Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing

5 files changed, 340 insertions, 11 deletions

diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
new file mode 100644
index 00000000..f9028f32
--- /dev/null
+++ b/wqflask/utility/authentication_tools.py
@@ -0,0 +1,96 @@
+from __future__ import absolute_import, print_function, division
+
+import json
+import requests
+
+from base import data_set, webqtlConfig
+
+from utility import hmac
+from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id
+Redis = get_redis_conn()
+
+from flask import Flask, g, redirect, url_for
+
+import logging
+logger = logging.getLogger(__name__ )
+
+def check_resource_availability(dataset, trait_id=None):
+
+    #ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy
+    if g.user_session.user_id in Redis.smembers("super_users"):
+       return webqtlConfig.SUPER_PRIVILEGES
+
+    response = None
+
+    #At least for now assume temporary entered traits are accessible#At least for now assume temporary entered traits are accessible
+    if type(dataset) == str:
+        return webqtlConfig.DEFAULT_PRIVILEGES
+    if dataset.type == "Temp":
+        return webqtlConfig.DEFAULT_PRIVILEGES
+
+    resource_id = get_resource_id(dataset, trait_id)
+
+    if resource_id:
+        resource_info = get_resource_info(resource_id)
+        if not resource_info:
+            return webqtlConfig.DEFAULT_PRIVILEGES
+    else:
+        return response #ZS: Need to substitute in something that creates the resource in Redis later
+
+    the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
+    try:
+        response = json.loads(requests.get(the_url).content)
+    except:
+        response = resource_info['default_mask']
+
+    if response:
+        return response
+    else: #ZS: No idea how this would happen, but just in case
+        return False
+
+def check_admin(resource_id=None):
+    the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
+    try:
+        response = json.loads(requests.get(the_url).content)['admin']
+    except:
+        response = resource_info['default_mask']['admin']
+
+    if 'edit-admins' in response:
+        return "edit-admins"
+    elif 'edit-access' in response:
+        return "edit-access"
+    else:
+        return "not-admin"
+
+def check_owner(dataset=None, trait_id=None, resource_id=None):
+    if resource_id:
+        resource_info = get_resource_info(resource_id)
+        if g.user_session.user_id == resource_info['owner_id']:
+            return resource_id
+    else:
+        resource_id = get_resource_id(dataset, trait_id)
+        if resource_id:
+            resource_info = get_resource_info(resource_id)
+            if g.user_session.user_id == resource_info['owner_id']:
+                return resource_id
+
+    return False
+
+def check_owner_or_admin(dataset=None, trait_id=None, resource_id=None):
+    if not resource_id:
+        if dataset.type == "Temp":
+            return "not-admin"
+        else:
+            resource_id = get_resource_id(dataset, trait_id)
+
+    if g.user_session.user_id in Redis.smembers("super_users"):
+        return "owner"
+
+    resource_info = get_resource_info(resource_id)
+    if resource_info:
+        if g.user_session.user_id == resource_info['owner_id']:
+            return "owner"
+        else:
+            return check_admin(resource_id)
+
+    return "not-admin"
\ No newline at end of file
diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py
index e7c04fef..9ce809b6 100644
--- a/wqflask/utility/helper_functions.py
+++ b/wqflask/utility/helper_functions.py
@@ -1,7 +1,7 @@
 from __future__ import absolute_import, print_function, division
 
-from base.trait import GeneralTrait
 from base import data_set
+from base.trait import create_trait
 from base.species import TheSpecies
 
 from utility import hmac
@@ -11,7 +11,6 @@ from flask import Flask, g
 import logging
 logger = logging.getLogger(__name__ )
 
