diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/search_results.py | 33 | ||||
| -rw-r--r-- | wqflask/wqflask/static/packages/bootstrap/css/docs.css | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/search_result_page.html | 269 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 2 |
4 files changed, 106 insertions, 200 deletions
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index 8fc12b16..a2b0596c 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -182,6 +182,14 @@ class SearchResultPage(templatePage): 'GenbankId', 'UniGeneId', 'RefSeq_TranscriptId'] + self.header_fields = ['', + 'ID', + 'Symbol', + 'Description', + 'Location', + 'Mean Expr', + 'Max LRS', + 'Max LRS Location'] elif self.dataset.type == "Geno": self.search_fields = ['Name','Chr'] @@ -693,8 +701,7 @@ class SearchResultPage(templatePage): and ProbeSetXRef.ProbeSetFreezeId = %s """ % (self.db_conn.escape_string(search_term), self.db_conn.escape_string(str(self.dataset.id)))) - - print("query is:", query) + self.cursor.execute(query) #print("query is:", pf(self.query)) @@ -1252,19 +1259,25 @@ class SearchResultPage(templatePage): else: trait_location_value = ord(str(this_trait.chr).upper()[0])*1000 + this_trait.mb - trait_location_repr = 'Chr%s: %.6f' % (this_trait.chr, float(this_trait.mb) ) + trait_location_repr = 'Chr %s: %.4f Mb' % (this_trait.chr, float(this_trait.mb) ) this_trait.trait_location_repr = trait_location_repr #this_trait.trait_location_value = trait_location_value tr.append(TDCell(HT.TD(trait_location_repr, Class=className, nowrap="on"), trait_location_repr, trait_location_value)) #XZ, 01/12/08: This SQL query is much faster. - self.cursor.execute(""" - select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet - where ProbeSetXRef.ProbeSetFreezeId = %d and - ProbeSet.Id = ProbeSetXRef.ProbeSetId and - ProbeSet.Name = '%s' - """ % (this_trait.db.id, this_trait.name)) + query = ( +"""select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet + where ProbeSetXRef.ProbeSetFreezeId = %s and + ProbeSet.Id = ProbeSetXRef.ProbeSetId and + ProbeSet.Name = '%s' + """ % (self.db_conn.escape_string(str(this_trait.db.id)), + self.db_conn.escape_string(this_trait.name))) + + print("query is:", pf(query)) + + self.cursor.execute(query) result = self.cursor.fetchone() + if result: if result[0]: mean = result[0] @@ -1310,7 +1323,7 @@ class SearchResultPage(templatePage): this_trait.LRS_score_repr = LRS_score_repr = '%3.1f' % this_trait.lrs this_trait.LRS_score_value = LRS_score_value = this_trait.lrs - this_trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (LRS_Chr, float(LRS_Mb) ) + this_trait.LRS_location_repr = LRS_location_repr = 'Chr %s: %.4f Mb' % (LRS_Chr, float(LRS_Mb) ) LRS_flag = 0 #tr.append(TDCell(HT.TD(HT.Href(text=LRS_score_repr,url="javascript:showIntervalMapping('%s', '%s : %s')" % (formName, this_trait.db.shortname, this_trait.name), Class="fs12 fwn"), Class=className, align='right', nowrap="on"),LRS_score_repr, LRS_score_value)) diff --git a/wqflask/wqflask/static/packages/bootstrap/css/docs.css b/wqflask/wqflask/static/packages/bootstrap/css/docs.css index a6fff3c3..7efd72cd 100644 --- a/wqflask/wqflask/static/packages/bootstrap/css/docs.css +++ b/wqflask/wqflask/static/packages/bootstrap/css/docs.css @@ -560,7 +560,7 @@ h2 + .row { /* Echo out a label for the example */ .bs-docs-example:after { - content: "Example"; + content: "Results"; position: absolute; top: -1px; left: -1px; diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index 06458818..abf2dba7 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -2,195 +2,88 @@ {% block title %}Search Results{% endblock %} {% block content %} <!