Update dcicsnovault with fix for uuid not appearing in frame=raw view…

CHANGELOG.rst

@@ -6,6 +6,12 @@ cgap-portal
 Change Log
 ----------
 
+15.6.0
+======
+* Update dcicsnovault (branch: dmichaels-20240709 - to become 11.20.0)
+  with fix for uuid not appearing in frame=raw view for search results.
+
+
 15.5.0
 ======
 * Use snovault search modules rather than the local ones (in the src/encoded/search directory).

Makefile

@@ -90,17 +90,20 @@ download-genes: # grabs latest gene list from the below link, unzips and drops i
 	mv gene_inserts_v0.4.6.json src/encoded/annotations/gene_inserts_v0.4.6.json
 
 deploy1:  # starts postgres/ES locally and loads inserts, and also starts ingestion engine
-	@DEBUGLOG=`pwd` SNOVAULT_DB_TEST_PORT=`grep 'sqlalchemy[.]url =' development.ini | sed -E 's|.*:([0-9]+)/.*|\1|'` dev-servers development.ini --app-name app --clear --init --load
+	# @DEBUGLOG=`pwd` SNOVAULT_DB_TEST_PORT=`grep 'sqlalchemy[.]url =' development.ini | sed -E '/^[[:space:]]*#/d' | sed -E 's|.*:([0-9]+)/.*|\1|'` dev-servers development.ini --app-name app --clear --init --load
+	@DEBUGLOG=`pwd` dev-servers development.ini --app-name app --clear --init --load
 
 deploy1a:  # starts postgres/ES locally and loads inserts, but does not start the ingestion engine
-	@DEBUGLOG=`pwd` SNOVAULT_DB_TEST_PORT=`grep 'sqlalchemy[.]url =' development.ini | sed -E 's|.*:([0-9]+)/.*|\1|'` dev-servers development.ini --app-name app --clear --init --load --no_ingest
-#	@DEBUGLOG=`pwd` SNOVAULT_DB_TEST_PORT=`grep 'sqlalchemy[.]url =' development.ini | sed -E 's|.*:([0-9]+)/.*|\1|'` dev-servers development.ini --app-name app --clear --init --load
+	# @DEBUGLOG=`pwd` SNOVAULT_DB_TEST_PORT=`grep 'sqlalchemy[.]url =' development.ini | sed -E '/^[[:space:]]*#/d' | sed -E 's|.*:([0-9]+)/.*|\1|'` dev-servers development.ini --app-name app --clear --init --load --no_ingest
+	@DEBUGLOG=`pwd` dev-servers development.ini --app-name app --clear --init --load --no_ingest
 
 deploy1b:  # starts ingestion engine separately so it can be easily stopped and restarted for debugging in foreground
-	@echo "Starting ingestion listener. Press ^C to exit." && DEBUGLOG=`pwd` SNOVAULT_DB_TEST_PORT=`grep 'sqlalchemy[.]url =' development.ini | sed -E 's|.*:([0-9]+)/.*|\1|'` poetry run ingestion-listener development.ini --app-name app
+	# @echo "Starting ingestion listener. Press ^C to exit." && DEBUGLOG=`pwd` SNOVAULT_DB_TEST_PORT=`grep 'sqlalchemy[.]url =' development.ini | sed -E '/^[[:space:]]*#/d' | sed -E 's|.*:([0-9]+)/.*|\1|'` poetry run ingestion-listener development.ini --app-name app
+	@echo "Starting ingestion listener. Press ^C to exit." && DEBUGLOG=`pwd` poetry run ingestion-listener development.ini --app-name app
 
