcodeinfo[14] else ''%>"/></td></tr>
-             <tr><td>Obsolete (Y or N)</td><td><input type="text" name="obsolete_status" id="obsolete_status" value="<%=barcodeinfo[15] if barcodeinfo[15] else ''%>"/></td></tr>
+             <table
+             <tr><td><input class="checkbox" type="checkbox" name="biomass_remaining" id="biomass_remaining_checked" value="biomass_remaining_checked"<%=biomass_check%>/>
+             <label for="biomass_remaining"> Biomass Remaining (current:<%=biomass_remaining%>)</label></td></tr>
+             <tr><td>Sequencing Status</td><td><input type="text" name="sequencing_status" id="sequencing_status" value="<%=sequencing_status%>"/></td></tr>
+             <tr><td>Obsolete (Y or N)</td><td><input type="text" maxlength="1" name="obsolete_status" id="obsolete_status" value="<%=obsolete%>"/></td></tr>
              </table>
              </li>
              <li>
-             <tr><td>Project</td><td><select name="project" id="project" >
+             <tr><td>Project </td><td><select name="project" id="project" >
 <%
         project_names = data_access.getProjectNames()
         current_project = data_access.getBarcodeProjType(barcode)
@@ -286,10 +288,10 @@ try:
             </select></td></tr>
             </li>
              <li>
-               Send an email notification (previously sent: <%=barcodeinfo[7]%>): <br />
+               Send an email notification (previously sent: <%=date_of_last_email%>): <br />
                <table><tr>
                   <td> <input class="checkbox" type="checkbox" name="send_email" id="send_email" value="send_email" style="float:left;" /> </td>
-                  <td><label for="send_email" style="display:block;">send kit owner <%=barcodeinfo[12]%> (<%=barcodeinfo[11]%>) an email </label> </td></tr>
+                  <td><label for="send_email" style="display:block;">send kit owner <%=email%> (<%=name%>) an email </label> </td></tr>
 
 <%
         if email_type == '0':
@@ -327,8 +329,8 @@ try:
         elif email_type == '1':
             # indent
 %>
-            <input type="hidden" name="sample_time" value="<%=barcodeinfo[2]%>" />
-            <input type="hidden" name="sample_date" value="<%=barcodeinfo[1]%>" />
+            <input type="hidden" name="sample_time" value="<%=sample_time%>" />
+            <input type="hidden" name="sample_date" value="<%=sample_date%>" />
 <%
         # de-indent
 %>
diff --git a/www/wwwadmin/edit_barcode.psp b/www/wwwadmin/edit_barcode.psp
deleted file mode 100644
index 02743a66..00000000
--- a/www/wwwadmin/edit_barcode.psp
+++ /dev/null
@@ -1,119 +0,0 @@
-<script src="../americangut/js/jquery.ui.timepicker.js"></script>
-
-<%@ include file="common_vars.psp" %>
-
-<form action="fusebox.psp" method="post" name="submit_data" id="submit_data">
-    <input type="hidden" name="page" value="select_task.psp"/>
-    <input type="hidden" name="message" value="Barcode was updated successfully."/>
-</form>
-
-<%
-qiime_data_access = data_access = data_access_factory(ServerConfig.data_access_type)
-if 'sample_postmark_date' in form:
-	# Submit and redirect to fusebox
-	qiime_data_access.updateBarcodeStatus(form['status'], 
-		form['sample_postmark_date'], form['scan_date'], form['barcode'],
-		form['biomass_remaining'], form['sequencing_status'], 
-		form['obsolete'])
-	qiime_data_access.setBarcodeProjType(form['project'], form['barcode'])
-	req.write('<script>document.submit_data.submit();</script>')
-
-
-if 'barcode' in form:
-	barcode = form['barcode']
-	if len(barcode) != 9:
-		req.write('Barcode does not exist')
-	else:
-		details = qiime_data_access.getBarcodeDetails(barcode)
-		if len(details) == 0:
-			req.write('Barcode does not exist')
-		else: 
-			date_created = details['create_date']
-			status = '' if details['status'] is None else details['status']
-			scan_date = '' if details['scan_date'] is None else \
-				details['scan_date']
-			sample_postmark_date = '' if details['sample_postmark_date'] is None \
-				else details['sample_postmark_date']
-			sequencing_status = '' if details['sequencing_status'] is None\
-				else details['sequencing_status']
-			biomass_remaining = '' if details['biomass_remaining'] is None \
-				else details['biomass_remaining']
-			obsolete = '' if details['obsolete'] is None else details['obsolete']
-			#Indent
-%>
-<form action="fusebox.psp?page=edit_barcode.psp" method="post" name"edit_barcode_submit"=>
-<table>
-<tr>
-<td>Barcode</td>
-<td> <%=barcode%> </td>
-</tr>
-<tr>
-<td>Date Created</td>
-<td> <%=date_created%> </td>
-</tr>
-<tr>
-<td>Status</td>
-<td><input type="text" name="status" id="status" value="<%=status%>"/></td>
-</tr>
-<tr>
-<td> Scan Date </td>
-<td><input type="text" name="scan_date" id="scan_date" value="<%=scan_date%>"/></td>
-</tr>
-<tr>
-<td>Sample Postmark Date</td>
-<td><input type="text" name="sample_postmark_date" id="sample_postmark_date" value="<%=sample_postmark_date%>"/></td>
-</tr>
-<tr>
-<td>Sequencing Status</td>
-<td><input type="text" name="sequencing_status" id="sequencing_status" value="<%=sequencing_status%>"/></td>
-</tr>
-<tr>
-<td>Biomass Remaining (Y or N)</td>
-<td><input type="text" maxlength="1" name="biomass_remaining" id="biomass_remaining" value="<%=biomass_remaining%>"/></td>
-</tr>
-<tr>
-<td>Obsolete (Y or N)</td>
-<td><input type="text" maxlength="1" name="obsolete" id="obsolete" value="<%=obsolete%>"/></td>
-<tr><td>Project</td><td><select name="project" id="project" >
-<%
-			project_names = qiime_data_access.getProjectNames()
-			current_project = qiime_data_access.getBarcodeProjType(barcode)
-			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 Indent
-%>
-		</select></td></tr>
-</tr>
-<td><input type="submit" id="submit_flag" value="Submit"/></td>
-</table>
-<input type="hidden" name="barcode" id="barcode" value="<%=barcode%>"/>
-<input type="hidden" name="date_created" id="date_created" value="<%=date_created%>"/>
-</form>
-
-<%
-#End Indent
-else:
-	#indent
-%>
-
-<form method="post" name="edit_barcode" id="edit_barcode" action="fusebox.psp?page=edit_barcode.psp">
-	<input type="hidden" name="submit_flag" id="submit_flag" value="0"/>
-	<table>
-		<tr>
-			<td>Barcode</td>
-			<td>
-				<input type="text" name="barcode" id="barcode" />
-			</td>
-		</tr>
-		<tr>
-		<td></td><td> <input type="submit" value="Go" style="width:50px;"></td>
-		</tr>
-	</table>
-</form>
-
-<% 
-#end indent
-%>
diff --git a/www/wwwadmin/header.psp b/www/wwwadmin/header.psp
index 2fffa4ee..0c0f3109 100644
--- a/www/wwwadmin/header.psp
+++ b/www/wwwadmin/header.psp
@@ -72,11 +72,6 @@ else:
             <input type="hidden" name="page_title" value="Manage Fast UniFrac limits">
         </form>
 
-        <form action="fusebox.psp" method="post" name="edit_barcode" id="edit_barcode">
-            <input type="hidden" name="page" value="edit_barcode.psp">
-            <input type="hidden" name="page_title" value="Edit Barcode">
-        </form>
-
         <!-- American Gut Utilities -->
 
         <form action="fusebox.psp" method="post" name="ag_search" id="ag_search">
@@ -165,7 +160,6 @@ else:
         <h3>General Project Utilities</h3>
         <ul class="mainmenu">
             <li><a href="" onclick="document.barcode_util.submit(); return false;">Scan Barcode</a></li>
-            <li><a href="" onclick="document.edit_barcode.submit(); return false;">Edit Barcode</a></li>
         </ul>
 
         <h3>Legacy Web App Utilities</h3>

From 83417154ba38df8a8feed81c71c15a1c9c02c829 Mon Sep 17 00:00:00 2001
From: teravest <ejteravest@gmail.com>
Date: Thu, 20 Feb 2014 10:34:47 -0700
Subject: [PATCH 06/16] Update barcode scanner to edit barcode fields

This add the ability to change biomass_remaining,
sequencing_status and obsolete from the barcode scanner
---
 .../procedures/get_sequencing_statuses.sql    | 14 +++++++++
 python_code/data_access/qiime_data_access.py  |  8 +++++
 www/wwwadmin/barcode_util.psp                 | 30 +++++++++++++++----
 3 files changed, 47 insertions(+), 5 deletions(-)
 create mode 100644 database/procedures/get_sequencing_statuses.sql

diff --git a/database/procedures/get_sequencing_statuses.sql b/database/procedures/get_sequencing_statuses.sql
new file mode 100644
index 00000000..672bdd1b
--- /dev/null
+++ b/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_;
+*/
\ No newline at end of file
diff --git a/python_code/data_access/qiime_data_access.py b/python_code/data_access/qiime_data_access.py
index cb7efaaf..24f54dd2 100755
--- a/python_code/data_access/qiime_data_access.py
+++ b/python_code/data_access/qiime_data_access.py
@@ -2998,6 +2998,14 @@ 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 getBarcodeDetails(self, barcode):
         """returns a dictionary of barcode deatails
diff --git a/www/wwwadmin/barcode_util.psp b/www/wwwadmin/barcode_util.psp
index 25a96544..87c73194 100644
--- a/www/wwwadmin/barcode_util.psp
+++ b/www/wwwadmin/barcode_util.psp
@@ -152,7 +152,7 @@ try:
         name = '' if barcodeinfo[12] == None else barcodeinfo[12]
         biomass_remaining = '' if barcodeinfo[13] == None else barcodeinfo[13]
         sequencing_status = '' if barcodeinfo[14] == None else barcodeinfo[14]
-        obsolete = '' if barcodeinfo[15] == None else barcodeinfo[15]
+        obsolete = 'N' if barcodeinfo[15] == None else barcodeinfo[15]
         biomass_check = 'checked' if biomass_remaining == 'Y' else ''
         moldy_checked = "checked" if moldy in ('Y','y') else ""
         overloaded_checked = "checked" if overloaded in ('Y','y') else ""
@@ -188,7 +188,7 @@ try:
         #indent
 %>
         
-        <div id="{div_id}" class="verification_color">
+        <div id="<%=div_id%>" class="verification_color">
            <div class="verification_text_wrapper">
               <br />
                
@@ -269,8 +269,28 @@ try:
              <table
              <tr><td><input class="checkbox" type="checkbox" name="biomass_remaining" id="biomass_remaining_checked" value="biomass_remaining_checked"<%=biomass_check%>/>
              <label for="biomass_remaining"> Biomass Remaining (current:<%=biomass_remaining%>)</label></td></tr>
-             <tr><td>Sequencing Status</td><td><input type="text" name="sequencing_status" id="sequencing_status" value="<%=sequencing_status%>"/></td></tr>
-             <tr><td>Obsolete (Y or N)</td><td><input type="text" maxlength="1" name="obsolete_status" id="obsolete_status" value="<%=obsolete%>"/></td></tr>
+             <tr><td>Sequencing Status</td><td><select name="sequencing_status" id="sequencing_status">
+<%
+        seq_statuses = data_access.getSequencingStatuses()
+        for status in seq_statuses:
+            if sequencing_status == status:
+              req.write('<option value="{0}" selected>{0}</option>'.format(status))
+            else:
+                req.write('<option value="{0}">{0}</option>'.format(status))
+        #END Indent
+%>
+        </select></td></tr>
+             <tr><td>Obsolete</td><td><select name="obsolete_status" id="obsolete_status">
+<%
+        if obsolete == 'N':
+          req.write('<option value="{0}" selected>{0}</option>'.format(obsolete))
+          req.write('<option value="Y">Y</option>')
+        else:
+          req.write('<option value="N">N</option>')
+          req.write('<option value="{0}" selected>{0}</option>'.format(obsolete))
+        #END Indent
+%>
+             </select></td></tr>
              </table>
              </li>
              <li>
@@ -291,7 +311,7 @@ try:
                Send an email notification (previously sent: <%=date_of_last_email%>): <br />
                <table><tr>
                   <td> <input class="checkbox" type="checkbox" name="send_email" id="send_email" value="send_email" style="float:left;" /> </td>
-                  <td><label for="send_email" style="display:block;">send kit owner <%=email%> (<%=name%>) an email </label> </td></tr>
+                  <td><label for="send_email" style="display:block;">send kit owner <%=name%> (<%=email%>) an email </label> </td></tr>
 
 <%
         if email_type == '0':

From 97363aece70588bc27582e14c0e529b674371992 Mon Sep 17 00:00:00 2001
From: teravest <ejteravest@gmail.com>
Date: Thu, 20 Feb 2014 10:39:39 -0700
Subject: [PATCH 07/16] clean up qiime_data_access.py

---
 python_code/data_access/qiime_data_access.py | 22 --------------------
 1 file changed, 22 deletions(-)

diff --git a/python_code/data_access/qiime_data_access.py b/python_code/data_access/qiime_data_access.py
index 24f54dd2..4a153aaa 100755
--- a/python_code/data_access/qiime_data_access.py
+++ b/python_code/data_access/qiime_data_access.py
@@ -3006,25 +3006,3 @@ def getSequencingStatuses(self):
         con.cursor().callproc('get_sequencing_statuses', [result])
         seq_statuses = [row[0] for row in result]
         return seq_statuses
-
-    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()
-        try:
-            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]
-                }
-        except TypeError :
-            #no results mean barcode doesn't exist 
-            return {}
-        return barcode_details
\ No newline at end of file

From d7a3683352a1496b58e45ae2e0e37348dae7559c Mon Sep 17 00:00:00 2001
From: teravest <ejteravest@gmail.com>
Date: Thu, 20 Feb 2014 14:08:55 -0700
Subject: [PATCH 08/16] adding barcode status

---
 database/procedures/get_barcode_statuses.sql | 16 ++++++++++++
 python_code/data_access/qiime_data_access.py | 10 ++++++++
 www/wwwadmin/barcode_util.psp                | 26 ++++++++++++++------
 3 files changed, 45 insertions(+), 7 deletions(-)
 create mode 100644 database/procedures/get_barcode_statuses.sql

diff --git a/database/procedures/get_barcode_statuses.sql b/database/procedures/get_barcode_statuses.sql
new file mode 100644
index 00000000..5badf0d1
--- /dev/null
+++ b/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;
+*/
\ No newline at end of file
diff --git a/python_code/data_access/qiime_data_access.py b/python_code/data_access/qiime_data_access.py
index 4a153aaa..622fe054 100755
--- a/python_code/data_access/qiime_data_access.py
+++ b/python_code/data_access/qiime_data_access.py
@@ -2998,6 +2998,7 @@ 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
         """
@@ -3006,3 +3007,12 @@ def getSequencingStatuses(self):
         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
diff --git a/www/wwwadmin/barcode_util.psp b/www/wwwadmin/barcode_util.psp
index 87c73194..37dc39e4 100644
--- a/www/wwwadmin/barcode_util.psp
+++ b/www/wwwadmin/barcode_util.psp
@@ -24,7 +24,7 @@ if prev_barcode:
         biomass_remaining_value = form.get('biomass_remaining', [])
         biomass_remaining = 'N'
         if 'biomass_remaining_checked' in biomass_remaining_value: biomass_remaining = 'Y'
-        data_access.updateBarcodeStatus('Received', form['postmark_date'],
+        data_access.updateBarcodeStatus(form['bstatus'], form['postmark_date'],
                                         form['scan_date'], prev_barcode,
                                         biomass_remaining,
                                         form['sequencing_status'], 
@@ -145,7 +145,7 @@ try:
         other = 'NA' if barcodeinfo[5] == None else barcodeinfo[5]
         other_text = '' if barcodeinfo[6] == None else barcodeinfo[6]
         date_of_last_email = '' if barcodeinfo[7] == None else barcodeinfo[7]
-        status = '' if barcodeinfo[8] == None else barcodeinfo[8]
+        status = 'Received' if barcodeinfo[8] == None else barcodeinfo[8]
         scan_date = 'NA' if barcodeinfo[9] == None else barcodeinfo[9]
         sample_postmark_date = 'NA' if barcodeinfo[10] == None else barcodeinfo[10]
         email = '' if barcodeinfo[11] == None else barcodeinfo[11]
@@ -266,17 +266,29 @@ try:
                   (please follow the format mm/dd/yyyy. Example: 12/25/2012)
              </li>
              <li>General Sample Information: <br>
-             <table
+             <table>
+             <tr><td>Barcode Status</td><td><select name="bstatus" id="bstatus">
+<%
+        bar_statuses = data_access.getBarcodeStatuses()
+        for bstatus in bar_statuses:
+            if bstatus == status:
+                req.write('<option value="{0}" selected>{0}</option>'.format(bstatus))
+            else:
+                req.write('<option value="{0}">{0}</option>'.format(bstatus))
+        #END Indent
+%>
+
+             </select></td></tr>
              <tr><td><input class="checkbox" type="checkbox" name="biomass_remaining" id="biomass_remaining_checked" value="biomass_remaining_checked"<%=biomass_check%>/>
              <label for="biomass_remaining"> Biomass Remaining (current:<%=biomass_remaining%>)</label></td></tr>
              <tr><td>Sequencing Status</td><td><select name="sequencing_status" id="sequencing_status">
 <%
         seq_statuses = data_access.getSequencingStatuses()
-        for status in seq_statuses:
-            if sequencing_status == status:
-              req.write('<option value="{0}" selected>{0}</option>'.format(status))
+        for sstatus in seq_statuses:
+            if sequencing_status == sstatus:
+                req.write('<option value="{0}" selected>{0}</option>'.format(sstatus))
             else:
-                req.write('<option value="{0}">{0}</option>'.format(status))
+                req.write('<option value="{0}">{0}</option>'.format(sstatus))
         #END Indent
 %>
         </select></td></tr>

