Further UI improvements

d1c0f578 · Peter Eastman · 3515f0da · d1c0f578 · d1c0f578 · d1c0f578
Commit d1c0f578 authored Sep 06, 2013 by Peter Eastman
11 changed files
--- a/html/addHeavyAtoms.html
+++ b/html/addHeavyAtoms.html
-<html>
-<head><title>PDB Fixer</title></head>
-<body>
 The following residues are missing heavy atoms, which will be added.
 <p>
 <form method="post" action="/">
@@ -11,5 +8,8 @@ The following residues are missing heavy atoms, which will be added.
 <p>
 <input type="submit" value="Continue"/>
 </form>
+<script>
+setCurrentStep(5)
+</script>
 </body>
 <html>
--- a/html/addHydrogens.html
+++ b/html/addHydrogens.html
-<html>
-<head><title>PDB Fixer</title>
 <script>
 function validateForm() {
    if (document.getElementById("addCheckbox").checked) {
@@ -11,8 +9,6 @@ function validateForm() {
    }
 }
 </script>
-</head>
-<body>
 Add missing hydrogen atoms?
 <p>
 <form method="post" action="/" onsubmit="return validateForm()">
@@ -20,5 +16,8 @@ Add missing hydrogen atoms?
 <p>
 <input type="submit" value="Continue"/>
 </form>
+<script>
+setCurrentStep(6)
+</script>
 </body>
 <html>
\ No newline at end of file
--- a/html/addResidues.html
+++ b/html/addResidues.html
-<html>
-<head>
-<title>PDB Fixer</title>
-<script>
-function setCheckboxes(selected) {
-    checkboxes = document.getElementById("table").getElementsByTagName("input");
-    for (var i = 0; i < checkboxes.length; i++)
-        checkboxes[i].checked = selected
-}
-</script>
-</head>
-<body>
 The SEQRES records in this PDB file include residues that are missing from the atom data section.  Do you want to add the missing residues?
 <p>
 <form method="post" action="/">
@@ -21,5 +9,8 @@ The SEQRES records in this PDB file include residues that are missing from the a
 <p>
 <input type="submit" value="Continue"/>
 </form>
+<script>
+setCurrentStep(3)
+</script>
 </body>
 <html>
--- a/html/convertResidues.html
+++ b/html/convertResidues.html
-<html>
-<head>
-<title>PDB Fixer</title>
-<script>
-function setCheckboxes(selected) {
-    checkboxes = document.getElementById("table").getElementsByTagName("input");
-    for (var i = 0; i < checkboxes.length; i++)
-        checkboxes[i].checked = selected
-}
-</script>
-</head>
-<body>
 This PDB file contains non-standard residues.  Do you want to convert them to the corresponding standard residues?
 <p>
 <form method="post" action="/">
@@ -21,5 +9,8 @@ This PDB file contains non-standard residues.  Do you want to convert them to th
 <p>
 <input type="submit" value="Continue"/>
 </form>
+<script>
+setCurrentStep(4)
+</script>
 </body>
 <html>
\ No newline at end of file
--- a/html/header.html
+++ b/html/header.html
+<html>
+<head>
+<title>PDBFixer</title>
+<script>
+function setCurrentStep(step) {
+    for (var i = 1; i < step; i++)
+        document.getElementById("step"+i).style.color="black"
+    document.getElementById("step"+step).style.color="red"
+    for (var i = step+1; i < 8; i++)
+        document.getElementById("step"+i).style.color="gray"
+    if (step == 1)
+        document.getElementById("newfile").disabled=true
+}
+function setCheckboxes(selected) {
+    checkboxes = document.getElementById("table").getElementsByTagName("input");
+    for (var i = 0; i < checkboxes.length; i++)
+        checkboxes[i].checked = selected
+}
+</script>
+</head>
+<body>
+<div style="background-color:LightSkyBlue;font-style:italic;font-size:xx-large;text-align:center">PDBFixer</div>
+<span style="background-color:LightSkyBlue;font-style:italic;font-size:large;float:right;height:100%;padding:0px 10px">
+    <form method="post" action="/controls">
+        <input type="submit" name="newfile" value="New File" id="newfile"/>
+        <input type="submit" name="quit" value="Quit" style="float:right"/>
+    </form>
+    <p id="step1">Load File</p>
+    <p id="step2">Select Chains</p>
+    <p id="step3">Add Residues</p>
+    <p id="step4">Convert Residues</p>
+    <p id="step5">Add Heavy Atoms</p>
+    <p id="step6">Add Hydrogens</p>
+    <p id="step7">Save File</p>
+</span>
+<p/>
\ No newline at end of file
--- a/html/quit.html
+++ b/html/quit.html
+<html>
+<head>
+<title>PDBFixer</title>
+</head>
+<body>
+<h1 style="text-align:center">See You Again Soon!</h1>
+PDBFixer has exited.  You can close your browser window.
