Resolved conflicts for pulling from testing branch

4 files changed, 175 insertions, 18 deletions

diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
new file mode 100644
index 00000000..1dba357d
--- /dev/null
+++ b/wqflask/utility/elasticsearch_tools.py
@@ -0,0 +1,58 @@
+from elasticsearch import Elasticsearch, TransportError
+import logging
+
+from utility.logger import getLogger
+logger = getLogger(__name__)
+
+from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT
+
+def test_elasticsearch_connection():
+    es = Elasticsearch(['http://'+ELASTICSEARCH_HOST+":"+ELASTICSEARCH_PORT+'/'], verify_certs=True)
+    if not es.ping():
+        logger.warning("Elasticsearch is DOWN")
+
+def get_elasticsearch_connection():
+    """Return a connection to ES. Returns None on failure"""
+    logger.info("get_elasticsearch_connection")
+    es = None
+    try:
+        assert(ELASTICSEARCH_HOST)
+        assert(ELASTICSEARCH_PORT)
+        logger.info("ES HOST",ELASTICSEARCH_HOST)
+
+        es = Elasticsearch([{
+            "host": ELASTICSEARCH_HOST, "port": ELASTICSEARCH_PORT
+        }]) if (ELASTICSEARCH_HOST and ELASTICSEARCH_PORT) else None
+
+        es_logger = logging.getLogger("elasticsearch")
+        es_logger.setLevel(logging.INFO)
+        es_logger.addHandler(logging.NullHandler())
+    except:
+        logger.error("Failed to get elasticsearch connection")
+        es = None
+
+    return es
+
+def get_user_by_unique_column(es, column_name, column_value, index="users", doc_type="local"):
+    return get_item_by_unique_column(es, column_name, column_value, index=index, doc_type=doc_type)
+
+def save_user(es, user, user_id):
+    es_save_data(es, "users", "local", user, user_id)
+
+def get_item_by_unique_column(es, column_name, column_value, index, doc_type):
+    item_details = None
+    try:
+        response = es.search(
+            index = index, doc_type = doc_type, body = {
+                "query": { "match": { column_name: column_value } }
+            })
+        if len(response["hits"]["hits"]) > 0:
+            item_details = response["hits"]["hits"][0]["_source"]
+    except TransportError as te:
+        pass
+    return item_details
+
+def es_save_data(es, index, doc_type, data_item, data_id,):
+    from time import sleep
+    es.create(index, doc_type, body=data_item, id=data_id)
+    sleep(1) # Delay 1 second to allow indexing
diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py
new file mode 100644
index 00000000..5a62cc50
--- /dev/null
+++ b/wqflask/utility/startup_config.py
@@ -0,0 +1,39 @@
+
+from wqflask import app
+from utility.tools import WEBSERVER_MODE, show_settings, get_setting_int, get_setting, get_setting_bool
+
+import utility.logger
+logger = utility.logger.getLogger(__name__ )
+
+BLUE  = '\033[94m'
+GREEN = '\033[92m'
+BOLD  = '\033[1m'
+ENDC  = '\033[0m'
+
+def app_config():
+    app.config['SESSION_TYPE'] = 'filesystem'
+    if not app.config.get('SECRET_KEY'):
+        import os
+        app.config['SECRET_KEY'] = str(os.urandom(24))
+
+    mode = WEBSERVER_MODE
+    if mode == "DEV" or mode == "DEBUG":
+        app.config['TEMPLATES_AUTO_RELOAD'] = True
+        # if mode == "DEBUG":
+        #     app.config['EXPLAIN_TEMPLATE_LOADING'] = True <--- use overriding app param instead
+    print("==========================================")
+    show_settings()
+
+    port = get_setting_int("SERVER_PORT")
+
+    if get_setting_bool("USE_GN_SERVER"):
+        print("GN2 API server URL is ["+BLUE+get_setting("GN_SERVER_URL")+ENDC+"]")
+        import requests
+        page = requests.get(get_setting("GN_SERVER_URL"))
+        if page.status_code != 200:
+            raise Exception("API server not found!")
+
+    import utility.elasticsearch_tools as es
+    es.test_elasticsearch_connection()
+
+    print("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % (BLUE,str(port),ENDC,get_setting("WEBSERVER_URL")))
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index d3113302..ea216a35 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -54,7 +54,7 @@ def get_setting(command_id,guess=None):
     # print("Looking for "+command_id+"\n")
     command = value(os.environ.get(command_id))
     if command is None or command == "":
-        command = OVERRIDES.get(command_id)
+        command = OVERRIDES.get(command_id) # currently not in use
         if command is None:
             # ---- Check whether setting exists in app
             command = value(app.config.get(command_id))
@@ -220,7 +220,7 @@ def show_settings():
 
     logger.info(OVERRIDES)
     logger.info(BLUE+"Mr. Mojo Risin 2"+ENDC)
-    print "runserver.py: ****** Webserver configuration ******"
+    print "runserver.py: ****** Webserver configuration - k,v pairs from app.config ******"
     keylist = app.config.keys()
     keylist.sort()
     for k in keylist:
@@ -251,6 +251,31 @@ assert_dir(JS_GUIX_PATH)
 JS_GN_PATH         = get_setting('JS_GN_PATH')
 # assert_dir(JS_GN_PATH)
 
