Excipient server restart - Revision history

Frodo: asdf

2024-05-17T21:48:27Z

asdf

← Older revision		Revision as of 21:48, 17 May 2024
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	DB should be now fully populated.		DB should be now fully populated.


			[[Category:Excipients]]

Frodo: Frodo moved page Excipients to Excipient server restart without leaving a redirect: more informative name

2024-05-17T21:48:09Z

Frodo moved page Excipients to Excipient server restart without leaving a redirect: more informative name

← Older revision

Revision as of 21:48, 17 May 2024

Enkhjargal at 18:47, 24 July 2017

2017-07-24T18:47:55Z

← Older revision		Revision as of 18:47, 24 July 2017
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	python /home/enkhjargal/PycharmProjects/Excipients/manage-excipients.py manage-db migrate		python /home/enkhjargal/PycharmProjects/Excipients/manage-excipients.py manage-db migrate

	4. Load the openfda regulatory_status data (populates 'Status' table in db):		4. Load the openfda regulatory_status data (populates 'Status' table in db, last updated April/2017):
	-> create a file named regulatory_status.csv		-> create a file named regulatory_status.csv
	touch regulatory_status.csv		touch regulatory_status.csv
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	python /home/enkhjargal/PycharmProjects/Excipients/manage-excipients.py parse_status_definition /home/enkhjargal/PycharmProjects/Excipients/data/regulatory_status.csv		python /home/enkhjargal/PycharmProjects/Excipients/manage-excipients.py parse_status_definition /home/enkhjargal/PycharmProjects/Excipients/data/regulatory_status.csv

	5. Load the openfda excipients function data (populates 'Function' table in db):		5. Load the openfda excipients function data (populates 'Function' table in db, last updated April/2017):
	python /home/enkhjargal/PycharmProjects/Excipients/manage-excipients.py parse_function_definition /home/enkhjargal/PycharmProjects/Excipients/data/function_definition.csv		python /home/enkhjargal/PycharmProjects/Excipients/manage-excipients.py parse_function_definition /home/enkhjargal/PycharmProjects/Excipients/data/function_definition.csv

Enkhjargal at 22:10, 24 April 2017

2017-04-24T22:10:41Z

← Older revision		Revision as of 22:10, 24 April 2017
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	----		----

	[[HowTos for the ~~brand~~ new version of Excipients]]		[[HowTos for the new version of Excipients]]

	1. Create a copy of existing production database		1. Create a copy of existing production database

Enkhjargal: Enkhjargal moved page Deployment to Excipients

2017-04-24T22:10:13Z

Enkhjargal moved page Deployment to Excipients

← Older revision

Revision as of 22:10, 24 April 2017

Enkhjargal at 22:04, 24 April 2017

2017-04-24T22:04:04Z

← Older revision		Revision as of 22:04, 24 April 2017
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	9. Pull Zincids for populated Substance data. (populate the zincid and smiles column in substance table)		9. Pull Zincids for populated Substance data. (populate the zincid and smiles column in substance table)
	-> python /home/enkhjargal/PycharmProjects/Excipients/manage-excipients.py parse_fda_label_data		-> python /home/enkhjargal/PycharmProjects/Excipients/manage-excipients.py parse_fda_label_data

			DB should be now fully populated.

Enkhjargal at 22:03, 24 April 2017

2017-04-24T22:03:22Z

← Older revision		Revision as of 22:03, 24 April 2017
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	1. Create a copy of existing production database		1. Create a copy of existing production database

	2. In the flask code, change the database url to the newly created db		2. In the flask code, change the database url to the newly created db