+</body>
+</html>
\ No newline at end of file
--- a/html/removeChains.html
+++ b/html/removeChains.html
-<html>
-<head>
-<title>PDB Fixer</title>
-<script>
-function setCheckboxes(selected) {
-    checkboxes = document.getElementById("table").getElementsByTagName("input");
-    for (var i = 0; i < checkboxes.length; i++)
-        checkboxes[i].checked = selected
-}
-</script>
-</head>
-<body>
 This PDB file contains %d chains.  Select which ones to include.
 <p>
 <form method="post" action="/">
@@ -21,5 +9,8 @@ This PDB file contains %d chains.  Select which ones to include.
 <p>
 <input type="submit" value="Continue"/>
 </form>
+<script>
+setCurrentStep(2)
+</script>
 </body>
 <html>
\ No newline at end of file
--- a/html/saveFile.html
+++ b/html/saveFile.html
-<html>
-<head><title>PDB Fixer</title></head>
-<body>
 The fixed PDB file is ready to save.
 <p>
 <form method="post" action="/">
 <input type="submit" name="save" value="Save File"/>
 <input type="submit" name="newfile" value="Process Another File"/>
 </form>
+<script>
+setCurrentStep(7)
+</script>
 </body>
 <html>
--- a/html/start.html
+++ b/html/start.html
-<html>
-<head><title>PDBFixer</title></head>
-<body>
 <h1>Welcome To PDBFixer!</h1>
 Select a PDB file to load.  It will be analyzed for problems.
 <p>
@@ -9,5 +6,8 @@ PDB File: <input type="file" name="pdbfile" onchange="document.getElementById('s
 <p>
 <input type="submit" id="submit" value="Analyze File" disabled/>
 </form>
+<script>
+setCurrentStep(1)
+</script>
 </body>
 </html>
--- a/ui.py
+++ b/ui.py
@@ -11,6 +11,13 @@ def loadHtmlFile(name):
    file = os.path.join(htmlPath, name)
    return open(file).read()
+def controlsCallback(parameters, handler):
+    if 'newfile' in parameters:
+        displayStartPage()
+    if 'quit' in parameters:
+        handler.sendResponse(loadHtmlFile("quit.html"))
+        uiserver.server.shutdown()
 def startPageCallback(parameters, handler):
    if 'pdbfile' in parameters:
        global fixer
@@ -56,7 +63,7 @@ def saveFilePageCallback(parameters, handler):
 def displayStartPage():
    uiserver.setCallback(startPageCallback)
-    uiserver.setContent(loadHtmlFile("start.html"))
+    uiserver.setContent(header+loadHtmlFile("start.html"))
 def displayDeleteChainsPage():
    uiserver.setCallback(deleteChainsPageCallback)
@@ -79,7 +86,7 @@ def displayDeleteChainsPage():
        else:
            content = ', '.join(set(residues))
        table += '    <tr><td>%d</td><td>%d</td><td>%s</td><td><input type="checkbox" name="include%d" checked></td></tr>\n' % (chain.index+1, len(residues), content, i)
-    uiserver.setContent(loadHtmlFile("removeChains.html") % (numChains, table))
+    uiserver.setContent(header+loadHtmlFile("removeChains.html") % (numChains, table))
 def displayAddResiduesPage():
    uiserver.setCallback(addResiduesPageCallback)
@@ -91,7 +98,7 @@ def displayAddResiduesPage():
    for i, key in enumerate(sorted(fixer.missingResidues)):
        residues = fixer.missingResidues[key]
        table += '    <tr><td>%d</td><td>%d to %d</td><td>%s</td><td><input type="checkbox" name="add%d" checked></td></tr>\n' % (key[0]+1, key[1]+1, key[1]+len(residues), ', '.join(residues), i)
-    uiserver.setContent(loadHtmlFile("addResidues.html") % table)
+    uiserver.setContent(header+loadHtmlFile("addResidues.html") % table)
 def displayConvertResiduesPage():
    uiserver.setCallback(convertResiduesPageCallback)
@@ -106,7 +113,7 @@ def displayConvertResiduesPage():
    table = ""
    for i, residue in enumerate(fixer.nonstandardResidues):
