harvdev-proforma-testdb

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docker build . -t proformatestdb

docker run -p 127.0.0.1:5436:5432 proformatestdb:latest

psql -h 127.0.0.1 -p 5436 -U tester -d fb_test  (password is *tester*)

Example sql.

SELECT f.name, f.uniquename, cvt.name 
  FROM feature f, cvterm cvt 
  WHERE f.type_id = cvt.cvterm_id;

    name     | uniquename  |             name             
-------------+-------------+------------------------------
 2L          | 2L          | chromosome_arm
 unspecified | unspecified | chromosome
 2L          | 2L          | chromosome
 symbol-5    | FBgn0000005 | gene
 symbol-4    | FBgn0000004 | gene
 symbol-3    | FBgn0000003 | gene
 symbol-2    | FBgn0000002 | gene
 symbol-1    | FBgn0000001 | gene
 symbol-5RA  | FBtr0000005 | mRNA
 symbol-4RA  | FBtr0000004 | mRNA
 symbol-3RA  | FBtr0000003 | mRNA
 symbol-2RA  | FBtr0000002 | mRNA
 symbol-1RA  | FBtr0000001 | mRNA
 2L          | 2L          | golden_path_region
 P-element   | FBte0000001 | natural_transposable_element

Using this testdb locally for testing.

You may want to update the testdb and test that before commiting. If you create a test db image docker build . -t testdb Then when you run the test add the --local_testdb flag.

Use FlyBase dockerhub image

docker run -p 127.0.0.1:5436:5432 flybase/proformatestdb:latest

Viewing Postgres logs

• The container must be running in order to view the logs.

• Connect to the running container.

  • docker exec -it proformatestdb /bin/bash

• Navigate to the log directory.

  • cd /var/log/postgresql

• Use tail, head, or cat to view the logs.

  • The log filename will change depending on the date.
  • tail -f postgresql-2019-07-23_200159.log