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manage_projects.html
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manage_projects.html
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{% extends "sitebase.html" %}
{% block head %}
<link rel="stylesheet" type="text/css" href="/static/vendor/DataTables/DataTables-1.10.21/css/jquery.dataTables.css">
<link rel="stylesheet" type="text/css" href="/static/vendor/DataTables/Buttons-1.6.2/css/buttons.dataTables.css">
<style>
th { white-space: normal; }
div.dataTables_wrapper {
width: 1000px;
margin: 0 auto;
}
.modal-backdrop {
/* bug fix - no overlay */
display: none;
}
</style>
<script src="/static/vendor/DataTables/DataTables-1.10.21/js/jquery.dataTables.js"></script>
<script src="/static/vendor/DataTables/Buttons-1.6.2/js/dataTables.buttons.js"></script>
<script src="/static/vendor/DataTables/Buttons-1.6.2/js/buttons.colVis.js"></script>
<script class="init">
// set up for DataTable of project info:
var projectTable = undefined; //defined on document ready
const numCols = 49;
// from https://davidwalsh.name/fill-array-javascript
const fillRange = (start, end) => {
return Array(end - start + 1).fill().map((item, index) => start + index);
};
// NB: zero-based
const hideableColNums = fillRange(3, numCols - 1);
// end from https://davidwalsh.name/fill-array-javascript
const basicGroupColNums = fillRange(3, 14);
const dispositionGroupColNums = fillRange(15, 18);
const sampleTypeGroupColNums = fillRange(19, 23);
const profilingGroupColNums = fillRange(24, 34);
const brandingGroupColNums = fillRange(35, 36);
const kitsGroupColNums = fillRange(37, 41);
const samplesGroupColNums = fillRange(42, 48);
function showAllCols(){
projectTable.columns().visible(true);
}
// end datatable set-up
// functions for resetting, populating, and displaying the
// create/update modal
function resetModal(){
showAllCols();
document.getElementById("project_form").reset();
}
function readRow(projId){
showAllCols();
let projIdSuffix = "_" + projId;
let projRowIdSelector = "#tr_project" + projIdSuffix;
$(projRowIdSelector).children('td').each(function () {
// any non-data columns (like edit button column)
// don't have an id, so we know to skip them
if (this.id) {
// get the form element in the modal edit form
// that has the same base id as the data cell we're examining
let formElmId = this.id.replace("td_", "");
formElmId = formElmId.replace(projIdSuffix, "");
let formElm = $("#" + formElmId);
// if we got an editable element with this id (which we
// won't always--e.g., no editable element for num_received_samples
// bc that is read-only from db)
if (formElm.length === 1){
// if the element is a checkbox, it needs special
// finicky handling to set its value
if (formElm.is(":checkbox")) {
// set checked property to boolean value of data field
let isChecked = (this.innerText.toLowerCase() === "true");
formElm.prop('checked', isChecked);
// trigger onchange event manually via jquery
formElm.change();
} else {
// set the value of the form element to the value
// of the relevant cell in the projects table
formElm.val(this.innerText);
}
}
}
});
}
// called when the modal submit is clicked (NOT at onsubmit, which is too late)
function unhideAllPanels() {
// make all the panels visible. This is a kludge needed because input elements
// that are not visible are not included when the form is posted :(
$(".collapse").addClass("show").css("height","auto");
// disable the submit button
$('#modal_submit').addClass('disabled');
// show a wait message since the page reload is not instant
$('#wait_msg').show();
}
function loadByActiveStatus(statusSelect){
let manage_projects_url = "/manage_projects";
let active_status_filter = statusSelect.value;
if (active_status_filter !== "all"){
manage_projects_url+= "?is_active="+ active_status_filter;
}
showWait(manage_projects_url);
}
$(document).ready(function() {
// set active status drop-down value; note that this code-level change
// does NOT trigger the drop-down's onchange event (which reloads the page)
let urlParams = new URLSearchParams(window.location.search);
let is_active_val = "all";
if (urlParams.has('is_active')){
is_active_val = urlParams.get('is_active');
}
$('#is_active_val').val(is_active_val);
document.getElementById('bank_samples').onchange = function() {
// the 'plating_start_date input field is disabled if
// the 'bank_samples' checkbox is NOT checked, and enabled if it is.