        table += '    <tr><td>%d</td><td>%s %d</td><td>%s</td><td><input type="checkbox" name="convert%d" checked></td></tr>\n' % (residue.chain.index+1, residue.name, indexInChain[residue], substitutions[residue.name], i)
-    uiserver.setContent(loadHtmlFile("convertResidues.html") % table)
+    uiserver.setContent(header+loadHtmlFile("convertResidues.html") % table)
 def displayMissingAtomsPage():
    uiserver.setCallback(missingAtomsPageCallback)
@@ -128,17 +135,20 @@ def displayMissingAtomsPage():
        if residue in fixer.missingTerminals:
            atoms.extend(atom for atom in fixer.missingTerminals[residue])
        table += '    <tr><td>%d</td><td>%s %d</td><td>%s</td></tr>\n' % (residue.chain.index+1, residue.name, indexInChain[residue], ', '.join(atoms))
-    uiserver.setContent(loadHtmlFile("addHeavyAtoms.html")% table)
+    uiserver.setContent(header+loadHtmlFile("addHeavyAtoms.html")% table)
 def displayAddHydrogensPage():
    uiserver.setCallback(addHydrogensPageCallback)
-    uiserver.setContent(loadHtmlFile("addHydrogens.html"))
+    uiserver.setContent(header+loadHtmlFile("addHydrogens.html"))
 def displaySaveFilePage():
    uiserver.setCallback(saveFilePageCallback)
-    uiserver.setContent(loadHtmlFile("saveFile.html"))
+    uiserver.setContent(header+loadHtmlFile("saveFile.html"))
 def launchUI():
+    global header
+    header = loadHtmlFile("header.html")
    uiserver.beginServing()
+    uiserver.setCallback(controlsCallback, "/controls")
    displayStartPage()
    webbrowser.open('http://localhost:'+str(uiserver.server.server_address[1]))
\ No newline at end of file
--- a/uiserver.py
+++ b/uiserver.py
@@ -13,25 +13,34 @@ class _Handler(BaseHTTPRequestHandler):
                parameters = parse_qs(self.path[queryStart+1:])
            else:
                parameters = {}
-            result = callback(parameters, self)
+            self.invokeCallback(parameters)
        if not self.hasSentResponse:
            self.sendResponse(content)
    def do_POST(self):
        self.hasSentResponse = False
-        if callback is not None:
+        parameters = cgi.FieldStorage(fp=self.rfile, headers=self.headers, environ={'REQUEST_METHOD':'POST', 'CONTENT_TYPE':self.headers['Content-Type']})
-            parameters = cgi.FieldStorage(fp=self.rfile, headers=self.headers, environ={'REQUEST_METHOD':'POST', 'CONTENT_TYPE':self.headers['Content-Type']})
+        self.invokeCallback(parameters)
-            callback(parameters, self)
        if not self.hasSentResponse:
            self.sendResponse(content)
+    def log_message(self, format, *args):
+        return
+    def invokeCallback(self, parameters):
+        path = self.path
+        if '?' in path:
+            path = path[:path.find('?')]
+        if path in callback:
+            callback[path](parameters, self)
    def sendResponse(self, response):
        self.hasSentResponse = True
        self.send_response(200)
        self.send_header("Content-type", "text/html")
-        self.send_header("Content-length", str(len(content)))
+        self.send_header("Content-length", str(len(response)))
        self.end_headers()
-        self.wfile.write(content)
+        self.wfile.write(response)
    def sendDownload(self, download, filename):
        self.hasSentResponse = True
@@ -46,7 +55,7 @@ class _ThreadingHTTPServer(ThreadingMixIn, HTTPServer):
    pass
 content = ""
-callback = None
+callback = {}
 server = _ThreadingHTTPServer(("localhost", 8000), _Handler)
 def beginServing():
@@ -56,7 +65,6 @@ def setContent(newContent):
    global content
    content = newContent
-def setCallback(newCallback):
+def setCallback(newCallback, path="/"):
    global callback
-    callback = newCallback
+    callback[path] = newCallback