From f3316e2d8ea4f81f9115faec4eee8721aa606bab Mon Sep 17 00:00:00 2001
From: teravest <ejteravest@gmail.com>
Date: Fri, 21 Feb 2014 11:14:19 -0700
Subject: [PATCH 09/16] updated biomass and made headers for general vs project

---
 www/wwwadmin/ag_edit_kit.psp  |  16 -----
 www/wwwadmin/barcode_util.psp | 114 ++++++++++++++++++++--------------
 2 files changed, 66 insertions(+), 64 deletions(-)

diff --git a/www/wwwadmin/ag_edit_kit.psp b/www/wwwadmin/ag_edit_kit.psp
index 815ffdb3..d81c10d0 100644
--- a/www/wwwadmin/ag_edit_kit.psp
+++ b/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>
 
 
diff --git a/www/wwwadmin/barcode_util.psp b/www/wwwadmin/barcode_util.psp
index 37dc39e4..4ec9a85a 100644
--- a/www/wwwadmin/barcode_util.psp
+++ b/www/wwwadmin/barcode_util.psp
@@ -16,7 +16,7 @@ current_date = date.today().strftime("%m/%d/%Y")
 
 prev_barcode = form.get('prev_barcode', None)
 if prev_barcode:
-    try: # try to update barcode current status.
+        # try to update barcode current status.
         # do not change scan_date if it's already in the database.
         # it's gotten from the html form, so use str representation of None.
         # if form['scan_date'] == 'None': scan_date = current_date
@@ -26,7 +26,7 @@ if prev_barcode:
         if 'biomass_remaining_checked' in biomass_remaining_value: biomass_remaining = 'Y'
         data_access.updateBarcodeStatus(form['bstatus'], form['postmark_date'],
                                         form['scan_date'], prev_barcode,
-                                        biomass_remaining,
+                                        form['biomass_remaining'],
                                         form['sequencing_status'], 
                                         form['obsolete_status'])
         data_access.setBarcodeProjType(form['project'], prev_barcode)
@@ -105,8 +105,8 @@ Thank you for your participation!
         ag_data_access.updateAKB(prev_barcode, moldy, overloaded, other,
                                  form['other_text'], sent_date)
         req.write("Barcode %s was sucessfully updated<br/>" % prev_barcode)
-    except:
-        req.write("Barcode %s update failed!!!<br/>" % prev_barcode)
+    # except:
+    #     req.write("Barcode %s update failed!!!<br/>" % prev_barcode)
 # de-indent
 %>
 
@@ -150,7 +150,7 @@ try:
         sample_postmark_date = 'NA' if barcodeinfo[10] == None else barcodeinfo[10]
         email = '' if barcodeinfo[11] == None else barcodeinfo[11]
         name = '' if barcodeinfo[12] == None else barcodeinfo[12]
-        biomass_remaining = '' if barcodeinfo[13] == None else barcodeinfo[13]
+        biomass_remaining = 'Unknown' if barcodeinfo[13] == None else barcodeinfo[13]
         sequencing_status = '' if barcodeinfo[14] == None else barcodeinfo[14]
         obsolete = 'N' if barcodeinfo[15] == None else barcodeinfo[15]
         biomass_check = 'checked' if biomass_remaining == 'Y' else ''
@@ -200,6 +200,7 @@ try:
         </div>
 
         <div id="barcode_form">
+
         <form action="fusebox.psp?page=barcode_util.psp" method="post"
          onsubmit="return confirm('Are you sure to submit and update database?')"
          onreset="return confirm('Are you sure to reset?')">
@@ -212,28 +213,9 @@ try:
           <input type="hidden" name="sample_time" id="sample_time" value="<%=sample_time%>"/>
           <input type="hidden" name="sample_site" id="sample_site" value="<%=sample_site%>"/>
           <ul>
-             <li>
-             Sample details: <br/>
-             <table>
-             <tr><td>Sample Date</td><td><%=sample_date%></td></tr>
-             <tr><td>Sample Time</td><td><%=sample_time%></td></tr>
-             <tr><td>Sample Site</td><td><%=sample_site%></td></tr>
-             </table>
-             </li>
-             <li>
-               Sample issues: <br />
-                  <input class="checkbox" type="checkbox" name="sample_issue" id="moldy" value="moldy" <%=moldy_checked%>/> 
-                    <label for="moldy"> moldy (current: <%=moldy%>) </label> <br />
-                  <input class="checkbox" type="checkbox" name="sample_issue" id="overloaded" value="overloaded" <%=overloaded_checked%>/>
-                    <label for="overloaded"> overloaded (current: <%=overloaded%>) </label> <br />
-                  <input class="checkbox" type="checkbox" name="sample_issue" id="other" value="other" <%=other_checked%>/>
-                    <label for="other"> other (current: <%=other%>) </label> <br />
-             </li>
-             <li>
-               Other notes: <br />
-                  <textarea name="other_text" onclick="this.select()"><%=other_text%></textarea>
-             </li>
-             <li>
+          <table cellspacing="40"><tr><td>
+          <h2> General Barcode Details </h2>
+            <li>
                Sample postmark date (current: <%=sample_postmark_date%>) : <br />
                   <input type="text" name="postmark_date" id="postmark_date" value="<%=sample_postmark_date if sample_postmark_date != 'NA' else ''%>" onclick="this.select()" /> <br />
                         <script>
@@ -265,9 +247,8 @@ try:
                         </script>
                   (please follow the format mm/dd/yyyy. Example: 12/25/2012)
              </li>
-             <li>General Sample Information: <br>
-             <table>
-             <tr><td>Barcode Status</td><td><select name="bstatus" id="bstatus">
+             <li>
+             Barcode Status:<br /><select name="bstatus" id="bstatus">
 <%
         bar_statuses = data_access.getBarcodeStatuses()
         for bstatus in bar_statuses:
@@ -278,10 +259,23 @@ try:
         #END Indent
 %>
 
-             </select></td></tr>
-             <tr><td><input class="checkbox" type="checkbox" name="biomass_remaining" id="biomass_remaining_checked" value="biomass_remaining_checked"<%=biomass_check%>/>
-             <label for="biomass_remaining"> Biomass Remaining (current:<%=biomass_remaining%>)</label></td></tr>
-             <tr><td>Sequencing Status</td><td><select name="sequencing_status" id="sequencing_status">
+             </select></li>
+             <li>Biomass Remaining: <br /><select name="biomass_remaining" id="biomass_remaining">
+<%
+        for bmass in ['N', 'Y', 'Unknown']:
+            selected = ''
+            if biomass_remaining == bmass:
+                selected = 'selected'
+            if bmass == 'Y':
+                req.write("<option value='Y' {0}>Yes</option>".format(selected))
+            elif bmass == 'N':
+                req.write("<option value='N' {0}>No</option>".format(selected))
+            elif bmass == 'Unknown':
+                req.write("<option value='' {0}>Unknown</option>".format(selected))
+        #END Indent
+%>
+             </select></li>
+             <li>Sequencing Status<br /><select name="sequencing_status" id="sequencing_status">
 <%
         seq_statuses = data_access.getSequencingStatuses()
         for sstatus in seq_statuses:
@@ -291,34 +285,54 @@ try:
                 req.write('<option value="{0}">{0}</option>'.format(sstatus))
         #END Indent
 %>
-        </select></td></tr>
-             <tr><td>Obsolete</td><td><select name="obsolete_status" id="obsolete_status">
+        </select></li>
+             <li>Obsolete<br /><select name="obsolete_status" id="obsolete_status">
 <%
         if obsolete == 'N':
-          req.write('<option value="{0}" selected>{0}</option>'.format(obsolete))
-          req.write('<option value="Y">Y</option>')
+          req.write('<option value="N" selected>No</option>')
+          req.write('<option value="Y">Yes</option>')
         else:
-          req.write('<option value="N">N</option>')
-          req.write('<option value="{0}" selected>{0}</option>'.format(obsolete))
+          req.write('<option value="N">No</option>')
+          req.write('<option value="Y" selected>Yes</option>')
         #END Indent
 %>
-             </select></td></tr>
-             </table>
-             </li>
+             </select></li>
              <li>
-             <tr><td>Project </td><td><select name="project" id="project" >
+             Project <br /><select name="project" id="project" >
 <%
         project_names = data_access.getProjectNames()
-        current_project = data_access.getBarcodeProjType(barcode)
         for project in project_names:
-            if project == current_project:
+            if project == proj_type:
                 req.write('<option value="{0}" selected>{0}</option>'.format(project))
             else:
                 req.write('<option value="{0}">{0}</option>'.format(project))
         #End Indent
 %>
-            </select></td></tr>
-            </li>
+            </select>
+            </li></td><td>
+            <h2><%=proj_type%> details</h2>
+             <li>
+             Sample details: <br/>
+             <table>
+             <tr><td>Sample Date</td><td><%=sample_date%></td></tr>
+             <tr><td>Sample Time</td><td><%=sample_time%></td></tr>
+             <tr><td>Sample Site</td><td><%=sample_site%></td></tr>
+             </table>
+             </li>
+             <li>
+               Sample issues: <br />
+                  <input class="checkbox" type="checkbox" name="sample_issue" id="moldy" value="moldy" <%=moldy_checked%>/> 
+                    <label for="moldy"> moldy (current: <%=moldy%>) </label> <br />
+                  <input class="checkbox" type="checkbox" name="sample_issue" id="overloaded" value="overloaded" <%=overloaded_checked%>/>
+                    <label for="overloaded"> overloaded (current: <%=overloaded%>) </label> <br />
+                  <input class="checkbox" type="checkbox" name="sample_issue" id="other" value="other" <%=other_checked%>/>
+                    <label for="other"> other (current: <%=other%>) </label> <br />
+             </li>
+             <li>
+               Other notes: <br />
+                  <textarea name="other_text" onclick="this.select()"><%=other_text%></textarea>
+             </li>
+            
              <li>
                Send an email notification (previously sent: <%=date_of_last_email%>): <br />
                <table><tr>
@@ -368,7 +382,11 @@ try:
 %>
             </table>
            </li>
+           <li>
+        <a href="fusebox.psp?page=ag_edit_barcode.psp&barcode=<%=barcode%>">Edit American Gut Barcode</a>
+           </li>
           </ul>
+          </tr></td></table><br /><br />
               <input type="submit" value="Submit">
               <input type="reset" value="Reset!">
         </form>

From 285d76973781043571db317ea491a8a49a59742f Mon Sep 17 00:00:00 2001
From: teravest <ejteravest@gmail.com>
Date: Fri, 21 Feb 2014 15:30:36 -0700
Subject: [PATCH 10/16] added project group and display by project group

---
 database/procedures/get_project_group.sql    |  17 ++
 python_code/data_access/qiime_data_access.py |  14 ++
 www/wwwadmin/barcode_util.psp                | 184 +++++++++++--------
 3 files changed, 136 insertions(+), 79 deletions(-)
 create mode 100644 database/procedures/get_project_group.sql

diff --git a/database/procedures/get_project_group.sql b/database/procedures/get_project_group.sql
new file mode 100644
index 00000000..11bb1b43
--- /dev/null
+++ b/database/procedures/get_project_group.sql
@@ -0,0 +1,17 @@
+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;
+  null;
+end get_project_group;
+
+
+/*variable x REFCURSOR;
+execute get_project_group('Handout Kits', :x);
+print x;
+*/
\ No newline at end of file
diff --git a/python_code/data_access/qiime_data_access.py b/python_code/data_access/qiime_data_access.py
index 622fe054..b4780a2e 100755
--- a/python_code/data_access/qiime_data_access.py
+++ b/python_code/data_access/qiime_data_access.py
@@ -3016,3 +3016,17 @@ def getBarcodeStatuses(self):
         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
+        """
+        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
diff --git a/www/wwwadmin/barcode_util.psp b/www/wwwadmin/barcode_util.psp
index 4ec9a85a..20888b8f 100644
--- a/www/wwwadmin/barcode_util.psp
+++ b/www/wwwadmin/barcode_util.psp
@@ -2,7 +2,8 @@
 <%
 __author__ = "Doug Wendel"
 __copyright__ = "Copyright 2009-2013, Qiime Web Analysis"
-__credits__ = ["Doug Wendel", "Zhenjiang Xu", "Adam Robbins-Pianka"]
+__credits__ = ["Doug Wendel", "Zhenjiang Xu", "Adam Robbins-Pianka",
+               "Emily TerAvest"]
 __license__ = "GPL"
 __version__ = "1.0.0.dev"
 __email__ = "zhenjiang.xu@colorado.edu"
@@ -11,102 +12,117 @@ __status__ = "Production"
 from utils.mail import send_email
 from datetime import date
 
-# scan_date = date.today().isoformat()
+
 current_date = date.today().strftime("%m/%d/%Y")
 
 prev_barcode = form.get('prev_barcode', None)
 if prev_barcode:
-        # try to update barcode current status.
-        # do not change scan_date if it's already in the database.
-        # it's gotten from the html form, so use str representation of None.
-        # if form['scan_date'] == 'None': scan_date = current_date
-        # else: scan_date = form['scan_date']
+        # try to update general barcode information.
         biomass_remaining_value = form.get('biomass_remaining', [])
         biomass_remaining = 'N'
         if 'biomass_remaining_checked' in biomass_remaining_value: biomass_remaining = 'Y'
-        data_access.updateBarcodeStatus(form['bstatus'], form['postmark_date'],
-                                        form['scan_date'], prev_barcode,
-                                        form['biomass_remaining'],
-                                        form['sequencing_status'], 
-                                        form['obsolete_status'])
-        data_access.setBarcodeProjType(form['project'], prev_barcode)
+        try:
+            data_access.updateBarcodeStatus(form['bstatus'], form['postmark_date'],
+                                            form['scan_date'], prev_barcode,
+                                            form['biomass_remaining'],
+                                            form['sequencing_status'], 
+                                            form['obsolete_status'])
+            data_access.setBarcodeProjType(form['project'], prev_barcode)
+            req.write("General Barcode Information Updated<br>")
+        except:
+            req.write("Failed to updated General Barcode Information<br>")
     
-        sent_date = form['sent_date']
+        if form['proj_group'] in 'American Gut':
+            #if we are also updated the american gut form
+            sent_date = form['sent_date']
 
-        general_name = "American Gut participant"
+            general_name = "American Gut participant"
 
-        login_user = form['login_user'] # kit owner name
-        if login_user=="None": login_user = general_name
+            login_user = form['login_user'] # kit owner name
+            if login_user=="None": login_user = general_name
 
-        if "send_email" in form:
-            email_type = form['email_type']
-            subject = body_message = ""
-            sample_time = form['sample_time']
-            sample_date = form['sample_date']
-            if email_type == '0':
-                subject='Follow up on Your American Gut Sample with Barcode %s' % prev_barcode
-                body_message='''
-Dear {name},
+            if "send_email" in form:
+                email_type = form['email_type']
+                subject = body_message = ""
+                sample_time = form['sample_time']
+                sample_date = form['sample_date']
+                if email_type == '0':
+                    subject='Follow up on Your American Gut Sample with Barcode %s' % prev_barcode
+                    body_message='''
+    Dear {name},
 
-We have recently received your sample barcode: {barcode}, but we cannot process your sample until the online forms have been completed.  Information about your sample is tracked through the American Gut participant website, and you are required to log in and complete the online process in order for your sample to be processed. 
+    We have recently received your sample barcode: {barcode}, but we cannot process your sample until the online forms have been completed.  
+    Information about your sample is tracked through the American Gut participant website, and you are required to log in and complete the online 
+    process in order for your sample to be processed. 
 
-If it is a human sample, we require formal consent, questionnaire results and sample details (type, date, and time of collection). If it is a pet or environmental sample we require sample details (type, date and time of collection). If you have already filled out the consent form and questionnaire, then it is likely that the sample simply needs to be associated with the appropriate participant.
+    The most common reason for receiving this email is the sample was not logged. Logging the sample associates the sample with a participant in our records.
+    This needs to be done so the we know that the sample has consent before we can process it. 
 
-In order to help you in adding these details, the side of the sample tube {barcode} reads:
-   sample date: {sample_date} 
-   sample time: {sample_time}
+    If it is a human sample, we require formal consent, questionnaire results and sample details (type, date, and time of collection). 
+    If it is a pet or environmental sample we require sample details (type, date and time of collection). If you have already filled out the 
+    consent form and questionnaire, then it is likely that the sample simply needs to be associated with the appropriate participant.
 
-Instructions about the required procedures can be found here: http://www.microbio.me/americangut/img/full_instructions.pdf
+    In order to help you in adding these details, the side of the sample tube {barcode} reads:
+       sample date: {sample_date} 
+       sample time: {sample_time}
 
-These procedures are in place to protect your privacy, and please be sure that we are properly associating your sample to your survey results. We realize that some of these steps may not be completely intuitive. However, our kits are designed to support multiple participants and sample types, which necessitates the added complexity of explicitly requiring participants to associate samples with themselves so that we can guarantee compliance with human subjects research protocols.
+    Instructions about the required procedures can be found here: http://www.microbio.me/americangut/img/full_instructions.pdf
 
-Please log back into the American Gut website (http://www.microbio.me/americangut) as soon as possible and complete the online process. If you have any questions or concerns, please contact us at info@americangut.org.
+    These procedures are in place to protect your privacy, and please be sure that we are properly associating your sample to your 
+    survey results. We realize that some of these steps may not be completely intuitive. However, our kits are designed to support 
+    multiple participants and sample types, which necessitates the added complexity of explicitly requiring participants to associate 
+    samples with themselves so that we can guarantee compliance with human subjects research protocols.
 
-Thank you,
+    Please log back into the American Gut website (http://www.microbio.me/americangut) as soon as possible and complete the online process. 
+    If you have any questions or concerns, please contact us at info@americangut.org.
 
