From 6b1ff5e1b8390ee88319b4f252acee5d27f4ba97 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Sat, 17 Dec 2016 13:41:33 +0100 Subject: [PATCH 1/3] uwsgi changes --- hicbrowser/views.py | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/hicbrowser/views.py b/hicbrowser/views.py index 249844b..bb5cfa3 100644 --- a/hicbrowser/views.py +++ b/hicbrowser/views.py @@ -128,6 +128,7 @@ def check_static_img_folders(): return dir_path + '/images' +app = Flask(__name__) def main(config_file, port, numProc, template_folder=None, debug=False): @@ -139,7 +140,7 @@ def main(config_file, port, numProc, template_folder=None, debug=False): sys.stderr.write("setting template folder to\n {}\n".format(template_folder)) kwargs['template_folder'] = template_folder - app = Flask(__name__, **kwargs) + #app = Flask(__name__, **kwargs) from flask import Blueprint img_path = check_static_img_folders() @@ -147,6 +148,7 @@ def main(config_file, port, numProc, template_folder=None, debug=False): # register an static path for images using Blueprint images_static = Blueprint('site', __name__, static_url_path='/images', + template_folder=template_folder, static_folder=img_path) app.register_blueprint(images_static) @@ -372,4 +374,15 @@ def get_image(): return None # run the app - app.run(host='0.0.0.0', debug=debug, use_reloader=False, port=port, processes=numProc) + # app.run(host='0.0.0.0', debug=debug, use_reloader=False, port=port, processes=numProc) + +main(config_file='/data/browserConfig.ini', port=8080, template_folder=None, numProc=1, debug=True, create_app=False) + +if __name__ == "__main__": + # run the app + app.run(host='0.0.0.0', debug=True, use_reloader=False, port=8080, processes=2) + + + + + From a9485170c14f57cd4e19b9cef7410c3c6c0a349d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Sat, 17 Dec 2016 14:20:47 +0100 Subject: [PATCH 2/3] Update views.py --- hicbrowser/views.py | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/hicbrowser/views.py b/hicbrowser/views.py index bb5cfa3..30ae6eb 100644 --- a/hicbrowser/views.py +++ b/hicbrowser/views.py @@ -376,13 +376,9 @@ def get_image(): # run the app # app.run(host='0.0.0.0', debug=debug, use_reloader=False, port=port, processes=numProc) -main(config_file='/data/browserConfig.ini', port=8080, template_folder=None, numProc=1, debug=True, create_app=False) +main(config_file='/data/browserConfig.ini', port=8080, template_folder=None, numProc=1, debug=True) if __name__ == "__main__": # run the app app.run(host='0.0.0.0', debug=True, use_reloader=False, port=8080, processes=2) - - - - From 0b893ed4101c7442b5606d7e902ede71a9a0ed32 Mon Sep 17 00:00:00 2001 From: E Rasche Date: Fri, 8 Sep 2017 11:22:02 +0200 Subject: [PATCH 3/3] Remove all slashes and directory traversing --- hicbrowser/client/html/index.html | 24 ++--- hicbrowser/client/js/models/browser.js | 4 +- hicbrowser/client/js/models/config.js | 4 +- hicbrowser/client/js/models/gene.js | 4 +- hicbrowser/client/js/templates.js | 22 ++-- hicbrowser/client/js/views/browser.js | 40 ++++---- hicbrowser/client/templates/gene.hbs | 2 +- hicbrowser/client/templates/index.hbs | 4 +- hicbrowser/client/templates/loading.hbs | 6 +- hicbrowser/static/js/App.js | 130 ++++++++++++++---------- hicbrowser/static/js/App.min.js | 40 ++++---- hicbrowser/templates/index.html | 23 ++--- hicbrowser/views.py | 8 +- 13 files changed, 166 insertions(+), 145 deletions(-) diff --git a/hicbrowser/client/html/index.html b/hicbrowser/client/html/index.html index 76be64c..a5d94d6 100644 --- a/hicbrowser/client/html/index.html +++ b/hicbrowser/client/html/index.html @@ -8,15 +8,15 @@ HiCBrowser - - + + -
+
@@ -24,7 +24,7 @@
- +
@@ -50,21 +50,21 @@

HiCBrowser

- - + +
- - + +
- - + +
@@ -74,8 +74,8 @@

HiCBrowser

- - + + + diff --git a/hicbrowser/views.py b/hicbrowser/views.py index 30ae6eb..099e540 100644 --- a/hicbrowser/views.py +++ b/hicbrowser/views.py @@ -279,10 +279,10 @@ def browser(query): img_code = [] img_content = [] for trp_idx in range(len(trp_list)): - figure_path = "/get_image?region={}:{}-{}&id={}".format(chromosome, _range[0], _range[1], trp_idx) + figure_path = "get_image?region={}:{}-{}&id={}".format(chromosome, _range[0], _range[1], trp_idx) img_code.append(figure_path) - figure_content_path = "/get_image?region={}:|+start+|-|+end+|&id={}".format(chromosome, trp_idx) + figure_content_path = "get_image?region={}:|+start+|-|+end+|&id={}".format(chromosome, trp_idx) img_content.append(figure_content_path) tracks.append(img_code) @@ -293,10 +293,10 @@ def browser(query): img_code = [] img_content = [] for trp_idx in range(len(trp_list)): - figure_path = "/get_image?region={}:{}-{}&id={}".format(chromosome, start, end, trp_idx) + figure_path = "get_image?region={}:{}-{}&id={}".format(chromosome, start, end, trp_idx) img_code.append(figure_path) - figure_content_path = "/get_image?region={}:|+start+|-|+end+|&id={}".format(chromosome, trp_idx) + figure_content_path = "get_image?region={}:|+start+|-|+end+|&id={}".format(chromosome, trp_idx) img_content.append(figure_content_path) tracks.append(img_code)