From ad73c7d39d93683aba1b065b6660c4b5a98554bf Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 17 Mar 2017 22:53:07 -0400
Subject: [PATCH] Remove mako

---
 templates/user/dbkeys.mako | 249 -------------------------------------
 1 file changed, 249 deletions(-)
 delete mode 100644 templates/user/dbkeys.mako

diff --git a/templates/user/dbkeys.mako b/templates/user/dbkeys.mako
deleted file mode 100644
index e331a07ae28..00000000000
--- a/templates/user/dbkeys.mako
+++ /dev/null
@@ -1,249 +0,0 @@
-<%!
-    def inherit(context):
-        if context.get('use_panels'):
-            return '/webapps/galaxy/base_panels.mako'
-        else:
-            return '/base.mako'
-%>
-<%inherit file="${inherit(context)}"/>
-
-<%def name="init()">
-<%
-    self.has_left_panel=False
-    self.has_right_panel=False
-    self.message_box_visible=False
-    self.active_view="user"
-    self.overlay_visible=False
-%>
-</%def>
-
-<%def name="title()">Custom Database Builds</%def>
-
-<%def name="stylesheets()">
-    ${parent.stylesheets()}
-    <style type="text/css">
-        #custom_dbkeys * {
-            min-width: 100px;
-            vertical-align: text-top;
-        }
-        pre {
-            padding: 0;
-            margin: 0;
-        }
-        ## If page is displayed in panels, pad from edges for readability.
-        %if context.get('use_panels'):
-        div#center {
-            padding: 10px;
-        }
-        %endif
-        div.def_tab {
-            float: left;
-            padding: 0.2em 0.5em;
-            background-color: white;
-        }
-        div.def_tab.active {
-            background-color: #CCF;
-            border: solid 1px #66A;
-        }
-    </style>
-</%def>
-
-<%def name="javascripts()">
-   ${parent.javascripts()}
-   
-    <script type="text/javascript">
-
-    $(function() {
-        $(".db_hide").each(function() {
-            var pre = $(this);
-            pre.hide();
-            pre.siblings("span").wrap( "<a href='javascript:void(0);'></a>" ).click( function() {
-                pre.toggle();
-            });     
-        });
-        $("#installed_builds").hide();
-        $("#show_installed_builds").click(function() {
-            $("#installed_builds").show();
-        });
-        
-        // Set up behavior for build definition tab controls.
-        $("div.def_tab > a").each(function() {
-            $(this).click(function() {
-                var tab_id = $(this).attr("id");
-
-                // Hide all build inputs, help.
-                $("div.build_definition").children(":input").hide();
-                $(".infomessagesmall > div").hide();
-                
-                // Show input item, help corresponding to tab id.
-                $("#" + tab_id + "_input").show();
-                $("." + tab_id + "_help").show();
-                
-                // Update tabs.
-                $("div.def_tab").removeClass("active");
-                $(this).parent().addClass("active");
-            });
-        });
-        
-        ## If there are fasta HDAs available, show fasta tab; otherwise show len file tab.
-        // Set starting tab.
-        % if fasta_hdas.first():
-            $("#fasta").click();
-        % else:
-            $("#len_file").click();
-        % endif
-        
-        // Before submit, remove inputs not associated with the active tab.
