| Previous changeset 15:648b3b7437da (2014-05-12) Next changeset 17:8e61627a87f1 (2014-05-13) |
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Commit message:
fix validation, reindent |
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modified:
blast_html.html.jinja blast_html.py |
| b |
| diff -r 648b3b7437da -r db7e4ee3be03 blast_html.html.jinja --- a/blast_html.html.jinja Mon May 12 17:33:08 2014 +0200 +++ b/blast_html.html.jinja Tue May 13 12:22:35 2014 +0200 |
| [ |
| b'@@ -4,10 +4,10 @@\n <meta charset="UTF-8">\n \n <title>Blast output</title>\n-\n+ \n <style>\n body {\n- color: #33333;\n+ color: #333333;\n font-family: Arial,Sans-Serif;\n }\n \n@@ -86,20 +86,18 @@\n \n \n \n+ .graphics .grey {\n+ text-align: center;\n+ }\n+\n .graphic {\n background-color: white;\n border: 2px solid black;\n padding: .5em 1.5em;\n- align: center;\n margin: auto;\n }\n \n- #graphics .grey {\n- text-align: center;\n- }\n-\n .centered, #defline, div.legend, div.tablewrapper {\n- align: center;\n margin-left: auto;\n margin-right: auto;\n }\n@@ -250,7 +248,7 @@\n }\n \n .title .hittitle {\n- color: #22222;\n+ color: #222222;\n margin-bottom: .3em;\n }\n .title .titleinfo {\n@@ -331,11 +329,11 @@\n \n <script type="text/javascript">\n function toggle_visibility(id) {\n-\t var e = document.getElementById(id);\n-\t if(e.style.display != \'block\')\n-\t e.style.display = \'block\';\n-\t else\n-\t e.style.display = \'none\';\n+ var e = document.getElementById(id);\n+ if(e.style.display != \'block\')\n+ e.style.display = \'block\';\n+ else\n+ e.style.display = \'none\';\n }\n </script>\n \n@@ -346,29 +344,29 @@\n <div id=content>\n <h1>Nucleotide Sequence ({{length}} letters)</h1>\n \n- <div id=header>\n+ <div class=header>\n \n <table class=headerdata>\n {% for param, value in params %}\n <tr><td class=param>{{param}}:</td><td>{{value}}</td></tr>\n {% endfor %}\n </table>\n- \n+ \n </div>\n \n {% if not (blast.BlastOutput_iterations.findall(\'Iteration\') and\n blast.BlastOutput_iterations.Iteration.Iteration_hits.findall(\'Hit\')) %}\n- <div id=nodata>\n-\t<h2>No Results</h2>\n-\t<div class=grey>\n-\t No Matches\n-\t</div>\n+ <div class=nodata>\n+ <h2>No Results</h2>\n+ <div class=grey>\n+ No Matches\n+ </div>\n </div>\n {% else %}\n \n \n \n- <div id=graphics>\n+ <div class=graphics>\n <h2>Graphic Summary</h2>\n \n <div class=grey>\n@@ -378,41 +376,40 @@\n \n <div class=graphic>\n <h4 class=darkHeader>Color key for alignment scores</h4>\n-\t <div class=legend><div class=graphicrow>\n-\t\t<div class=graphicitem style="background-color: {{colors[0]}}"><40</div>\n-\t\t<div class=graphicitem style="background-color: {{colors[1]}}">40\xe2\x80\x9350</div>\n-\t\t<div class=graphicitem style="background-color: {{colors[2]}}">50\xe2\x80\x9380</div>\n-\t\t<div class=graphicitem style="background-color: {{colors[3]}}">80\xe2\x80\x93200</div>\n-\t\t<div class=graphicitem style="background-color: {{colors[4]}}">200\xe2\x89\xa4</div>\n+ <div class=legend><div class=graphicrow>\n+ <div class=graphicitem style="background-color: {{colors[0]}}"><40</div>\n+ <div