From f2bafcc586034da96bf7e9455935dd458c543b5e Mon Sep 17 00:00:00 2001
From: Floreal Cabanettes <floreal.cabanettes@inra.fr>
Date: Tue, 20 Feb 2018 09:11:58 +0100
Subject: [PATCH] Add load of example data in run form, Implements #21
---
application.properties | 4 +++
src/dgenies/INSTALL.md | 10 ++++++-
src/dgenies/config_reader.py | 12 ++++++++
src/dgenies/lib/fasta.py | 22 ++++++++------
src/dgenies/lib/job_manager.py | 5 +++-
src/dgenies/static/js/dgenies.run.js | 24 +++++++++++++--
src/dgenies/templates/run.html | 5 +++-
src/dgenies/views.py | 45 +++++++++++++++++++---------
8 files changed, 98 insertions(+), 29 deletions(-)
diff --git a/application.properties b/application.properties
index aa579d9..d69fec3 100644
--- a/application.properties
+++ b/application.properties
@@ -93,3 +93,7 @@ clean_freq = 1
run_local = 1
data_prepare = 2
max_concurrent_dl = 5
+
+[example]
+query =
+target =
diff --git a/src/dgenies/INSTALL.md b/src/dgenies/INSTALL.md
index 2e1923c..58e6a0b 100644
--- a/src/dgenies/INSTALL.md
+++ b/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
diff --git a/src/dgenies/config_reader.py b/src/dgenies/config_reader.py
index 5c36c0c..28cc5f0 100644
--- a/src/dgenies/config_reader.py
+++ b/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 ""
diff --git a/src/dgenies/lib/fasta.py b/src/dgenies/lib/fasta.py
index c4755dc..504ba22 100644
--- a/src/dgenies/lib/fasta.py
+++ b/src/dgenies/lib/fasta.py
@@ -1,20 +1,24 @@
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
diff --git a/src/dgenies/lib/job_manager.py b/src/dgenies/lib/job_manager.py
index ca0e9bf..afcfcaf 100644
--- a/src/dgenies/lib/job_manager.py
+++ b/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
diff --git a/src/dgenies/static/js/dgenies.run.js b/src/dgenies/static/js/dgenies.run.js
index 051dd44..7d23ae9 100644
--- a/src/dgenies/static/js/dgenies.run.js
+++ b/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();
};
diff --git a/src/dgenies/templates/run.html b/src/dgenies/templates/run.html
index 5ea6076..a06c93b 100644
--- a/src/dgenies/templates/run.html
+++ b/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">
diff --git a/src/dgenies/views.py b/src/dgenies/views.py
index 3577106..9c1432d 100644
--- a/src/dgenies/views.py
+++ b/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:
--
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