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Makefile
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Makefile
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REDISCLI=${HOME}/redis-3.2.6/src/redis-cli
test_db:
date
curl -s http://127.0.0.1:7379/FLUSHALL > /dev/null
redbiom admin scripts-writable
redbiom admin create-context --name "test" --description "test context"
redbiom admin load-sample-metadata --metadata test.txt
redbiom admin load-sample-metadata-search --metadata test.txt
redbiom admin load-sample-data --table test.biom --context test
# with test_has_alts, the input has some overlapping samples (i.e., a
# different prep) and some novel IDs.
# this metadata file contains some new entries and some overlap with the
# test context above, so we expect that 2 samples will load
redbiom admin load-sample-metadata --metadata test_with_alts.txt
redbiom admin load-sample-metadata-search --metadata test_with_alts.txt
# only the "novel" samples should load.
redbiom admin load-sample-data --table test_with_alts.biom --context test
# now lets create a separate context to represent a totally different prep
# and lets just cram it full of the alt data. No additional metadata
# should get loaded as it is already represented.
redbiom admin create-context --name "test-alt" --description "test context"
# we can load metadata, but nothing will get loaded since it already got
# loaded above. **IMPORTANT** prep specific information is not yet
# supported, so this means **ONLY** sample metadata is stored
redbiom admin load-sample-metadata --metadata test_with_alts.txt
redbiom admin load-sample-data --table test_with_alts.biom --context test-alt
redbiom admin scripts-read-only
date
test: test_db
/bin/bash test.sh
nosetests
/bin/bash test_failures.sh # this blows away the db
/bin/bash test_external.sh # relies on public redbiom instance
test_bulk: test_db_bulk
/bin/bash test.sh
/bin/bash test_failures.sh # this blows away the db
test_db_bulk:
date
curl -s http://127.0.0.1:7379/FLUSHALL > /dev/null
redbiom admin scripts-writable
redbiom admin create-context --name "test" --description "test context"
redbiom admin load-sample-metadata --metadata test.txt
redbiom admin load-sample-metadata-search --metadata test.txt
redbiom admin load-sample-data --table test.biom --context test --mass-insertion | ${REDISCLI} --pipe
# with test_has_alts, the input has some overlapping samples (i.e., a
# different prep) and some novel IDs.
# this metadata file contains some new entries and some overlap with the
# test context above, so we expect that 2 samples will load
redbiom admin load-sample-metadata --metadata test_with_alts.txt
redbiom admin load-sample-metadata-search --metadata test_with_alts.txt
# only the "novel" samples should load.
redbiom admin load-sample-data --table test_with_alts.biom --context test --mass-insertion | ${REDISCLI} --pipe
# now lets create a separate context to represent a totally different prep
# and lets just cram it full of the alt data. No additional metadata
# should get loaded as it is already represented.
redbiom admin create-context --name "test-alt" --description "test context"
# we can load metadata, but nothing will get loaded since it already got
# loaded above. **IMPORTANT** prep specific information is not yet
# supported, so this means **ONLY** sample metadata is stored
redbiom admin load-sample-metadata --metadata test_with_alts.txt
redbiom admin load-sample-data --table test_with_alts.biom --context test-alt --mass-insertion | ${REDISCLI} --pipe
redbiom admin scripts-read-only
date