-- Start of body --> - <TR> - <TD bgColor=#eeeeee class="solidBorder"> - <Table width= "100%" cellSpacing=0 cellPadding=5> - <TR> - <TD valign="top" height="200" width="100%" bgcolor="#eeeeee"> - <P class="title">Search Results</P> - <BLOCKQUOTE>GeneNetwork searched: - <a href="/dbdoc/{{dataset.fullname}}">{{ dataset.fullname }}</a> - <br /> - - For all records that match: - <ul> - {% if search_terms %} - <li> - {% for word in search_terms %} - <strong>{{word.search_term}}</strong> {% if not loop.last %} or {% endif %} - {% endfor %} - </li> - {% endif %} - </ul> + <header class="jumbotron subhead" id="overview"> + <div class="container"> + <h1>Search Results</h1> + <p class="lead"> + GeneNetwork found {{ numify(results|count, "record", "records") }}. + </p> + </div> + </header> - <P>GeneNetwork found <strong>{{ numify(results|count, "record", "records") }}</strong>.</P> - - <P>To study a record, click on its ID below.</P> - - <P>To add one or more records to your Selection window, use the checkbox and then click the <STRONG>Add to Collection</STRONG> button.</P> - </BLOCKQUOTE> - <FORM METHOD="GET" ACTION="/search" ENCTYPE="multipart/form-data" NAME="show_trait"> - - <INPUT TYPE="hidden" NAME="database" VALUE="_"> - <INPUT TYPE="hidden" NAME="incparentsf1" VALUE="ON"> - <INPUT TYPE="hidden" NAME="FormID" VALUE="showDatabase"> - <INPUT TYPE="hidden" NAME="ProbeSetID" VALUE="_"> - <INPUT TYPE="hidden" NAME="RISet" VALUE="BXD"> - <INPUT TYPE="hidden" NAME="CellID" VALUE="_"> - <P> - <TABLE border="0" cellpadding="0" cellspacing="2" width="100%"> - <TR> - <TD> - <TABLE border="0" cellpadding="0" cellspacing="2" width="20%"> - <TR> - <TD width="25%"> - <A HREF="#" onClick="checkAll(document.getElementsByName('show_trait')[0]);"> - <IMG src="/images/select_all2_final.jpg" alt="Select All" name="selectall" style="border:none;" title="Select All"></A> - </TD> - <TD width="25%"> - <A HREF="#" onClick="checkNone(document.getElementsByName('show_trait')[0]);"> - <IMG src="/images/select_none2_final.jpg" alt="Select None" style="border:none;" title="Select None"> - </A> - </TD> - <TD width="25%"> - <A HREF="#" onClick="checkInvert(document.getElementsByName('show_trait')[0]);"> - <IMG src="/images/invert_selection2_final.jpg" alt="Invert Selection" name="selectinvert" style="border:none;" title="Invert Selection"> - </A> - </TD> - <TD width="25%"> - <A HREF="#"> - <IMG src="/images/add_collection1_final.jpg" alt="Add To Collection" name="addselect" style="border:none;" title="Add To Collection"> - </A> - </TD> - </TR> - <TR> - <TD width="25%"> Select</TD> - <TD width="255"> Deselect</TD> - <TD width="25%"> Invert</TD> - <TD width="25%"> Add</TD> - </TR></TABLE> - </TD> - </TR> - <TR> - <TD height="40"> - <INPUT TYPE="button" NAME="Default_Name" class="button" VALUE="Download Table" onClick="location.href='/tmp/Search_fYr7h2Hn.xls'"> - </TD> - </TR> - <TR> - <TD> - <DIV id="sortable"> - <TABLE class="collap b2" cellpadding="5" cellspacing="1"> - <TR> - <TD class="fs13 fwb ffl b1 cw cbrb" nowrap="ON"> - </TD> - <TD class="fs13 fwb ffl b1 cw cbrb"> - Record - <BR>ID<BR> - <DIV style="float: bottom;"> - <A HREF="javascript:xmlhttpPost('/webqtl/main.py?FormID=AJAX_table', 'sortable', 'sort=record_id&order=up&file=Search_fYr7h2Hn&tableID=sortable&addIndex=1&hiddenColumns=')"> - <IMG src="/images/sortup.gif" alt="sortup.gif" border="0"> - </A> - <A HREF="javascript:xmlhttpPost('/webqtl/main.py?FormID=AJAX_table', 'sortable', 'sort=record_id&order=down&file=Search_fYr7h2Hn&tableID=sortable&addIndex=1&hiddenColumns=')"> - <IMG src="/images/sortdown.gif" alt="sortdown.gif" border="0"> - </A> - </DIV> - </TD> - <TD