-
 def get_species_dataset_trait(self, start_vars):
     #assert type(read_genotype) == type(bool()), "Expecting boolean value for read_genotype"
     if "temp_trait" in start_vars.keys():
@@ -24,7 +23,7 @@ def get_species_dataset_trait(self, start_vars):
     logger.debug("After creating dataset")
     self.species = TheSpecies(dataset=self.dataset)
     logger.debug("After creating species")
-    self.this_trait = GeneralTrait(dataset=self.dataset,
+    self.this_trait = create_trait(dataset=self.dataset,
                                    name=start_vars['trait_id'],
                                    cellid=None,
                                    get_qtl_info=True)
@@ -34,7 +33,6 @@ def get_species_dataset_trait(self, start_vars):
     #self.dataset.group.read_genotype_file()
     #self.genotype = self.dataset.group.genotype
 
-
 def get_trait_db_obs(self, trait_db_list):
     if isinstance(trait_db_list, basestring):
         trait_db_list = trait_db_list.split(",")
@@ -49,10 +47,11 @@ def get_trait_db_obs(self, trait_db_list):
             dataset_ob = data_set.create_dataset(dataset_name=dataset_name, dataset_type="Temp", group_name=trait_name.split("_")[2])
         else:
             dataset_ob = data_set.create_dataset(dataset_name)
-        trait_ob = GeneralTrait(dataset=dataset_ob,
+        trait_ob = create_trait(dataset=dataset_ob,
                                name=trait_name,
                                cellid=None)
-        self.trait_list.append((trait_ob, dataset_ob))
+        if trait_ob:
+            self.trait_list.append((trait_ob, dataset_ob))
 
 def get_species_groups():
 
diff --git a/wqflask/utility/hmac.py b/wqflask/utility/hmac.py
index d8a0eace..b08be97e 100644
--- a/wqflask/utility/hmac.py
+++ b/wqflask/utility/hmac.py
@@ -3,6 +3,8 @@ from __future__ import print_function, division, absolute_import
 import hmac
 import hashlib
 
+from flask import url_for
+
 from wqflask import app
 
 def hmac_creation(stringy):
diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index 0754e16f..6c912a23 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -1,17 +1,26 @@
 from __future__ import print_function, division, absolute_import
 
+import uuid
 import simplejson as json
+import datetime
 
 import redis # used for collections
-Redis = redis.StrictRedis()
 
 import logging
 
 from flask import (render_template, flash)
 
+from utility import hmac
+
 from utility.logger import getLogger
 logger = getLogger(__name__)
 
+def get_redis_conn():
+    Redis = redis.StrictRedis(port=6379)
+    return Redis
+
+Redis = get_redis_conn()
+
 def is_redis_available():
     try:
         Redis.ping()
@@ -21,6 +30,7 @@ def is_redis_available():
 
 def get_user_id(column_name, column_value):
     user_list = Redis.hgetall("users")
+    key_list = []
     for key in user_list:
         user_ob = json.loads(user_list[key])
         if column_name in user_ob and user_ob[column_name] == column_value:
@@ -42,6 +52,30 @@ def get_user_by_unique_column(column_name, column_value):
 
     return item_details
 
+def get_users_like_unique_column(column_name, column_value):
+    """
+    Like previous function, but this only checks if the input is a subset of a field and can return multiple results
+    """
+    matched_users = []
+
+    if column_value != "":
+        user_list = Redis.hgetall("users")
+        if column_name != "user_id":
+            for key in user_list:
+                user_ob = json.loads(user_list[key])
+                if "user_id" not in user_ob:
+                    set_user_attribute(key, "user_id", key)
+                    user_ob["user_id"] = key
+                if column_name in user_ob:
+                    if column_value in user_ob[column_name]:
+                        matched_users.append(user_ob)
+        else:
+            matched_users.append(json.loads(user_list[column_value]))
+
+    return matched_users
+
+# def search_users_by_unique_column(column_name, column_value):
+
 def set_user_attribute(user_id, column_name, column_value):
     user_info = json.loads(Redis.hget("users", user_id))
     user_info[column_name] = column_value
@@ -70,11 +104,209 @@ def check_verification_code(code):
     email_address = None
     user_details = None
     email_address = Redis.hget("verification_codes", code)
-    return email_address
 
