From ea7d508ea7f199f189557023dbb8e42858c8681b Mon Sep 17 00:00:00 2001
From: Jose Navas <josenavasmolina@gmail.com>
Date: Fri, 29 May 2015 19:09:43 -0700
Subject: [PATCH] Removing unused files

---
 .../prep_template_panel.html                  | 112 ---------------
 .../raw_data_editor_tab.html                  | 127 ------------------
 2 files changed, 239 deletions(-)
 delete mode 100644 qiita_pet/templates/study_description_templates/prep_template_panel.html
 delete mode 100644 qiita_pet/templates/study_description_templates/raw_data_editor_tab.html

diff --git a/qiita_pet/templates/study_description_templates/prep_template_panel.html b/qiita_pet/templates/study_description_templates/prep_template_panel.html
deleted file mode 100644
index 9923b24cc..000000000
--- a/qiita_pet/templates/study_description_templates/prep_template_panel.html
+++ /dev/null
@@ -1,112 +0,0 @@
-{% from os.path import basename %}
-{% from qiita_pet.handlers.util import download_link_or_path %}
-
-<!-- modal view to enter preprocessing parameters -->
-<div class="modal fade" id="preprocess-modal-view-{{prep_id}}" tabindex="-1" role="dialog" aria-labelledby="myModalLabel" aria-hidden="true">
-  <div class="modal-dialog">
-    <div class="modal-content">
-      <div class="modal-header">
-        <button type="button" class="close" data-dismiss="modal" aria-hidden="true">&times;</button>
-        <h4 class="modal-title" id="myModalLabel">Choose preprocessing parameters</h4>
-      </div>
-      <form action="/study/preprocess" method="post" onsubmit='return submit_preprocess({{prep_id}});'>
-        <div class="modal-body">
-          <div>
-            <div class="form-group">
-              <table>
-                <tr>
-                  <td>
-                    <select id="preprocessing_parameters_{{prep_id}}" name="preprocessing_parameters_id" class="form-control" onchange="$('#display-extra-info-{{prep_id}}').html($(this).children(':selected').attr('extra-info'))">
-                      <option value="0" extra-info="">Select an option ...</option>
-                      {% for idx, name, text in preprocess_options %}
-                        <option value="{{idx}}" extra-info="{% raw text %}">{{name}}</option>
-                      {% end %}
-                    </select>
-                  </td>
-                  <td>&nbsp; &nbsp;</td>
-                  <td>
-                    <input type='submit' id='start_preprocess_submit' class='btn btn-success' value="Start preprocessing">
-                    <input type='hidden' name='study_id' value="{{study_id}}">
-                    <input type='hidden' name='prep_template_id' value="{{prep_id}}">
-                  </td>
-                </tr>
-                <tr><td>&nbsp;</td></tr>
-                <tr><td colspan="3">
-                  Here you are selecting the parameters to use for preprocessing. This is the demultiplexing and quality control
-                  step for multiplexed sequencing. For more information visit:
-                  <a target="_blank" href="http://qiime.org/scripts/split_libraries.html">454</a> and
-                  <a target="_blank" href="http://qiime.org/scripts/split_libraries_fastq.html">Illumina</a>.
