From 4c2ce5580a0891d89fc35c48da06d25fb4c8df76 Mon Sep 17 00:00:00 2001 From: Muriithi Frederick Muriuki Date: Thu, 22 Mar 2018 06:09:39 +0300 Subject: Fix 'def' statement * End the 'def' statement with a colon (:) * Add an empty line between lines at different indentation levels for clarity. --- wqflask/base/anon_collection.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/base/anon_collection.py b/wqflask/base/anon_collection.py index 8ee73296..dd1aa27f 100644 --- a/wqflask/base/anon_collection.py +++ b/wqflask/base/anon_collection.py @@ -1,6 +1,6 @@ class AnonCollection(TraitCollection): - def __init__(self, anon_id) + def __init__(self, anon_id): self.anon_id = anon_id self.collection_members = Redis.smembers(self.anon_id) print("self.collection_members is:", self.collection_members) @@ -12,6 +12,7 @@ class AnonCollection(TraitCollection): print("traits_to_remove:", traits_to_remove) for trait in traits_to_remove: Redis.srem(self.anon_id, trait) + members_now = self.collection_members - traits_to_remove print("members_now:", members_now) print("Went from {} to {} members in set.".format(len(self.collection_members), len(members_now))) -- cgit v1.2.3 From cfce6d80be4fb38573c37d1943db2687d54cf2fc Mon Sep 17 00:00:00 2001 From: Muriithi Frederick Muriuki Date: Thu, 22 Mar 2018 06:28:01 +0300 Subject: Change raise statement * Change the raise statement to use an Exception object rather than using a string for compatibility with Python3. --- wqflask/utility/svg.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py index 512bc9e6..db13b9d1 100644 --- a/wqflask/utility/svg.py +++ b/wqflask/utility/svg.py @@ -1029,7 +1029,7 @@ class drawing: try: xv.feed(svg) except: - raise "SVG is not well formed, see messages above" + raise Exception("SVG is not well formed, see messages above") else: print "SVG well formed" if __name__=='__main__': -- cgit v1.2.3 From 9396ba78aa204a7f9474c314ca5a519c48ba042c Mon Sep 17 00:00:00 2001 From: Muriithi Frederick Muriuki Date: Fri, 13 Apr 2018 15:41:31 +0300 Subject: Check email provided on forgot password * Ensure that the user actually provides an email address when they try to use the forgot password feature. --- wqflask/wqflask/user_manager.py | 32 +++++++++++++++++--------------- 1 file changed, 17 insertions(+), 15 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py index 5f6c818e..9d09dbf6 100644 --- a/wqflask/wqflask/user_manager.py +++ b/wqflask/wqflask/user_manager.py @@ -727,31 +727,33 @@ def logout(): return response -@app.route("/n/forgot_password") +@app.route("/n/forgot_password", methods=['GET']) def forgot_password(): """Entry point for forgotten password""" - return render_template("new_security/forgot_password.html") + print("ARGS: ", request.args) + errors = {"no-email": request.args.get("no-email")} + print("ERRORS: ", errors) + return render_template("new_security/forgot_password.html", errors=errors) @app.route("/n/forgot_password_submit", methods=('POST',)) def forgot_password_submit(): """When a forgotten password form is submitted we get here""" params = request.form email_address = params['email_address'] - logger.debug("Wants to send password E-mail to ",email_address) - es = get_elasticsearch_connection() - user_details = get_user_by_unique_column(es, "email_address", email_address) - if user_details: - ForgotPasswordEmail(user_details["email_address"]) - # try: - # user = model.User.query.filter_by(email_address=email_address).one() - # except orm.exc.NoResultFound: - # flash("Couldn't find a user associated with the email address {}. Sorry.".format( - # email_address)) - # return redirect(url_for("login")) - # ForgotPasswordEmail(user) - return render_template("new_security/forgot_password_step2.html", + next_page = None + if email_address != "": + logger.debug("Wants to send password E-mail to ",email_address) + es = get_elasticsearch_connection() + user_details = get_user_by_unique_column(es, "email_address", email_address) + if user_details: + ForgotPasswordEmail(user_details["email_address"]) + return render_template("new_security/forgot_password_step2.html", subject=ForgotPasswordEmail.subject) + else: + flash("You MUST provide an email", "alert-danger") + return redirect(url_for("forgot_password")) + @app.errorhandler(401) def unauthorized(error): return redirect(url_for('login')) -- cgit v1.2.3 From ea099c2820fbca3f935fb8dc657b88e71224cded Mon Sep 17 00:00:00 2001 From: Muriithi Frederick Muriuki Date: Sun, 15 Apr 2018 09:53:21 +0300 Subject: Fix issue with indentation * Ensure the return is at the correct indentation level so that it is executed correctly. --- wqflask/wqflask/user_manager.