Add button to delete a job + some minor fixes and refactoring, Implements #120

src/dgenies/lib/functions.py

@@ -234,4 +234,15 @@ class Functions:
                 "mem_peak": Functions.get_readable_size(item.job.mem_peak),
                 "time_elapsed": Functions.get_readable_time(item.job.time_elapsed)
             })
-        return items
\ No newline at end of file
+        return items
+
+    @staticmethod
+    def is_in_gallery(id_job, mode):
+        if mode == "webserver":
+            from dgenies.database import Gallery, Job
+            from peewee import DoesNotExist
+            try:
+                return len(Gallery.select().where(Gallery.job == Job.get(id_job=id_job))) > 0
+            except DoesNotExist:
+                return False
+        return False

src/dgenies/lib/job_manager.py

@@ -30,7 +30,7 @@ import binascii
 from dgenies.database import Job
 
 if MODE == "webserver":
-    from dgenies.database import Session
+    from dgenies.database import Session, Gallery
     from peewee import DoesNotExist
 
 
@@ -969,3 +969,19 @@ class JobManager:
                 return {"status": status, "mem_peak": None, "time_elapsed": None, "error": error}
             except FileNotFoundError:
                 return {"status": "unknown", "error": ""}
+
+    def delete(self):
+        if not os.path.exists(self.output_dir) or not os.path.isdir(self.output_dir):
+            return False, "Job does not exists"
+        if MODE == "webserver":
+            try:
+                job = Job.get(id_job=self.id_job)
+            except DoesNotExist:
+                pass
+            else:
+                is_gallery = Gallery.select().where(Gallery.job == job)
+                if is_gallery:
+                    return False, "Delete a job that is in gallery is forbidden"
+                job.delete_instance()
+        shutil.rmtree(self.output_dir)
+        return True, ""
\ No newline at end of file

src/dgenies/static/css/style.css

@@ -685,4 +685,25 @@ h2.status {
 
 h2.status,div.status-body {
     margin-left: 55px;
+}
+
+div#sidebar {
+    position: relative;
+}
+
+div#sidebar p.bottom {
+    position: absolute;
+    bottom: 0;
+    right: 0;
+    width: 100px;
+}
+
+div#sidebar p.bottom input#delete-job {
+    background: #ffbba8 !important;
+}
+
+ul.nav ul.dropdown-menu {
+    max-height: 300px;
+    overflow-y: auto;
+
 }
\ No newline at end of file

src/dgenies/static/js/d3.boxplot.js

@@ -86,6 +86,7 @@ d3.boxplot.init = function (id_res=null, from_file=false) {
                 }
                 else {
                     $("#supdraw").html($("<p>").html("This job does not exist!").css("margin-top", "15px"));
+                    dgenies.result.remove_job_from_cookie(dgenies.result.id_res);
                 }
             }
         )

src/dgenies/static/js/dgenies.js

@@ -2,6 +2,30 @@ dgenies = {};
 dgenies.loading = "#loading";
 dgenies.noise = true;
 
+dgenies.init = function() {
+    let cookies = $.cookie("results");
+    cookies = (cookies !== undefined && cookies.length > 0) ? cookies.split("|") : [];
+    dgenies.update_results(cookies);
+};
+
+dgenies.update_results = function(results) {
+    let job_list_item = $("ul.nav li.result ul");
+    job_list_item.html("");
+    if (results.length > 0) {
+        for (let i=0; i<results.length; i++) {
+            let result = results[i];
+            job_list_item.append($("<li>").append($("<a>")
+            .attr("href", `/result/${result}`)
+            .text(result)))
+        }
+    }
+    else {
+        job_list_item.append($("<li>").append($("<a>")
+            .attr("href", "/run")
+            .text("Please run a job!")))
+    }
+};
+
 dgenies.notify = function (text, type="warning", delay=5000) {
     $.notify({
         message: text