-                </td></tr>
-                <tr><td>&nbsp;</td></tr>
-                <tr>
-                  <td id="display-extra-info-{{prep_id}}" colspan="2"></td>
-                </tr>
-              </table>
-            </div>
-          </div>
-        </div>
-        <div class="modal-footer">
-        </div>
-      </form>
-    </div>
-  </div>
-</div>
-
-<div class="panel panel-default">
-  <div class="panel-heading">
-    <h4 class="panel-title">
-      <a data-parent="#prep-accordion" href="#collapse{{prep_id}}" style="pointer-events: none; cursor: default;">{{data_type}} (ID: {{prep_id}})</a>&nbsp;
-        <div class="{{status_class1}}" style="color: {{status_color}};"></div>
-        <div class="{{status_class2}}" style="color: {{status_color}};"></div>
-        <button class="close" title="Remove this prep template" type="button" onclick="delete_prep_template('{{data_type}}', {{prep_id}})">&nbsp; ×</button>
-    </h4>
-  </div>
-  <div id="collapse{{prep_id}}" class="panel-collapse collapse in">
-    <div class="panel-body">
-      <b>Files:</b><br/>
-      <table border="0" style="margin-left: 10px;">
-        <tr>
-          <td style="padding:3px;">
-            <a class="btn btn-default" href="/metadata_summary/?study_id={{study_id}}&prep_template={{prep_id}}">
-                Show prep template summary
-            </a>
-          </td>
-        </tr>
-        {% for ptid, ptpath, ptype in filepaths %}
-          <tr>
-            <td>
-            {% raw download_link_or_path(is_local_request, ptpath, ptid, ptype) %}
-            </td>
-          </tr>
-        {% end %}
-      </table>
-      <br/>
-      {% if is_editable %}
-        <!-- We pass a 0 as a preprocessed data id here, since the preprocessed data 0 does not exists -->
-        {% module EditInvestigationType(ena_terms, user_defined_terms, prep_id, investigation_type, 0) %}
-      {% end %}
-      <br/>
-      {% if not preprocessed_data or preprocessing_status.startswith('failed') %}
-        {% if study_status == 'sandbox' %}
-          {% if show_preprocess_btn %}
-            <a class="btn btn-primary glyphicon glyphicon-play" data-toggle="modal" data-target="#preprocess-modal-view-{{prep_id}}" style="word-spacing: -10px;"> Preprocess</a>
-          {% else %}
-            <b>{{ no_preprocess_msg }}</b>
-          {% end %}
-        {% end %}
-          <br>
-          <i>Status:</i> {{preprocessing_status}}
-          <br>
-          {% if 'zero-size array' in preprocessing_status %}
-            <b>Your barcodes do not seem to match your prep template info</b>
-          {% end %}
-      {% else %}
-        <b>Preprocessed data generated: </b>
-        <a href="#" onClick="display_tab('preprocessed_data_tab', {{preprocessed_data[0]}});">{{preprocessed_data[0]}}</a>
-        {% for pdi in preprocessed_data[1:] %}
-          , <a href="#" onClick="display_tab('preprocessed_data_tab', {{pdi}});">{{pdi}}</a>
-        {% end %}
-      {% end %}
-    </div>
-  </div>
-</div>
diff --git a/qiita_pet/templates/study_description_templates/raw_data_editor_tab.html b/qiita_pet/templates/study_description_templates/raw_data_editor_tab.html
deleted file mode 100644
index e8bd3ef21..000000000
--- a/qiita_pet/templates/study_description_templates/raw_data_editor_tab.html
+++ /dev/null
@@ -1,127 +0,0 @@
-{% from os.path import basename %}
-
-<div class="tab-pane" id="raw_data_info_{{raw_data_id}}" style="padding: 10px;">
-  <table border="0">
-    <tr>
-      <td style="vertical-align:top;padding:10px;">
-
-      <!-- Add prep template section -->
-      {% if is_editable %}
-        <h4>Add prep template to this raw data</h4>
-        To add a prep template you need to:
-        <ol>
-          <!-- Step 1: choose the prep template file -->
-          <li>
-            Select your prep template file <br/>
-            (only files with the "txt" and "tsv" file extensions will be displayed here):
-            <select id="add_prep_template_{{raw_data_id}}">
-              {% for f in files %}
-                {% if f.endswith(('txt', 'tsv')) %}
-                <option value="{{f}}">{{f}}</option>
-                {% end %}
-              {% end %}
-            </select>,
-          </li>
-          <!-- Step 2: choose the prep template data type -->