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py index 9d09dbf6..d652f2e9 100644 --- a/wqflask/wqflask/user_manager.py +++ b/wqflask/wqflask/user_manager.py @@ -747,8 +747,9 @@ def forgot_password_submit(): user_details = get_user_by_unique_column(es, "email_address", email_address) if user_details: ForgotPasswordEmail(user_details["email_address"]) - return render_template("new_security/forgot_password_step2.html", - subject=ForgotPasswordEmail.subject) + + return render_template("new_security/forgot_password_step2.html", + subject=ForgotPasswordEmail.subject) else: flash("You MUST provide an email", "alert-danger") -- cgit v1.2.3 From fdd28defcaf3326f3c6b6507124708d83a1da119 Mon Sep 17 00:00:00 2001 From: Muriithi Frederick Muriuki Date: Sun, 15 Apr 2018 11:57:09 +0300 Subject: Deactivate analysis of email_address field * Prevent elasticsearch from analysing and tokenising the email_address field so as to avoid issue with getting back all email addresses with the same domain as the one being searched for. --- wqflask/utility/elasticsearch_tools.py | 13 +++++++++++++ 1 file changed, 13 insertions(+) (limited to 'wqflask') diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py index d35cb5ee..7d2ee8c9 100644 --- a/wqflask/utility/elasticsearch_tools.py +++ b/wqflask/utility/elasticsearch_tools.py @@ -24,6 +24,8 @@ def get_elasticsearch_connection(): "host": ELASTICSEARCH_HOST, "port": ELASTICSEARCH_PORT }]) if (ELASTICSEARCH_HOST and ELASTICSEARCH_PORT) else None + setup_users_index(es) + es_logger = logging.getLogger("elasticsearch") es_logger.setLevel(logging.INFO) es_logger.addHandler(logging.NullHandler()) @@ -33,6 +35,17 @@ def get_elasticsearch_connection(): return es +def setup_users_index(es_connection): + if es_connection: + index_settings = { + "properties": { + "email_address": { + "type": "string" + , "index": "not_analyzed"}}} + + es_connection.indices.create(index='users', ignore=400) + es_connection.indices.put_mapping(body=index_settings, index="users", doc_type="local") + 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) -- cgit v1.2.3 From dda4697505aea2cd950533dfb3a0dfb0e66ec018 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Mon, 16 Apr 2018 09:00:52 +0000 Subject: Docs on elasticsearch use --- README.md | 24 ++++++++++++++------ bin/test-website | 2 +- wqflask/utility/elasticsearch_tools.py | 41 ++++++++++++++++++++++++++++++++++ 3 files changed, 59 insertions(+), 8 deletions(-) (limited to 'wqflask') diff --git a/README.md b/README.md index 3e7e64d0..59645994 100644 --- a/README.md +++ b/README.md @@ -17,25 +17,35 @@ deploy GN2 and dependencies as a self contained unit on any machine. The database can be run separately as well as the source tree (for developers). See the [installation docs](doc/README.org). -## Test +## Run Once installed GN2 can be run online through a browser interface ```sh -./bin/genenetwork2 +genenetwork2 ``` -(default is http://localhost:5003/). For more examples, including running scripts and a Python REPL -see the startup script [./bin/genenetwork2](https://github.com/genenetwork/genenetwork2/blob/testing/bin/genenetwork2). +(default is http://localhost:5003/). For full examples (you'll need to +set a number of environment variables), including running scripts and +a Python REPL, see the startup script +[./bin/genenetwork2](https://github.com/genenetwork/genenetwork2/blob/testing/bin/genenetwork2). +## Testing -We are building up automated -testing using [mechanize](https://github.com/genenetwork/genenetwork2/tree/master/test/lib) which can be run with +We are building 'Mechanical Rob' automated testing using Python +[requests](https://github.com/genenetwork/genenetwork2/tree/master/test/lib) +which can be run with something like ```sh -./bin/test-website +env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -c ../test/requests/test-website.py -a http://localhost:5003 ``` +The GN2_PROFILE is the Guix profile that contains all +dependencies. The ./bin/genenetwork2 script sets up the environment +and executes test-website.py in a Python interpreter. The -a switch +says to run all tests and the