     if email_address:
         user_details = get_user_by_unique_column('email_address', email_address)
-        return user_details
+        if user_details:
+            return user_details
+        else:
+            return None
+    else:
+        return None
+
+def get_user_groups(user_id):
+    #ZS: Get the groups where a user is an admin or a member and return lists corresponding to those two sets of groups
+    admin_group_ids = []  #ZS: Group IDs where user is an admin
+    user_group_ids = []   #ZS: Group IDs where user is a regular user
+    groups_list = Redis.hgetall("groups")
+    for key in groups_list:
+        try:
+            group_ob = json.loads(groups_list[key])
+            group_admins = set(group_ob['admins'])
+            group_members = set(group_ob['members'])
+            if user_id in group_admins:
+                admin_group_ids.append(group_ob['id'])
+            elif user_id in group_members:
+                user_group_ids.append(group_ob['id'])
+            else:
+                continue
+        except:
+            continue
+
+    admin_groups = []
+    user_groups = []
+    for the_id in admin_group_ids:
+        admin_groups.append(get_group_info(the_id))
+    for the_id in user_group_ids:
+        user_groups.append(get_group_info(the_id))
+
+    return admin_groups, user_groups
+
+def get_group_info(group_id):
+    group_json = Redis.hget("groups", group_id)
+    group_info = None
+    if group_json:
+        group_info = json.loads(group_json)
+
+    return group_info
+
+def get_group_by_unique_column(column_name, column_value):
+    """ Get group by column; not sure if there's a faster way to do this """
+
+    matched_groups = []
+
+    all_group_list = Redis.hgetall("groups")
+    for key in all_group_list:
+        group_info = json.loads(all_group_list[key])
+        if column_name == "admins" or column_name == "members": #ZS: Since these fields are lists, search in the list
+            if column_value in group_info[column_name]:
+                matched_groups.append(group_info)
+        else:
+            if group_info[column_name] == column_value:
+                matched_groups.append(group_info)
+
+    return matched_groups
+
+def get_groups_like_unique_column(column_name, column_value):
+    """
+    Like previous function, but this only checks if the input is a subset of a field and can return multiple results
+    """
+    matched_groups = []
+
+    if column_value != "":
+        group_list = Redis.hgetall("groups")
+        if column_name != "group_id":
+            for key in group_list:
+                group_info = json.loads(group_list[key])
+                if column_name == "admins" or column_name == "members": #ZS: Since these fields are lists, search in the list
+                    if column_value in group_info[column_name]:
+                        matched_groups.append(group_info)
+                else:
+                    if column_name in group_info:
+                        if column_value in group_info[column_name]:
+                            matched_groups.append(group_info)
+        else:
+            matched_groups.append(json.loads(group_list[column_value]))
+
+    return matched_groups
+
+def create_group(admin_user_ids, member_user_ids = [], group_name = "Default Group Name"):
+    group_id = str(uuid.uuid4())
+    new_group = {
+        "id"    : group_id,
+        "admins": admin_user_ids,
+        "members" : member_user_ids,
+        "name"  : group_name,
+        "created_timestamp": datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'),
+        "changed_timestamp": datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
+    }
+
+    Redis.hset("groups", group_id, json.dumps(new_group))
+
+    return new_group
+
+def delete_group(user_id, group_id):
+    #ZS: If user is an admin of a group, remove it from the groups hash
+    group_info = get_group_info(group_id)
+    if user_id in group_info["admins"]:
+        Redis.hdel("groups", group_id)
+        return get_user_groups(user_id)
+    else:
+        None
+
+def add_users_to_group(user_id, group_id, user_emails = [], admins = False): #ZS "admins" is just to indicate whether the users should be added to the groups admins or regular users set
+    group_info = get_group_info(group_id)