---American Gut Team--
-'''
+    Thank you,
 
-                body_message = body_message.format(name=login_user, barcode=prev_barcode,
-                                                   sample_date=sample_date,
-                                                   sample_time=sample_time)
-            elif email_type == '1':
-                subject = 'American Gut Sample with Barcode %s is Received.' % prev_barcode
-                body_message = '''
-Dear {name},
+    --American Gut Team--
+    '''
 
-We have recently received your sample with barcode {barcode} dated {sample_date} {sample_time} and we have begun processing it.  Please see our FAQ section for when you can expect results. (http://www.microbio.me/americangut/FAQ.psp#faq4)
+                    body_message = body_message.format(name=login_user, barcode=prev_barcode,
+                                                       sample_date=sample_date,
+                                                       sample_time=sample_time)
+                elif email_type == '1':
+                    subject = 'American Gut Sample with Barcode %s is Received.' % prev_barcode
+                    body_message = '''
+    Dear {name},
 
-Thank you for your participation!
+    We have recently received your sample with barcode {barcode} dated {sample_date} {sample_time} and we have begun processing it.  
+    Please see our FAQ section for when you can expect results. (http://www.microbio.me/americangut/FAQ.psp#faq4)
 
---American Gut Team--
-'''
-                body_message = body_message.format(name=login_user, barcode=prev_barcode,
-                                                   sample_date=sample_date, sample_time=sample_time)
+    Thank you for your participation!
 
-            
+    --American Gut Team--
+    '''
+                    body_message = body_message.format(name=login_user, barcode=prev_barcode,
+                                                       sample_date=sample_date, sample_time=sample_time)
 
-            login_email = form['login_email']
+                
 
- 
-            if login_email != "None":
-                try:
-                    send_email(body_message, subject, login_email)
-                    sent_date = current_date
-                    req.write("Sent email successfully to kit owner %s<br/>" % login_email)
-                except:
-                    req.write("Email sending to (%s) failed failed (barcode: %s)!!!<br/>" % (login_email, prev_barcode))
-    
-        sample_issue = form.get('sample_issue', [])
-        moldy = overloaded = other = 'N'
-        if 'moldy' in sample_issue: moldy = 'Y'
-        if 'overloaded' in sample_issue: overloaded = 'Y'
-        if 'other' in sample_issue: other = 'Y'
-        ag_data_access.updateAKB(prev_barcode, moldy, overloaded, other,
-                                 form['other_text'], sent_date)
-        req.write("Barcode %s was sucessfully updated<br/>" % prev_barcode)
-    # except:
-    #     req.write("Barcode %s update failed!!!<br/>" % prev_barcode)
+                login_email = form['login_email']
+
+     
+                if login_email != "None":
+                    try:
+                        send_email(body_message, subject, login_email)
+                        sent_date = current_date
+                        req.write("Sent email successfully to kit owner %s<br/>" % login_email)
+                    except:
+                        req.write("Email sending to (%s) failed failed (barcode: %s)!!!<br/>" % (login_email, prev_barcode))
+        
+            sample_issue = form.get('sample_issue', [])
+            moldy = overloaded = other = 'N'
+            if 'moldy' in sample_issue: moldy = 'Y'
+            if 'overloaded' in sample_issue: overloaded = 'Y'
+            if 'other' in sample_issue: other = 'Y'
+            try:
+                ag_data_access.updateAKB(prev_barcode, moldy, overloaded, other,
+                                     form['other_text'], sent_date)
+                req.write("Barcode %s American Gut Info was sucessfully updated<br/>" % prev_barcode)
+            except:
+                req.write("Barcode %s American Gut Info update failed!!!<br/>" % prev_barcode)
 # de-indent
 %>
 
@@ -125,6 +141,7 @@ try:
     barcodeinfo = ag_data_access.checkBarcode(barcode)
     barcode_metadata = ag_data_access.AGGetBarcodeMetadata(barcode)
     proj_type = data_access.getBarcodeProjType(barcode)
+    proj_group = data_access.getProjectGroup(proj_type)
     if len(barcodeinfo)==0:
         req.write('''
          <div id="invalid_barcode" class="verification_color">
@@ -212,6 +229,7 @@ try:
           <input type="hidden" name="sample_date" id="sample_date" value="<%=sample_date%>"/>
           <input type="hidden" name="sample_time" id="sample_time" value="<%=sample_time%>"/>
           <input type="hidden" name="sample_site" id="sample_site" value="<%=sample_site%>"/>
+          <input type="hidden" name="proj_group" id="proj_group" value="<%=proj_group%>"/>
           <ul>
           <table cellspacing="40"><tr><td>
           <h2> General Barcode Details </h2>
@@ -310,7 +328,11 @@ try:
 %>
             </select>
             </li></td><td>
-            <h2><%=proj_type%> details</h2>
+<%
+        if proj_group== 'American Gut':
+            #Indent
+%>
+            <h2><%=proj_type%> Details</h2>
              <li>
              Sample details: <br/>
              <table>
@@ -335,13 +357,14 @@ try:
             
              <li>
                Send an email notification (previously sent: <%=date_of_last_email%>): <br />
+
                <table><tr>
                   <td> <input class="checkbox" type="checkbox" name="send_email" id="send_email" value="send_email" style="float:left;" /> </td>
                   <td><label for="send_email" style="display:block;">send kit owner <%=name%> (<%=email%>) an email </label> </td></tr>
 
 <%
-        if email_type == '0':
-            # indent
+            if email_type == '0':
+                # indent
 %>
             <tr><td></td><td>
             sample date: <input type="text" name="sample_date" id="sample_date" style="width:100px"/> <br/>
@@ -372,21 +395,24 @@ try:
                   </script>
             </td></tr>
 <%
-        elif email_type == '1':
-            # indent
+            elif email_type == '1':
+                # indent
 %>
             <input type="hidden" name="sample_time" value="<%=sample_time%>" />
             <input type="hidden" name="sample_date" value="<%=sample_date%>" />
 <%
-        # de-indent
+            # de-indent
 %>
             </table>
            </li>
            <li>
-        <a href="fusebox.psp?page=ag_edit_barcode.psp&barcode=<%=barcode%>">Edit American Gut Barcode</a>
+            <a href="fusebox.psp?page=ag_edit_barcode.psp&barcode=<%=barcode%>">Edit American Gut Barcode</a>
            </li>
           </ul>
-          </tr></td></table><br /><br />
+<%
+        #End Indent
+%>
+          </td></tr></table><br /><br />
               <input type="submit" value="Submit">
               <input type="reset" value="Reset!">
         </form>

From 0152739d9ee25bb367659b286136833283c7cf25 Mon Sep 17 00:00:00 2001
From: teravest <ejteravest@gmail.com>
Date: Mon, 24 Feb 2014 15:45:09 -0700
Subject: [PATCH 11/16] fixed separation of barcode vs project info

---
 .../procedures/ag_get_barcode_details.sql     |   5 +-
 database/procedures/get_barcode_details.sql   |  18 +
 python_code/data_access/ag_data_access.py     |  38 +-
 python_code/data_access/qiime_data_access.py  |  22 +
 www/wwwadmin/barcode_util.psp                 | 540 +++++++++---------
 5 files changed, 350 insertions(+), 273 deletions(-)
 create mode 100644 database/procedures/get_barcode_details.sql

diff --git a/database/procedures/ag_get_barcode_details.sql b/database/procedures/ag_get_barcode_details.sql
index 7f8b5f64..5955eaf9 100644
--- a/database/procedures/ag_get_barcode_details.sql
+++ b/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_;
 */
 
-
- 
\ No newline at end of file
diff --git a/database/procedures/get_barcode_details.sql b/database/procedures/get_barcode_details.sql
new file mode 100644
index 00000000..048ed7f8
--- /dev/null
+++ b/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_;
+*/
\ No newline at end of file
diff --git a/python_code/data_access/ag_data_access.py b/python_code/data_access/ag_data_access.py
index 2def2356..9bf8d8e4 100755
--- a/python_code/data_access/ag_data_access.py
+++ b/python_code/data_access/ag_data_access.py
@@ -154,21 +154,29 @@ 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],
-            'refunded' : barcode_details[10],
-            'withdrawn' : barcode_details[11]
-        }
-
+        try:
+            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]
+            }
+        except TypeError:
+            row_dict = {}
         return row_dict
 
     def getAGKitDetails(self, supplied_kit_id):
diff --git a/python_code/data_access/qiime_data_access.py b/python_code/data_access/qiime_data_access.py
index b4780a2e..1ad635a2 100755
--- a/python_code/data_access/qiime_data_access.py
+++ b/python_code/data_access/qiime_data_access.py
@@ -3030,3 +3030,25 @@ def getProjectGroup(self, project_name):
             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()
+        try:
+            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]
+                }
+        except TypeError :
+            #no results mean barcode doesn't exist 
+            return {}
+        return barcode_details
diff --git a/www/wwwadmin/barcode_util.psp b/www/wwwadmin/barcode_util.psp
index 20888b8f..09356d19 100644
--- a/www/wwwadmin/barcode_util.psp
+++ b/www/wwwadmin/barcode_util.psp
@@ -19,12 +19,10 @@ prev_barcode = form.get('prev_barcode', None)
 if prev_barcode:
         # try to update general barcode information.
         biomass_remaining_value = form.get('biomass_remaining', [])
-        biomass_remaining = 'N'
-        if 'biomass_remaining_checked' in biomass_remaining_value: biomass_remaining = 'Y'
         try:
             data_access.updateBarcodeStatus(form['bstatus'], form['postmark_date'],
                                             form['scan_date'], prev_barcode,
-                                            form['biomass_remaining'],
+                                            form['biomass_remaining_value'],
                                             form['sequencing_status'], 
                                             form['obsolete_status'])
             data_access.setBarcodeProjType(form['project'], prev_barcode)
@@ -32,7 +30,7 @@ if prev_barcode:
         except:
             req.write("Failed to updated General Barcode Information<br>")
     
-        if form['proj_group'] in 'American Gut':
+        if form['proj_group'] == 'American Gut':
             #if we are also updated the american gut form
             sent_date = form['sent_date']
 
@@ -138,286 +136,318 @@ if prev_barcode:
 <%
 try:
     barcode = form['barcode']
-    barcodeinfo = ag_data_access.checkBarcode(barcode)
-    barcode_metadata = ag_data_access.AGGetBarcodeMetadata(barcode)
-    proj_type = data_access.getBarcodeProjType(barcode)
-    proj_group = data_access.getProjectGroup(proj_type)
-    if len(barcodeinfo)==0:
-        req.write('''
-         <div id="invalid_barcode" class="verification_color">
-            <div class="verification_text_wrapper">
-               <br />
-                 <h2 class="verification_text">Barcode <br>
-                 "%s"
-                 <br> does not exist in the database!</h2>
-             </div>
+except(KeyError):
+    pass
+    #will get here on first load of this page since there should be no barcode key in the form dict
+
+barcode_details = data_access.getBarcodeDetails(barcode)
+proj_type = data_access.getBarcodeProjType(barcode)
+proj_group = data_access.getProjectGroup(proj_type)
+
+if len(barcode_details)==0:
+    req.write('''
+     <div id="invalid_barcode" class="verification_color">
+        <div class="verification_text_wrapper">
+           <br />
+             <h2 class="verification_text">Barcode <br>
+             "%s"
+             <br> does not exist in the database!</h2>
          </div>
-        ''' % barcode)
-    else: 
-        sample_site = '' if barcodeinfo[0] == None else barcodeinfo[0]
-        sample_date = '' if barcodeinfo[1] == None else barcodeinfo[1]
-        sample_time = '' if barcodeinfo[2] == None else barcodeinfo[2]
-        moldy = 'NA' if barcodeinfo[3] == None else barcodeinfo[3]
-        overloaded = 'NA' if barcodeinfo[4] == None else barcodeinfo[4]
-        other = 'NA' if barcodeinfo[5] == None else barcodeinfo[5]
-        other_text = '' if barcodeinfo[6] == None else barcodeinfo[6]
-        date_of_last_email = '' if barcodeinfo[7] == None else barcodeinfo[7]
-        status = 'Received' if barcodeinfo[8] == None else barcodeinfo[8]
-        scan_date = 'NA' if barcodeinfo[9] == None else barcodeinfo[9]
-        sample_postmark_date = 'NA' if barcodeinfo[10] == None else barcodeinfo[10]
-        email = '' if barcodeinfo[11] == None else barcodeinfo[11]
-        name = '' if barcodeinfo[12] == None else barcodeinfo[12]
-        biomass_remaining = 'Unknown' if barcodeinfo[13] == None else barcodeinfo[13]
-        sequencing_status = '' if barcodeinfo[14] == None else barcodeinfo[14]
-        obsolete = 'N' if barcodeinfo[15] == None else barcodeinfo[15]
-        biomass_check = 'checked' if biomass_remaining == 'Y' else ''
-        moldy_checked = "checked" if moldy in ('Y','y') else ""
-        overloaded_checked = "checked" if overloaded in ('Y','y') else ""
-        other_checked = "checked" if other in ('Y','y') else "",
-        div_id = message = email_type = ""
-
-        if (barcodeinfo[15] == "Y"):
-                #the barcode is obsolete
-                div_id = "obsolete"
-                message = "Barcode is Obsolete"
-        elif not (sample_date == sample_site == sample_time == ''):
-            # it has all sample details (sample time, date, site)
-            if len(barcode_metadata) == 1:
-                # and we can successfully retrieve sample metadata
-                div_id = "verified"
-                message = "All good"
-                email_type = "1"
-            elif len(barcode_metadata) == 0:
-                # we cannot retrieve metadata
-                div_id = "no_metadata"
-                message = "Cannot retrieve metadata"
+     </div>
+    ''' % barcode)
+else: 
+    #barcode exists get general info 
+    status = 'Received' if barcode_details['status'] == None \
+            else barcode_details['status']
+    scan_date = 'NA' if barcode_details['scan_date'] == None \
+            else barcode_details['scan_date']
+    sample_postmark_date = 'NA' if barcode_details['sample_postmark_date'] \
+            == None else barcode_details['sample_postmark_date']
+    
+    biomass_remaining = 'Unknown' if barcode_details['biomass_remaining'] \
+            == None else barcode_details['biomass_remaining']
+    sequencing_status = '' if barcode_details['sequencing_status'] \
+            == None else barcode_details['sequencing_status']
+    obsolete = 'N' if barcode_details['obsolete'] == None \
+            else barcode_details['obsolete']
+    div_id = message = email_type = ""
+
+    if (obsolete == "Y"):
+            #the barcode is obsolete
+            div_id = "obsolete"
+            message = "Barcode is Obsolete"
+    #get project info for div 
+    elif proj_group == 'American Gut':
+        ag_details = ag_data_access.getAGBarcodeDetails(barcode)
+        if len(ag_details) > 0:
+            sample_site = '' if ag_details['site_sampled'] == None \
+                        else ag_details['site_sampled']
+            sample_date = '' if ag_details['sample_date'] == None else \
+                        ag_details['sample_date']
+            sample_time = '' if ag_details['sample_time'] == None else \
+                        ag_details['sample_time']
+            moldy = 'NA' if ag_details['moldy'] == None else ag_details['moldy']
+            overloaded = 'NA' if ag_details['overloaded'] == None else \
+                        ag_details['overloaded']
+            other = 'NA' if ag_details['other'] == None else ag_details['other']
+            other_text = '' if ag_details['other_text'] == None else \
+                        ag_details['other_text']
+            date_of_last_email = '' if ag_details['date_of_last_email'] == None \
+                        else ag_details['date_of_last_email']
+            email = '' if ag_details['email'] == None else ag_details['email']
+            name = '' if ag_details['kit_name'] == None else ag_details['kit_name']
+            moldy_checked = "checked" if moldy in ('Y','y') else ""
+            overloaded_checked = "checked" if overloaded in ('Y','y') else ""
+            other_checked = "checked" if other in ('Y','y') else ""
+            barcode_metadata = ag_data_access.AGGetBarcodeMetadata(barcode)
+            if not (sample_date == sample_site == sample_time == ''):
+                # it has all sample details (sample time, date, site)
+                if len(barcode_metadata) == 1:
+                    # and we can successfully retrieve sample metadata
+                    div_id = "verified"
+                    message = "All good"
+                    email_type = "1"
+                elif len(barcode_metadata) == 0:
+                    # we cannot retrieve metadata
+                    div_id = "no_metadata"
+                    message = "Cannot retrieve metadata"
+                else:
+                    # should never get here (this would happen if the metadata
+                    # pulldown returned more than one row for a single barcode)
+                    div_id = "md_pulldown_error"
+                    message = ("This barcode has multiple entries in the "
+                               "database, which should never happeen. Please "
+                               "notify someone on the database crew.")
             else:
-                # should never get here (this would happen if the metadata
-                # pulldown returned more than one row for a single barcode)
-                div_id = "md_pulldown_error"
-                message = ("This barcode has multiple entries in the "
-                           "database, which should never happeen. Please "
-                           "notify someone on the database crew.")
+                div_id = "not_assigned"
+                message = "Missing info"
+                email_type = "0"
         else:
             div_id = "not_assigned"
-            message = "Missing info"
-            email_type = "0"
-        #indent
+            message = ("In American Gut project group but No " 
+                       "Amerincan Gut info for barcode")
+    else:
+        div_id = "verified"
+        message = "Barcode Info is correct"
+    #INDENT
+    #Below this point is general barcode code. 
 %>
-        
-        <div id="<%=div_id%>" class="verification_color">
-           <div class="verification_text_wrapper">
-              <br />
-               
-                <h2 class="verification_text">
-                 Project type: <%=proj_type%> <br><br>
-                 Barcode: <%=barcode%><br><br>
-                <%=message%></h2>
-            </div>
+    
+    <div id="<%=div_id%>" class="verification_color">
+       <div class="verification_text_wrapper">
+          <br />
+           
+            <h2 class="verification_text">
+             Project type: <%=proj_type%> <br><br>
+             Barcode: <%=barcode%><br><br>
+            <%=message%></h2>
         </div>
+    </div>
+
+    <div id="barcode_form">
 
