Merge remote-tracking branch 'origin/pride' into pride

.Dockerfile

@@ -30,7 +30,7 @@ RUN mkdir -p /home/appuser/logs
 COPY static ./static
 COPY templates ./templates
 COPY tests ./tests
-COPY xi_web_api ./xi_web_api
+COPY xiview_server ./xiview_server
 COPY .env .
 COPY default.database.ini .
 COPY logging.ini .

.env

@@ -1,3 +1,3 @@
 PYTHONHASHSEED=0
-FLASK_APP="xi_web_api/pride_loader.py"
+FLASK_APP="xiview_server/pride_loader.py"
 XI2XIVIEWLOADER_SETTINGS=config

logging.ini

@@ -15,7 +15,12 @@ handlers=fileHandler, console_handler
 class=FileHandler
 level=DEBUG
 formatter=simpleFormatter
-args=('logs/xi_web_api.log',)
+args=('logs/xiview_server.log',)
+
+[handler_console_handler]
+class = StreamHandler
+formatter = simpleFormatter
+args = (sys.stdout,)
 
 [handler_console_handler]
 class = StreamHandler

setup.cfg

@@ -1,7 +1,7 @@
 [tool:pytest]
 pep8maxlinelength = 100
 flake8-max-line-length = 100
-#addopts = --cov=xi_web_api --cov-report html --cov-branch --cov-fail-under=90 --flake8
+#addopts = --cov=xiview_server --cov-report html --cov-branch --cov-fail-under=90 --flake8
 
 [flake8]
 ignore = F403,E226,F405,W503

static/network.html

@@ -165,8 +165,8 @@
     //<![CDATA[
     //     window.xiSpecBaseDir = "/spectrum/"; // you may need to edit this depending on where xiView_container is in web server folder
     window.xiAnnotRoot = "xiAnnotator/";
-    window.peakListUrl = "get_peaklist";
-    xiview.main("PRIDE", "get_data");
+    window.peakListUrl = "http://www.ebi.ac.uk/pride/archive/xiview/data/get_peaklist";
+    xiview.main("PRIDE", "http://www.ebi.ac.uk/pride/archive/xiview/data/get_xiview_data");
 
     //]]>
     </script>

static/pride.css

@@ -92,4 +92,8 @@
 
 #xiNetButtonBar > span.layoutLabel.noBreak.sectionDividerLeft {
     border-left: 0;
+}
+
+#helpDropdownPlaceholder > div > ul > li:nth-child(1) {
+    display: none !important;
 }