document.getElementById('plating_start_date').disabled = !this.checked;
};
// from https://getbootstrap.com/docs/4.0/components/modal/
$('#exampleModal').on('show.bs.modal', function (event) {
let button = $(event.relatedTarget); // Button that triggered the modal
let action = button.data('action'); // Extract info from data-action attribute
let modal = $(this);
// set modal title and submit button text based on type of activity
// being performed (either create or update)
modal.find('.modal-title').text(action + ' Project');
$("#modal_submit").text(action);
});
// end from https://getbootstrap.com/docs/4.0/components/modal/
projectTable = $('#projects_list').DataTable({
// Set the "Branding Associated Instructions" column to display
// its content as a link if they contain :// (as in http://, https://, etc)
"columnDefs": [{
"targets": 35,
"render": function (data, type, row, meta) {
let result = data;
if (data.indexOf("://") > -1) {
result = '<a href="' + data + '">' + data + '</a>';
}
return result;
}
}],
// Enable horizontal scrolling of DataTable
"scrollX": true,
// Define groups of columns that will be showed/hidden by named buttons
// modified from https://datatables.net/extensions/buttons/examples/column_visibility/columnGroups.html#:~:text=SearchPanes-,Column%20groups,provides%20this%20ability%20for%20Buttons
dom: 'Bfrtip',
buttons: [
{
extend: 'colvisGroup',
text: 'Show all',
show: ':hidden'
},
{
extend: 'colvisGroup',
text: 'Basics',
show: basicGroupColNums,
hide: hideableColNums.filter(i => !basicGroupColNums.includes(i))
},
{
extend: 'colvisGroup',
text: 'Disposition',
show: dispositionGroupColNums,
hide: hideableColNums.filter(i => !dispositionGroupColNums.includes(i))
},
{
extend: 'colvisGroup',
text: 'Sample Types',
show: sampleTypeGroupColNums,
hide: hideableColNums.filter(i => !sampleTypeGroupColNums.includes(i))
},
{
extend: 'colvisGroup',
text: 'Profiling',
show: profilingGroupColNums,
hide: hideableColNums.filter(i => !profilingGroupColNums.includes(i))
},
{
extend: 'colvisGroup',
text: 'Branding',
show: brandingGroupColNums,
hide: hideableColNums.filter(i => !brandingGroupColNums.includes(i))
},
{
extend: 'colvisGroup',
text: 'Kits',
show: kitsGroupColNums,
hide: hideableColNums.filter(i => !kitsGroupColNums.includes(i))
},
{
extend: 'colvisGroup',
text: 'Samples',
show: samplesGroupColNums,
hide: hideableColNums.filter(i => !samplesGroupColNums.includes(i))
}
]
// end modified from https://datatables.net/extensions/buttons/examples/column_visibility/columnGroups.html#:~:text=SearchPanes-,Column%20groups,provides%20this%20ability%20for%20Buttons
});
} );
</script>
{% endblock %}
{% block content %}
<h3>Projects</h3>
{% if 'error_message' in result %}
<p>{{ result['error_message'] }}</p>
{% else %}
<div>
<div class="result_container">
<div class="dataTables_wrapper">
<div>
<select id="is_active_val" onchange="loadByActiveStatus(this);">
<option value="true">Active</option>
<option value="false">Inactive</option>
<option value="all">All</option>
</select>
</div>
<br />
<table id="projects_list" class="display wrap" style="width:100%">
<thead>
<tr>
<th>Edit</th>
<th>ID</th>
<th>Study Name</th>
<!--Basics group-->
<th>Flight Sub-Project Name</th>
<th>Alias</th>
<th>Is Microsetta</th>
<th>Sponsor</th>
<th>Coordination</th>
<th>POC</th>
<th>Additional POC</th>
<th>POC e-mail address</th>
<th>Deadlines</th>
<th># Subjects</th>
<th>Timepoints</th>
<th>Start Date</th>
<!--Disposition group-->
