Add load of example data in run form, Implements #21

application.properties

@@ -93,3 +93,7 @@ clean_freq = 1
 run_local = 1
 data_prepare = 2
 max_concurrent_dl = 5
+
+[example]
+query =
+target = 

src/dgenies/INSTALL.md

@@ -172,7 +172,7 @@ Configuration
 
 Changing the default configuration is not required for standalone mode, but you can want to custom some parts of the program.
 
-Configuration is stored in the `/etc/dgenies/application.properties` file (linux) or in the `application.properties` file of the install folder (windows). The file is divided in 8 parts described below.
+Configuration is stored in the `/etc/dgenies/application.properties` file (linux) or in the `application.properties` file of the install folder (windows). The file is divided in 9 parts described below.
 
 To change this file, please copy it into `application.properties.local` (at the same location) to avoid erase of the file on upgrades.
 
@@ -281,6 +281,14 @@ Several parameters for jobs:
 * `data_prepare`: max number of data prepare jobs launched locally.
 * `max_concurrent_dl`: max number of concurrent upload of files allowed.
 
+### Example
+
+Here, you can fill example data. At least target is required to enable example data.
+
+Fill for target and query the absolute local path of the file. This path will not be shown to the client. Only the file name will be shown.
+
+If at least target is filled, a button "Load example" will be shown in the run form. Click on it will load example data in the form.
+
 
 
 Maintenance

src/dgenies/config_reader.py

@@ -403,3 +403,15 @@ class AppConfigReader:
         except (NoOptionError, NoSectionError):
             pass
         return allowed_ip
+
+    def _get_example_query(self):
+        try:
+            return self.reader.get("example", "query")
+        except (NoOptionError, NoSectionError):
+            return ""
+
+    def _get_example_target(self):
+        try:
+            return self.reader.get("example", "target")
+        except (NoOptionError, NoSectionError):
+            return ""

src/dgenies/lib/fasta.py

 class Fasta:
-    def __init__(self, name, path, type_f):
-        self.__name = name
-        self.__path = path
-        self.__type = type_f
+    def __init__(self, name, path, type_f, example=False):
+        self._name = name
+        self._path = path
+        self._type = type_f
+        self._example = example
 
     def set_path(self, path):
-        self.__path = path
+        self._path = path
 
     def get_path(self):
-        return self.__path
+        return self._path
 
     def set_name(self, name):
-        self.__name = name
+        self._name = name
 
     def get_name(self):
-        return self.__name
+        return self._name
 
     def get_type(self):
-        return self.__type
+        return self._type
+
+    def is_example(self):
+        return self._example

src/dgenies/lib/job_manager.py

@@ -371,7 +371,10 @@ class JobManager:
 
     def __getting_local_file(self, fasta: Fasta, type_f):
         finale_path = os.path.join(self.output_dir, type_f + "_" + os.path.basename(fasta.get_path()))
-        shutil.move(fasta.get_path(), finale_path)
+        if fasta.is_example():
+            shutil.copy(fasta.get_path(), finale_path)
+        else:
+            shutil.move(fasta.get_path(), finale_path)
         with open(os.path.join(self.output_dir, "." + type_f), "w") as save_file:
             save_file.write(finale_path)
         return finale_path

src/dgenies/static/js/dgenies.run.js

@@ -10,11 +10,15 @@ dgenies.run.max_upload_file_size = -1
 dgenies.run.files = [undefined, undefined];
 dgenies.run.allow_upload = false;
 dgenies.run.ping_interval = null;
+dgenies.run.target_example = "";
+dgenies.run.query_example = "";
 
-dgenies.run.init = function (s_id, allowed_ext, max_upload_file_size=1073741824) {
+dgenies.run.init = function (s_id, allowed_ext, max_upload_file_size=1073741824, target_example="", query_example="") {
     dgenies.run.s_id = s_id;
     dgenies.run.allowed_ext = allowed_ext;
-    dgenies.run.max_upload_file_size = max_upload_file_size
+    dgenies.run.max_upload_file_size = max_upload_file_size;
+    dgenies.run.target_example = target_example;
+    dgenies.run.query_example = query_example;
     dgenies.run.restore_form();
     dgenies.run.set_events();
     dgenies.run.init_fileuploads();
@@ -154,6 +158,15 @@ dgenies.run.get_file_size_str = function(size) {
     return Math.round(size / 1073741824) + " Go";
 };
 
