Merge branch 'dev'

Author: kmoad

cravat/admin_util.py

@@ -921,6 +921,8 @@ def get_system_conf(file_only=False):
             conf[constants.user_email_key] = constants.default_user_email
         if constants.user_email_opt_out_key not in conf:
             conf[constants.user_email_opt_out_key] = constants.default_user_email_opt_out
+        if constants.user_survey_key not in conf:
+            conf[constants.user_survey_key] = constants.default_user_survey
         if "custom_system_conf" in globals():
             global custom_system_conf
             for k, v in custom_system_conf.items():

cravat/constants.py

@@ -133,6 +133,10 @@
 default_user_email = ''
 default_user_email_opt_out = False
 
+# user survey
+user_survey_key = 'show_user_survey'
+default_user_survey = True
+
 # liftover
 liftover_chains_dir = os.path.join(packagedir, "liftover")
 liftover_chain_paths = {

cravat/cravat_web.py

@@ -559,7 +559,7 @@ def check_local_update(interval):
         except requests.exceptions.ConnectionError:
             pass
         print(
-            """
+            r"""
    ____                   __________  ___ _    _____  ______
   / __ \____  ___  ____  / ____/ __ \/   | |  / /   |/_  __/
  / / / / __ \/ _ \/ __ \/ /   / /_/ / /| | | / / /| | / /   

cravat/util.py

@@ -18,6 +18,24 @@
 import math
 
 
+def discretize_scalar(score, cutoffs):
+    """Locate the location of `score` in a list[tuple(float, str)] of
+    `cutoffs`, where the float cutoff is the maximum value, inclusive
+    of the value, for that label. The last tuple should typically have
+    `float("inf")` as the cutoff, otherwise the function may retun
+    `None`
+
+    The cutoffs must be sorted in increasing value.
+    """
+    prev_cutoff = None
+    for cutoff, label in cutoffs:
+        if score <= cutoff:
+            return label
+        if prev_cutoff is not None and prev_cutoff > cutoff:
+            raise ValueError("cutoffs are not sorted")
+        prev_cutoff = cutoff
+
+
 def get_ucsc_bins(start, stop=None):
     if stop is None:
         stop = start + 1
@@ -141,12 +159,12 @@ def aa_abbv_to_let(abbvs):
 
 
 tmap_re = re.compile(
-    "\*?(?P<transcript>[A-Z_]+\d+\.\d+):"
-    + "(?P<ref>[A-Z_\*]+)"
-    + "(?P<pos>\d+|NA)"
-    + "(?P<alt>[A-Z_\*]+)"
-    + "\((?P<so>\w+)\)"
-    + "\((?P<hugo>\w+)\)"
+    r"\*?(?P<transcript>[A-Z_]+\d+\.\d+):"
+    + r"(?P<ref>[A-Z_\*]+)"
+    + r"(?P<pos>\d+|NA)"
+    + r"(?P<alt>[A-Z_\*]+)"
+    + r"\((?P<so>\w+)\)"
+    + r"\((?P<hugo>\w+)\)"
 )
 
 codon_table = {
@@ -473,6 +491,7 @@ def humanize_bytes(num, binary=False):
         quot_str = quot_str.rstrip("0").rstrip(".")
     return "{quotient} {unit}".format(quotient=quot_str, unit=unit)
 
+
 def write_log_msg(logger, e):
     if hasattr(e, "msg"):
         if type(e.msg) == list:
@@ -485,4 +504,3 @@ def write_log_msg(logger, e):
     else:
         logger.info(e)
         print(e)
-

cravat/webresult/webresult.py

@@ -268,7 +268,7 @@ async def get_status (request):
     job_id, dbpath = await get_jobid_dbpath(request)
     conn = await get_db_conn(dbpath)
     cursor = await conn.cursor()
-    q = 'select * from info where colkey not like "\_%" escape "\\"'
+    q = r'select * from info where colkey not like "\_%" escape "\\"'
     await cursor.execute(q)
     content = {}
     for row in await cursor.fetchall():
@@ -418,7 +418,7 @@ async def get_jobid_dbpath (request):
     else:
         dbpath = ''
     if dbpath == '':
-        if 'job_id' != '':
+        if job_id != '':
             global wu
             dbpath = await wu.filerouter.job_db(request, job_id, given_username=given_username)
         else:

cravat/webstore/nocache/webstore.js

@@ -1355,9 +1355,13 @@ function onClickModuleDetailUpdateButton(evt) {
     var btn = evt.target;
     var btnModuleName = btn.getAttribute('module');
     var installSize = OC.updates[btnModuleName].size;
+    btn.disabled = true;
     $.ajax({
         url: '/store/freemodulesspace',
         ajax: true,
+        always: function (response) {
+            btn.disabled = false;
+        },
         success: function(response) {
             var freeSpace = response;
             var noSpace = false;

cravat/websubmit/clipboard-check-solid-white.svg

@@ -42,6 +42,12 @@
         <div id='admindiv_tabhead' class='tabhead' value='admindiv' disabled='t' style='display: none;'>
             ADMIN
         </div>
+        <a href="https://docs.google.com/forms/d/1xK1nJre7d_d85QScVFFhdUri3rj9Bs_M0VIhHR8398o" target="_blank" id="survey-button-link" title="User Survey">
+        <div id='survey-button' >
+            <div id='survey-button-icon' class='button-icon' title='User Survey' ></div>
+            User Survey
+        </div>
+        </a>
     </div>
     <div id='header-right'>
         <div id='top-menu'>

cravat/websubmit/clipboard-check-solid.svg

@@ -291,7 +291,7 @@ function getModuleDetailInstallButton(moduleName, td, buttonDiv) {
     } else {
         buttonText = 'Install';
         button.style.backgroundColor = '#beeaff';
-        button.addEventListener('click', () => OC.mediator.publish('moduleinfo.install'));
+        button.addEventListener('click', (evt) => OC.mediator.publish('moduleinfo.install', evt));
     }
     button.textContent = buttonText;
     button.style.padding = '8px';
@@ -321,7 +321,7 @@ function getModuleDetailUpdateButton(moduleName) {
         var titleText = 'Update blocked by: ' + blockString + '. Uninstall blocking modules to update.';
         button.setAttribute('title', titleText);
     }
-    button.addEventListener('click', () => OC.mediator.publish('moduleinfo.update'));
+    button.addEventListener('click', (evt) => OC.mediator.publish('moduleinfo.update', evt));
     return button;
 }
 
@@ -408,6 +408,7 @@ function makeModuleDetailDialog(moduleName, moduleListName, moduleListPos) {
         sdiv.style.marginTop = '10px';
         sdiv.style.fontSize = '12px';
         if (OC.installInfo[moduleName] != undefined) {
+            button.disabled = true;
             sdiv.textContent = OC.installInfo[moduleName]['msg'];
         }
         addEl(td, sdiv);
@@ -619,6 +620,9 @@ function makeModuleDetailDialog(moduleName, moduleListName, moduleListPos) {
                 addEl(d, span);
                 var button = getModuleDetailUpdateButton(moduleName);
                 addEl(buttonDiv, button);
+                if (OC.installInfo[moduleName] !== undefined) {
+                    button.disabled = true;
+                }
             }
         }
     }