<th>Bank Samples (was Disposition)</th>
<th>Plating Start Date</th>
<th>Disposition Comments</th>
<th>Collection</th>
<!--Sample Types group -->
<th>Fecal</th>
<th>Saliva</th>
<th>Skin</th>
<th>Blood</th>
<th>Other Type</th>
<!--Profiling group-->
<th>16s</th>
<th>Shallow Shotgun</th>
<th>Shotgun</th>
<th>RT-qPCR</th>
<th>Serology</th>
<th>Meta-transcriptomics</th>
<th>Mass Spec</th>
<th>Mass Spec Comments</th>
<th>Mass Spec Contact</th>
<th>POC email</th>
<th>Other Profiling</th>
<!--Branding group -->
<th>Branding Associated Instructions</th>
<th>Branding Status</th>
<!--Kits group -->
<th>Num Unique Sources</th>
<th>Num Kits</th>
<th>Num Partially Returned Kits</th>
<th>Num Fully Returned Kits</th>
<th>Num Kits with Problem Sample(s)</th>
<!--Samples group -->
<th>Num Samples</th>
<th>Num Samples Received</th>
<th>Num Valid Samples</th>
<th>Num Samples of Unknown Validity</th>
<th>Num Samples w/o Account</th>
<th>Num Samples w/o Source</th>
<th>Num Samples w/o Collection Info</th>
</tr>
</thead>
<tbody>
{% for project in result['projects'] %}
{% set curr_id = project['project_id'] %}
<tr id = "tr_project_{{ curr_id }}">
<td>
<button type="button" data-toggle="modal" data-target="#exampleModal" data-action="Update" onclick="readRow({{ curr_id }});">
Edit
</button>
</td>
<td id="td_project_id_{{ curr_id }}">{{ project['project_id'] }}</td>
<td id="td_project_name_{{ curr_id }}">{{ project['project_name'] }}</td>
<td id="td_subproject_name_{{ curr_id }}">{{ project['subproject_name'] }}</td>
<td id="td_alias_{{ curr_id }}">{{ project['alias'] }}</td>
<td id="td_is_microsetta_{{ curr_id }}">{{ project['is_microsetta'] }}</td>
<td id="td_sponsor_{{ curr_id }}">{{ project['sponsor'] }}</td>
<td id="td_coordination_{{ curr_id }}">{{ project['coordination'] }}</td>
<td id="td_contact_name_{{ curr_id }}">{{ project['contact_name'] }}</td>
<td id="td_addtl_contact_name_{{ curr_id }}">{{ project['additional_contact_name'] }}</td>
<td id="td_contact_email_{{ curr_id }}">{{ project['contact_email'] }}</td>
<td id="td_deadlines_{{ curr_id }}">{{ project['deadlines'] }}</td>
<td id="td_num_subjects_{{ curr_id }}">{{ project['num_subjects'] }}</td>
<td id="td_num_timepoints_{{ curr_id }}">{{ project['num_timepoints'] }}</td>
<td id="td_start_date_{{ curr_id }}">{{ project['start_date'] }}</td>
<td id="td_bank_samples_{{ curr_id }}">{{ project['bank_samples'] }}</td>
<td id="td_plating_start_date_{{ curr_id }}">{{ project['plating_start_date'] }}</td>
<td id="td_disposition_comments_{{ curr_id }}">{{ project['disposition_comments'] }}</td>
<td id="td_collection_{{ curr_id }}">{{ project['collection'] }}</td>
<td id="td_is_fecal_{{ curr_id }}">{{ project['is_fecal'] }}</td>
<td id="td_is_saliva_{{ curr_id }}">{{ project['is_saliva'] }}</td>
<td id="td_is_skin_{{ curr_id }}">{{ project['is_skin'] }}</td>
<td id="td_is_blood_{{ curr_id }}">{{ project['is_blood'] }}</td>
<td id="td_is_other_{{ curr_id }}">{{ project['is_other'] }}</td>
<td id="td_do_16s_{{ curr_id }}">{{ project['do_16s'] }}</td>
<td id="td_do_shallow_shotgun_{{ curr_id }}">{{ project['do_shallow_shotgun'] }}</td>
<td id="td_do_shotgun_{{ curr_id }}">{{ project['do_shotgun'] }}</td>
<td id="td_do_rt_qpcr_{{ curr_id }}">{{ project['do_rt_qpcr'] }}</td>
<td id="td_do_serology_{{ curr_id }}">{{ project['do_serology'] }}</td>
<td id="td_do_metatranscriptomics_{{ curr_id }}">{{ project['do_metatranscriptomics'] }}</td>