class=graphicitem style="background-color: {{colors[1]}}">40\xe2\x80\x9350</div>\n+ <div class=graphicitem style="background-color: {{colors[2]}}">50\xe2\x80\x9380</div>\n+ <div class=graphicitem style="background-color: {{colors[3]}}">80\xe2\x80\x93200</div>\n+ <div class=graphicitem style="background-color: {{colors[4]}}">200\xe2\x89\xa4</div>\n </div></div>\n-\t <div style="clear: left"></div>\n+ <div style="clear: left"></div>\n \n <div class=tablewrapper>\n \n <div class=scale>\n <div>query:</div>\n-\t\t<div class=graphicrow>\n- {% for s in queryscale %}\n- <div class=graphicitem\n-\t\t\t style="width: {{s.width|safe}}%">\n-\t\t <div>{{s.label|safe}}</div>\n-\t\t </div>\n- {% endfor %}\n-\t\t</div>\n-\t\t<div style="clear: left"></div>\n+ <div class=graphicrow>\n+ {% for s in queryscale %}\n+ <div class=graphicitem style="width: {{s.width}}%">\n+ '..b'<a class=showmoretitles onclick="toggle_visibility(\'moretitles{{hit.Hit_num}}\'); return false;" href=\'\'>\n-\t\tSee {{hit|othertitles|length}} more title(s)\n-\t </a>\n+ {% if hit|othertitles|length %}\n+ <a class=showmoretitles onclick="toggle_visibility(\'moretitles{{hit.Hit_num|js_string_escape}}\'); return false;" href=\'\'>\n+ See {{hit|othertitles|length}} more title(s)\n+ </a>\n \n-\t <div class=moretitles id=moretitles{{hit.Hit_num}} style="display: none">\n-\t\t{% for title in hit|othertitles %}\n-\t\t<div class=title>\n-\t\t <p class=hittitle>{{title.title}}</p>\n-\t\t <p class=titleinfo>\n-\t\t <span class=b>Sequence ID:</span> <a href="{{genelink(title.hitid)}}">{{title.id}}</a>\n-\t\t </p>\n-\t\t</div>\n-\t\t{% endfor %}\n-\t </div>\n-\t {% endif %}\n+ <div class=moretitles id=moretitles{{hit.Hit_num}} style="display: none">\n+ {% for title in hit|othertitles %}\n+ <div class=title>\n+ <p class=hittitle>{{title.title}}</p>\n+ <p class=titleinfo>\n+ <span class=b>Sequence ID:</span> <a href="{{genelink(title.hitid)}}">{{title.id}}</a>\n+ </p>\n+ </div>\n+ {% endfor %}\n+ </div>\n+ {% endif %}\n \n-\t {% for hsp in hit.Hit_hsps.Hsp %}\n-\t <div class=hotspot>\n-\t\t<p class=range>\n-\t\t <span class=range>Range {{hsp.Hsp_num}}: {{hsp[\'Hsp_hit-from\']}} to {{hsp[\'Hsp_hit-to\']}}</span>\n-\t\t <a class=range href="{{genelink(hit|hitid, \'genbank\', hsp)}}">GenBank</a>\n-\t\t <a class=range href="{{genelink(hit|hitid, \'graph\', hsp)}}">Graphics</a>\n-\t\t</p>\n+ {% for hsp in hit.Hit_hsps.Hsp %}\n+ <div class=hotspot>\n+ <p class=range>\n+ <span class=range>Range {{hsp.Hsp_num}}: {{hsp[\'Hsp_hit-from\']}} to {{hsp[\'Hsp_hit-to\']}}</span>\n+ <a class=range href="{{genelink(hit|hitid, \'genbank\', hsp)}}">GenBank</a>\n+ <a class=range href="{{genelink(hit|hitid, \'graph\', hsp)}}">Graphics</a>\n+ </p>\n \n-\t\t<table class=hotspotstable>\n-\t\t <tr>\n-\t\t <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>\n-\t\t </tr>\n-\t\t <tr>\n-\t\t <td>{{hsp[\'Hsp_bit-score\']|fmt(\'.1f\')}} bits({{hsp.Hsp_score}})</td>\n-\t\t <td>{{hsp.Hsp_evalue|fmt(\'.1f\')}}</td>\n-\t\t <td>{{ hsp.Hsp_identity }}/{{ hsp|len }}({{\n-\t\t (hsp.Hsp_identity/hsp|len) |fmt(\'.0%\') }})</td>\n-\t\t <td>{{ hsp.Hsp_gaps }}/{{ hsp|len\n-\t\t }}({{ (hsp.Hsp_gaps / hsp|len) | fmt(\'.0%\') }})</td>\n-\t\t <td>{{ hsp[\'Hsp_query-frame\']|asframe }}/{{ hsp[\'Hsp_hit-frame\']|asframe }}</td>\n-\t\t </tr>\n-\t\t</table>\n+ <table class=hotspotstable>\n+ <tr>\n+ <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>\n+ </tr>\n+ <tr>\n+ <td>{{hsp[\'Hsp_bit-score\']|fmt(\'.1f\')}} bits({{hsp.Hsp_score}})</td>\n+ <td>{{hsp.Hsp_evalue|fmt(\'.1f\')}}</td>\n+ <td>{{ hsp.Hsp_identity }}/{{ hsp|len }}({{\n+ (hsp.Hsp_identity/hsp|len) |fmt(\'.0%\') }})</td>\n+ <td>{{ hsp.Hsp_gaps }}/{{ hsp|len\n+ }}({{ (hsp.Hsp_gaps / hsp|len) | fmt(\'.0%\') }})</td>\n+ <td>{{ hsp[\'Hsp_query-frame\']|asframe }}/{{ hsp[\'Hsp_hit-frame\']|asframe }}</td>\n+ </tr>\n+ </table>\n \n-\t\t<pre class=alignmentgraphic>{{hsp|alignment_pre}}</pre>\n-\t </div>\n-\t {% endfor %}\n-\t \n-\t </div>\n+ <pre class=alignmentgraphic>{{hsp|alignment_pre}}</pre>\n+ </div>\n+ {% endfor %}\n+ \n+ </div>\n \n-\t {% endfor %}\n-\t</div></div>\n+ {% endfor %}\n+ </div></div>\n </div>\n \n {% endif %}\n@@ -540,3 +537,9 @@\n </body>\n </html>\n \n+{#\n+Local Variables:\n+tab-width: 2\n+indent-tabs-mode: nil\n+End:\n+#}\n' |
| b |
| diff -r 648b3b7437da -r db7e4ee3be03 blast_html.py --- a/blast_html.py Mon May 12 17:33:08 2014 +0200 +++ b/blast_html.py Tue May 13 12:22:35 2014 +0200 |
| [ |
| @@ -94,8 +94,44 @@ link = "http://www.ncbi.nlm.nih.gov/nucleotide/{}?report={}&log$=nuclalign".format(hit, type) if hsp != None: link += "&from={}&to={}".format(hsp['Hsp_hit-from'], hsp['Hsp_hit-to']) - return jinja2.Markup(link) + return link + + +# javascript escape filter based on Django's, from https://github.com/dsissitka/khan-website/blob/master/templatefilters.py#L112-139 +# I've removed the html escapes, since html escaping is already being performed by the template engine. +_base_js_escapes = ( + ('\\', r'\u005C'), + ('\'', r'\u0027'), + ('"', r'\u0022'), + # ('>', r'\u003E'), + # ('<', r'\u003C'), + # ('&', r'\u0026'), + # ('=', r'\u003D'), + # ('-', r'\u002D'), + # (';', r'\u003B'), + # (u'\u2028', r'\u2028'), + # (u'\u2029', r'\u2029') +) + +# Escape every ASCII character with a value less than 32. This is +# needed a.o. to prevent parsers from jumping out of javascript +# parsing mode. +_js_escapes = (_base_js_escapes + + tuple(('%c' % z, '\\u%04X' % z) for z in range(32))) + +@filter +def js_string_escape(value): + """Escape javascript string literal escapes. Note that this only works + within javascript string literals, not in general javascript + snippets.""" + + value = str(value) + + for bad, good in _js_escapes: + value = value.replace(bad, good) + + return value @@ -175,10 +211,10 @@ if table[i] == last: count += 1 continue - matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'none')) + matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'transparent')) last = table[i] count = 1 - matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'none')) + matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'transparent')) yield dict(colors=matches, link="#hit"+hit.Hit_num.text, defline=firsttitle(hit)) |