-          <li>
-            select the prep template data type
-            <select id="data_type_{{raw_data_id}}">
-              {% for name, value in data_types %}
-                <option value="{{value}}">{{name}}</option>
-              {% end %}
-            </select>
-          </li>
-          <!-- Step 3 (optional): select investigation type -->
-          <li>
-            (optional but required for EBI submission) select an investigation type:
-            <select onclick="investigationTypeChanged({{raw_data_id}})" onchange="investigationTypeChanged({{raw_data_id}})" id="investigation-type-{{raw_data_id}}">
-              <option value="None Selected">None Selected</option>
-              {% raw ena_terms %}
-            </select>
-            <table id="investigation-type-table" name="investigation-types" class="investigation-type-table">
-              <tr id="user-defined-investigation-types-{{raw_data_id}}" style="display:none;">
-                <td>
-                  Select one of the user defined investigation types:
-                </td>
-                <td>
-                  <select onclick="newInvestigationTypeChanged({{raw_data_id}})" onchange="newInvestigationTypeChanged({{raw_data_id}})" id="user-defined-investigation-type-{{raw_data_id}}">
-                  {% for term in user_defined_terms %}
-                    <option value="{{term}}">{{term}}</option>
-                  {% end %}
-                  </select>
-                </td>
-              </tr>
-              <tr id="new-investigation-type-entry-{{raw_data_id}}" style="display:none;">
-                <td>
-                  Enter a new investigation type:
-                </td>
-                <td>
-                  <input type="text" id="new-investigation-type-{{raw_data_id}}" name="new-investigation-type" class="form-control">
-                </td>
-              </tr>
-            </table>
-          </li>
-        </ol>
-        <br/>
-        <a class="btn btn-primary" onclick="add_prep_template({{raw_data_id}});">Add prep template</a>
-        <br/>
-        <hr/>
-      {% end %}
-
-
-        <!-- Uploaded prep templates (table) -->
-        <h4>Prep templates uploaded</h4>
-        <div class="panel-group" id="prep-accordion-{{raw_data_id}}">
-          {% for prep in available_prep_templates %}
-            {% module PrepTemplatePanel(prep, study_id, is_editable, ena_terms, study_status, user_defined_terms, raw_data_files) %}
-          {% end %}
-        </div>
-      </td>
-
-      <!-- Files linked to the raw data -->
-      <td style="vertical-align:top;padding:10px;">
-        <h4>Linked files to this raw data</h4>
-          {% if show_unlink_btn %}
-            <a class="btn btn-danger" onclick="unlink_all_files({{raw_data_id}})">Unlink all files</a><br/>
-          {% end %}
-          <i><b style="color:red">{{link_msg}}</b></i><br/>
-        {% for fpid, f, t in raw_data_files %}
-            <i>{{basename(f)}}:</i> {{t[4:]}} <br/>
-        {% end %}
-          <br/>
-        {% if is_editable and not show_unlink_btn %}
-          <h4>Link uploaded files with raw data</h4>
-          <table border="0">
-            <tr>
-              <th>File</th>
-              <th>&nbsp;&nbsp;&nbsp;</th>
-              <th>File type</th>
-            </tr>
-            {% for f in files %}
-            <tr>
-              <td>{{f}}</td>
-              <td>&nbsp;</td>
-              <td>
-                <select id="{{f}}" name="upload_file_{{raw_data_id}}">
-                  <option value="">Ignore ...</option>
-                  {% for fp_type in filepath_types %}
-                    <option value="{{fp_type}}">{{fp_type}}</option>
-                  {% end %}
-                </select>
-              </td>
-            </tr>
-            {% end %}
-        </table>
-        <br/>
-        <a onclick="link_files_to_raw_data({{raw_data_id}});"
-          {% if disable_link_btn %}
-            class="btn btn-default" style=" pointer-events: none; cursor: default; background-color:grey;"
-          {% else %}
-            class="btn btn-primary"
-          {% end %}>
-          Link raw files to: {{raw_data_filetype}} (ID: {{raw_data_id}})
-        </a>
-        {% end %}
-      </td>
-    </table>
-</div>