<td id="td_do_mass_spec_{{ curr_id }}">{{ project['do_mass_spec'] }}</td>
<td id="td_mass_spec_comments_{{ curr_id }}">{{ project['mass_spec_comments'] }}</td>
<td id="td_mass_spec_contact_name_{{ curr_id }}">{{ project['mass_spec_contact_name'] }}</td>
<td id="td_mass_spec_contact_email_{{ curr_id }}">{{ project['mass_spec_contact_email'] }}</td>
<td id="td_do_other_{{ curr_id }}">{{ project['do_other'] }}</td>
<td id="td_branding_associated_instructions_{{ curr_id }}">{{ project['branding_associated_instructions'] }}</td>
<td id="td_branding_status_{{ curr_id }}">{{ project['branding_status'] }}</td>
<td id="td_num_unique_sources_{{ curr_id }}">{{ project['computed_stats']['num_unique_sources'] }}</td>
<td id="td_num_kits_{{ curr_id }}">{{ project['computed_stats']['num_kits'] }}</td>
<td id="td_num_partially_returned_kits_{{ curr_id }}">{{ project['computed_stats']['num_partially_returned_kits'] }}</td>
<td id="td_num_fully_returned_kits_{{ curr_id }}">{{ project['computed_stats']['num_fully_returned_kits'] }}</td>
<td id="td_num_kits_w_problems_{{ curr_id }}">{{ project['computed_stats']['num_kits_w_problems'] }}</td>
<td id="td_num_samples_{{ curr_id }}">{{ project['computed_stats']['num_samples'] }}</td>
<td id="td_num_samples_received_{{ curr_id }}">{{ project['computed_stats']['num_samples_received'] }}</td>
<td id="td_num_sample_is_valid_{{ curr_id }}">{{ project['computed_stats']['num_sample_is_valid'] }}</td>
<td id="td_num_received_unknown_validity_{{ curr_id }}">{{ project['computed_stats']['num_received_unknown_validity'] }}</td>
<td id="td_num_no_registered_account_{{ curr_id }}">{{ project['computed_stats']['num_no_registered_account'] }}</td>
<td id="td_num_no_associated_source_{{ curr_id }}">{{ project['computed_stats']['num_no_associated_source'] }}</td>
<td id="td_num_no_collection_info_{{ curr_id }}">{{ project['computed_stats']['num_no_collection_info'] }}</td>
</tr>
{% endfor %}
</tbody>
</table>
</div>
</div>
</div>
<button type="button" data-toggle="modal" data-target="#exampleModal" data-action="Create" onClick="resetModal();">Create New Project</button>
<button type="button" onClick="showWait(); window.location.reload();">Refresh Results</button>
{% endif %}
<form name="project_form" id="project_form" method="POST">
<div class="modal fade" id="exampleModal" tabindex="-1" role="dialog" aria-labelledby="exampleModalLabel" aria-hidden="true">
<div class="modal-dialog" role="document">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title" id="exampleModalLabel">Edit Project</h5>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">×</span>
</button>
</div>
<div class="modal-body">
<input type="hidden" name="project_id" id="project_id" value="" />
<table>
<tr>
<td><label for="project_name">Project Name: </label></td>
<td><input type="text" name="project_name" id="project_name" /></td>
</tr>
</table>
<p></p>
<div class="accordion" id="myAccordion">
<div class="card">
<div class="card-header" id="headingOne">
<h2 class="mb-0">
<button type="button" class="btn btn-link"
data-toggle="collapse" data-target="#collapseOne">
Basics
</button>
</h2>
</div>
<div id="collapseOne" class="collapse" aria-labelledby="headingOne">
<div class="card-body">
<table>
<tr>
<td><label for="subproject_name">Sub-Project Name: </label></td>
<td><input type="text" name="subproject_name" id="subproject_name" /></td>
</tr>
<tr>
<td><label for="alias">Alias: </label></td>
<td><input type="text" name="alias" id="alias" /></td>
</tr>
<tr>