-        <div id="barcode_form">
-
-        <form action="fusebox.psp?page=barcode_util.psp" method="post"
-         onsubmit="return confirm('Are you sure to submit and update database?')"
-         onreset="return confirm('Are you sure to reset?')">
-          <input type="hidden" name="prev_barcode" value="<%=barcode%>" />
-          <input type="hidden" name="sent_date" value="<%=date_of_last_email%>" />
-          <input type="hidden" name="login_user"  value="<%=name%>" />
-          <input type="hidden" name="login_email" value="<%=email%>" />
-          <input type="hidden" name="email_type" value="<%=email_type%>" />
-          <input type="hidden" name="sample_date" id="sample_date" value="<%=sample_date%>"/>
-          <input type="hidden" name="sample_time" id="sample_time" value="<%=sample_time%>"/>
-          <input type="hidden" name="sample_site" id="sample_site" value="<%=sample_site%>"/>
-          <input type="hidden" name="proj_group" id="proj_group" value="<%=proj_group%>"/>
-          <ul>
-          <table cellspacing="40"><tr><td>
-          <h2> General Barcode Details </h2>
-            <li>
-               Sample postmark date (current: <%=sample_postmark_date%>) : <br />
-                  <input type="text" name="postmark_date" id="postmark_date" value="<%=sample_postmark_date if sample_postmark_date != 'NA' else ''%>" onclick="this.select()" /> <br />
-                        <script>
-                          $(function() {
-                            $( "#postmark_date" ).datepicker({
-                                    changeMonth: true,
-                                    maxDate: '+0m',
-                                    onSelect: function(dateText, inst) {
-                                        $(this).focus();
-                                    }
-                            });
-                          });
-                        </script>
-                  (please follow the format mm/dd/yyyy. Example: 12/25/2012)
-             </li>
-             <li>
-               Scan date (current: <%=scan_date%>): <br />
-               <input type="text" name="scan_date" id="scan_date" value="<%=scan_date if scan_date != 'NA' else ''%>" onclick="this.select()" /> <br />
-                        <script>
-                          $(function() {
-                            $( "#scan_date" ).datepicker({
-                                    changeMonth: true,
-                                    maxDate: '+0m',
-                                    onSelect: function(dateText, inst) {
-                                        $(this).focus();
-                                    }
-                            });
-                          });
-                        </script>
-                  (please follow the format mm/dd/yyyy. Example: 12/25/2012)
-             </li>
-             <li>
-             Barcode Status:<br /><select name="bstatus" id="bstatus">
+    <form action="fusebox.psp?page=barcode_util.psp" method="post"
+     onsubmit="return confirm('Are you sure to submit and update database?')"
+     onreset="return confirm('Are you sure to reset?')">
+      <input type="hidden" name="prev_barcode" value="<%=barcode%>" />
+      <input type="hidden" name="proj_group" id="proj_group" value="<%=proj_group%>"/>
+      <ul>
+      <table cellspacing="40"><tr><td>
+      <h2> General Barcode Details </h2>
+        <li>
+           Sample postmark date (current: <%=sample_postmark_date%>) : <br />
+              <input type="text" name="postmark_date" id="postmark_date" value="<%=sample_postmark_date if sample_postmark_date != 'NA' else ''%>" onclick="this.select()" /> <br />
+                    <script>
+                      $(function() {
+                        $( "#postmark_date" ).datepicker({
+                                changeMonth: true,
+                                maxDate: '+0m',
+                                onSelect: function(dateText, inst) {
+                                    $(this).focus();
+                                }
+                        });
+                      });
+                    </script>
+              (please follow the format mm/dd/yyyy. Example: 12/25/2012)
+         </li>
+         <li>
+           Scan date (current: <%=scan_date%>): <br />
+           <input type="text" name="scan_date" id="scan_date" value="<%=scan_date if scan_date != 'NA' else ''%>" onclick="this.select()" /> <br />
+                    <script>
+                      $(function() {
+                        $( "#scan_date" ).datepicker({
+                                changeMonth: true,
+                                maxDate: '+0m',
+                                onSelect: function(dateText, inst) {
+                                    $(this).focus();
+                                }
+                        });
+                      });
+                    </script>
+              (please follow the format mm/dd/yyyy. Example: 12/25/2012)
+         </li>
+         <li>
+         Barcode Status:<br /><select name="bstatus" id="bstatus">
 <%
-        bar_statuses = data_access.getBarcodeStatuses()
-        for bstatus in bar_statuses:
-            if bstatus == status:
-                req.write('<option value="{0}" selected>{0}</option>'.format(bstatus))
-            else:
-                req.write('<option value="{0}">{0}</option>'.format(bstatus))
-        #END Indent
+    bar_statuses = data_access.getBarcodeStatuses()
+    for bstatus in bar_statuses:
+        if bstatus == status:
+            req.write('<option value="{0}" selected>{0}</option>'.format(bstatus))
+        else:
+            req.write('<option value="{0}">{0}</option>'.format(bstatus))
+    #END Indent
 %>
 
-             </select></li>
-             <li>Biomass Remaining: <br /><select name="biomass_remaining" id="biomass_remaining">
+         </select></li>
+         <li>Biomass Remaining: <br /><select name="biomass_remaining" id="biomass_remaining">
 <%
-        for bmass in ['N', 'Y', 'Unknown']:
-            selected = ''
-            if biomass_remaining == bmass:
-                selected = 'selected'
-            if bmass == 'Y':
-                req.write("<option value='Y' {0}>Yes</option>".format(selected))
-            elif bmass == 'N':
-                req.write("<option value='N' {0}>No</option>".format(selected))
-            elif bmass == 'Unknown':
-                req.write("<option value='' {0}>Unknown</option>".format(selected))
-        #END Indent
+    for bmass in ['N', 'Y', 'Unknown']:
+        selected = ''
+        if biomass_remaining == bmass:
+            selected = 'selected'
+        if bmass == 'Y':
+            req.write("<option value='Y' {0}>Yes</option>".format(selected))
+        elif bmass == 'N':
+            req.write("<option value='N' {0}>No</option>".format(selected))
+        elif bmass == 'Unknown':
+            req.write("<option value='' {0}>Unknown</option>".format(selected))
+    #END Indent
 %>
-             </select></li>
-             <li>Sequencing Status<br /><select name="sequencing_status" id="sequencing_status">
+         </select></li>
+         <li>Sequencing Status<br /><select name="sequencing_status" id="sequencing_status">
 <%
-        seq_statuses = data_access.getSequencingStatuses()
-        for sstatus in seq_statuses:
-            if sequencing_status == sstatus:
-                req.write('<option value="{0}" selected>{0}</option>'.format(sstatus))
-            else:
-                req.write('<option value="{0}">{0}</option>'.format(sstatus))
-        #END Indent
+    seq_statuses = data_access.getSequencingStatuses()
+    for sstatus in seq_statuses:
+        if sequencing_status == sstatus:
+            req.write('<option value="{0}" selected>{0}</option>'.format(sstatus))
+        else:
+            req.write('<option value="{0}">{0}</option>'.format(sstatus))
+    if sequencing_status == '':
+        req.write('<option value="" selected>Unknown</option>')
+    else: 
+        req.write('<option value="">Unknown</option>')
+    #END Indent
 %>
-        </select></li>
-             <li>Obsolete<br /><select name="obsolete_status" id="obsolete_status">
+    </select></li>
+         <li>Obsolete<br /><select name="obsolete_status" id="obsolete_status">
 <%
-        if obsolete == '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
+    if obsolete == '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></li>
-             <li>
-             Project <br /><select name="project" id="project" >
+         </select></li>
+         <li>
+         Project <br /><select name="project" id="project" >
 <%
-        project_names = data_access.getProjectNames()
-        for project in project_names:
-            if project == proj_type:
-                req.write('<option value="{0}" selected>{0}</option>'.format(project))
-            else:
-                req.write('<option value="{0}">{0}</option>'.format(project))
-        #End Indent
+    project_names = data_access.getProjectNames()
+    for project in project_names:
+        if project == proj_type:
+            req.write('<option value="{0}" selected>{0}</option>'.format(project))
+        else:
+            req.write('<option value="{0}">{0}</option>'.format(project))
+    #End Indent
 %>
-            </select>
-            </li></td><td>
+    </select>
+    </li></td><td>
 <%
-        if proj_group== 'American Gut':
-            #Indent
+    if proj_group== 'American Gut' and len(ag_details) > 0:
+        #Displaying project specific information
+        #Indent
 %>
-            <h2><%=proj_type%> Details</h2>
-             <li>
-             Sample details: <br/>
-             <table>
-             <tr><td>Sample Date</td><td><%=sample_date%></td></tr>
-             <tr><td>Sample Time</td><td><%=sample_time%></td></tr>
-             <tr><td>Sample Site</td><td><%=sample_site%></td></tr>
-             </table>
-             </li>
-             <li>
-               Sample issues: <br />
-                  <input class="checkbox" type="checkbox" name="sample_issue" id="moldy" value="moldy" <%=moldy_checked%>/> 
-                    <label for="moldy"> moldy (current: <%=moldy%>) </label> <br />
-                  <input class="checkbox" type="checkbox" name="sample_issue" id="overloaded" value="overloaded" <%=overloaded_checked%>/>
-                    <label for="overloaded"> overloaded (current: <%=overloaded%>) </label> <br />
-                  <input class="checkbox" type="checkbox" name="sample_issue" id="other" value="other" <%=other_checked%>/>
-                    <label for="other"> other (current: <%=other%>) </label> <br />
-             </li>
-             <li>
-               Other notes: <br />
-                  <textarea name="other_text" onclick="this.select()"><%=other_text%></textarea>
-             </li>
-            
-             <li>
-               Send an email notification (previously sent: <%=date_of_last_email%>): <br />
-
-               <table><tr>
-                  <td> <input class="checkbox" type="checkbox" name="send_email" id="send_email" value="send_email" style="float:left;" /> </td>
-                  <td><label for="send_email" style="display:block;">send kit owner <%=name%> (<%=email%>) an email </label> </td></tr>
+      <input type="hidden" name="sent_date" value="<%=date_of_last_email%>" />
+      <input type="hidden" name="login_user"  value="<%=name%>" />
+      <input type="hidden" name="login_email" value="<%=email%>" />
+      <input type="hidden" name="email_type" value="<%=email_type%>" />
+      <input type="hidden" name="sample_date" id="sample_date" value="<%=sample_date%>"/>
+      <input type="hidden" name="sample_time" id="sample_time" value="<%=sample_time%>"/>
+      <input type="hidden" name="sample_site" id="sample_site" value="<%=sample_site%>"/>
+        <h2><%=proj_type%> Details</h2>
+         <li>
+         Sample details: <br/>
+         <table>
+         <tr><td>Sample Date</td><td><%=sample_date%></td></tr>
+         <tr><td>Sample Time</td><td><%=sample_time%></td></tr>
+         <tr><td>Sample Site</td><td><%=sample_site%></td></tr>
+         </table>
+         </li>
+         <li>
+           Sample issues: <br />
+              <input class="checkbox" type="checkbox" name="sample_issue" id="moldy" value="moldy" <%=moldy_checked%>/> 
+                <label for="moldy"> moldy (current: <%=moldy%>) </label> <br />
+              <input class="checkbox" type="checkbox" name="sample_issue" id="overloaded" value="overloaded" <%=overloaded_checked%>/>
+                <label for="overloaded"> overloaded (current: <%=overloaded%>) </label> <br />
+              <input class="checkbox" type="checkbox" name="sample_issue" id="other" value="other" <%=other_checked%>/>
+                <label for="other"> other (current: <%=other%>) </label> <br />
+         </li>
+         <li>
+           Other notes: <br />
+              <textarea name="other_text" onclick="this.select()"><%=other_text%></textarea>
+         </li>
+        
+         <li>
+           Send an email notification (previously sent: <%=date_of_last_email%>): <br />
+
+           <table><tr>
+              <td> <input class="checkbox" type="checkbox" name="send_email" id="send_email" value="send_email" style="float:left;" /> </td>
+              <td><label for="send_email" style="display:block;">send kit owner <%=name%> (<%=email%>) an email </label> </td></tr>
 
 <%
-            if email_type == '0':
-                # indent
+        if email_type == '0':
+            # indent
 %>
-            <tr><td></td><td>
-            sample date: <input type="text" name="sample_date" id="sample_date" style="width:100px"/> <br/>
-                        <script>
-                          $(function() {
-                            $( "#sample_date" ).datepicker({
-                                    changeMonth: true,
-                                    maxDate: '+0m',
-                                    onSelect: function(dateText, inst) {
-                                        $(this).focus();
-                                    }
-                            });
-                          });
-                        </script>
-            </td></tr>
-            <tr><td></td><td>
-            sample time: <input type="text" name="sample_time" id="sample_time" style="width:100px"/> <br />
-                  <script>
+        <tr><td></td><td>
+        sample date: <input type="text" name="sample_date" id="sample_date" style="width:100px"/> <br/>
+                    <script>
                       $(function() {
-                        $( "#sample_time" ).timepicker({
-                           showPeriod: true,
-                           showLeadingZero: true,
-                           onSelect: function(dateText, inst) {
-                              $(this).focus();
-                           }
+                        $( "#sample_date" ).datepicker({
+                                changeMonth: true,
+                                maxDate: '+0m',
+                                onSelect: function(dateText, inst) {
+                                    $(this).focus();
+                                }
                         });
                       });
-                  </script>
-            </td></tr>
+                    </script>
+        </td></tr>
+        <tr><td></td><td>
+        sample time: <input type="text" name="sample_time" id="sample_time" style="width:100px"/> <br />
+              <script>
+                  $(function() {
+                    $( "#sample_time" ).timepicker({
+                       showPeriod: true,
+                       showLeadingZero: true,
+                       onSelect: function(dateText, inst) {
+                          $(this).focus();
+                       }
+                    });
+                  });
+              </script>
+        </td></tr>
 <%
-            elif email_type == '1':
-                # indent
+        elif email_type == '1':
+            # indent
 %>
-            <input type="hidden" name="sample_time" value="<%=sample_time%>" />
-            <input type="hidden" name="sample_date" value="<%=sample_date%>" />
+        <input type="hidden" name="sample_time" value="<%=sample_time%>" />
+        <input type="hidden" name="sample_date" value="<%=sample_date%>" />
 <%
-            # de-indent
+        # de-indent
 %>
-            </table>
-           </li>
-           <li>
-            <a href="fusebox.psp?page=ag_edit_barcode.psp&barcode=<%=barcode%>">Edit American Gut Barcode</a>
-           </li>
-          </ul>
+        </table>
+       </li>
+       <li>
+        <a href="fusebox.psp?page=ag_edit_barcode.psp&barcode=<%=barcode%>">Edit American Gut Barcode</a>
+       </li>
+      </ul>
 <%
-        #End Indent
-%>
-          </td></tr></table><br /><br />
-              <input type="submit" value="Submit">
-              <input type="reset" value="Reset!">
-        </form>
-        </div>
-<%
-except(KeyError):
-    #will get here on first load of this page since there should be no barcode key in the form dict
+    #End Indent
+    #below here is barcode general 
 %>
+      </td></tr></table><br /><br />
+          <input type="submit" value="Submit">
+          <input type="reset" value="Reset!">
+    </form>
+    </div>

From 539f8964846e2060d3357d296bb7e255924ec818 Mon Sep 17 00:00:00 2001
From: teravest <ejteravest@gmail.com>
Date: Mon, 3 Mar 2014 09:36:21 -0700
Subject: [PATCH 12/16] remove try except in favor of if statment