src/dgenies/static/js/dgenies.result.controls.js

@@ -7,6 +7,7 @@ dgenies.result.controls.init = function () {
     $("#sort-contigs").click(dgenies.result.controls.launch_sort_contigs);
     $("#hide-noise").click(dgenies.result.controls.launch_hide_noise);
     $("#summary").click(dgenies.result.controls.summary);
+    $("#delete-job").click(dgenies.result.controls.delete_job);
     $("form#select-zone input.submit").click(dgenies.result.controls.select_zone);
     $("form#export select").change(dgenies.result.export.export);
 };
@@ -120,4 +121,51 @@ dgenies.result.controls.select_zone = function() {
     else {
         dgenies.notify("Please select zones into zoom!", "danger", 2000);
     }
+};
+
+dgenies.result.controls.do_delete_job = function () {
+    dgenies.post(`/delete/${dgenies.result.id_res}`,
+        {},
+        function(data) {
+            if (data["success"]) {
+                dgenies.notify("Your job has been deleted!", "success", 1500);
+                window.setTimeout(() => {
+                    dgenies.result.remove_job_from_cookie(dgenies.result.id_res);
+                    window.location = "/";
+                }, 1500);
+            }
+            else {
+                dgenies.notify("error" in data ? data["error"] : "An error has occurred. Please contact the support",
+                    "danger")
+            }
+        })
+};
+
+dgenies.result.controls.delete_job = function () {
+    let dialog = $("<div>")
+        .attr("id", "dialog-confirm")
+        .attr("title", "Delete job?");
+    let icon = $("<span>")
+        .attr("class", "ui-icon ui-icon-help")
+        .css("float", "left")
+        .css("margin", "12px 12px 20px 0");
+    let body = $("<p>");
+    body.append(icon);
+    body.append("Confirm deletion of this job? This operation is definitive.");
+    dialog.append(body);
+    dialog.dialog({
+        resizable: false,
+        height: "auto",
+        width: 500,
+        modal: true,
+        buttons: {
+            "Yes": function() {
+                $( this ).dialog( "close" );
+                dgenies.result.controls.do_delete_job();
+            },
+            "No": function () {
+                $( this ).dialog( "close" );
+            }
+        }
+    });
 };
\ No newline at end of file

src/dgenies/static/js/dgenies.result.export.js

@@ -115,7 +115,7 @@ dgenies.result.export.ask_export_fasta = function () {
                 $( this ).dialog( "close" );
             }
         }
-    })
+    });
 };
 
 dgenies.result.export.export_association_table = function () {

src/dgenies/static/js/dgenies.result.js

@@ -8,5 +8,36 @@ dgenies.result.id_res = null;
 
 dgenies.result.init = function(id_res) {
     dgenies.result.id_res = id_res;
+    dgenies.result.update_cookies();
     d3.boxplot.init();
 };
+
+dgenies.result.update_cookies = function () {
+    let cookies = $.cookie("results");
+    cookies = (cookies !== undefined && cookies.length > 0) ? cookies.split("|") : [];
+    let index = cookies.indexOf(dgenies.result.id_res);
+    let need_update = false;
+    if (index === -1) {
+        need_update = true;
+        cookies.unshift(dgenies.result.id_res)
+    }
+    $.cookie("results", cookies.join("|"), {path: '/'});
+    if (need_update) {
+        dgenies.update_results(cookies);
+    }
+};
+
+dgenies.result.remove_job_from_cookie = function(job) {
+    let cookies = $.cookie("results");
+    cookies = cookies !== undefined ? cookies.split("|") : [];
+    let index = cookies.indexOf(job);
+    let need_update = false;
+    if (index > -1) {
+        need_update = true;
+        cookies.splice(index, 1);
+    }
+    $.cookie("results", cookies.join("|"), {path: '/'});
+    if (need_update) {
+        dgenies.update_results(cookies);
+    }
+};
\ No newline at end of file

