--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/templates/html_selectable_report.py	Mon Mar 02 20:46:00 2015 -0500
@@ -0,0 +1,399 @@
+import os.path
+import time
+import csv
+import collections
+import re
+import common
+
+HTML_REPORT_HEADER_FILE = 'html_report_header.html'
+
+class HTMLReport(object):
+	
+	""" This receives and sets up the general meta-data fields available to the html rendering engine 
+
+	"""
+	def __init__(self, tagGroup, options, query_stats = []):
+
+		self.columns = tagGroup.columns
+		self.display_columns = [field for field in self.columns if field['group']=='column']
+		self.row_limit = options.row_limit
+		self.section_bins = {}
+		self.todo = collections.deque([]) # stack of things to do
+		self.query_stats = query_stats
+		self.empty_queries = [query['id'] for query in query_stats if query['filtered_rows'] == 0]
+		self.initialized = False
+
+		# These items are available for display in html generation via dictionary string replacement: [string ... %(filters)s ...] % self.lookup
+		self.lookup = {
+			'depth': 0,
+			'filters': 'Filters: ' + options.filters_HTML if len(options.filters_HTML) else '',
+			'timestamp': time.strftime('%Y/%m/%d'),
+			'visible_limit': 20,
+			'column_count': str(len([field for field in self.columns if field['group']=='column'])),
+			'table_rows':0,
+			'select_row':0,
+			'row_limit': self.row_limit,
+			'label':'',
+			'value':'',
+			'link':'',
+			'cssClass':'',
+			'table_header': self._tableHeader(),
+			'section_bins':'',
+			'section_counter':1
+		}
+		
+		if hasattr(options,'dataset_selection_id'):
+			self.lookup['dataset_selection_id'] = options.dataset_selection_id
+			self.initialized = True
+		
+		else:
+			self.lookup['dataset_selection_id'] = 0
+			self.errorNotice = '<div style="width:400px;margin:auto"><h3>This Selectable HTML Report needs the "Basic Report Field Output" to include the qseq and sseq sequence fields (aligned part of query sequence and subject sequence).  Add these fields or try a selection that has more than 12 columns.</h3></div>'
+
+	"""		
+	_processTagStack()
+	In the production of html, start tags and template bits are added to the outgoing html when 
+	designated section columns of data change value.  the self.todo stack keeps track of all the 
+	tag closings that have to occur when a section or table section comes to an end (and new one 
+	begins or end of document occurs).
+
+	This dynamically executes any functions listed in stack that are greater than given tag depth.
+	Generally the functions return html closing content.
+	
+	@param depth integer >= 0
+	@uses self.todo stack of [depth, function_name] items	
+	"""
+	def _processTagStack(self, depth = 0):
+		html = ''
+		while len(self.todo) and self.todo[0][0] >= depth: 
+			html += getattr(self, self.todo.popleft()[1] )()
+		return html 
+
+
+
+	############################### HTML REPORT RENDERING ############################## 
+	""" render() produces the html.  Takes in tabular data + metainformation about that file,
+	 and iterates through rows.  This approach depends on detecting changes in stated report 
+	section columns and table section columns, and triggers appropriate section start and end, 
+	and table / table section start and end tags.
+
+	@param in_file string	Full file path
+	@param out_html_file string	Full output html data file path to write to.
+	"""
+	def render (self, in_file, out_html_file):
+
+		try:
+			
+			fp_in = open(in_file, "rb")
+			fp_out = open(out_html_file, 'w')
+
+			fp_out.write( self._header(HTML_REPORT_HEADER_FILE) )
+				
+			if self.initialized:
+
+				fp_out.write( self._bodyStart() )
+				self.todo.appendleft([0,'_bodyEnd'])
+				
+				reader = csv.reader(fp_in, delimiter="\t")
+
+				for row in reader:
+
+					html = ''
+					self.rowdata = []
+					row_bins = []
+					section_reset = False
+					
+					for (idx, field) in enumerate(self.columns):
+
+						value = field['value'] = row[idx]
+						depth = idx + 1
+
+						# If a bin is mentioned on this row, its put into self.selection_bins.