-        $("#submit").click(function() {
-            var id = $(this).parents("form").find(".active > a").attr("id");
-            $("div.build_definition").children(":input").each(function() {
-                if ( $(this).attr("id") !== (id + "_input")  ) {
-                    $(this).remove();
-                }
-            });
-        });
-    });
-
-    </script>
-</%def>
-
-<%def name="center_panel()">
-    ${self.body()}
-</%def>
-
-<%def name="body()">
-    % if message:
-        <div class="errormessagelarge">${message}</div>
-    % elif lines_skipped > 0:
-        <div class="warningmessagelarge">Skipped ${lines_skipped} lines that could not be parsed. (Line was either blank or not 2-column, with 2nd column being an integer)</div>
-    % endif
-
-    <h3>Current Custom Builds:</h3>
-
-    % if dbkeys:
-        <table id="custom_dbkeys" class="colored" cellspacing="0" cellpadding="0">
-            <tr class="header">
-                <th>Name</th>
-                <th>Key</th>
-                <th>Number of chroms/contigs</th>
-                <th></th>
-            </tr>
-        % for key, dct in dbkeys.iteritems():
-            <tr>
-                <td>${dct['name'] | h}</td>
-                <td>${key | h}</td>
-                <td>
-    ##                <span>${len(dct["chroms"])} entries</span>
-    ##                <pre id="pre_${key}" class="db_hide">
-    ##                    <table cellspacing="0" cellpadding="0">
-    ##                        <tr><th>Chrom</th><th>Length</th></tr>
-    ##                        % for chrom, chrom_len in dct["chroms"].iteritems():
-    ##                            <tr><td>${chrom | h}</td><td>${chrom_len | h}</td></tr>
-    ##                        % endfor
-    ##                    </table>
-    ##                </pre>
-                    % if 'count' in dct:
-                        ${dct['count']}
-                    % else:
-                        Processing
-                    % endif
-                </td>
-                <td><form action="dbkeys" method="post"><input type="hidden" name="key" value="${key | h}" /><input type="submit" name="delete" value="Delete" /></form></td>
-            </tr>
-        % endfor
-        </table>
-    % else:
-        <p>You currently have no custom builds.</p>
-    % endif
-    
-    <p>
-        <a id="show_installed_builds" href="javascript:void(0);">Show loaded, system-installed builds</a>
-        <blockquote id="installed_builds">${installed_len_files}</blockquote>
-    </p>
-    
-    <hr />
-    <h3>Add a Custom Build</h3>
-    <form action="dbkeys" method="post" enctype="multipart/form-data">
-        ## Include hidden param for panels:
-        %if use_panels:
-            <input type="hidden" name="use_panels" value="True">
-        %endif
-        ## Custom build via fasta in history.
-        <div class="toolForm" style="float: left;">
-            <div class="toolFormTitle">New Build</div>
-            <div class="toolFormBody">
-                <div class="form-row">
-                    <label for="name">Name (eg: Hamster):</label>
-                    <input type="text" id="name" name="name" />
-                </div>
-                <div class="form-row">
-                    <label for="key">Key (eg: hamster_v1):</label>
-                    <input type="text" id="key" name="key" />
-                </div>
-                <div class="form-row build_definition">
-                    <label>Definition:</label>
-                    <div class="def_tab">
-                        <a id="fasta" href="javascript:void(0)">FASTA</a>
-                    </div>
-                    <div class="def_tab">
-                        <a id="len_file" href="javascript:void(0)">Len File</a>
-                    </div>
-                    <div class="def_tab">
-                        <a id="len_entry" href="javascript:void(0)">Len Entry</a>
-                    </div>
-                    <div style="clear: both; padding-bottom: 0.5em"></div>
-                    <select id="fasta_input" name="dataset_id">
-                    %for dataset in fasta_hdas:
-                        <option value="${trans.security.encode_id( dataset.id )}">${dataset.hid | h}: ${dataset.name | h}</option>
-                    %endfor
-                    </select>
-                    <input type="file" id="len_file_input" name="len_file" /></input>
-                    <textarea id="len_entry_input" name="len_text" cols="30" rows="8"></textarea>
-                </div>            
-                <div class="form-row"><input id="submit" type="submit" name="add" value="Submit"/></div>
-            </div>
-        </div>
-    </form>
-    <div class="infomessagesmall" style="float: left; margin-left: 10px; width: 40%;">
-        <div class="fasta_help">
-            <h3>FASTA format</h3>
-            <p>
-                This is a multi-fasta file from your current history that provides the genome 
-                sequences for each chromosome/contig in your build.
-            </p>
-            
-            <p>
-                Here is a snippet from an example multi-fasta file:
-                <pre>
-    >chr1
-    ATTATATATAAGACCACAGAGAGAATATTTTGCCCGG...
-    >chr2
-    GGCGGCCGCGGCGATATAGAACTACTCATTATATATA...
-    ...
-                </pre>
-            </p>
-        </div>
-        <div class="len_file_help len_entry_help">
-            <h3>Length Format</h3>
-            <p>
-                The length format is two-column, separated by whitespace, of the form:
-                <pre>chrom/contig   length of chrom/contig</pre>
-            </p>
-            <p>
-                For example, the first few entries of <em>mm9.len</em> are as follows:
-                <pre>
-    chr1    197195432
-    chr2    181748087
-    chr3    159599783
-    chr4    155630120
-    chr5    152537259
-                </pre>
-            </p>
-        
-            <p>Trackster uses this information to populate the select box for chrom/contig, and
-            to set the maximum basepair of the track browser. You may either upload a .len file
-            of this format (Len File option), or directly enter the information into the box 
-            (Len Entry option).</p>
-        </div>
-    </div>
-</%def>