src/dgenies/static/js/jquery.cookie-1.4.1.min.js

+/*! jquery.cookie v1.4.1 | MIT */
+!function(a){"function"==typeof define&&define.amd?define(["jquery"],a):"object"==typeof exports?a(require("jquery")):a(jQuery)}(function(a){function b(a){return h.raw?a:encodeURIComponent(a)}function c(a){return h.raw?a:decodeURIComponent(a)}function d(a){return b(h.json?JSON.stringify(a):String(a))}function e(a){0===a.indexOf('"')&&(a=a.slice(1,-1).replace(/\\"/g,'"').replace(/\\\\/g,"\\"));try{return a=decodeURIComponent(a.replace(g," ")),h.json?JSON.parse(a):a}catch(b){}}function f(b,c){var d=h.raw?b:e(b);return a.isFunction(c)?c(d):d}var g=/\+/g,h=a.cookie=function(e,g,i){if(void 0!==g&&!a.isFunction(g)){if(i=a.extend({},h.defaults,i),"number"==typeof i.expires){var j=i.expires,k=i.expires=new Date;k.setTime(+k+864e5*j)}return document.cookie=[b(e),"=",d(g),i.expires?"; expires="+i.expires.toUTCString():"",i.path?"; path="+i.path:"",i.domain?"; domain="+i.domain:"",i.secure?"; secure":""].join("")}for(var l=e?void 0:{},m=document.cookie?document.cookie.split("; "):[],n=0,o=m.length;o>n;n++){var p=m[n].split("="),q=c(p.shift()),r=p.join("=");if(e&&e===q){l=f(r,g);break}e||void 0===(r=f(r))||(l[q]=r)}return l};h.defaults={},a.removeCookie=function(b,c){return void 0===a.cookie(b)?!1:(a.cookie(b,"",a.extend({},c,{expires:-1})),!a.cookie(b))}});
\ No newline at end of file

src/dgenies/templates/base.html

@@ -9,6 +9,7 @@
         <script src="{{ url_for('static', filename='js/bootstrap.min.js') }}" type="text/JavaScript"></script>
         <script src="{{ url_for('static', filename='js/bootstrap-notify.min.js') }}" type="text/JavaScript"></script>
         <script src="{{ url_for('static', filename='js/jquery-ui.min.js') }}" type="text/JavaScript"></script>
+        <script src="{{ url_for('static', filename='js/jquery.cookie-1.4.1.min.js') }}" type="text/JavaScript"></script>
         <script src="{{ url_for('static', filename='js/dgenies.js') }}" type="text/JavaScript"></script>
         <script src="{{ url_for('static', filename='js/dgenies.prototypes.js') }}" type="text/JavaScript"></script>
     {% endblock %}
@@ -19,7 +20,7 @@
     <link rel="stylesheet" href="{{ url_for('static', filename='css/style.css') }}" type="text/css">
     <link rel="shortcut icon" href="{{ url_for('static', filename='images/favicon.ico') }}">
 </head>
-<body role="document" onload="{% block onload %}{% endblock %}">
+<body role="document" onload="{% block onload %}dgenies.init();{% endblock %}">
 {% block body %}
     <div id="main-wrapper">
         <!-- Fixed navbar -->
@@ -39,24 +40,10 @@
                     <ul class="nav navbar-nav">
                         <li class="{% if(menu == 'index') %}active{% endif %}"><a href="/">About</a></li>
                         <li class="{% if(menu == 'run') %}active{% endif %}"><a href="/run">Run</a></li>
-                        <li class="dropdown {% if(menu == 'result') %}active{% endif %}">
+                        <li class="dropdown result {% if(menu == 'result') %}active{% endif %}">
                             <a href="#" class="dropdown-toggle" data-toggle="dropdown">Results<span
                                     class="caret"></span></a>
                             <ul class="dropdown-menu" role="menu">
-                                {% block results %}
-                                    {% set has_job = False %}
-                                    {% if current_result and current_result not in results %}
-                                        {% set has_job = True %}
-                                        <li><a href="/result/{{ current_result }}">{{ current_result }}</a></li>
-                                    {% endif %}
-                                    {% if results | length > 0 %}
-                                        {% for result in results %}
-                                            <li><a href="/result/{{ result }}">{{ result }}</a></li>
-                                        {% endfor %}
-                                    {% elif not has_job %}
-                                        <li><a href="/run">Please run a job!</a></li>
-                                    {% endif %}
-                                {% endblock %}
                             </ul>
                         </li>
                         {% if mode == "webserver" %}

src/dgenies/templates/result.html

@@ -16,7 +16,10 @@
     <script src="{{ url_for('static', filename='js/BootstrapMenu.min.js') }}" type="text/JavaScript"></script>
     <link rel="stylesheet" href="{{ url_for('static', filename='css/chosen.min.css') }}" type="text/css">
 {% endblock %}
-{% block onload %}dgenies.result.init('{{ id }}');{% endblock %}
+{% block onload %}
+    {{ super() }}
+    dgenies.result.init('{{ id }}');
+{% endblock %}
 {% block content %}
 {{ super() }}
 