+dgenies.run.fill_examples = function () {
+    $("select.target").val("1").trigger("change");
+    $("input#target").val("example://" + dgenies.run.target_example);
+    if (dgenies.run.query_example !== "") {
+        $("select.query").val("1").trigger("change");
+        $("input#query").val("example://" + dgenies.run.query_example);
+    }
+};
+
 dgenies.run.set_events = function() {
     let max_file_size_txt = dgenies.run.get_file_size_str(dgenies.run.max_upload_file_size);
     $("input.file-query").change(function () {
@@ -204,6 +217,9 @@ dgenies.run.set_events = function() {
     $("select.target").change(function() {
         dgenies.run.change_fasta_type("target", $("select.target").find(":selected").text().toLowerCase())
     });
+    $("button#example").click(function() {
+        dgenies.run.fill_examples();
+    });
 };
 
 dgenies.run.change_fasta_type = function (fasta, type, keep_url=false) {
@@ -381,7 +397,8 @@ dgenies.run.ping_upload = function () {
 };
 
 dgenies.run.check_url = function (url) {
-    return url.startsWith("http://") || url.startsWith("https://") || url.startsWith("ftp://");
+    return url.startsWith("http://") || url.startsWith("https://") || url.startsWith("ftp://") ||
+        url.startsWith("example://");
 };
 
 dgenies.run.start_uploads = function() {
@@ -427,6 +444,7 @@ dgenies.run.start_uploads = function() {
 
 dgenies.run.show_global_loading = function () {
     $("button#submit").hide();
+    $("button#example").hide();
     $("div#uploading-loading").show();
 };
 

src/dgenies/templates/run.html

@@ -11,7 +11,7 @@
 {% endblock %}
 {% block onload %}
     {{ super() }}
-    dgenies.run.init('{{ s_id }}',{{ allowed_ext }}, {{ max_upload_file_size }});
+    dgenies.run.init('{{ s_id }}',{{ allowed_ext }}, {{ max_upload_file_size }}, '{{ target }}', '{{ query }}');
 {% endblock %}
 {% block content %}
     <form id="submit_minimap" method=post action="#">
@@ -107,6 +107,9 @@
             <p class="afterworlff">* We will send you results by mail.</p>
             <p class="afterworlff">** Can be gzipped.</p>
             <button type="button" id="submit">Submit</button>
+            {% if example %}
+            <button type="button" id="example">Load example</button>
+            {% endif %}
         </div>
         <div id="uploading-loading" style="display:none;">Uploading files...</div>
         <div class="hidden-input-files">

src/dgenies/views.py

@@ -64,7 +64,10 @@ def run():
         email = request.args["email"]
     return render_template("run.html", id_job=id_job, email=email,
                            menu="run", allowed_ext=ALLOWED_EXTENSIONS, s_id=s_id,
-                           max_upload_file_size=config_reader.max_upload_file_size)
+                           max_upload_file_size=config_reader.max_upload_file_size,
+                           example=config_reader.example_target != "",
+                           target=os.path.basename(config_reader.example_target),
+                           query=os.path.basename(config_reader.example_query))
 
 
 @app.route("/run-test", methods=['GET'])
@@ -134,20 +137,34 @@ def launch_analysis():
         # Save files:
         query = None
         if file_query != "":
-            query_name = os.path.splitext(file_query.replace(".gz", ""))[0] if file_query_type == "local" else None
-            query_path = os.path.join(app.config["UPLOAD_FOLDER"], upload_folder, file_query) \
-                if file_query_type == "local" else file_query
-            if file_query_type == "local" and not os.path.exists(query_path):
-                errors.append("Query file not correct!")
+            example = False
+            if file_query.startswith("example://"):
+                example = True
+                query_path = config_reader.example_query
+                query_name = os.path.basename(query_path)
+                file_query_type = "local"
+            else:
+                query_name = os.path.splitext(file_query.replace(".gz", ""))[0] if file_query_type == "local" else None
+                query_path = os.path.join(app.config["UPLOAD_FOLDER"], upload_folder, file_query) \
+                    if file_query_type == "local" else file_query
+                if file_query_type == "local" and not os.path.exists(query_path):
+                    errors.append("Query file not correct!")
+                    form_pass = False
+            query = Fasta(name=query_name, path=query_path, type_f=file_query_type, example=example)
+        example = False
+        if file_target.startswith("example://"):
+            example = True
+            target_path = config_reader.example_target
+            target_name = os.path.basename(target_path)
+            file_target_type = "local"
+        else:
+            target_name = os.path.splitext(file_target.replace(".gz", ""))[0] if file_target_type == "local" else None
+            target_path = os.path.join(app.config["UPLOAD_FOLDER"], upload_folder, file_target) \
+                if file_target_type == "local" else file_target
+            if file_target_type == "local" and not os.path.exists(target_path):
+                errors.append("Target file not correct!")
                 form_pass = False
-            query = Fasta(name=query_name, path=query_path, type_f=file_query_type)
-        target_name = os.path.splitext(file_target.replace(".gz", ""))[0] if file_target_type == "local" else None
-        target_path = os.path.join(app.config["UPLOAD_FOLDER"], upload_folder, file_target) \
-            if file_target_type == "local" else file_target
-        if file_target_type == "local" and not os.path.exists(target_path):
-            errors.append("Target file not correct!")
-            form_pass = False
-        target = Fasta(name=target_name, path=target_path, type_f=file_target_type)
+        target = Fasta(name=target_name, path=target_path, type_f=file_target_type, example=example)
 
         if form_pass:
             # Launch job: