diff options
| -rw-r--r-- | misc/notes.txt | 16 | ||||
| -rw-r--r-- | wqflask/cfg/default_settings.py | 3 | ||||
| -rw-r--r-- | wqflask/cfg/zach_settings.py | 5 | ||||
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pylmmKinship.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/base.html | 82 |
5 files changed, 60 insertions, 48 deletions
diff --git a/misc/notes.txt b/misc/notes.txt index 976573a6..cdd353ea 100644 --- a/misc/notes.txt +++ b/misc/notes.txt @@ -11,6 +11,9 @@ git add -A Get the default path being used when a command is typed: which _______ +Change default path python looks at when importing +export PYTHONPATH="/home/zas1024/gene/wqflask" + Get the paths checked when a user types a command: echo $PATH @@ -67,7 +70,11 @@ Deactivate virtual environment: deactivate (just type deactivate) To set WQFLASK_SETTINGS environment variable: -export WQFLASK_SETTINGS=~/gene/wqflask/cfg/zach_settings.py (or wherever file is located) +export WQFLASK_SETTINGS=~/zach_settings.py (or wherever file is located) + +zach_settings.py is the local config file with the DB_URI +default_settings.py is the config file with the configuration information that would apply +to any running instance of GeneNetwork To change screen environment variable (if man not working or to get color, for example): export TERM=screen @@ -84,6 +91,13 @@ python runserver.py =========================================== +Update user password: +use mysql; +UPDATE user SET password=PASSWORD('whatever') WHERE user='webqtl'; +FLUSH PRIVILEGES; + +=========================================== + Redis things Restart redis server: diff --git a/wqflask/cfg/default_settings.py b/wqflask/cfg/default_settings.py index 1811ccfd..53b5a96e 100644 --- a/wqflask/cfg/default_settings.py +++ b/wqflask/cfg/default_settings.py @@ -3,3 +3,6 @@ LOGFILE = """/tmp/flask_gn_log""" #This is needed because Flask turns key errors into a #400 bad request response with no exception/log TRAP_BAD_REQUEST_ERRORS = True + +#SECURITY_CONFIRMABLE = True +SECURITY_TRACKABLE = True \ No newline at end of file diff --git a/wqflask/cfg/zach_settings.py b/wqflask/cfg/zach_settings.py deleted file mode 100644 index 1970bd9c..00000000 --- a/wqflask/cfg/zach_settings.py +++ /dev/null @@ -1,5 +0,0 @@ -LOGFILE = """/tmp/flask_gn_log""" - -TRAP_BAD_REQUEST_ERRORS = True - -DB_URI = """mysql://webqtl:f2ZypIflRM@gn.cazhbciu2y1i.us-east-1.rds.amazonaws.com/db_webqtl""" diff --git a/wqflask/wqflask/my_pylmm/pylmmKinship.py b/wqflask/wqflask/my_pylmm/pylmmKinship.py index 403e739d..db1449a4 100644 --- a/wqflask/wqflask/my_pylmm/pylmmKinship.py +++ b/wqflask/wqflask/my_pylmm/pylmmKinship.py @@ -122,7 +122,7 @@ np.savetxt(outFile,K) if options.saveEig: if options.verbose: sys.stderr.write("Obtaining Eigendecomposition\n") - Kva,Kve = linalg.eigh(K) + Kva, Kve = linalg.eigh(K) if options.verbose: sys.stderr.write("Saving eigendecomposition to %s.[kva | kve]\n" % outFile) np.savetxt(outFile+".kva",Kva) diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index 590f5789..71c12941 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -26,49 +26,49 @@ <!-- Navbar ================================================== --> <div class="navbar navbar-inverse navbar-fixed-top"> - <div class="navbar-inner"> - <div class="container"> - <button type="button" class="btn btn-navbar" data-toggle="collapse" data-target=".nav-collapse"> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <a class="brand" href="/">GeneNetwork</a> - <div class="nav-collapse collapse"> - <ul class="nav"> - <li class="active"> - <a href="/">Home</a> - </li> - <li class="dropdown"> - <a id="drop1" href="#" role="button" class="dropdown-toggle" data-toggle="dropdown"> - Search <b class="caret"></b> - </a> - <ul class="dropdown-menu" role="menu" aria-labelledby="drop1"> - <li><a tabindex="-1" href="/webqtl/main.py?FormID=tissueCorrelation">Tissue Corrleation</a></li> - <li><a tabindex="-1" href="/webqtl/main.py?FormID=snpBrowser">SNP Browser</a></li> - <li class="divider"></li> - <li><a tabindex="-1" href="/webqtl/main.py?FormID=geneWiki">Gene Wiki</a></li> + <div class="navbar-inner"> + <div class="container"> + <button type="button" class="btn btn-navbar" data-toggle="collapse" data-target=".nav-collapse"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="brand" href="/">GeneNetwork</a> + <div class="nav-collapse collapse"> + <ul class="nav"> + <li class="active"> + <a href="/">Home</a> + </li> + <li class="dropdown"> + <a id="drop1" href="#" role="button" class="dropdown-toggle" data-toggle="dropdown"> + Search <b class="caret"></b> + </a> + <ul class="dropdown-menu" role="menu" aria-labelledby="drop1"> + <li><a tabindex="-1" href="/webqtl/main.py?FormID=tissueCorrelation">Tissue Corrleation</a></li> + <li><a tabindex="-1" href="/webqtl/main.py?FormID=snpBrowser">SNP Browser</a></li> + <li class="divider"></li> + <li><a tabindex="-1" href="/webqtl/main.py?FormID=geneWiki">Gene Wiki</a></li> + </ul> + </li> + <li class=""> + <a href="#">Help</a> + </li> + <li class=""> + <a href="/whats_new">News</a> + </li> + <li class=""> + <a href="./reference.html">References</a> + </li> + <li class=""> + <a href="./policies">Policies</a> + </li> + <li class=""> + <a href="./links">Links</a> + </li> </ul> - </li> - <li class=""> - <a href="#">Help</a> - </li> - <li class=""> - <a href="/whats_new">News</a> - </li> - <li class=""> - <a href="./reference.html">References</a> - </li> - <li class=""> - <a href="./policies">Policies</a> - </li> - <li class=""> - <a href="./links">Links</a> - </li> - </ul> - </div> + </div> + </div> </div> - </div> </div> {% block content %}{% endblock %} |