+GITHUB_CLIENT_ID = get_setting('GITHUB_CLIENT_ID')
+GITHUB_CLIENT_SECRET = get_setting('GITHUB_CLIENT_SECRET')
+GITHUB_AUTH_URL = None
+if GITHUB_CLIENT_ID != 'UNKNOWN' and GITHUB_CLIENT_SECRET:
+    GITHUB_AUTH_URL = "https://github.com/login/oauth/authorize?client_id=" + \
+                      GITHUB_CLIENT_ID+"&client_secret="+GITHUB_CLIENT_SECRET
+    GITHUB_API_URL = get_setting('GITHUB_API_URL')
+
+ORCID_CLIENT_ID = get_setting('ORCID_CLIENT_ID')
+ORCID_CLIENT_SECRET = get_setting('ORCID_CLIENT_SECRET')
+ORCID_AUTH_URL = None
+if ORCID_CLIENT_ID != 'UNKNOWN' and ORCID_CLIENT_SECRET:
+    ORCID_AUTH_URL = "https://sandbox.orcid.org/oauth/authorize?response_type=code&scope=/authenticate&show_login=true&client_id=" + \
+                      ORCID_CLIENT_ID+"&client_secret="+ORCID_CLIENT_SECRET
+    ORCID_TOKEN_URL = get_setting('ORCID_TOKEN_URL')
+
+ELASTICSEARCH_HOST = get_setting('ELASTICSEARCH_HOST')
+ELASTICSEARCH_PORT = get_setting('ELASTICSEARCH_PORT')
+import utility.elasticsearch_tools as es
+es.test_elasticsearch_connection()
+
+SMTP_CONNECT = get_setting('SMTP_CONNECT')
+SMTP_USERNAME = get_setting('SMTP_USERNAME')
+SMTP_PASSWORD = get_setting('SMTP_PASSWORD')
+
 PYLMM_COMMAND      = app_set("PYLMM_COMMAND",pylmm_command())
 GEMMA_COMMAND      = app_set("GEMMA_COMMAND",gemma_command())
 assert(GEMMA_COMMAND is not None)
@@ -260,23 +285,16 @@ TEMPDIR            = tempdir() # defaults to UNIX TMPDIR
 assert_dir(TEMPDIR)
 
 # ---- Handle specific JS modules
+JS_GUIX_PATH = get_setting("JS_GUIX_PATH")
+assert_dir(JS_GUIX_PATH)
+assert_dir(JS_GUIX_PATH+'/cytoscape-panzoom')
+CSS_PATH = "UNKNOWN"
+# assert_dir(JS_PATH)
 JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("Twitter-Post-Fetcher"))
 assert_dir(JS_TWITTER_POST_FETCHER_PATH)
-
-from six import string_types
-
-if os.environ.get('WQFLASK_OVERRIDES'):
-    jsonfn = get_setting('WQFLASK_OVERRIDES')
-    logger.info("WQFLASK_OVERRIDES: %s" % jsonfn)
-    with open(jsonfn) as data_file:
-        overrides = json.load(data_file)
-        for k in overrides:
-            cmd = overrides[k]
-            if isinstance(cmd, string_types):
-                OVERRIDES[k] = eval(cmd)
-            else:
-                OVERRIDES[k] = cmd
-            logger.debug(OVERRIDES)
+assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js")
+JS_CYTOSCAPE_PATH = get_setting("JS_CYTOSCAPE_PATH",js_path("cytoscape"))
+assert_dir(JS_CYTOSCAPE_PATH)
+assert_file(JS_CYTOSCAPE_PATH+'/cytoscape.min.js')
 
 # assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData")
-assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js")
diff --git a/wqflask/utility/type_checking.py b/wqflask/utility/type_checking.py
new file mode 100644
index 00000000..220e5f62
--- /dev/null
+++ b/wqflask/utility/type_checking.py
@@ -0,0 +1,42 @@
+# Type checking functions
+
+def is_float(value):
+    try:
+        float(value)
+        return True
+    except:
+        return False
+
+def is_int(value):
+    try:
+        int(value)
+        return True
+    except:
+        return False
+
+def is_str(value):
+    if value is None:
+        return False
+    try:
+        str(value)
+        return True
+    except:
+        return False
+
+def get_float(vars,name,default=None):
+    if name in vars:
+        if is_float(vars[name]):
+            return float(vars[name])
+    return None
+
+def get_int(vars,name,default=None):
+    if name in vars:
+        if is_int(vars[name]):
+            return float(vars[name])
+    return default
+
+def get_string(vars,name,default=None):
+    if name in vars:
+        if not vars[name] is None:
+            return str(vars[name])
+    return default