---
 www/wwwadmin/barcode_util.psp | 575 +++++++++++++++++-----------------
 1 file changed, 286 insertions(+), 289 deletions(-)

diff --git a/www/wwwadmin/barcode_util.psp b/www/wwwadmin/barcode_util.psp
index 09356d19..6c7be72f 100644
--- a/www/wwwadmin/barcode_util.psp
+++ b/www/wwwadmin/barcode_util.psp
@@ -134,320 +134,317 @@ if prev_barcode:
 </form>
 </div>
 <%
-try:
-    barcode = form['barcode']
-except(KeyError):
-    pass
-    #will get here on first load of this page since there should be no barcode key in the form dict
-
-barcode_details = data_access.getBarcodeDetails(barcode)
-proj_type = data_access.getBarcodeProjType(barcode)
-proj_group = data_access.getProjectGroup(proj_type)
-
-if len(barcode_details)==0:
-    req.write('''
-     <div id="invalid_barcode" class="verification_color">
-        <div class="verification_text_wrapper">
-           <br />
-             <h2 class="verification_text">Barcode <br>
-             "%s"
-             <br> does not exist in the database!</h2>
-         </div>
-     </div>
-    ''' % barcode)
-else: 
-    #barcode exists get general info 
-    status = 'Received' if barcode_details['status'] == None \
-            else barcode_details['status']
-    scan_date = 'NA' if barcode_details['scan_date'] == None \
-            else barcode_details['scan_date']
-    sample_postmark_date = 'NA' if barcode_details['sample_postmark_date'] \
-            == None else barcode_details['sample_postmark_date']
-    
-    biomass_remaining = 'Unknown' if barcode_details['biomass_remaining'] \
-            == None else barcode_details['biomass_remaining']
-    sequencing_status = '' if barcode_details['sequencing_status'] \
-            == None else barcode_details['sequencing_status']
-    obsolete = 'N' if barcode_details['obsolete'] == None \
-            else barcode_details['obsolete']
-    div_id = message = email_type = ""
-
-    if (obsolete == "Y"):
-            #the barcode is obsolete
-            div_id = "obsolete"
-            message = "Barcode is Obsolete"
-    #get project info for div 
-    elif proj_group == 'American Gut':
-        ag_details = ag_data_access.getAGBarcodeDetails(barcode)
-        if len(ag_details) > 0:
-            sample_site = '' if ag_details['site_sampled'] == None \
-                        else ag_details['site_sampled']
-            sample_date = '' if ag_details['sample_date'] == None else \
-                        ag_details['sample_date']
-            sample_time = '' if ag_details['sample_time'] == None else \
-                        ag_details['sample_time']
-            moldy = 'NA' if ag_details['moldy'] == None else ag_details['moldy']
-            overloaded = 'NA' if ag_details['overloaded'] == None else \
-                        ag_details['overloaded']
-            other = 'NA' if ag_details['other'] == None else ag_details['other']
-            other_text = '' if ag_details['other_text'] == None else \
-                        ag_details['other_text']
-            date_of_last_email = '' if ag_details['date_of_last_email'] == None \
-                        else ag_details['date_of_last_email']
-            email = '' if ag_details['email'] == None else ag_details['email']
-            name = '' if ag_details['kit_name'] == None else ag_details['kit_name']
-            moldy_checked = "checked" if moldy in ('Y','y') else ""
-            overloaded_checked = "checked" if overloaded in ('Y','y') else ""
-            other_checked = "checked" if other in ('Y','y') else ""
-            barcode_metadata = ag_data_access.AGGetBarcodeMetadata(barcode)
-            if not (sample_date == sample_site == sample_time == ''):
-                # it has all sample details (sample time, date, site)
-                if len(barcode_metadata) == 1:
-                    # and we can successfully retrieve sample metadata
-                    div_id = "verified"
-                    message = "All good"
-                    email_type = "1"
-                elif len(barcode_metadata) == 0:
-                    # we cannot retrieve metadata
-                    div_id = "no_metadata"
-                    message = "Cannot retrieve metadata"
-                else:
-                    # should never get here (this would happen if the metadata
-                    # pulldown returned more than one row for a single barcode)
-                    div_id = "md_pulldown_error"
-                    message = ("This barcode has multiple entries in the "
-                               "database, which should never happeen. Please "
-                               "notify someone on the database crew.")
-            else:
-                div_id = "not_assigned"
-                message = "Missing info"
-                email_type = "0"
-        else:
-            div_id = "not_assigned"
-            message = ("In American Gut project group but No " 
-                       "Amerincan Gut info for barcode")
-    else:
-        div_id = "verified"
-        message = "Barcode Info is correct"
-    #INDENT
-    #Below this point is general barcode code. 
+if 'barcode' in form:
+  barcode = form['barcode']
+
+  barcode_details = data_access.getBarcodeDetails(barcode)
+  proj_type = data_access.getBarcodeProjType(barcode)
+  proj_group = data_access.getProjectGroup(proj_type)
+
+  if len(barcode_details)==0:
+      req.write('''
+       <div id="invalid_barcode" class="verification_color">
+          <div class="verification_text_wrapper">
+             <br />
+               <h2 class="verification_text">Barcode <br>
+               "%s"
+               <br> does not exist in the database!</h2>
+           </div>
+       </div>
+      ''' % barcode)
+  else: 
+      #barcode exists get general info 
+      status = 'Received' if barcode_details['status'] == None \
+              else barcode_details['status']
+      scan_date = 'NA' if barcode_details['scan_date'] == None \
+              else barcode_details['scan_date']
+      sample_postmark_date = 'NA' if barcode_details['sample_postmark_date'] \
+              == None else barcode_details['sample_postmark_date']
+      
+      biomass_remaining = 'Unknown' if barcode_details['biomass_remaining'] \
+              == None else barcode_details['biomass_remaining']
+      sequencing_status = '' if barcode_details['sequencing_status'] \
+              == None else barcode_details['sequencing_status']
+      obsolete = 'N' if barcode_details['obsolete'] == None \
+              else barcode_details['obsolete']
+      div_id = message = email_type = ""
+
+      if (obsolete == "Y"):
+              #the barcode is obsolete
+              div_id = "obsolete"
+              message = "Barcode is Obsolete"
+      #get project info for div 
+      elif proj_group == 'American Gut':
+          ag_details = ag_data_access.getAGBarcodeDetails(barcode)
+          if len(ag_details) > 0:
+              sample_site = '' if ag_details['site_sampled'] == None \
+                          else ag_details['site_sampled']
+              sample_date = '' if ag_details['sample_date'] == None else \
+                          ag_details['sample_date']
+              sample_time = '' if ag_details['sample_time'] == None else \
+                          ag_details['sample_time']
+              moldy = 'NA' if ag_details['moldy'] == None else ag_details['moldy']
+              overloaded = 'NA' if ag_details['overloaded'] == None else \
+                          ag_details['overloaded']
+              other = 'NA' if ag_details['other'] == None else ag_details['other']
+              other_text = '' if ag_details['other_text'] == None else \
+                          ag_details['other_text']
+              date_of_last_email = '' if ag_details['date_of_last_email'] == None \
+                          else ag_details['date_of_last_email']
+              email = '' if ag_details['email'] == None else ag_details['email']
+              name = '' if ag_details['kit_name'] == None else ag_details['kit_name']
+              moldy_checked = "checked" if moldy in ('Y','y') else ""
+              overloaded_checked = "checked" if overloaded in ('Y','y') else ""
+              other_checked = "checked" if other in ('Y','y') else ""
+              barcode_metadata = ag_data_access.AGGetBarcodeMetadata(barcode)
+              if not (sample_date == sample_site == sample_time == ''):
+                  # it has all sample details (sample time, date, site)
+                  if len(barcode_metadata) == 1:
+                      # and we can successfully retrieve sample metadata
+                      div_id = "verified"
+                      message = "All good"
+                      email_type = "1"
+                  elif len(barcode_metadata) == 0:
+                      # we cannot retrieve metadata
+                      div_id = "no_metadata"
+                      message = "Cannot retrieve metadata"
+                  else:
+                      # should never get here (this would happen if the metadata
+                      # pulldown returned more than one row for a single barcode)
+                      div_id = "md_pulldown_error"
+                      message = ("This barcode has multiple entries in the "
+                                 "database, which should never happeen. Please "
+                                 "notify someone on the database crew.")
+              else:
+                  div_id = "not_assigned"
+                  message = "Missing info"
+                  email_type = "0"
+          else:
+              div_id = "not_assigned"
+              message = ("In American Gut project group but No " 
+                         "Amerincan Gut info for barcode")
+      else:
+          div_id = "verified"
+          message = "Barcode Info is correct"
+      #INDENT
+      #Below this point is general barcode code. 
 %>
-    
-    <div id="<%=div_id%>" class="verification_color">
-       <div class="verification_text_wrapper">
-          <br />
-           
-            <h2 class="verification_text">
-             Project type: <%=proj_type%> <br><br>
-             Barcode: <%=barcode%><br><br>
-            <%=message%></h2>
-        </div>
-    </div>
-
-    <div id="barcode_form">
-
-    <form action="fusebox.psp?page=barcode_util.psp" method="post"
-     onsubmit="return confirm('Are you sure to submit and update database?')"
-     onreset="return confirm('Are you sure to reset?')">
-      <input type="hidden" name="prev_barcode" value="<%=barcode%>" />
-      <input type="hidden" name="proj_group" id="proj_group" value="<%=proj_group%>"/>
-      <ul>
-      <table cellspacing="40"><tr><td>
-      <h2> General Barcode Details </h2>
-        <li>
-           Sample postmark date (current: <%=sample_postmark_date%>) : <br />
-              <input type="text" name="postmark_date" id="postmark_date" value="<%=sample_postmark_date if sample_postmark_date != 'NA' else ''%>" onclick="this.select()" /> <br />
-                    <script>
-                      $(function() {
-                        $( "#postmark_date" ).datepicker({
-                                changeMonth: true,
-                                maxDate: '+0m',
-                                onSelect: function(dateText, inst) {
-                                    $(this).focus();
-                                }
+      
+      <div id="<%=div_id%>" class="verification_color">
+         <div class="verification_text_wrapper">
+            <br />
+             
+              <h2 class="verification_text">
+               Project type: <%=proj_type%> <br><br>
+               Barcode: <%=barcode%><br><br>
+              <%=message%></h2>
+          </div>
+      </div>
+
+      <div id="barcode_form">
+
+      <form action="fusebox.psp?page=barcode_util.psp" method="post"
+       onsubmit="return confirm('Are you sure to submit and update database?')"
+       onreset="return confirm('Are you sure to reset?')">
+        <input type="hidden" name="prev_barcode" value="<%=barcode%>" />
+        <input type="hidden" name="proj_group" id="proj_group" value="<%=proj_group%>"/>
+        <ul>
+        <table cellspacing="40"><tr><td>
+        <h2> General Barcode Details </h2>
+          <li>
+             Sample postmark date (current: <%=sample_postmark_date%>) : <br />
+                <input type="text" name="postmark_date" id="postmark_date" value="<%=sample_postmark_date if sample_postmark_date != 'NA' else ''%>" onclick="this.select()" /> <br />
+                      <script>
+                        $(function() {
+                          $( "#postmark_date" ).datepicker({
+                                  changeMonth: true,
+                                  maxDate: '+0m',
+                                  onSelect: function(dateText, inst) {
+                                      $(this).focus();
+                                  }
+                          });
                         });
-                      });
-                    </script>
-              (please follow the format mm/dd/yyyy. Example: 12/25/2012)
-         </li>
-         <li>
-           Scan date (current: <%=scan_date%>): <br />
-           <input type="text" name="scan_date" id="scan_date" value="<%=scan_date if scan_date != 'NA' else ''%>" onclick="this.select()" /> <br />
-                    <script>
-                      $(function() {
-                        $( "#scan_date" ).datepicker({
-                                changeMonth: true,
-                                maxDate: '+0m',
-                                onSelect: function(dateText, inst) {
-                                    $(this).focus();
-                                }
+                      </script>
+                (please follow the format mm/dd/yyyy. Example: 12/25/2012)
+           </li>
+           <li>
+             Scan date (current: <%=scan_date%>): <br />
+             <input type="text" name="scan_date" id="scan_date" value="<%=scan_date if scan_date != 'NA' else ''%>" onclick="this.select()" /> <br />
+                      <script>
+                        $(function() {
+                          $( "#scan_date" ).datepicker({
+                                  changeMonth: true,
+                                  maxDate: '+0m',
+                                  onSelect: function(dateText, inst) {
+                                      $(this).focus();
+                                  }
+                          });
                         });
-                      });
-                    </script>
-              (please follow the format mm/dd/yyyy. Example: 12/25/2012)
-         </li>
-         <li>
-         Barcode Status:<br /><select name="bstatus" id="bstatus">
+                      </script>
+                (please follow the format mm/dd/yyyy. Example: 12/25/2012)
+           </li>
+           <li>
+           Barcode Status:<br /><select name="bstatus" id="bstatus">
 <%
-    bar_statuses = data_access.getBarcodeStatuses()
-    for bstatus in bar_statuses:
-        if bstatus == status:
-            req.write('<option value="{0}" selected>{0}</option>'.format(bstatus))
-        else:
-            req.write('<option value="{0}">{0}</option>'.format(bstatus))
-    #END Indent
+      bar_statuses = data_access.getBarcodeStatuses()
+      for bstatus in bar_statuses:
+          if bstatus == status:
+              req.write('<option value="{0}" selected>{0}</option>'.format(bstatus))
+          else:
+              req.write('<option value="{0}">{0}</option>'.format(bstatus))
+      #END Indent
 %>
 
-         </select></li>
-         <li>Biomass Remaining: <br /><select name="biomass_remaining" id="biomass_remaining">
+           </select></li>
+           <li>Biomass Remaining: <br /><select name="biomass_remaining" id="biomass_remaining">
 <%
-    for bmass in ['N', 'Y', 'Unknown']:
-        selected = ''
-        if biomass_remaining == bmass:
-            selected = 'selected'
-        if bmass == 'Y':
-            req.write("<option value='Y' {0}>Yes</option>".format(selected))
-        elif bmass == 'N':
-            req.write("<option value='N' {0}>No</option>".format(selected))
-        elif bmass == 'Unknown':
-            req.write("<option value='' {0}>Unknown</option>".format(selected))
-    #END Indent
+      for bmass in ['N', 'Y', 'Unknown']:
+          selected = ''
+          if biomass_remaining == bmass:
+              selected = 'selected'
+          if bmass == 'Y':
+              req.write("<option value='Y' {0}>Yes</option>".format(selected))
+          elif bmass == 'N':
+              req.write("<option value='N' {0}>No</option>".format(selected))
+          elif bmass == 'Unknown':
+              req.write("<option value='' {0}>Unknown</option>".format(selected))
+      #END Indent
 %>
-         </select></li>
-         <li>Sequencing Status<br /><select name="sequencing_status" id="sequencing_status">
+           </select></li>
+           <li>Sequencing Status<br /><select name="sequencing_status" id="sequencing_status">
 <%
-    seq_statuses = data_access.getSequencingStatuses()
-    for sstatus in seq_statuses:
-        if sequencing_status == sstatus:
-            req.write('<option value="{0}" selected>{0}</option>'.format(sstatus))
-        else:
-            req.write('<option value="{0}">{0}</option>'.format(sstatus))
-    if sequencing_status == '':
-        req.write('<option value="" selected>Unknown</option>')
-    else: 
-        req.write('<option value="">Unknown</option>')
-    #END Indent
+      seq_statuses = data_access.getSequencingStatuses()
+      for sstatus in seq_statuses:
+          if sequencing_status == sstatus:
+              req.write('<option value="{0}" selected>{0}</option>'.format(sstatus))
+          else:
+              req.write('<option value="{0}">{0}</option>'.format(sstatus))
+      if sequencing_status == '':
+          req.write('<option value="" selected>Unknown</option>')
+      else: 
+          req.write('<option value="">Unknown</option>')
+      #END Indent
 %>
-    </select></li>
-         <li>Obsolete<br /><select name="obsolete_status" id="obsolete_status">
+      </select></li>
+           <li>Obsolete<br /><select name="obsolete_status" id="obsolete_status">
 <%
-    if obsolete == '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
+      if obsolete == '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></li>
-         <li>
-         Project <br /><select name="project" id="project" >
+           </select></li>
+           <li>
+           Project <br /><select name="project" id="project" >
 <%
-    project_names = data_access.getProjectNames()
-    for project in project_names:
-        if project == proj_type:
-            req.write('<option value="{0}" selected>{0}</option>'.format(project))
-        else:
-            req.write('<option value="{0}">{0}</option>'.format(project))
-    #End Indent
+      project_names = data_access.getProjectNames()
+      for project in project_names:
+          if project == proj_type:
+              req.write('<option value="{0}" selected>{0}</option>'.format(project))
+          else:
+              req.write('<option value="{0}">{0}</option>'.format(project))
+      #End Indent
 %>
-    </select>
-    </li></td><td>
+      </select>
+      </li></td><td>
 <%
-    if proj_group== 'American Gut' and len(ag_details) > 0:
-        #Displaying project specific information
-        #Indent
+      if proj_group== 'American Gut' and len(ag_details) > 0:
+          #Displaying project specific information
+          #Indent
 %>
-      <input type="hidden" name="sent_date" value="<%=date_of_last_email%>" />
-      <input type="hidden" name="login_user"  value="<%=name%>" />
-      <input type="hidden" name="login_email" value="<%=email%>" />
-      <input type="hidden" name="email_type" value="<%=email_type%>" />
-      <input type="hidden" name="sample_date" id="sample_date" value="<%=sample_date%>"/>
-      <input type="hidden" name="sample_time" id="sample_time" value="<%=sample_time%>"/>
-      <input type="hidden" name="sample_site" id="sample_site" value="<%=sample_site%>"/>
-        <h2><%=proj_type%> Details</h2>
-         <li>
-         Sample details: <br/>
-         <table>
-         <tr><td>Sample Date</td><td><%=sample_date%></td></tr>
-         <tr><td>Sample Time</td><td><%=sample_time%></td></tr>
-         <tr><td>Sample Site</td><td><%=sample_site%></td></tr>
-         </table>
-         </li>
-         <li>
-           Sample issues: <br />
-              <input class="checkbox" type="checkbox" name="sample_issue" id="moldy" value="moldy" <%=moldy_checked%>/> 
-                <label for="moldy"> moldy (current: <%=moldy%>) </label> <br />
-              <input class="checkbox" type="checkbox" name="sample_issue" id="overloaded" value="overloaded" <%=overloaded_checked%>/>
-                <label for="overloaded"> overloaded (current: <%=overloaded%>) </label> <br />
-              <input class="checkbox" type="checkbox" name="sample_issue" id="other" value="other" <%=other_checked%>/>
-                <label for="other"> other (current: <%=other%>) </label> <br />
-         </li>
-         <li>
-           Other notes: <br />
-              <textarea name="other_text" onclick="this.select()"><%=other_text%></textarea>
-         </li>
-        
-         <li>
-           Send an email notification (previously sent: <%=date_of_last_email%>): <br />
-
-           <table><tr>
-              <td> <input class="checkbox" type="checkbox" name="send_email" id="send_email" value="send_email" style="float:left;" /> </td>
-              <td><label for="send_email" style="display:block;">send kit owner <%=name%> (<%=email%>) an email </label> </td></tr>
+        <input type="hidden" name="sent_date" value="<%=date_of_last_email%>" />
+        <input type="hidden" name="login_user"  value="<%=name%>" />
+        <input type="hidden" name="login_email" value="<%=email%>" />
+        <input type="hidden" name="email_type" value="<%=email_type%>" />
+        <input type="hidden" name="sample_date" id="sample_date" value="<%=sample_date%>"/>
+        <input type="hidden" name="sample_time" id="sample_time" value="<%=sample_time%>"/>
+        <input type="hidden" name="sample_site" id="sample_site" value="<%=sample_site%>"/>
+          <h2><%=proj_type%> Details</h2>
+           <li>
+           Sample details: <br/>
+           <table>
+           <tr><td>Sample Date</td><td><%=sample_date%></td></tr>
+           <tr><td>Sample Time</td><td><%=sample_time%></td></tr>
+           <tr><td>Sample Site</td><td><%=sample_site%></td></tr>
+           </table>
+           </li>
+           <li>
+             Sample issues: <br />
+                <input class="checkbox" type="checkbox" name="sample_issue" id="moldy" value="moldy" <%=moldy_checked%>/> 
+                  <label for="moldy"> moldy (current: <%=moldy%>) </label> <br />
+                <input class="checkbox" type="checkbox" name="sample_issue" id="overloaded" value="overloaded" <%=overloaded_checked%>/>
+                  <label for="overloaded"> overloaded (current: <%=overloaded%>) </label> <br />
+                <input class="checkbox" type="checkbox" name="sample_issue" id="other" value="other" <%=other_checked%>/>
+                  <label for="other"> other (current: <%=other%>) </label> <br />
+           </li>
+           <li>
+             Other notes: <br />
+                <textarea name="other_text" onclick="this.select()"><%=other_text%></textarea>
+           </li>
+          
+           <li>
+             Send an email notification (previously sent: <%=date_of_last_email%>): <br />
+
+             <table><tr>
+                <td> <input class="checkbox" type="checkbox" name="send_email" id="send_email" value="send_email" style="float:left;" /> </td>
+                <td><label for="send_email" style="display:block;">send kit owner <%=name%> (<%=email%>) an email </label> </td></tr>
 