<td><label for="is_microsetta">Microsetta Project: </label></td>
<td><input type="checkbox" name="is_microsetta" id="is_microsetta" value='true' /></td>
</tr>
<tr>
<td><label for="sponsor">Sponsor: </label></td>
<td><input type="text" name="sponsor" id="sponsor" /></td>
</tr>
<tr>
<td><label for="coordination">Coordination: </label></td>
<td><input type="text" name="coordination" id="coordination" /></td>
</tr>
<tr>
<td><label for="contact_name">Contact Name: </label></td>
<td><input type="text" name="contact_name" id="contact_name" /></td>
</tr>
<tr>
<td><label for="addtl_contact_name">Additional Contact Name: </label></td>
<td><input type="text" name="addtl_contact_name" id="addtl_contact_name" /></td>
</tr>
<tr>
<td><label for="contact_email">Contact Email: </label></td>
<td><input type="email" name="contact_email" id="contact_email" /></td>
</tr>
<tr>
<td><label for="deadlines">Deadlines: </label></td>
<td><input type="text" name="deadlines" id="deadlines" /></td>
</tr>
<tr>
<td><label for="num_subjects">Number of Subjects: </label></td>
<td><input type="text" name="num_subjects" id="num_subjects" /></td>
</tr>
<tr>
<td><label for="num_timepoints">Number of Timepoints: </label></td>
<td><input type="text" name="num_timepoints" id="num_timepoints" /></td>
</tr>
<tr>
<td><label for="start_date">Start Date: </label></td>
<td><input type="text" name="start_date" id="start_date" /></td>
</tr>
</table>
</div>
</div>
</div>
<div class="card">
<div class="card-header" id="headingTwo">
<h2 class="mb-0">
<button type="button" class="btn btn-link"
data-toggle="collapse" data-target="#collapseTwo">
Disposition
</button>
</h2>
</div>
<div id="collapseTwo" class="collapse" aria-labelledby="headingTwo">
<div class="card-body">
<table>
<tr>
<td><label for="bank_samples">Bank Samples: </label></td>
<td><input type="checkbox" name="bank_samples" id="bank_samples" value='true' /></td>
</tr>
<tr>
<td><label for="plating_start_date">Plate On (Optional): </label></td>
<td><input type="text" name="plating_start_date" id="plating_start_date" placeholder="2020-07-04"
pattern="[0-9]{4}-[0-9]{2}-[0-9]{2}" disabled /><br>
<small>Format: YYYY-MM-DD</small>
</td>
</tr>
<tr>
<td><label for="disposition_comments">Disposition Comments: </label></td>
<td><input type="text" name="disposition_comments" id="disposition_comments" /></td>
</tr>
<tr>
<td><label for="collection">Collection: </label></td>
<td><input type="text" name="collection" id="collection" /></td>
</tr>
</table>
</div>
</div>
</div>
<div class="card">
<div class="card-header" id="headingThree">
<h2 class="mb-0">
<button type="button" class="btn btn-link"
data-toggle="collapse" data-target="#collapseThree">
Sample Types
</button>
</h2>
</div>
<div id="collapseThree" class="collapse" aria-labelledby="headingThree">
<div class="card-body">
<table>
<tr>
<td><label for="is_fecal">Fecal: </label></td>
<td>
<select name="is_fecal" id="is_fecal">
<option value=""></option>
<option value="X">X</option>
<option value="?">?</option>
</select>
</td>
</tr>
<tr>
<td><label for="is_saliva">Saliva: </label></td>
<td>
<select name="is_saliva" id="is_saliva">
<option value=""></option>
<option value="X">X</option>
<option value="?">?</option>
</select>
</td>
</tr>
<tr>
<td><label for="is_skin">Skin: </label></td>
<td>
<select name="is_skin" id="is_skin">
<option value=""></option>
<option value="X">X</option>
<option value="?">?</option>
</select>
</td>
</tr>
<tr>
