Merge remote-tracking branch 'origin/testing' into feature/add_rqtl_pairscan

2 files changed, 114 insertions, 0 deletions

diff --git a/doc/configurations.org b/doc/configurations.org
new file mode 100644
index 00000000..54c97d52
--- /dev/null
+++ b/doc/configurations.org
@@ -0,0 +1,92 @@
+#+TITLE: Configurations for GeneNetwork2 Service
+#+OPTIONS: toc:3
+
+* Configuration Variables
+
+** Basic Configurations
+
+- *GN_VERSION*: The current version of GN2
+- *GN2_PROXY*: URL to the GN2 proxy service
+- *GN_SERVER_URL*:  URL to the GN3 REST API server
+- *GN2_BASE_URL*: ??
+- *GN2_BRANCH_URL*:
+- *SERVER_PORT*: The port on which to run GN2. This is passed on to Flask.
+- *SECRET_HMAC_CODE*:
+- *GENENETWORK_FILES*: Base directory for all static data files
+- *HOME*: The home directory of the user that GN2 runs as
+
+** Redis Configurations
+
+- *REDIS_URL*: The url to use to connect to the running redis instance
+- *USE_REDIS*: Redis caching
+
+
+** Database (MySQL) Configurations
+
+- *SQL_URI*: The URI to the database server in the form
+   ~mysql://<username>:<password>@<host>:<port>/<dbname>~. Replace the items in
+    the angle brackets with the appropriate values for each item.
+- *SQL_ALCHEMY_POOL_RECYCLE*: Probably obsoleted - the use of ORMs (ha/i)s
+   be(en/ing) phased off
+
+# ---- Flask configuration (see website)
+** Flask-Specific Configurations
+- *TRAP_BAD_REQUEST_ERRORS*:
+- *SECURITY_CONFIRMABLE*:
+- *SECURITY_TRACKABLE*:
+- *SECURITY_REGISTERABLE*:
+- *SECURITY_RECOVERABLE*:
+- *SECURITY_EMAIL_SENDER*:
+- *SECURITY_POST_LOGIN_VIEW*:
+
+** External Services
+
+*** GitHub Configurations
+
+- *GITHUB_CLIENT_ID*: Client identifier key for GitHub OAuth authentication
+- *GITHUB_CLIENT_SECRET*: Client authentication token for github
+- *GITHUB_AUTH_URL*: The url to use for authenticating the client (GN2) with
+  GitHub. Default: https://github.com/login/oauth/authorize
+- *GITHUB_API_URL*: Once the client (GN2) is authenticated with GitHub, this URI
+  is the used to authenticate users using GitHub. The default value is
+   https://api.github.com/user
+
+*** ORCID Configurations
+
+- *ORCID_CLIENT_ID*: Client identifier key for ORCID OAuth authentication
+- *ORCID_CLIENT_SECRET*: Client authentication token for ORCID
+- *ORCID_AUTH_URL*: The url to use for authenticating the client (GN2) with
+  ORCID. Default: https://orcid.org/oauth/authorize
+- *ORCID_TOKEN_URL*: The URI to acquire a token once GN2 has been authenticated
+  with ORCID. This token is used to authenticate users with the ORCID service.
+  The default value is https://orcid.org/oauth/token
+
+** Mail Configurations
+- *SMTP_CONNECT*:
+- *SMTP_USERNAME*:
+- *SMTP_PASSWORD*:
+
+** Javascript Configurations
+- *JS_GN_PATH*: Path to local javascript libraries for development purposes only.
+   See [[./development.org]] for more details
+
+** External Commands Configurations
+- *REAPER_COMMAND*: The path to the reaper command/executable
+
+** Behavioral Settings
+# ---- Behavioural settings (defaults) note that logger and log levels can
+#      be overridden at the module level and with enviroment settings
+- *WEBSERVER_MODE*: Determines how the service is run.
+  If the value is ~DEBUG~, the service is run in debug mode - debug tools are
+  activated for the application.
+  If the value is ~DEV~, the service is run in development mode; logging is
+  activated.
+- *WEBSERVER_BRANDING*: Probably unused - verify and remove.
+- *WEBSERVER_DEPLOY*: Probably unused - verify and remove.
+- *WEBSERVER_URL*: Probably unused - verify and remove.
+- *LOG_LEVEL*:
+- *LOG_LEVEL_DEBUG*:
+- *LOG_SQL*:
+- *LOG_SQL_ALCHEMY*:
+- *LOG_BENCH*:
+- *USE_GN_SERVER*: ??
diff --git a/doc/database.org b/doc/database.org
index d5462d4e..32f1f8e0 100644
--- a/doc/database.org
+++ b/doc/database.org
@@ -1370,6 +1370,28 @@ Empty set (0.00 sec)
 
 Hmmm. This is the test database. Then there are the plink files and VCF files.
 
+** How to fetch case attribute data
+
+To fetch case attribute data, you need the PublixshXRef Id and it's
+PhenotypeId.  Run the following query (as an example):
+
+#+begin_src sql
+SELECT concat(st.Name, ',', ifnull(pd.value, 'x'), ',',
+       ifnull(ps.error, 'x'), ',', ifnull(ns.count, 'x')) as 'Data',
+       ifnull(ca.Name, 'x') as 'CaseAttr', ifnull(cxref.value, 'x') as 'Value'
+FROM PublishFreeze pf
+JOIN PublishXRef px ON px.InbredSetId = pf.InbredSetId
+JOIN PublishData pd ON pd.Id = px.DataId
+JOIN Strain st ON pd.StrainId = st.Id
+LEFT JOIN PublishSE ps ON ps.DataId = pd.Id AND ps.StrainId = pd.StrainId
+LEFT JOIN NStrain ns ON ns.DataId = pd.Id AND ns.StrainId = pd.StrainId
+LEFT JOIN CaseAttributeXRefNew cxref ON
+           (cxref.InbredSetId = px.InbredSetId AND
+            cxref.StrainId = st.Id)
+LEFT JOIN CaseAttribute ca ON ca.Id = cxref.CaseAttributeId
+WHERE px.Id = 10006 AND px.PhenotypeId = 28409 LIMIT 10;
+#+end_src
+
 * Optimize SQL?
 
 We were facing some issues with slow queries. A query