@@ -71,6 +74,9 @@
                 <p><input type="button" id="sort-contigs" value="Sort contigs"/></p>
                 <p><input type="button" id="hide-noise" value="Hide noise"/></p>
                 <p><input type="button" id="summary" value="Summary"/></p>
+                {% if not is_gallery %}
+                    <p class="bottom"><input type="button" id="delete-job" value="Delete job"/></p>
+                {% endif %}
             </form>
         </div>
     </div>

src/dgenies/templates/run.html

@@ -9,7 +9,10 @@
     <script src="{{ url_for('static', filename='js/jquery.fileupload-validate.js') }}"></script>
     <script src="{{ url_for('static', filename='js/dgenies.run.js') }}" type="text/JavaScript"></script>
 {% endblock %}
-{% block onload %}dgenies.run.init('{{ s_id }}',{{ allowed_ext }}, {{ max_upload_file_size }}, '{{ mode }}');{% endblock %}
+{% block onload %}
+    {{ super() }}
+    dgenies.run.init('{{ s_id }}',{{ allowed_ext }}, {{ max_upload_file_size }}, '{{ mode }}');
+{% endblock %}
 {% block content %}
     <form id="submit_minimap" method=post action="#">
         <h2 class="title-launch">Launch map analysis</h2>

src/dgenies/templates/status.html

@@ -3,7 +3,10 @@
     {{ super() }}
         <script src="{{ url_for('static', filename='js/dgenies.status.js') }}" type="text/JavaScript"></script>
 {% endblock %}
-{% block onload %}dgenies.status.init('{{ status }}', '{{ mode }}');{% endblock %}
+{% block onload %}
+    {{ super() }}
+    dgenies.status.init('{{ status }}', '{{ mode }}');
+{% endblock %}
 {% block content %}
     <h2 class="status">Job name: {{ id_job }}</h2>
     <div class="status-body">

src/dgenies/views.py

@@ -20,12 +20,6 @@ if MODE == "webserver":
     from peewee import DoesNotExist
 
 
-@app.context_processor
-def get_launched_results():
-    cookie = request.cookies.get("results")
-    return {"results": cookie.split("|") if cookie is not None else set()}
-
-
 # Main
 @app.route("/", methods=['GET'])
 def main():
@@ -182,15 +176,8 @@ def status(id_job):
 # Results path
 @app.route("/result/<id_res>", methods=['GET'])
 def result(id_res):
-    my_render = render_template("result.html", title=app_title, id=id_res, menu="result", current_result=id_res,
-                                mode=MODE)
-    response = app.make_response(my_render)
-    cookie = request.cookies.get("results")
-    cookie = cookie.split("|") if cookie is not None else []
-    if id_res not in cookie:
-        cookie.insert(0, id_res)
-    response.set_cookie(key="results", value="|".join(cookie), path="/")
-    return response
+    return render_template("result.html", title=app_title, id=id_res, menu="result", current_result=id_res, mode=MODE,
+                           is_gallery=Functions.is_in_gallery(id_res, MODE))
 
 
 @app.route("/gallery", methods=['GET'])
@@ -222,7 +209,7 @@ def get_file(file, gzip=False):  # pragma: no cover
     except FileNotFoundError:
         abort(404)
     except IOError as exc:
-        print(exc)
+        print(exc.__traceback__)
         abort(500)
 
 
@@ -664,3 +651,13 @@ def send_mail(id_res):
         return "OK"
     else:
         abort(403)
+
+
+@app.route("/delete/<id_res>", methods=['POST'])
+def delete_job(id_res):
+    job = JobManager(id_job=id_res)
+    success, error = job.delete()
+    return jsonify({
+        "success": success,
+        "error": error
+    })