diff options
Diffstat (limited to 'wqflask/utility')
| -rw-r--r-- | wqflask/utility/elasticsearch_tools.py | 58 | ||||
| -rw-r--r-- | wqflask/utility/startup_config.py | 39 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 54 | ||||
| -rw-r--r-- | wqflask/utility/type_checking.py | 42 |
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 |