+						if field['type'] == 'bin' and value != '': 
+							row_bins.append(value)
+							if not value in self.section_bins:
+								self.section_bins[value] = field['label']
+
+						grouping = field['group']
+						# Section or table grouping here: 
+						if grouping == 'section' or grouping == 'table':	
+
+							# Check to see if a new section or table section is triggered by change in field's value:
+							if section_reset or (not 'valueOld' in field) or value != field['valueOld']:
+								
+								self.lookup['value'] = value
+								self.lookup['label'] = field['label']
+
+								html += self._processTagStack(depth)
+
+								if grouping == 'section':
+									section_reset = True 
+									self.lookup['section_depth'] = depth
+									self.lookup['section_counter'] += 1
+									self.lookup['table_rows'] = 0
+									self.section_bins = {}
+
+									html += self._sectionStart()
+
+									html += self._sectionFormStart()
+									self.todo.appendleft([depth,'_sectionFormEnd'])
+
+									self.todo.appendleft([depth,'_sectionEnd'])
+
+								elif grouping == 'table': 
+									
+									lastToDo = self.todo[0]
+									if lastToDo[1] == '_sectionEnd': #Just started a section
+										html += self._tableStart()
+										self.todo.appendleft([lastToDo[0]+1,'_tableEnd'])
+
+									html += self._tbodyHeader() + self._tbodyStart()
+									self.todo.appendleft([lastToDo[0]+2,'_tbodyEnd'])
+
+							field['valueOld'] = value
+
+						else:
+							
+							if grouping == 'column': self.rowdata.append(row[idx])
+
+					lastToDo = self.todo[0]
+					# No table level, instead going right from section to column field:
+					if lastToDo[1] == '_sectionEnd': 
+						html += self._tableStart() + self._tbodyStart()
+						self.todo.appendleft([lastToDo[0]+1,'_tableEnd'])
+						self.todo.appendleft([lastToDo[0]+2,'_tbodyEnd'])
+
+					self.lookup['row_bins'] = ",".join(row_bins)
+
+					fp_out.write(html)
+
+					self.lookup['table_rows'] += 1
+
+					# Now output table row of data:
+					fp_out.write( self._tableRow() )
+
+		
+			#Not initialized here, so just write created error notice.
+			else:
+
+				fp_out.write('<h3>' + self.errorNotice + '</body></html>')
+				
+			fp_out.write( self._processTagStack() )
+				
+		except IOError as e:
+			print 'Operation failed: %s' % e.strerror
+
+		fp_in.close()
+		fp_out.close()
+
+
+	############################### HTML REPORT PART TEMPLATES ############################## 
+	def _header(self, filename):
+
+		with open(os.path.join(os.path.dirname(__file__), filename), "r") as fphtml:
+			data = fphtml.read()
+		
+		return data
+		
+		
+	def _bodyStart(self):
+		# The form enables the creation of a dataset from selected entries.  It passes selections (based on a certain column's value) to the "Select tabular rows" tool, which then creates a dataset from the selected rows. 
+		with open(os.path.join(os.path.dirname(__file__), "html_selectable_report_tool_state.txt"), "r") as form_code_file:
+			self.lookup['form_state'] = form_code_file.readline().strip()
+		
+		html = """
+				<script>
+					// Toggle checkbox inputs of given table according to state of checkbox
+					function toggleInputs(mycheckbox, table) {
+						var checkboxes = table.getElementsByTagName('INPUT');
+						// Loop skips first toggler checkbox
+						for (var ptr = 1; ptr < checkboxes.length; ptr ++ ) {
+							checkboxes[ptr].checked = mycheckbox.checked;
+						}
+						return true; // prevents click processing
+					}
+					
+					//Drops hidden section id from form submission when no section items were selected
+					function formCheck() {
+						var tables = document.getElementsByTagName('TABLE');
+						for (var ptr = 0; ptr < tables.length; ptr ++) {
+							var inputs = tables[ptr].getElementsByTagName('INPUT');
+							var selected = 0;
+							// 1st item in table is select-all toggle
+							for (var ptr2 = 1; ptr2 < inputs.length; ptr2 ++) { 
+								if (inputs[ptr2].getAttribute('name') == 'select' && inputs[ptr2].checked) selected ++;
+							}
+							if (selected==0) {	
+								id = tables[ptr].getAttribute("id");
+								secInput = document.getElementById(id + '_start');
+								secInput.disabled = true;	
+								secInput.setAttribute('disabled','disabled');								
+								secInput.value='';								
+							}
+
+						}
+						return true;
+					}
+				</script>
+
+				<form id="tool_form" name="tool_form" action="../../../tool_runner"  target="galaxy_main" method="post" enctype="application/x-www-form-urlencoded">
+   					<input type="hidden" name="refresh" value="refresh"/>
+            		<input type="hidden" name="tool_id" value="bccdcSelectSubsets"/>