 <%
-        if email_type == '0':
-            # indent
+          if email_type == '0':
+              # indent
 %>
-        <tr><td></td><td>
-        sample date: <input type="text" name="sample_date" id="sample_date" style="width:100px"/> <br/>
-                    <script>
-                      $(function() {
-                        $( "#sample_date" ).datepicker({
-                                changeMonth: true,
-                                maxDate: '+0m',
-                                onSelect: function(dateText, inst) {
-                                    $(this).focus();
-                                }
+          <tr><td></td><td>
+          sample date: <input type="text" name="sample_date" id="sample_date" style="width:100px"/> <br/>
+                      <script>
+                        $(function() {
+                          $( "#sample_date" ).datepicker({
+                                  changeMonth: true,
+                                  maxDate: '+0m',
+                                  onSelect: function(dateText, inst) {
+                                      $(this).focus();
+                                  }
+                          });
                         });
+                      </script>
+          </td></tr>
+          <tr><td></td><td>
+          sample time: <input type="text" name="sample_time" id="sample_time" style="width:100px"/> <br />
+                <script>
+                    $(function() {
+                      $( "#sample_time" ).timepicker({
+                         showPeriod: true,
+                         showLeadingZero: true,
+                         onSelect: function(dateText, inst) {
+                            $(this).focus();
+                         }
                       });
-                    </script>
-        </td></tr>
-        <tr><td></td><td>
-        sample time: <input type="text" name="sample_time" id="sample_time" style="width:100px"/> <br />
-              <script>
-                  $(function() {
-                    $( "#sample_time" ).timepicker({
-                       showPeriod: true,
-                       showLeadingZero: true,
-                       onSelect: function(dateText, inst) {
-                          $(this).focus();
-                       }
                     });
-                  });
-              </script>
-        </td></tr>
+                </script>
+          </td></tr>
 <%
-        elif email_type == '1':
-            # indent
+          elif email_type == '1':
+              # indent
 %>
-        <input type="hidden" name="sample_time" value="<%=sample_time%>" />
-        <input type="hidden" name="sample_date" value="<%=sample_date%>" />
+          <input type="hidden" name="sample_time" value="<%=sample_time%>" />
+          <input type="hidden" name="sample_date" value="<%=sample_date%>" />
 <%
-        # de-indent
+          # de-indent
 %>
-        </table>
-       </li>
-       <li>
-        <a href="fusebox.psp?page=ag_edit_barcode.psp&barcode=<%=barcode%>">Edit American Gut Barcode</a>
-       </li>
-      </ul>
+          </table>
+         </li>
+         <li>
+          <a href="fusebox.psp?page=ag_edit_barcode.psp&barcode=<%=barcode%>">Edit American Gut Barcode</a>
+         </li>
+        </ul>
 <%
-    #End Indent
-    #below here is barcode general 
+      #End Indent
+      #below here is barcode general 
 %>
-      </td></tr></table><br /><br />
-          <input type="submit" value="Submit">
-          <input type="reset" value="Reset!">
-    </form>
-    </div>
+        </td></tr></table><br /><br />
+            <input type="submit" value="Submit">
+            <input type="reset" value="Reset!">
+      </form>
+      </div>

From 4bb433ec06222777dbc1eff3252bdeadace767b7 Mon Sep 17 00:00:00 2001
From: teravest <ejteravest@gmail.com>
Date: Thu, 6 Mar 2014 15:41:09 -0700
Subject: [PATCH 13/16] in the middle of addressing comments

---
 python_code/data_access/qiime_data_access.py |   9 +-
 www/wwwadmin/ag_edit_barcode.psp             |   3 +-
 www/wwwadmin/barcode_util.psp                | 623 ++++++++++---------
 3 files changed, 328 insertions(+), 307 deletions(-)

diff --git a/python_code/data_access/qiime_data_access.py b/python_code/data_access/qiime_data_access.py
index 1ad635a2..c9bd7621 100755
--- a/python_code/data_access/qiime_data_access.py
+++ b/python_code/data_access/qiime_data_access.py
@@ -2962,11 +2962,14 @@ 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, biomass_remaining, sequencing_status, obsolete):
+    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, biomass_remaining, sequencing_status, obsolete])
+        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.
@@ -3020,7 +3023,7 @@ def getBarcodeStatuses(self):
     def getProjectGroup(self, project_name):
         """Returns a project group name
 
-        project_name is the name of the project
+        project_name is the name of the project from the table project
         """
         con = self.getMetadataDatabaseConnection()
         result = con.cursor()
diff --git a/www/wwwadmin/ag_edit_barcode.psp b/www/wwwadmin/ag_edit_barcode.psp
index b27ac248..c627b8ad 100644
--- a/www/wwwadmin/ag_edit_barcode.psp
+++ b/www/wwwadmin/ag_edit_barcode.psp
@@ -28,7 +28,8 @@ if 'submit_flag' in form:
   });
 </script>
 -->
-
+<!-- This from is called ag_edit_barcode1 to avoid naming conflists with 
+     the forms in header.psp -->
 <form method="post" name="ag_edit_barcode1" id="ag_edit_barcode1" action="fusebox.psp?page=ag_edit_barcode.psp">
 	<input type="hidden" name="submit_flag" id="submit_flag" value="0"/>
 	<table>
diff --git a/www/wwwadmin/barcode_util.psp b/www/wwwadmin/barcode_util.psp
index 6c7be72f..bc58ab7b 100644
--- a/www/wwwadmin/barcode_util.psp
+++ b/www/wwwadmin/barcode_util.psp
@@ -18,7 +18,6 @@ current_date = date.today().strftime("%m/%d/%Y")
 prev_barcode = form.get('prev_barcode', None)
 if prev_barcode:
         # try to update general barcode information.
-        biomass_remaining_value = form.get('biomass_remaining', [])
         try:
             data_access.updateBarcodeStatus(form['bstatus'], form['postmark_date'],
                                             form['scan_date'], prev_barcode,
@@ -46,32 +45,32 @@ if prev_barcode:
                 sample_date = form['sample_date']
                 if email_type == '0':
                     subject='Follow up on Your American Gut Sample with Barcode %s' % prev_barcode
-                    body_message='''
+                    body_message=('''
     Dear {name},
 
-    We have recently received your sample barcode: {barcode}, but we cannot process your sample until the online forms have been completed.  
-    Information about your sample is tracked through the American Gut participant website, and you are required to log in and complete the online 
+    We have recently received your sample barcode: {barcode}, but we cannot process your sample until the online forms have been completed.  \
+    Information about your sample is tracked through the American Gut participant website, and you are required to log in and complete the online \
     process in order for your sample to be processed. 
 
-    The most common reason for receiving this email is the sample was not logged. Logging the sample associates the sample with a participant in our records.
+    The most common reason for receiving this email is the sample was not logged. Logging the sample associates the sample with a participant in our records.\
     This needs to be done so the we know that the sample has consent before we can process it. 
 
-    If it is a human sample, we require formal consent, questionnaire results and sample details (type, date, and time of collection). 
-    If it is a pet or environmental sample we require sample details (type, date and time of collection). If you have already filled out the 
+    If it is a human sample, we require formal consent, questionnaire results and sample details (type, date, and time of collection). \
+    If it is a pet or environmental sample we require sample details (type, date and time of collection). If you have already filled out the \
     consent form and questionnaire, then it is likely that the sample simply needs to be associated with the appropriate participant.
 
-    In order to help you in adding these details, the side of the sample tube {barcode} reads:
-       sample date: {sample_date} 
+    In order to help you in adding these details, the side of the sample tube {barcode} reads: \
+       sample date: {sample_date} \
        sample time: {sample_time}
 
-    Instructions about the required procedures can be found here: http://www.microbio.me/americangut/img/full_instructions.pdf
+    Instructions about the required procedures can be found here: http://www.microbio.me/americangut/img/full_instructions.pdf \
 
-    These procedures are in place to protect your privacy, and please be sure that we are properly associating your sample to your 
-    survey results. We realize that some of these steps may not be completely intuitive. However, our kits are designed to support 
-    multiple participants and sample types, which necessitates the added complexity of explicitly requiring participants to associate 
+    These procedures are in place to protect your privacy, and please be sure that we are properly associating your sample to your \
+    survey results. We realize that some of these steps may not be completely intuitive. However, our kits are designed to support \
+    multiple participants and sample types, which necessitates the added complexity of explicitly requiring participants to associate \
     samples with themselves so that we can guarantee compliance with human subjects research protocols.
 
-    Please log back into the American Gut website (http://www.microbio.me/americangut) as soon as possible and complete the online process. 
+    Please log back into the American Gut website (http://www.microbio.me/americangut) as soon as possible and complete the online process. \
     If you have any questions or concerns, please contact us at info@americangut.org.
 
     Thank you,
@@ -111,10 +110,10 @@ if prev_barcode:
                         req.write("Email sending to (%s) failed failed (barcode: %s)!!!<br/>" % (login_email, prev_barcode))
         
             sample_issue = form.get('sample_issue', [])
-            moldy = overloaded = other = 'N'
-            if 'moldy' in sample_issue: moldy = 'Y'
-            if 'overloaded' in sample_issue: overloaded = 'Y'
-            if 'other' in sample_issue: other = 'Y'
+            moldy = 'Y' if 'moldy' in sample_issue else moldy = 'N'
+            overloaded = 'Y' if 'overloaded' in sample_issue \
+                        else overloaded = 'N'
+            other = 'Y' if other in sample_issue else other = 'N'
             try:
                 ag_data_access.updateAKB(prev_barcode, moldy, overloaded, other,
                                      form['other_text'], sent_date)
@@ -135,316 +134,334 @@ if prev_barcode:
 </div>
 <%
 if 'barcode' in form:
-  barcode = form['barcode']
-
-  barcode_details = data_access.getBarcodeDetails(barcode)
-  proj_type = data_access.getBarcodeProjType(barcode)
-  proj_group = data_access.getProjectGroup(proj_type)
-
-  if len(barcode_details)==0:
-      req.write('''
-       <div id="invalid_barcode" class="verification_color">
-          <div class="verification_text_wrapper">
-             <br />
-               <h2 class="verification_text">Barcode <br>
-               "%s"
-               <br> does not exist in the database!</h2>
-           </div>
-       </div>
-      ''' % barcode)
-  else: 
-      #barcode exists get general info 
-      status = 'Received' if barcode_details['status'] == None \
-              else barcode_details['status']
-      scan_date = 'NA' if barcode_details['scan_date'] == None \
-              else barcode_details['scan_date']
-      sample_postmark_date = 'NA' if barcode_details['sample_postmark_date'] \
-              == None else barcode_details['sample_postmark_date']
-      
-      biomass_remaining = 'Unknown' if barcode_details['biomass_remaining'] \
-              == None else barcode_details['biomass_remaining']
-      sequencing_status = '' if barcode_details['sequencing_status'] \
-              == None else barcode_details['sequencing_status']
-      obsolete = 'N' if barcode_details['obsolete'] == None \
-              else barcode_details['obsolete']
-      div_id = message = email_type = ""
-
-      if (obsolete == "Y"):
-              #the barcode is obsolete
-              div_id = "obsolete"
-              message = "Barcode is Obsolete"
-      #get project info for div 
-      elif proj_group == 'American Gut':
-          ag_details = ag_data_access.getAGBarcodeDetails(barcode)
-          if len(ag_details) > 0:
-              sample_site = '' if ag_details['site_sampled'] == None \
-                          else ag_details['site_sampled']
-              sample_date = '' if ag_details['sample_date'] == None else \
-                          ag_details['sample_date']
-              sample_time = '' if ag_details['sample_time'] == None else \
-                          ag_details['sample_time']
-              moldy = 'NA' if ag_details['moldy'] == None else ag_details['moldy']
-              overloaded = 'NA' if ag_details['overloaded'] == None else \
-                          ag_details['overloaded']
-              other = 'NA' if ag_details['other'] == None else ag_details['other']
-              other_text = '' if ag_details['other_text'] == None else \
-                          ag_details['other_text']
-              date_of_last_email = '' if ag_details['date_of_last_email'] == None \
-                          else ag_details['date_of_last_email']
-              email = '' if ag_details['email'] == None else ag_details['email']
-              name = '' if ag_details['kit_name'] == None else ag_details['kit_name']
-              moldy_checked = "checked" if moldy in ('Y','y') else ""
-              overloaded_checked = "checked" if overloaded in ('Y','y') else ""
-              other_checked = "checked" if other in ('Y','y') else ""
-              barcode_metadata = ag_data_access.AGGetBarcodeMetadata(barcode)
-              if not (sample_date == sample_site == sample_time == ''):
-                  # it has all sample details (sample time, date, site)
-                  if len(barcode_metadata) == 1:
-                      # and we can successfully retrieve sample metadata
-                      div_id = "verified"
-                      message = "All good"
-                      email_type = "1"
-                  elif len(barcode_metadata) == 0:
-                      # we cannot retrieve metadata
-                      div_id = "no_metadata"
-                      message = "Cannot retrieve metadata"
-                  else:
-                      # should never get here (this would happen if the metadata
-                      # pulldown returned more than one row for a single barcode)
-                      div_id = "md_pulldown_error"
-                      message = ("This barcode has multiple entries in the "
-                                 "database, which should never happeen. Please "
-                                 "notify someone on the database crew.")
-              else:
-                  div_id = "not_assigned"
-                  message = "Missing info"
-                  email_type = "0"
-          else:
-              div_id = "not_assigned"
-              message = ("In American Gut project group but No " 
-                         "Amerincan Gut info for barcode")
-      else:
-          div_id = "verified"
-          message = "Barcode Info is correct"
-      #INDENT
-      #Below this point is general barcode code. 
+    barcode = form['barcode']
+
+    barcode_details = data_access.getBarcodeDetails(barcode)
+    proj_type = data_access.getBarcodeProjType(barcode)
+    proj_group = data_access.getProjectGroup(proj_type)
+
+    if len(barcode_details)==0:
+        req.write('''
+         <div id="invalid_barcode" class="verification_color">
+            <div class="verification_text_wrapper">
+               <br />
+                 <h2 class="verification_text">Barcode <br>
+                 "%s"
+                 <br> does not exist in the database!</h2>
+             </div>
+         </div>
+        ''' % barcode)
+    else: 
+        #barcode exists get general info 
+        if barcode_details['status'] is None:
+            status = 'Received'
+        else: 
+            status = barcode_details['status']
+        if barcode_details['scan_date'] is None:
+            scan_date = 'NA'
+        else:
+            scan_date = barcode_details['scan_date']
+        if barcode_details['sample_postmark_date'] is None:
+            sample_postmark_date = 'NA'
+        else:
+            sample_postmark_date = barcode_details['sample_postmark_date']
+        if barcode_details['biomass_remaining'] is None:
+            biomass_remaining = 'Unknown'
+        else:
+            biomass_remaining = barcode_details['biomass_remaining']
+        if barcode_details['sequencing_status'] is None:
+            sequencing_status = ''
+        else:
+            sequencing_status = barcode_details['sequencing_status']
+        if barcode_details['obsolete'] is None:
+            obsolete = 'N'
+        else:
+            obsolete = barcode_details['obsolete']
+        div_id = message = email_type = ""
+
+        if (obsolete == "Y"):
+                #the barcode is obsolete
+                div_id = "obsolete"
+                message = "Barcode is Obsolete"
+        #get project info for div 
+        elif proj_group == 'American Gut':
+            ag_details = ag_data_access.getAGBarcodeDetails(barcode)
+            if len(ag_details) > 0:
+                if ag_details['site_sampled'] is None:
+                    sample_site = '' 
+                else: 
+                    sample_site = ag_details['site_sampled']
+                if ag_details['sample_date'] is None:
+                    sample_date = ''
+                else:
+                    sample_date = ag_details['sample_date']
+               
+
+               
+                sample_time = '' if ag_details['sample_time'] == None else \
+                            ag_details['sample_time']
+                moldy = 'NA' if ag_details['moldy'] == None else ag_details['moldy']
+                overloaded = 'NA' if ag_details['overloaded'] == None else \
+                            ag_details['overloaded']
+                other = 'NA' if ag_details['other'] == None else ag_details['other']
+                other_text = '' if ag_details['other_text'] == None else \
+                            ag_details['other_text']
+                date_of_last_email = '' if ag_details['date_of_last_email'] == None \
+                            else ag_details['date_of_last_email']
+                email = '' if ag_details['email'] == None else ag_details['email']
+                name = '' if ag_details['kit_name'] == None else ag_details['kit_name']
+                moldy_checked = "checked" if moldy in ('Y','y') else ""
+                overloaded_checked = "checked" if overloaded in ('Y','y') else ""
+                other_checked = "checked" if other in ('Y','y') else ""
+                barcode_metadata = ag_data_access.AGGetBarcodeMetadata(barcode)
+                if not (sample_date == sample_site == sample_time == ''):
+                    # it has all sample details (sample time, date, site)
+                    if len(barcode_metadata) == 1:
+                        # and we can successfully retrieve sample metadata
+                        div_id = "verified"
+                        message = "All good"
+                        email_type = "1"
+                    elif len(barcode_metadata) == 0:
+                        # we cannot retrieve metadata
+                        div_id = "no_metadata"
+                        message = "Cannot retrieve metadata"
+                    else:
+                        # should never get here (this would happen if the metadata
+                        # pulldown returned more than one row for a single barcode)
+                        div_id = "md_pulldown_error"
+                        message = ("This barcode has multiple entries in the "
+                                   "database, which should never happeen. Please "
+                                   "notify someone on the database crew.")
+                else:
+                    div_id = "not_assigned"
+                    message = "Missing info"
+                    email_type = "0"
+            else:
+                div_id = "not_assigned"
+                message = ("In American Gut project group but No " 
+                           "Amerincan Gut info for barcode")
+        else:
+            div_id = "verified"
+            message = "Barcode Info is correct"
+        #INDENT
+        #Below this point is general barcode code. 
 %>
-      
-      <div id="<%=div_id%>" class="verification_color">
-         <div class="verification_text_wrapper">
-            <br />
-             
-              <h2 class="verification_text">
-               Project type: <%=proj_type%> <br><br>
-               Barcode: <%=barcode%><br><br>
-              <%=message%></h2>
-          </div>
-      </div>
-
-      <div id="barcode_form">
-
-      <form action="fusebox.psp?page=barcode_util.psp" method="post"
-       onsubmit="return confirm('Are you sure to submit and update database?')"
-       onreset="return confirm('Are you sure to reset?')">
-        <input type="hidden" name="prev_barcode" value="<%=barcode%>" />
-        <input type="hidden" name="proj_group" id="proj_group" value="<%=proj_group%>"/>
-        <ul>
-        <table cellspacing="40"><tr><td>
-        <h2> General Barcode Details </h2>
-          <li>
-             Sample postmark date (current: <%=sample_postmark_date%>) : <br />
-                <input type="text" name="postmark_date" id="postmark_date" value="<%=sample_postmark_date if sample_postmark_date != 'NA' else ''%>" onclick="this.select()" /> <br />
-                      <script>
-                        $(function() {
-                          $( "#postmark_date" ).datepicker({
-                                  changeMonth: true,
-                                  maxDate: '+0m',
-                                  onSelect: function(dateText, inst) {
-                                      $(this).focus();
-                                  }
+        
+        <div id="<%=div_id%>" class="verification_color">
+           <div class="verification_text_wrapper">
+              <br />
+               
+                <h2 class="verification_text">
+                 Project type: <%=proj_type%> <br><br>
+                 Barcode: <%=barcode%><br><br>
+                <%=message%></h2>
+            </div>
+        </div>
+
+        <div id="barcode_form">
+
+        <form action="fusebox.psp?page=barcode_util.psp" method="post"
+         onsubmit="return confirm('Are you sure to submit and update database?')"
+         onreset="return confirm('Are you sure to reset?')">
+          <input type="hidden" name="prev_barcode" value="<%=barcode%>" />
+          <input type="hidden" name="proj_group" id="proj_group" value="<%=proj_group%>"/>
+          <ul>
+          <table cellspacing="40"><tr><td>
+          <h2> General Barcode Details </h2>
+            <li>
+               Sample postmark date (current: <%=sample_postmark_date%>) : <br />
+                  <input type="text" name="postmark_date" id="postmark_date" value="<%=sample_postmark_date if sample_postmark_date != 'NA' else ''%>" onclick="this.select()" /> <br />
+                        <script>
+                          $(function() {
+                            $( "#postmark_date" ).datepicker({
+                                    changeMonth: true,
+                                    maxDate: '+0m',
+                                    onSelect: function(dateText, inst) {
+                                        $(this).focus();
+                                    }
+                            });
                           });
-                        });
-                      </script>
-                (please follow the format mm/dd/yyyy. Example: 12/25/2012)
-           </li>
-           <li>
-             Scan date (current: <%=scan_date%>): <br />
-             <input type="text" name="scan_date" id="scan_date" value="<%=scan_date if scan_date != 'NA' else ''%>" onclick="this.select()" /> <br />
-                      <script>
-                        $(function() {
-                          $( "#scan_date" ).datepicker({
-                                  changeMonth: true,
-                                  maxDate: '+0m',
-                                  onSelect: function(dateText, inst) {
-                                      $(this).focus();
-                                  }
+                        </script>
+                  (please follow the format mm/dd/yyyy. Example: 12/25/2012)
+             </li>
+             <li>
+               Scan date (current: <%=scan_date%>): <br />
+               <input type="text" name="scan_date" id="scan_date" value="<%=scan_date if scan_date != 'NA' else ''%>" onclick="this.select()" /> <br />
+                        <script>
+                          $(function() {
+                            $( "#scan_date" ).datepicker({
+                                    changeMonth: true,
+                                    maxDate: '+0m',
+                                    onSelect: function(dateText, inst) {
+                                        $(this).focus();
+                                    }
+                            });
                           });
-                        });
-                      </script>
-                (please follow the format mm/dd/yyyy. Example: 12/25/2012)
-           </li>
-           <li>
-           Barcode Status:<br /><select name="bstatus" id="bstatus">
+                        </script>
+                  (please follow the format mm/dd/yyyy. Example: 12/25/2012)
+             </li>
+             <li>
+             Barcode Status:<br /><select name="bstatus" id="bstatus">
 <%
-      bar_statuses = data_access.getBarcodeStatuses()
-      for bstatus in bar_statuses:
-          if bstatus == status:
-              req.write('<option value="{0}" selected>{0}</option>'.format(bstatus))
-          else:
-              req.write('<option value="{0}">{0}</option>'.format(bstatus))
-      #END Indent
+        bar_statuses = data_access.getBarcodeStatuses()
+        for bstatus in bar_statuses:
+            if bstatus == status:
+                req.write('<option value="{0}" selected>{0}</option>'.format(bstatus))
+            else:
+                req.write('<option value="{0}">{0}</option>'.format(bstatus))
+        #END Indent
 %>
 