class="fs13 fwb ffl b1 cw cbrb"> - Symbol<BR><BR> - <DIV style="float: bottom;"> - <IMG src="/images/sortupon.gif" alt="sortupon.gif" border="0"> - <A HREF="javascript:xmlhttpPost('/webqtl/main.py?FormID=AJAX_table', 'sortable', 'sort=symbol&order=down&file=Search_fYr7h2Hn&tableID=sortable&addIndex=1&hiddenColumns=')"> - <IMG src="/images/sortdown.gif" alt="sortdown.gif" border="0"> - </A> - </DIV> - </TD> - <TD class="fs13 fwb ffl b1 cw cbrb"> - Description<BR><BR> - <DIV style="float: bottom;"> - <A HREF="javascript:xmlhttpPost('/webqtl/main.py?FormID=AJAX_table', 'sortable', 'sort=desc&order=up&file=Search_fYr7h2Hn&tableID=sortable&addIndex=1&hiddenColumns=')"> - <IMG src="/images/sortup.gif" alt="sortup.gif" border="0"> - </A> - <A HREF="javascript:xmlhttpPost('/webqtl/main.py?FormID=AJAX_table', 'sortable', 'sort=desc&order=down&file=Search_fYr7h2Hn&tableID=sortable&addIndex=1&hiddenColumns=')"> - <IMG src="/images/sortdown.gif" alt="sortdown.gif" border="0"> - </A> - </DIV> - </TD> - <TD class="fs13 fwb ffl b1 cw cbrb">Location<BR>Chr and Mb<BR> - <DIV style="float: bottom;"> - <A HREF="javascript:xmlhttpPost('/webqtl/main.py?FormID=AJAX_table', 'sortable', 'sort=location&order=up&file=Search_fYr7h2Hn&tableID=sortable&addIndex=1&hiddenColumns=')"> - <IMG src="/images/sortup.gif" alt="sortup.gif" border="0"> - </A> - <A HREF="javascript:xmlhttpPost('/webqtl/main.py?FormID=AJAX_table', 'sortable', 'sort=location&order=down&file=Search_fYr7h2Hn&tableID=sortable&addIndex=1&hiddenColumns=')"> - <IMG src="/images/sortdown.gif" alt="sortdown.gif" border="0"> - </A> - </DIV> - </TD> - <TD class="fs13 fwb ffl b1 cw cbrb">Mean<BR>Expr<BR> - <DIV style="float: bottom;"> - <A HREF="javascript:xmlhttpPost('/webqtl/main.py?FormID=AJAX_table', 'sortable', 'sort=mean&order=up&file=Search_fYr7h2Hn&tableID=sortable&addIndex=1&hiddenColumns=')"> - <IMG src="/images/sortup.gif" alt="sortup.gif" border="0"> - </A> - <A HREF="javascript:xmlhttpPost('/webqtl/main.py?FormID=AJAX_table', 'sortable', 'sort=mean&order=down&file=Search_fYr7h2Hn&tableID=sortable&addIndex=1&hiddenColumns=')"> - <IMG src="/images/sortdown.gif" alt="sortdown.gif" border="0"> - </A> - </DIV> - </TD> - <TD class="fs13 fwb ffl b1 cw cbrb" nowrap="ON">Max<BR>LRS<BR> - <DIV style="float: bottom;"> - <A HREF="javascript:xmlhttpPost('/webqtl/main.py?FormID=AJAX_table', 'sortable', 'sort=lrs&order=up&file=Search_fYr7h2Hn&tableID=sortable&addIndex=1&hiddenColumns=')"> - <IMG src="/images/sortup.gif" alt="sortup.gif" border="0"> - </A> - <A HREF="javascript:xmlhttpPost('/webqtl/main.py?FormID=AJAX_table', 'sortable', 'sort=lrs&order=down&file=Search_fYr7h2Hn&tableID=sortable&addIndex=1&hiddenColumns=')"> - <IMG src="/images/sortdown.gif" alt="sortdown.gif" border="0"> - </A> - </DIV> - </TD> - <TD class="fs13 fwb ffl b1 cw cbrb" nowrap="ON">Max LRS Location<BR>Chr and Mb<BR> - <DIV style="float: bottom;"> - <A HREF="javascript:xmlhttpPost('/webqtl/main.py?FormID=AJAX_table', 'sortable', 'sort=lrs_location&order=up&file=Search_fYr7h2Hn&tableID=sortable&addIndex=1&hiddenColumns=')"> - <IMG src="/images/sortup.gif" alt="sortup.gif" border="0"> - </A> - <A HREF="javascript:xmlhttpPost('/webqtl/main.py?FormID=AJAX_table', 'sortable', 'sort=lrs_location&order=down&file=Search_fYr7h2Hn&tableID=sortable&addIndex=1&hiddenColumns=')"> - <IMG src="/images/sortdown.gif" alt="sortdown.gif" border="0"> - </A> - </DIV> - </TD> - </TR> - {% for this_trait in trait_list %} - <TR id="{{ this_trait }}"> - <TD class="fs12 fwn ffl b1 c222" nowrap="on">{{ loop.index }} - <INPUT TYPE="checkbox" NAME="searchResult" class="checkbox" VALUE="{{ this_trait }}" onClick="highlight(this)"> - </TD> - <TD