URL points to the running GN2 http +server. + ## Documentation User documentation can be found diff --git a/bin/test-website b/bin/test-website index 5935f016..7fbcfd2f 100755 --- a/bin/test-website +++ b/bin/test-website @@ -2,6 +2,6 @@ if [ -z $GN2_PROFILE ]; then echo "Run request tests with something like" - echo env GN2_PROFILE=/home/wrk/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -c ../test/requests/test-website.py http://localhost:5003 + echo env GN2_PROFILE=/home/wrk/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -c ../test/requests/test-website.py -a http://localhost:5003 exit 1 fi diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py index 7d2ee8c9..4d4a9844 100644 --- a/wqflask/utility/elasticsearch_tools.py +++ b/wqflask/utility/elasticsearch_tools.py @@ -1,3 +1,44 @@ +# Elasticsearch support +# +# Some helpful commands to view the database: +# +# You can test the server being up with +# +# curl -H 'Content-Type: application/json' http://localhost:9200 +# +# List all indices +# +# curl -H 'Content-Type: application/json' 'localhost:9200/_cat/indices?v' +# +# To see the users index 'table' +# +# curl http://localhost:9200/users +# +# To list all user ids +# +# curl -H 'Content-Type: application/json' http://localhost:9200/users/local/_search?pretty=true -d ' +# { +# "query" : { +# "match_all" : {} +# }, +# "stored_fields": [] +# }' +# +# To view a record +# +# curl -H 'Content-Type: application/json' http://localhost:9200/users/local/_search?pretty=true -d ' +# { +# "query" : { +# "match" : { "email_address": "pjotr2017@thebird.nl"} +# } +# }' +# +# +# To delete the users index and data (dangerous!) +# +# curl -XDELETE -H 'Content-Type: application/json' 'localhost:9200/users' + + from elasticsearch import Elasticsearch, TransportError import logging -- cgit v1.2.3 From bc1672f8617c56684ae3aeda7018362e818c46d6 Mon Sep 17 00:00:00 2001 From: Muriithi Frederick Muriuki Date: Mon, 16 Apr 2018 17:25:14 +0300 Subject: Update mappings for Elasticsearch 6.2. Update logger * Update the indexes mappings to be compatible with the newer Elasticsearch 6.2.* series. Close the index before updating it, and reopen it after to help with the re-indexing of the data. * Update the error logger to include the exception that was thrown. --- wqflask/utility/elasticsearch_tools.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) (limited to 'wqflask') diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py index 7d2ee8c9..0dc59d43 100644 --- a/wqflask/utility/elasticsearch_tools.py +++ b/wqflask/utility/elasticsearch_tools.py @@ -29,8 +29,8 @@ def get_elasticsearch_connection(): es_logger = logging.getLogger("elasticsearch") es_logger.setLevel(logging.INFO) es_logger.addHandler(logging.NullHandler()) - except: - logger.error("Failed to get elasticsearch connection") + except Exception as e: + logger.error("Failed to get elasticsearch connection", e) es = None return es @@ -40,11 +40,12 @@ def setup_users_index(es_connection): index_settings = { "properties": { "email_address": { - "type": "string" - , "index": "not_analyzed"}}} + "type": "keyword"}}} es_connection.indices.create(index='users', ignore=400) + es_connection.indices.close(index="users") es_connection.indices.put_mapping(body=index_settings, index="users", doc_type="local") + es_connection.indices.open(index="users") 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) -- cgit v1.2.3 From ebbc8c67c13b44df98ea3c2b355e86f77572543b Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Mon, 16 Apr 2018 15:02:16 +0000 Subject: login messages improved --- wqflask/wqflask/templates/new_security/login_user.html | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/templates/new_security/login_user.html b/wqflask/wqflask/templates/new_security/login_user.html index 4a857c60..27b20ebf 100644 --- a/wqflask/wqflask/templates/new_security/login_user.html +++ b/wqflask/wqflask/templates/new_security/login_user.html @@ -31,16 +31,19 @@
{% if external_login["github"]: %} Login with Github + {% else %} +

Github login is not available right now

{% endif %} {% if external_login["orcid"]: %} Login with ORCID + {% else %} +

ORCID login is not available right now

{% endif %}
{% else: %}
-

You cannot login with external services at this time.
- Please try again later.

+

Sorry, you cannot login with Github or ORCID at this time.

{% endif %}
-- cgit v1.2.3