-           </select></li>
-           <li>Biomass Remaining: <br /><select name="biomass_remaining" id="biomass_remaining">
+             </select></li>
+             <li>Biomass Remaining: <br /><select name="biomass_remaining" id="biomass_remaining">
 <%
-      for bmass in ['N', 'Y', 'Unknown']:
-          selected = ''
-          if biomass_remaining == bmass:
-              selected = 'selected'
-          if bmass == 'Y':
-              req.write("<option value='Y' {0}>Yes</option>".format(selected))
-          elif bmass == 'N':
-              req.write("<option value='N' {0}>No</option>".format(selected))
-          elif bmass == 'Unknown':
-              req.write("<option value='' {0}>Unknown</option>".format(selected))
-      #END Indent
+        for bmass in ['N', 'Y', 'Unknown']:
+            selected = ''
+            if biomass_remaining == bmass:
+                selected = 'selected'
+            if bmass == 'Y':
+                req.write("<option value='Y' {0}>Yes</option>".format(selected))
+            elif bmass == 'N':
+                req.write("<option value='N' {0}>No</option>".format(selected))
+            elif bmass == 'Unknown':
+                req.write("<option value='' {0}>Unknown</option>".format(selected))
+        #END Indent
 %>
-           </select></li>
-           <li>Sequencing Status<br /><select name="sequencing_status" id="sequencing_status">
+             </select></li>
+             <li>Sequencing Status<br /><select name="sequencing_status" id="sequencing_status">
 <%
-      seq_statuses = data_access.getSequencingStatuses()
-      for sstatus in seq_statuses:
-          if sequencing_status == sstatus:
-              req.write('<option value="{0}" selected>{0}</option>'.format(sstatus))
-          else:
-              req.write('<option value="{0}">{0}</option>'.format(sstatus))
-      if sequencing_status == '':
-          req.write('<option value="" selected>Unknown</option>')
-      else: 
-          req.write('<option value="">Unknown</option>')
-      #END Indent
+        seq_statuses = data_access.getSequencingStatuses()
+        for sstatus in seq_statuses:
+            if sequencing_status == sstatus:
+                req.write('<option value="{0}" selected>{0}</option>'.format(sstatus))
+            else:
+                req.write('<option value="{0}">{0}</option>'.format(sstatus))
+        if sequencing_status == '':
+            req.write('<option value="" selected>Unknown</option>')
+        else: 
+            req.write('<option value="">Unknown</option>')
+        #END Indent
 %>
-      </select></li>
-           <li>Obsolete<br /><select name="obsolete_status" id="obsolete_status">
+        </select></li>
+             <li>Obsolete<br /><select name="obsolete_status" id="obsolete_status">
 <%
-      if obsolete == '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
+        if obsolete == '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></li>
-           <li>
-           Project <br /><select name="project" id="project" >
+             </select></li>
+             <li>
+             Project <br /><select name="project" id="project" >
 <%
-      project_names = data_access.getProjectNames()
-      for project in project_names:
-          if project == proj_type:
-              req.write('<option value="{0}" selected>{0}</option>'.format(project))
-          else:
-              req.write('<option value="{0}">{0}</option>'.format(project))
-      #End Indent
+        project_names = data_access.getProjectNames()
+        for project in project_names:
+            if project == proj_type:
+                req.write('<option value="{0}" selected>{0}</option>'.format(project))
+            else:
+                req.write('<option value="{0}">{0}</option>'.format(project))
+        #End Indent
 %>
-      </select>
-      </li></td><td>
+        </select>
+        </li></td><td>
 <%
-      if proj_group== 'American Gut' and len(ag_details) > 0:
-          #Displaying project specific information
-          #Indent
+        if proj_group== 'American Gut' and len(ag_details) > 0:
+            #Displaying project specific information
+            #Indent
 %>
-        <input type="hidden" name="sent_date" value="<%=date_of_last_email%>" />
-        <input type="hidden" name="login_user"  value="<%=name%>" />
-        <input type="hidden" name="login_email" value="<%=email%>" />
-        <input type="hidden" name="email_type" value="<%=email_type%>" />
-        <input type="hidden" name="sample_date" id="sample_date" value="<%=sample_date%>"/>
-        <input type="hidden" name="sample_time" id="sample_time" value="<%=sample_time%>"/>
-        <input type="hidden" name="sample_site" id="sample_site" value="<%=sample_site%>"/>
-          <h2><%=proj_type%> Details</h2>
-           <li>
-           Sample details: <br/>
-           <table>
-           <tr><td>Sample Date</td><td><%=sample_date%></td></tr>
-           <tr><td>Sample Time</td><td><%=sample_time%></td></tr>
-           <tr><td>Sample Site</td><td><%=sample_site%></td></tr>
-           </table>
-           </li>
-           <li>
-             Sample issues: <br />
-                <input class="checkbox" type="checkbox" name="sample_issue" id="moldy" value="moldy" <%=moldy_checked%>/> 
-                  <label for="moldy"> moldy (current: <%=moldy%>) </label> <br />
-                <input class="checkbox" type="checkbox" name="sample_issue" id="overloaded" value="overloaded" <%=overloaded_checked%>/>
-                  <label for="overloaded"> overloaded (current: <%=overloaded%>) </label> <br />
-                <input class="checkbox" type="checkbox" name="sample_issue" id="other" value="other" <%=other_checked%>/>
-                  <label for="other"> other (current: <%=other%>) </label> <br />
-           </li>
-           <li>
-             Other notes: <br />
-                <textarea name="other_text" onclick="this.select()"><%=other_text%></textarea>
-           </li>
-          
-           <li>
-             Send an email notification (previously sent: <%=date_of_last_email%>): <br />
-
-             <table><tr>
-                <td> <input class="checkbox" type="checkbox" name="send_email" id="send_email" value="send_email" style="float:left;" /> </td>
-                <td><label for="send_email" style="display:block;">send kit owner <%=name%> (<%=email%>) an email </label> </td></tr>
+          <input type="hidden" name="sent_date" value="<%=date_of_last_email%>" />
+          <input type="hidden" name="login_user"  value="<%=name%>" />
+          <input type="hidden" name="login_email" value="<%=email%>" />
+          <input type="hidden" name="email_type" value="<%=email_type%>" />
+          <input type="hidden" name="sample_date" id="sample_date" value="<%=sample_date%>"/>
+          <input type="hidden" name="sample_time" id="sample_time" value="<%=sample_time%>"/>
+          <input type="hidden" name="sample_site" id="sample_site" value="<%=sample_site%>"/>
+            <h2><%=proj_type%> Details</h2>
+             <li>
+             Sample details: <br/>
+             <table>
+             <tr><td>Sample Date</td><td><%=sample_date%></td></tr>
+             <tr><td>Sample Time</td><td><%=sample_time%></td></tr>
+             <tr><td>Sample Site</td><td><%=sample_site%></td></tr>
+             </table>
+             </li>
+             <li>
+               Sample issues: <br />
+                  <input class="checkbox" type="checkbox" name="sample_issue" id="moldy" value="moldy" <%=moldy_checked%>/> 
+                    <label for="moldy"> moldy (current: <%=moldy%>) </label> <br />
+                  <input class="checkbox" type="checkbox" name="sample_issue" id="overloaded" value="overloaded" <%=overloaded_checked%>/>
+                    <label for="overloaded"> overloaded (current: <%=overloaded%>) </label> <br />
+                  <input class="checkbox" type="checkbox" name="sample_issue" id="other" value="other" <%=other_checked%>/>
+                    <label for="other"> other (current: <%=other%>) </label> <br />
+             </li>
+             <li>
+               Other notes: <br />
+                  <textarea name="other_text" onclick="this.select()"><%=other_text%></textarea>
+             </li>
+            
+             <li>
+               Send an email notification (previously sent: <%=date_of_last_email%>): <br />
+
+               <table><tr>
+                  <td> <input class="checkbox" type="checkbox" name="send_email" id="send_email" value="send_email" style="float:left;" /> </td>
+                  <td><label for="send_email" style="display:block;">send kit owner <%=name%> (<%=email%>) an email </label> </td></tr>
 
 <%
-          if email_type == '0':
-              # indent
+            if email_type == '0':
+                # indent
 %>
-          <tr><td></td><td>
-          sample date: <input type="text" name="sample_date" id="sample_date" style="width:100px"/> <br/>
-                      <script>
-                        $(function() {
-                          $( "#sample_date" ).datepicker({
-                                  changeMonth: true,
-                                  maxDate: '+0m',
-                                  onSelect: function(dateText, inst) {
-                                      $(this).focus();
-                                  }
+            <tr><td></td><td>
+            sample date: <input type="text" name="sample_date" id="sample_date" style="width:100px"/> <br/>
+                        <script>
+                          $(function() {
+                            $( "#sample_date" ).datepicker({
+                                    changeMonth: true,
+                                    maxDate: '+0m',
+                                    onSelect: function(dateText, inst) {
+                                        $(this).focus();
+                                    }
+                            });
                           });
+                        </script>
+            </td></tr>
+            <tr><td></td><td>
+            sample time: <input type="text" name="sample_time" id="sample_time" style="width:100px"/> <br />
+                  <script>
+                      $(function() {
+                        $( "#sample_time" ).timepicker({
+                           showPeriod: true,
+                           showLeadingZero: true,
+                           onSelect: function(dateText, inst) {
+                              $(this).focus();
+                           }
                         });
-                      </script>
-          </td></tr>
-          <tr><td></td><td>
-          sample time: <input type="text" name="sample_time" id="sample_time" style="width:100px"/> <br />
-                <script>
-                    $(function() {
-                      $( "#sample_time" ).timepicker({
-                         showPeriod: true,
-                         showLeadingZero: true,
-                         onSelect: function(dateText, inst) {
-                            $(this).focus();
-                         }
                       });
-                    });
-                </script>
-          </td></tr>
+                  </script>
+            </td></tr>
 <%
-          elif email_type == '1':
-              # indent
+            elif email_type == '1':
+                # indent
 %>
-          <input type="hidden" name="sample_time" value="<%=sample_time%>" />
-          <input type="hidden" name="sample_date" value="<%=sample_date%>" />
+            <input type="hidden" name="sample_time" value="<%=sample_time%>" />
+            <input type="hidden" name="sample_date" value="<%=sample_date%>" />
 <%
-          # de-indent
+            # de-indent
 %>
-          </table>
-         </li>
-         <li>
-          <a href="fusebox.psp?page=ag_edit_barcode.psp&barcode=<%=barcode%>">Edit American Gut Barcode</a>
-         </li>
-        </ul>
+            </table>
+           </li>
+           <li>
+            <a href="fusebox.psp?page=ag_edit_barcode.psp&barcode=<%=barcode%>">Edit American Gut Barcode</a>
+           </li>
+          </ul>
 <%
-      #End Indent
-      #below here is barcode general 
+        #End Indent
+        #below here is barcode general 
 %>
-        </td></tr></table><br /><br />
-            <input type="submit" value="Submit">
-            <input type="reset" value="Reset!">
-      </form>
-      </div>
+          </td></tr></table><br /><br />
+              <input type="submit" value="Submit">
+              <input type="reset" value="Reset!">
+        </form>
+        </div>

From 2f852243410b8dc4dc2695974d7d4c2529f21779 Mon Sep 17 00:00:00 2001
From: teravest <ejteravest@gmail.com>
Date: Fri, 7 Mar 2014 09:09:18 -0700
Subject: [PATCH 14/16] changes based on review comments. I will deploy this to
 webdev after we deploy the mapmarker to live

---
 database/procedures/get_project_group.sql    |   1 -
 python_code/data_access/ag_data_access.py    |   5 +-
 python_code/data_access/qiime_data_access.py |   6 +-
 www/wwwadmin/barcode_util.psp                | 152 +++++++++++--------
 4 files changed, 92 insertions(+), 72 deletions(-)

diff --git a/database/procedures/get_project_group.sql b/database/procedures/get_project_group.sql
index 11bb1b43..94eb94ad 100644
--- a/database/procedures/get_project_group.sql
+++ b/database/procedures/get_project_group.sql
@@ -7,7 +7,6 @@ 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;
-  null;
 end get_project_group;
 
 
diff --git a/python_code/data_access/ag_data_access.py b/python_code/data_access/ag_data_access.py
index 9bf8d8e4..045d3005 100755
--- a/python_code/data_access/ag_data_access.py
+++ b/python_code/data_access/ag_data_access.py
@@ -154,7 +154,7 @@ def getAGBarcodeDetails(self, barcode):
         results = con.cursor()
         con.cursor().callproc('ag_get_barcode_details', [barcode, results])
         barcode_details = results.fetchone()
-        try:
+        if barcode_details is not None:
             row_dict = {
                 'email': barcode_details[0],
                 'ag_kit_barcode_id': barcode_details[1],
@@ -175,7 +175,8 @@ def getAGBarcodeDetails(self, barcode):
                 'overloaded' : barcode_details[16],
                 'kit_name' : barcode_details[17]
             }
-        except TypeError:
+        else:
+            #no results so return an empty dict 
             row_dict = {}
         return row_dict
 
diff --git a/python_code/data_access/qiime_data_access.py b/python_code/data_access/qiime_data_access.py
index c9bd7621..11ccea28 100755
--- a/python_code/data_access/qiime_data_access.py
+++ b/python_code/data_access/qiime_data_access.py
@@ -3041,7 +3041,7 @@ def getBarcodeDetails(self, barcode):
         results = con.cursor()
         con.cursor().callproc('get_barcode_details',[barcode, results])
         row = results.fetchone()
-        try:
+        if row is not None:
             barcode_details = {
                 'create_date' : row[0],
                 'status' : row[1],
@@ -3051,7 +3051,7 @@ def getBarcodeDetails(self, barcode):
                 'sequencing_status' : row[5],
                 'obsolete' : row[6]
                 }
-        except TypeError :
+        else:
             #no results mean barcode doesn't exist 
-            return {}
+            barcode_details = {}
         return barcode_details
diff --git a/www/wwwadmin/barcode_util.psp b/www/wwwadmin/barcode_util.psp
index bc58ab7b..19659fea 100644
--- a/www/wwwadmin/barcode_util.psp
+++ b/www/wwwadmin/barcode_util.psp
@@ -46,52 +46,53 @@ if prev_barcode:
                 if email_type == '0':
                     subject='Follow up on Your American Gut Sample with Barcode %s' % prev_barcode
                     body_message=('''
-    Dear {name},
+Dear {name},
 
-    We have recently received your sample barcode: {barcode}, but we cannot process your sample until the online forms have been completed.  \
-    Information about your sample is tracked through the American Gut participant website, and you are required to log in and complete the online \
-    process in order for your sample to be processed. 
+    We have recently received your sample barcode: {barcode}, but we cannot process your sample until the online forms have been completed. \
+Information about your sample is tracked through the American Gut participant website, and you are required to log in and complete the online \
+process in order for your sample to be processed. 
 