 deploy2:  # spins up waittress to serve the application
-	@DEBUGLOG=`pwd` SNOVAULT_DB_TEST_PORT=`grep 'sqlalchemy[.]url =' development.ini | sed -E 's|.*:([0-9]+)/.*|\1|'` pserve development.ini
+	# @DEBUGLOG=`pwd` SNOVAULT_DB_TEST_PORT=`grep 'sqlalchemy[.]url =' development.ini | sed -E '/^[[:space:]]*#/d' | sed -E 's|.*:([0-9]+)/.*|\1|'` pserve development.ini
+	@DEBUGLOG=`pwd` pserve development.ini
 
 deploy3:  # Uploads genes, consequences then ingests the VCF below
 	poetry run ingest-vcf src/encoded/annotations/GAPFIBVPFEP5_v0.5.4.reformat.altcounts.vcf dummy-accession hms-dbmi hms-dbmi development.ini --app-name app --post-variants --post-genes --post-conseq

README.rst

@@ -94,3 +94,17 @@ in numerous libaries, but importantly:
 * **dcicutils**
   [`pypi library <https://pypi.org/project/dcicutils/>`_]
   [`source repo <https://github.com/4dn-dcic/utils>`_]
+
+
+Running Locally on Different Ports
+==================================
+If you wish you run cgap-portal locally on different ports than the defaults, to, for example, allow you to run
+both cgap-portal and smaht-portal locally simultaneously, you will need to do the following:
+
+1. Change the 'sqlalchemy.url' property in development.ini to change its default port (5441) to something else, e.g. 5442.
+2. Change the 'sqlalchemy.url' property in development.ini to change its temporary directory (host) from its default (/tmp/snovault/pgdata) to something else, e.g. /tmp/snovault_cgap/pgdata).
+3. Change the 'elasticsearch.server' property in base.ini to change its default port (9200) to something else, e.g. 9202.
+4. Set the 'elasticsearch.server.transport_ports' property in base.ini to something other than its implicit default (9300-9305) to something else, e.g. 9400-9405.
+5. Change the 'port' propety in the '[server:main]' section in development from its default (6543) to something else, e.g. 7543.
+6. Change the 'server 127.0.0.1:6543' value in src/encoded/nginx-dev.conf to match the value in #5 above, e.g. 'server 127.0.0.1:7543'.
+7. Change the 'listen 8000' value in src/encoded/nginx-dev.conf to 'listen 8001'.

base.ini

@@ -6,17 +6,23 @@ retry.attempts = 3
 file_upload_bucket = cgap-unit-testing-files
 file_wfout_bucket = cgap-unit-testing-wfout
 # this really shouldn't be used with development, only uncomment if your sure - unknow
-# th
 # system_bucket = elasticbeanstalk-encoded-4dn-system
 elasticsearch.server = 127.0.0.1:9200
-# elasticsearch.server.actual_port = 9201
-# The above elasticsearch.server.actual_port property is useful (only) for running a localhost ElasticSearch
+
+# The elasticsearch.server.actual_port property is useful (only) for running a localhost ElasticSearch
 # proxy in order to observe traffic (requests/responses) between portal and ElasticSearch with a tool like
 # mitmweb; e.g. setting elasticsearch.server.actual_port to 9201 and elasticsearch.server to localhost:9200
 # will case ElasticSearch to actually run on port 9201 but will cause portal to talk to it via port 9200,
 # and then we can run mitmweb --mode reverse:http://localhost:9201 -p 9200 --web-port 8081 which will
 # allow us to browse to http://localhost:8081 locally to observe all of the ElasticSearch traffic;
 # and note to install mitmweb do: pip install mitmproxy
+# elasticsearch.server.actual_port = 9203
+
+# The elasticsearch.server.transport_ports property is useful (only) for defining the "transport"
+# ports for a localhost ElasticSearch instance. This can be useful if you want to (for example) ran
+# both smaht-port and cgap-portal simultaneously. The default value (if unspecified) is "9300-9305".
+# elasticsearch.server.transport_ports = 9400-9405
+
 ontology_path = %(here)s/ontology.json
 aws_ip_ranges_path = %(here)s/aws-ip-ranges.json
 #this is to reroute downloads to something other than aws s3