+    if user_id in group_info["admins"]: #ZS: Just to make sure that the user is an admin for the group, even though they shouldn't be able to reach this point unless they are
+        if admins:
+            group_users = set(group_info["admins"])
+        else:
+            group_users = set(group_info["members"])
+
+        for email in user_emails:
+            user_id = get_user_id("email_address", email)
+            group_users.add(user_id)
+
+        if admins:
+            group_info["admins"] = list(group_users)
+        else:
+            group_info["members"] = list(group_users)
+
+        group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
+        Redis.hset("groups", group_id, json.dumps(group_info))
+        return group_info
+    else:
+        return None
+
+def remove_users_from_group(user_id, users_to_remove_ids, group_id, user_type = "members"): #ZS: User type is because I assume admins can remove other admins
+    group_info = get_group_info(group_id)
+
+    if user_id in group_info["admins"]:
+        users_to_remove_set = set(users_to_remove_ids)
+        if user_type == "admins" and user_id in users_to_remove_set: #ZS: Make sure an admin can't remove themselves from a group, since I imagine we don't want groups to be able to become admin-less
+            users_to_remove_set.remove(user_id)
+        group_users = set(group_info[user_type])
+        group_users -= users_to_remove_set
+        group_info[user_type] = list(group_users)
+        group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
+        Redis.hset("groups", group_id, json.dumps(group_info))
+
+def change_group_name(user_id, group_id, new_name):
+    group_info = get_group_info(group_id)
+    if user_id in group_info["admins"]:
+        group_info["name"] = new_name
+        Redis.hset("groups", group_id, json.dumps(group_info))
+        return group_info
+    else:
+        return None
+
+def get_resources():
+    resource_list = Redis.hgetall("resources")
+    return resource_list
+
+def get_resource_id(dataset, trait_id=None):
+    if dataset.type == "Publish":
+        if trait_id:
+            resource_id = hmac.hmac_creation("{}:{}:{}".format('dataset-publish', dataset.id, trait_id))
+        else:
+            return False
+    elif dataset.type == "ProbeSet":
+        resource_id = hmac.hmac_creation("{}:{}".format('dataset-probeset', dataset.id))
+    elif dataset.type == "Geno":
+        resource_id = hmac.hmac_creation("{}:{}".format('dataset-geno', dataset.id))
+    else:
+        return False
+
+    return resource_id
+
+def get_resource_info(resource_id):
+    resource_info = Redis.hget("resources", resource_id)
+    if resource_info:
+        return json.loads(resource_info)
     else:
         return None
-        flash("Invalid code: Password reset code does not exist or might have expired!", "error")
+
+def add_resource(resource_info, update=True):
+    if 'trait' in resource_info['data']:
+        resource_id = hmac.hmac_creation('{}:{}:{}'.format(str(resource_info['type']), str(resource_info['data']['dataset']), str(resource_info['data']['trait'])))
+    else:
+        resource_id = hmac.hmac_creation('{}:{}'.format(str(resource_info['type']), str(resource_info['data']['dataset'])))
+
+    if not Redis.hexists("resources", resource_id):
+        Redis.hset("resources", resource_id, json.dumps(resource_info))
+
+    return resource_info
+
+def add_access_mask(resource_id, group_id, access_mask):
+    the_resource = get_resource_info(resource_id)
+    the_resource['group_masks'][group_id] = access_mask
+
+    Redis.hset("resources", resource_id, json.dumps(the_resource))
+
+    return the_resource
+
+def change_resource_owner(resource_id, new_owner_id):
+    the_resource= get_resource_info(resource_id)
+    the_resource['owner_id'] = new_owner_id
+
+    Redis.delete("resource")
+    Redis.hset("resources", resource_id, json.dumps(the_resource))
\ No newline at end of file
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 2914d354..89d88516 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -292,7 +292,7 @@ JS_GUIX_PATH = get_setting("JS_GUIX_PATH")
 assert_dir(JS_GUIX_PATH)
 assert_dir(JS_GUIX_PATH+'/cytoscape-panzoom')
 
-CSS_PATH = "UNKNOWN"
+CSS_PATH = JS_GUIX_PATH  # The CSS is bundled together with the JS
 # assert_dir(JS_PATH)
 
 JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("javascript-twitter-post-fetcher"))