+                  	<input type="hidden" name="tool_state" value="%(form_state)s">
+					<input type="hidden" name="input" value="%(dataset_selection_id)s"/>			
+					<input type="hidden" name="incl_excl" value="1"/>
+		""" % self.lookup
+
+		if len(self.empty_queries):
+			qnames = ''
+			for name in self.empty_queries:	qnames += '<li>' + name + '</li>\n'
+			html += """
+			<div class="headerMessage">The following %s queries yielded 0 results (check filters): 
+				<ul>
+				%s
+				</ul>
+			</div>""" % (len(self.empty_queries), qnames)
+
+		return html % self.lookup
+
+	# Repeated for each grouped section table display
+	def _sectionStart(self):
+		self.lookup['select_row'] +=1
+		return """
+			<div class="section section_depth%(section_depth)s">
+				<div class="section_title">%(label)s: %(value)s</div>
+		""" % self.lookup 
+
+
+
+	def _sectionFormStart (self):
+		# This sets up the selection form with the minimal necessary parameters  # 
+		return """
+					<input type="checkbox" name="select" value="%(select_row)s" id="secId_%(select_row)s_start" checked="checked" style="display:none">
+					<input type="submit" class="btn btn-primary nonprintable" name="runtool_btn" value="Submit" onclick="formCheck()">
+			""" % self.lookup 
+
+
+	def _tableStart (self):
+
+		return """
+			<div class="checkUncheckAllPlaceholder"></div>
+			<table class="report" id="secId_%(select_row)s">
+				%(table_header)s
+		"""  % self.lookup
+
+
+	def _tableHeader(self):
+
+		colTags = ''
+		thTags = ''
+		firstColumnFlag = True
+		# Style numeric fields
+		for field in self.columns: 
+			if field['group'] == 'column': 
+				colTags += ('<col />' if field['type'] == 'text' else '<col class="numeric" />')
+				if firstColumnFlag == True:
+					thTags += '''<th>
+						<input type="checkbox" class="sectionCheckbox nonprintable" value="1"/>
+						''' + field['label'] + '</th>'
+					firstColumnFlag = False
+				else:
+					thTags += '<th>' + field['label'] + '</th>'
+
+		return """
+				<colgroup>
+					%s
+				</colgroup>
+				<thead class="top">
+					<tr>%s</tr>
+				</thead>""" % (colTags, thTags)
+
+	def _tbodyHeader (self):
+		if self.lookup['value'] == '': self.lookup['value'] = '(no match)'
+		return """	
+				<thead class="inside">
+					<tr>
+						<th colspan="%(column_count)s">%(label)s: %(value)s</th>
+					</tr>
+				</thead>""" % self.lookup
+
+	def _tbodyStart (self):
+		return """
+				<tbody>""" % self.lookup
+
+
+	def _tableRow(self):
+		self.lookup['select_row'] +=1
+
+		tdTags = ''
+		for (col, field) in enumerate(self.display_columns):
+			value =  self.rowdata[col]
+			self.lookup['value'] = value
+			self.lookup['cssClass'] = ' class="numeric"' if field['type'] == 'numeric' else ''
+			#See http://www.ncbi.nlm.nih.gov/books/NBK21091/table/ch18.T.refseq_accession_numbers_and_mole/?report=objectonly
+			#See http://www.ncbi.nlm.nih.gov/Sequin/acc.html
+			accessionID = re.search(r'[a-z]+[_]?[0-9]+(.[0-9]+)*' ,value, re.I)
+			if (accessionID) :
+				self.lookup['link'] = '<a href="https://google.com/#q=%s+gene" target="search">%s</a>' % (accessionID.group(), value)
+			else:
+				self.lookup['link'] = value
+			# First column optionally gets bin indicator as well as row checkbox selector 
+			if (col == 0):
+				tdTags += '<td%(cssClass)s><input type="checkbox" name="select" value="%(select_row)s" />%(link)s<span class="super">%(row_bins)s</span></td>' % self.lookup
+			else:
+				tdTags += '<td%(cssClass)s>%(value)s</td>' % self.lookup
+
+		return """\n\t\t\t<tr>%s</tr>""" % tdTags
+
+
+	def _tbodyEnd (self):
+		return """
+				</tbody>"""
+
+	def _tableEnd (self):
+		if len(self.section_bins):
+			bins = []
+			for key in sorted(self.section_bins):
+				bins.append( '<span class="super">(%s)</span>%s' % (key, self.section_bins[key]) )
+			self.lookup['section_bins'] = 'Bins: ' + ', '.join(bins)
+		else:
+			self.lookup['section_bins'] = ''
+
+		return """
+				<tfoot>
+					<tr>
+						<td colspan="%(column_count)s">
+							<div class="footerCenter">
+								%(filters)s. 
+							</div>
+							<div class="footerLeft">
+								<span class="rowViewer0"></span> %(table_rows)s results. 
+								<span class="rowViewer1 nonprintable"></span>
+								%(section_bins)s
+							</div> 
+							<div class="footerRight">
+								Report produced on %(timestamp)s
+							</div>
+
+						</td>
+					</tr>
+				</tfoot>
+			</table>""" % self.lookup
+
+	def _sectionFormEnd (self):
+		return """
+			
+		""" 
+
+	def _sectionEnd (self):
+		return """
+	
+		</div>"""
+
+
+	def _bodyEnd (self):
+
+		return """
+			</form>\n\t</body>\n</html>"""
+
+