class="stdcell"> - {# <A HREF="javascript:showDatabase3('{{ thisFormName }}','{{this_trait.db.name}}','{{ this_trait.name }}','{{ this_trait.cellid }}')" class="fs12 fwn"> - </a> #} - <a href="{{ url_for('show_trait_page', database=this_trait.db.name, ProbeSetID=this_trait.name, incparentsf1='ON', RISet='BXD')}}" class="fs12 fwn"> - {{ this_trait.name.upper() }} - </a> - </TD> - <TD class="fs12 fwn b1 c222 fsI"> - <A HREF="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids={{this_trait.geneid}}" TARGET="_blank" class="font_black fs12 fwn"> - {{ this_trait.symbol }} - </A> - </TD> - <TD class="stdcell">{{ this_trait.description_display }}</TD> - <TD class="stdcell" nowrap="on">{{ this_trait.trait_location_repr }}</TD> - <TD class="stdcell" nowrap="ON" align="right">{{ this_trait.mean }}</TD> - <TD class="stdcell" nowrap="on" align="right">{{ this_trait.LRS_score_repr }}</TD> - <TD class="stdcell" nowrap="on">{{ this_trait.LRS_location_repr }}</TD> - </TR> - {% endfor %} - </TABLE> - </DIV> - </TD> - </TR> - </TABLE> - <INPUT TYPE="hidden" NAME="Default_Name"> - </FORM> - </TD> - </TR> - </TABLE> - </TD> - </TR> + <div class="container"> + <div class="page-header"> + <h1>Your Search</h1> + </div> + + <p>We searched <a href="/dbdoc/{{dataset.fullname}}">{{ dataset.fullname }}</a><//> + + <p>To find all records that match:</p> + <ul> + {% if search_terms %} + <li> + {% for word in search_terms %} + <strong>{{word.search_term}}</strong> {% if not loop.last %} or {% endif %} + {% endfor %} + </li> + {% endif %} + </ul> + + <p>To study a record, click on its ID below.<br /> + Check records below and click Add button to add to selection.</p> + + <div class="bs-docs-example"> + <table class="table table-hover"> + <thead> + <tr> + {% for header in header_fields %} + <th>{{header}}</th> + {% endfor %} + </thead> + + <tbody> + {% for this_trait in trait_list %} + <TR id="{{ this_trait }}"> + <TD> + <INPUT TYPE="checkbox" NAME="searchResult" class="checkbox" + VALUE="{{ this_trait }}"> + </TD> + <TD> + <a href="{{ url_for('show_trait_page', + database=this_trait.db.name, + ProbeSetID=this_trait.name, incparentsf1='ON', + RISet='BXD')}}"> + {{ this_trait.name.upper() }} + </a> + </TD> + <TD> + <A HREF= + "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids={{this_trait.geneid}}" TARGET="_blank"> + {{ this_trait.symbol }} + </A> + </TD> + <TD>{{ this_trait.description_display }}</TD> + <TD>{{ this_trait.trait_location_repr }}</TD> + <TD>{{ this_trait.mean }}</TD> + <TD>{{ this_trait.LRS_score_repr }}</TD> + <TD>{{ this_trait.LRS_location_repr }}</TD> + </TR> + {% endfor %} + </tbody> + + </table> + + <br /> + + <button class="btn"><i class="icon-ok"></i> Select</button> + <button class="btn"><i class="icon-remove"></i> Deselect</button> + <button class="btn"><i class="icon-resize-vertical"></i> Invert</button> + <button class="btn"><i class="icon-plus-sign"></i> Add</button> + <button class="btn btn-primary pull-right"><i class="icon-download icon-white"></i> Download Table</button> + </div> + + </div> + <!-- End of body --> {% endblock %} diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index dd95f7ca..41d1d714 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -64,7 +64,7 @@ def search_page(): print("calling search_results.SearchResultPage") the_search = search_results.SearchResultPage(request.args) print("template_vars is:", pf(the_search.__dict__)) - print("trait_list is:", pf(the_search.__dict__['trait_list'][0].__dict__)) + #print("trait_list is:", pf(the_search.__dict__['trait_list'][0].__dict__)) return render_template("search_result_page.html", **the_search.__dict__) |