-    The most common reason for receiving this email is the sample was not logged. Logging the sample associates the sample with a participant in our records.\
-    This needs to be done so the we know that the sample has consent before we can process it. 
+    The most common reason for receiving this email is the sample was not logged. Logging the sample associates the sample with a participant in our records. \
+This needs to be done so the we know that the sample has consent before we can process it. 
 
     If it is a human sample, we require formal consent, questionnaire results and sample details (type, date, and time of collection). \
-    If it is a pet or environmental sample we require sample details (type, date and time of collection). If you have already filled out the \
-    consent form and questionnaire, then it is likely that the sample simply needs to be associated with the appropriate participant.
+If it is a pet or environmental sample we require sample details (type, date and time of collection). If you have already filled out the \
+consent form and questionnaire, then it is likely that the sample simply needs to be associated with the appropriate participant.
 
-    In order to help you in adding these details, the side of the sample tube {barcode} reads: \
-       sample date: {sample_date} \
-       sample time: {sample_time}
+    In order to help you in adding these details, the side of the sample tube {barcode} reads: 
+        sample date: {sample_date} 
+        sample time: {sample_time}
 
-    Instructions about the required procedures can be found here: http://www.microbio.me/americangut/img/full_instructions.pdf \
+    Instructions about the required procedures can be found here: http://www.microbio.me/americangut/img/full_instructions.pdf 
 
     These procedures are in place to protect your privacy, and please be sure that we are properly associating your sample to your \
-    survey results. We realize that some of these steps may not be completely intuitive. However, our kits are designed to support \
-    multiple participants and sample types, which necessitates the added complexity of explicitly requiring participants to associate \
-    samples with themselves so that we can guarantee compliance with human subjects research protocols.
+survey results. We realize that some of these steps may not be completely intuitive. However, our kits are designed to support \
+multiple participants and sample types, which necessitates the added complexity of explicitly requiring participants to associate \
+samples with themselves so that we can guarantee compliance with human subjects research protocols.
 
     Please log back into the American Gut website (http://www.microbio.me/americangut) as soon as possible and complete the online process. \
-    If you have any questions or concerns, please contact us at info@americangut.org.
+If you have any questions or concerns, please contact us at info@americangut.org.
 
-    Thank you,
+Thank you,
 
-    --American Gut Team--
-    '''
+--American Gut Team--
+    ''')
 
-                    body_message = body_message.format(name=login_user, barcode=prev_barcode,
+                    body_message = body_message.format(name=login_user, 
+                                                       barcode=prev_barcode,
                                                        sample_date=sample_date,
                                                        sample_time=sample_time)
                 elif email_type == '1':
                     subject = 'American Gut Sample with Barcode %s is Received.' % prev_barcode
                     body_message = '''
-    Dear {name},
+Dear {name},
 
-    We have recently received your sample with barcode {barcode} dated {sample_date} {sample_time} and we have begun processing it.  
-    Please see our FAQ section for when you can expect results. (http://www.microbio.me/americangut/FAQ.psp#faq4)
+    We have recently received your sample with barcode {barcode} dated {sample_date} {sample_time} and we have begun processing it. \
+Please see our FAQ section for when you can expect results. (http://www.microbio.me/americangut/FAQ.psp#faq4)
 
-    Thank you for your participation!
+Thank you for your participation!
 
-    --American Gut Team--
+--American Gut Team--
     '''
                     body_message = body_message.format(name=login_user, barcode=prev_barcode,
                                                        sample_date=sample_date, sample_time=sample_time)
@@ -110,10 +111,18 @@ if prev_barcode:
                         req.write("Email sending to (%s) failed failed (barcode: %s)!!!<br/>" % (login_email, prev_barcode))
         
             sample_issue = form.get('sample_issue', [])
-            moldy = 'Y' if 'moldy' in sample_issue else moldy = 'N'
-            overloaded = 'Y' if 'overloaded' in sample_issue \
-                        else overloaded = 'N'
-            other = 'Y' if other in sample_issue else other = 'N'
+            if 'moldy' in sample_issue:
+                moldy = 'Y'
+            else:
+                moldy = 'N'
+            if 'overloaded' in sample_issue:
+                overloaded = 'Y'
+            else:
+                overloaded = 'N'
+            if 'other' in sample_issue:
+                other = 'Y'
+            else:
+                other = 'N'
             try:
                 ag_data_access.updateAKB(prev_barcode, moldy, overloaded, other,
                                      form['other_text'], sent_date)
@@ -195,24 +204,47 @@ if 'barcode' in form:
                     sample_date = ''
                 else:
                     sample_date = ag_details['sample_date']
-               
+                if ag_details['sample_time'] is None:
+                    sample_time = ''
+                else:
+                    sample_time = ag_details['sample_time']
+                if ag_details['moldy'] is None:
+                    moldy = 'NA'
+                else: 
+                    moldy = ag_details['moldy']
+                if ag_details['overloaded'] is None:
+                    overloaded = 'NA'
+                else: 
+                    overloaded = ag_details['overloaded']
+                if ag_details['other'] is None:
+                    other = 'NA'
+                else:
+                    other = ag_details['other']
+                if ag_details['other_text'] is None:
+                    other_text = ''
+                else:
+                    other_text = ag_details['other_text']
+                if ag_details['date_of_last_email'] is None:
+                    date_of_last_email = ''
+                else:
+                    date_of_last_email = ag_details['date_of_last_email']
+                if ag_details['email'] is None:
+                    email = ''
+                else:
+                    email = ag_details['email']
+                if moldy =='Y':
+                    moldy_checked = 'checked'
+                else:
+                    moldy_checked = ''
+                if overloaded == 'Y':
+                    overloaded_checked = 'checked'
+                else:
+                    overloaded_checked = ''
+                if other == 'Y':
+                    other_checked = 'checked' 
+                else:
+                    other_checked = ''
 
-               
-                sample_time = '' if ag_details['sample_time'] == None else \
-                            ag_details['sample_time']
-                moldy = 'NA' if ag_details['moldy'] == None else ag_details['moldy']
-                overloaded = 'NA' if ag_details['overloaded'] == None else \
-                            ag_details['overloaded']
-                other = 'NA' if ag_details['other'] == None else ag_details['other']
-                other_text = '' if ag_details['other_text'] == None else \
-                            ag_details['other_text']
-                date_of_last_email = '' if ag_details['date_of_last_email'] == None \
-                            else ag_details['date_of_last_email']
-                email = '' if ag_details['email'] == None else ag_details['email']
-                name = '' if ag_details['kit_name'] == None else ag_details['kit_name']
-                moldy_checked = "checked" if moldy in ('Y','y') else ""
-                overloaded_checked = "checked" if overloaded in ('Y','y') else ""
-                other_checked = "checked" if other in ('Y','y') else ""
                 barcode_metadata = ag_data_access.AGGetBarcodeMetadata(barcode)
                 if not (sample_date == sample_site == sample_time == ''):
                     # it has all sample details (sample time, date, site)
@@ -261,8 +293,8 @@ if 'barcode' in form:
         <div id="barcode_form">
 
         <form action="fusebox.psp?page=barcode_util.psp" method="post"
-         onsubmit="return confirm('Are you sure to submit and update database?')"
-         onreset="return confirm('Are you sure to reset?')">
+         onsubmit="return confirm('Are you sure you want to submit and update database?')"
+         onreset="return confirm('Are you sure you want to reset?')">
           <input type="hidden" name="prev_barcode" value="<%=barcode%>" />
           <input type="hidden" name="proj_group" id="proj_group" value="<%=proj_group%>"/>
           <ul>
@@ -315,16 +347,9 @@ if 'barcode' in form:
              </select></li>
              <li>Biomass Remaining: <br /><select name="biomass_remaining" id="biomass_remaining">
 <%
-        for bmass in ['N', 'Y', 'Unknown']:
-            selected = ''
-            if biomass_remaining == bmass:
-                selected = 'selected'
-            if bmass == 'Y':
-                req.write("<option value='Y' {0}>Yes</option>".format(selected))
-            elif bmass == 'N':
-                req.write("<option value='N' {0}>No</option>".format(selected))
-            elif bmass == 'Unknown':
-                req.write("<option value='' {0}>Unknown</option>".format(selected))
+        for bmass, option_name in [('N', 'No'), ('Y', 'Yes'), ('Unknown', 'Unknown')]:
+            selected = 'selected' if bmass == biomass_remaining else ''
+            req.write('<option value="{0}" {1}>{2}</option'.format(bmass, selected, option_name))
         #END Indent
 %>
              </select></li>
@@ -332,14 +357,9 @@ if 'barcode' in form:
 <%
         seq_statuses = data_access.getSequencingStatuses()
         for sstatus in seq_statuses:
-            if sequencing_status == sstatus:
-                req.write('<option value="{0}" selected>{0}</option>'.format(sstatus))
-            else:
-                req.write('<option value="{0}">{0}</option>'.format(sstatus))
-        if sequencing_status == '':
-            req.write('<option value="" selected>Unknown</option>')
-        else: 
-            req.write('<option value="">Unknown</option>')
+            selected = 'selected' if sstatus == sequencing_status else ''
+            req.write('<option value="{0}" {1}>{0}</option>'.format(sstatus, 
+                       selected))
         #END Indent
 %>
         </select></li>

From 5d3d31da95e1e17261245bdbc4f759d0a9e9fd61 Mon Sep 17 00:00:00 2001
From: teravest <ejteravest@gmail.com>
Date: Tue, 25 Mar 2014 15:14:24 -0600
Subject: [PATCH 15/16] cleanup bugs and edit barcode

---
 python_code/data_access/ag_data_access.py | 11 +++++--
 www/wwwadmin/ag_edit_barcode.psp          | 35 +++++++++++++++++++++--
 www/wwwadmin/barcode_util.psp             | 22 ++++++++------
 3 files changed, 55 insertions(+), 13 deletions(-)

diff --git a/python_code/data_access/ag_data_access.py b/python_code/data_access/ag_data_access.py
index 045d3005..467bce90 100755
--- a/python_code/data_access/ag_data_access.py
+++ b/python_code/data_access/ag_data_access.py
@@ -252,9 +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):
-        con = self.getMetadataDatabaseConnection()
-        con.cursor().callproc('ag_update_barcode', [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, refunded,
+                              withdrawn])
 
     def addAGHumanParticipant(self, ag_login_id, participant_name):
         con = self.getMetadataDatabaseConnection()
diff --git a/www/wwwadmin/ag_edit_barcode.psp b/www/wwwadmin/ag_edit_barcode.psp
index d12f3cc9..3fb10755 100644
--- a/www/wwwadmin/ag_edit_barcode.psp
+++ b/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
 %>
@@ -72,7 +72,8 @@ 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 +189,39 @@ 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
diff --git a/www/wwwadmin/barcode_util.psp b/www/wwwadmin/barcode_util.psp
index 19659fea..81336c5b 100644
--- a/www/wwwadmin/barcode_util.psp
+++ b/www/wwwadmin/barcode_util.psp
@@ -19,10 +19,11 @@ prev_barcode = form.get('prev_barcode', None)
 if prev_barcode:
         # try to update general barcode information.
         try:
-            data_access.updateBarcodeStatus(form['bstatus'], form['postmark_date'],
+            data_access.updateBarcodeStatus(form['bstatus'],
+                                            form['postmark_date'],
                                             form['scan_date'], prev_barcode,
                                             form['biomass_remaining_value'],
-                                            form['sequencing_status'], 
+                                            form['sequencing_status'],
                                             form['obsolete_status'])
             data_access.setBarcodeProjType(form['project'], prev_barcode)
             req.write("General Barcode Information Updated<br>")
@@ -35,8 +36,9 @@ if prev_barcode:
 
             general_name = "American Gut participant"
 
-            login_user = form['login_user'] # kit owner name
-            if login_user=="None": login_user = general_name
+            login_user = form['login_user']  # kit owner name
+            if login_user == "None":
+                login_user = general_name
 
             if "send_email" in form:
                 email_type = form['email_type']
@@ -187,12 +189,12 @@ if 'barcode' in form:
         else:
             obsolete = barcode_details['obsolete']
         div_id = message = email_type = ""
-
+        ag_details = []
         if (obsolete == "Y"):
                 #the barcode is obsolete
                 div_id = "obsolete"
                 message = "Barcode is Obsolete"
-        #get project info for div 
+        #get project info for div
         elif proj_group == 'American Gut':
             ag_details = ag_data_access.getAGBarcodeDetails(barcode)
             if len(ag_details) > 0:
@@ -232,6 +234,10 @@ if 'barcode' in form:
                     email = ''
                 else:
                     email = ag_details['email']
+                if ag_details['kit_name'] is None:
+                     login_user = ''
+                else:
+                    login_user = ag_details['kit_name']
                 if moldy =='Y':
                     moldy_checked = 'checked'
                 else:
@@ -393,7 +399,7 @@ if 'barcode' in form:
             #Indent
 %>
           <input type="hidden" name="sent_date" value="<%=date_of_last_email%>" />
-          <input type="hidden" name="login_user"  value="<%=name%>" />
+          <input type="hidden" name="login_user"  value="<%=login_user%>" />
           <input type="hidden" name="login_email" value="<%=email%>" />
           <input type="hidden" name="email_type" value="<%=email_type%>" />
           <input type="hidden" name="sample_date" id="sample_date" value="<%=sample_date%>"/>
@@ -427,7 +433,7 @@ if 'barcode' in form:
 
                <table><tr>
                   <td> <input class="checkbox" type="checkbox" name="send_email" id="send_email" value="send_email" style="float:left;" /> </td>
-                  <td><label for="send_email" style="display:block;">send kit owner <%=name%> (<%=email%>) an email </label> </td></tr>
+                  <td><label for="send_email" style="display:block;">send kit owner <%=login_user%> (<%=email%>) an email </label> </td></tr>
 
 <%
             if email_type == '0':

From c3472f38c6b44439e1ae7c97853574180c194538 Mon Sep 17 00:00:00 2001
From: teravest <ejteravest@gmail.com>
Date: Wed, 26 Mar 2014 11:33:29 -0600
Subject: [PATCH 16/16] fixed form name conflict

---
 www/wwwadmin/ag_edit_barcode.psp | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/www/wwwadmin/ag_edit_barcode.psp b/www/wwwadmin/ag_edit_barcode.psp
index 3fb10755..e1bcfc09 100644
--- a/www/wwwadmin/ag_edit_barcode.psp
+++ b/www/wwwadmin/ag_edit_barcode.psp
@@ -28,15 +28,14 @@ if 'submit_flag' in form:
   });
 </script>
 -->
-<!-- This from is called ag_edit_barcode1 to avoid naming conflists with 
-     the forms in header.psp -->
-<form method="post" name="ag_edit_barcode1" id="ag_edit_barcode1" action="fusebox.psp?page=ag_edit_barcode.psp">
+
+<form method="post" name="edit_barcode" id="edit_barcode" action="fusebox.psp?page=ag_edit_barcode.psp">
 	<input type="hidden" name="submit_flag" id="submit_flag" value="0"/>
 	<table>
 		<tr>
 			<td>Barcode</td>
 			<td>
-				<select name="barcode" id="barcode" onChange="document.ag_edit_barcode1.submit();">
+				<select name="barcode" id="barcode" onChange="document.edit_barcode.submit();">
 				<option value="">Please Select...</a>
 <%
 barcodes = ag_data_access.getAGBarcodes()