	3. Run db update + db migrate to create new tables and new columns for existing tables. (automatically done by flask db-migrate, mapping the model objects to postgres db)		3. Run db update + db migrate to create new tables and new columns for existing tables. (automatically done by flask db-migrate, mapping the model objects to postgres db)
	python /home/enkhjargal/PycharmProjects/Excipients/manage-excipients.py manage-db upgrade		python /home/enkhjargal/PycharmProjects/Excipients/manage-excipients.py manage-db upgrade
	python /home/enkhjargal/PycharmProjects/Excipients/manage-excipients.py manage-db migrate		python /home/enkhjargal/PycharmProjects/Excipients/manage-excipients.py manage-db migrate
	4. Load the openfda regulatory_status data (~~creates~~ 'Status' table in db)
			4. Load the openfda regulatory_status data (populates 'Status' table in db):
	-> create a file named regulatory_status.csv		-> create a file named regulatory_status.csv
	touch regulatory_status.csv		touch regulatory_status.csv
	-> copy over the regulatory_status definitions from		-> copy over the regulatory_status definitions from
	python /home/enkhjargal/PycharmProjects/Excipients/manage-excipients.py parse_status_definition /home/enkhjargal/PycharmProjects/Excipients/data/regulatory_status.csv		python /home/enkhjargal/PycharmProjects/Excipients/manage-excipients.py parse_status_definition /home/enkhjargal/PycharmProjects/Excipients/data/regulatory_status.csv
	5. Load the openfda excipients function data (~~creates~~ 'Function' table in db)
			5. Load the openfda excipients function data (populates 'Function' table in db):
	python /home/enkhjargal/PycharmProjects/Excipients/manage-excipients.py parse_function_definition /home/enkhjargal/PycharmProjects/Excipients/data/function_definition.csv		python /home/enkhjargal/PycharmProjects/Excipients/manage-excipients.py parse_function_definition /home/enkhjargal/PycharmProjects/Excipients/data/function_definition.csv
	6. Load the dye relation data:
			6. Load the dye relation data. (creates the relation for excipients to functions which are dye):
	-> https://www.fda.gov/ForIndustry/ColorAdditives/ColorAdditiveInventories/ucm106626.htm)		-> https://www.fda.gov/ForIndustry/ColorAdditives/ColorAdditiveInventories/ucm106626.htm)
	-> python /home/enkhjargal/PycharmProjects/Excipients/manage-excipients.py load_color_additives_relationship /home/enkhjargal/PycharmProjects/Excipients/data/FDA_color_additives_all		-> python /home/enkhjargal/PycharmProjects/Excipients/manage-excipients.py load_color_additives_relationship /home/enkhjargal/PycharmProjects/Excipients/data/FDA_color_additives_all
	7. Load the fda general additives data
			7. Load the fda general additives data.(creates all other function and status relations to excipients):
	-> create a file named FDA_additives		-> create a file named FDA_additives
	touch FDA_additives		touch FDA_additives
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	-> parse the file to load it to db table		-> parse the file to load it to db table
	python /home/enkhjargal/PycharmProjects/Excipients/manage-excipients.py load_function_and_status_relationship /home/enkhjargal/PycharmProjects/Excipients/data/FDA_additives		python /home/enkhjargal/PycharmProjects/Excipients/manage-excipients.py load_function_and_status_relationship /home/enkhjargal/PycharmProjects/Excipients/data/FDA_additives
	8. Load the openfda drug label:
			8. Load the openfda drug label. (populate brand and substance tables and their relations to existing excipients):
	-> https://open.fda.gov/downloads/ (6 json files to download)		-> https://open.fda.gov/downloads/ (6 json files to download)
	-> parse each of them:		-> parse each of them:
	python /home/enkhjargal/PycharmProjects/Excipients/manage-excipients.py parse_fda_label_data /home/enkhjargal/PycharmProjects/Excipients/data/drug-label-0005-of-0006.json		python /home/enkhjargal/PycharmProjects/Excipients/manage-excipients.py parse_fda_label_data /home/enkhjargal/PycharmProjects/Excipients/data/drug-label-0005-of-0006.json
	9.
			9. Pull Zincids for populated Substance data. (populate the zincid and smiles column in substance table)
			-> python /home/enkhjargal/PycharmProjects/Excipients/manage-excipients.py parse_fda_label_data

Enkhjargal at 21:53, 24 April 2017

2017-04-24T21:53:48Z

@@ Line 23: / Line 23: @@
 .
       gunicorn --access-logfile excipients.ucsf.bkslab.org.acc --max-requests 1000 --bind 10.20.0.31:8093 excipients:app --workers 5 --timeout 1000)
 ----
- [[HowTos for the brand new version of Excipients]]
+[[HowTos for the brand new version of Excipients]]
-.
+. Create a copy of existing production database

Enkhjargal at 20:35, 24 April 2017

2017-04-24T20:35:19Z

@@ Line 1: / Line 1: @@
-Excipient Server Restart:
+[[Excipient Server Restart:]]
 . ssh gimel
@@ Line 23: / Line 23: @@
 .
       gunicorn --access-logfile excipients.ucsf.bkslab.org.acc --max-requests 1000 --bind 10.20.0.31:8093 excipients:app --workers 5 --timeout 1000)

Enkhjargal at 20:32, 24 April 2017

2017-04-24T20:32:39Z

← Older revision		Revision as of 20:32, 24 April 2017
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	1. Go to the dev version of Excipients and set the version number set in the __init__.py file		1. Go to the dev version of Excipients and set the version number set in the __init__.py file

	2. Create the distribution file		2. Create the distribution file
	python setup.py sdist		python setup.py sdist

	3. ssh gimel		3. ssh gimel

	4. su - www		4. su - www

	5. activate the production server ->		5. activate the production server ->
	cd /nfs/soft/www/apps/excipients/envs/production/		cd /nfs/soft/www/apps/excipients/envs/production/
	source bin/activate		source bin/activate

	6. copy over the created dist folder in /nfs/soft/www/apps/excipients/envs/production/		6. copy over the created dist folder in /nfs/soft/www/apps/excipients/envs/production/

	7. Run ->		7. Run ->
	pip install dist/CERSI-Excipients-X.Y.Z.tar.gz		pip install dist/CERSI-Excipients-X.Y.Z.tar.gz

	8.		8.
	gunicorn --access-logfile excipients.ucsf.bkslab.org.acc --max-requests 1000 --bind 10.20.0.31:8093 excipients:app --workers 5 --timeout 1000)		gunicorn --access-logfile excipients.ucsf.bkslab.org.acc --max-requests 1000 --bind 10.20.0.31:8093 excipients:app --workers 5 --timeout 1000)