<td><label for="is_blood">Blood: </label></td>
<td>
<select name="is_blood" id="is_blood">
<option value=""></option>
<option value="X">X</option>
<option value="?">?</option>
</select>
</td>
</tr>
<tr>
<td><label for="is_other">Other </label></td>
<td><input type="text" name="is_other" id="is_other" /></td>
</tr>
</table>
</div>
</div>
</div>
<div class="card">
<div class="card-header" id="headingFour">
<h2 class="mb-0">
<button type="button" class="btn btn-link"
data-toggle="collapse" data-target="#collapseFour">
Profiling
</button>
</h2>
</div>
<div id="collapseFour" class="collapse" aria-labelledby="headingFour">
<div class="card-body">
<table>
<tr>
<td><label for="do_16s">16S: </label></td>
<td><input type="text" name="do_16s" id="do_16s" /></td>
</tr>
<tr>
<td><label for="do_shallow_shotgun">Shallow Shotgun: </label></td>
<td><input type="text" name="do_shallow_shotgun" id="do_shallow_shotgun" /></td>
</tr>
<tr>
<td><label for="do_shotgun">Shotgun: </label></td>
<td><input type="text" name="do_shotgun" id="do_shotgun" /></td>
</tr>
<tr>
<td><label for="do_rt_qpcr">RT-qPCR: </label></td>
<td><input type="text" name="do_rt_qpcr" id="do_rt_qpcr" /></td>
</tr>
<tr>
<td><label for="do_serology">Serology: </label></td>
<td><input type="text" name="do_serology" id="do_serology" /></td>
</tr>
<tr>
<td><label for="do_metatranscriptomics">Meta-transcriptomics: </label></td>
<td><input type="text" name="do_metatranscriptomics" id="do_metatranscriptomics" /></td>
</tr>
<tr>
<td><label for="do_mass_spec">Mass Spec: </label></td>
<td><input type="text" name="do_mass_spec" id="do_mass_spec" /></td>
</tr>
<tr>
<td><label for="mass_spec_comments">Mass Spec Comments: </label></td>
<td><input type="text" name="mass_spec_comments" id="mass_spec_comments" /></td>
</tr>
<tr>
<td><label for="mass_spec_contact_name">Mass Spec Contact: </label></td>
<td><input type="text" name="mass_spec_contact_name" id="mass_spec_contact_name" /></td>
</tr>
<tr>
<td><label for="mass_spec_contact_email">POC email: </label></td>
<td><input type="email" name="mass_spec_contact_email" id="mass_spec_contact_email" /></td>
</tr>
<tr>
<td><label for="do_other">Other: </label></td>
<td><input type="text" name="do_other" id="do_other" /></td>
</tr>
</table>
</div>
</div>
</div>
<div class="card">
<div class="card-header" id="headingFive">
<h2 class="mb-0">
<button type="button" class="btn btn-link"
data-toggle="collapse" data-target="#collapseFive">
Branding
</button>
</h2>
</div>
<div id="collapseFive" class="collapse" aria-labelledby="headingFive">
<div class="card-body">
<table>
<tr>
<td><label for="branding_associated_instructions">Associated Instructions: </label></td>
<td><input type="text" name="branding_associated_instructions" id="branding_associated_instructions" /></td>
</tr>
<tr>
<td><label for="branding_status">Status: </label></td>
<td><input type="text" name="branding_status" id="branding_status" /></td>
</tr>
</table>
</div>
</div>
</div>
</div>
</div>
<div class="modal-footer">
<div id="wait_msg" style="display:none;">
<div class="d-flex justify-content-center">
Saving data ...
</div>
<div class="d-flex justify-content-center">
<div class="spinner-grow" role="status">
<span class="sr-only">Loading...</span>
</div>
</div>
</div>
<button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
<button type="submit" class="btn btn-primary" id="modal_submit"
onclick="unhideAllPanels();">Update</button>
</div>
</div>
</div>
</div>
</form>
{% endblock %}