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BioplatformsAustralia / bpaotu

OTU database access for the Australian Microbiome
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Remove metagenome samples without lat/lon from ingest #241

Closed Smithmania closed 1 year ago

Smithmania commented 1 year ago

Can we add a filter to the Metagenomes that omits samples from ingest that do not have latitude/longitude data in the metadata database? We do this for the Amplicons

hou098 commented 1 year ago

@Smithmania It should be doing that for all samples regardless of amplicon. https://github.com/BioplatformsAustralia/bpaotu/blob/master/bpaotu/bpaotu/importer.py#L489

Can you give me a specific sample id?

Smithmania commented 1 year ago

Hi David

sorry for the delay the git reply goes to my non csiro email

you could look at these 2 examples

102.100.100/139599 - this id is in our sqlite DB but does not have a lat/lon (and never will as it is a control sample)

102.100.100/401602 - This ID is not yet in our DB as the submitter has not given me the metadata sheet to ingest

let me know if you need more examples

On 4 Oct 2022, at 1:05 pm, David Houlder @.***> wrote:

It should be doing that for all samples regardless of amplicon. https://github.com/BioplatformsAustralia/bpaotu/blob/master/bpaotu/bpaotu/importer.py#L489 https://github.com/BioplatformsAustralia/bpaotu/blob/master/bpaotu/bpaotu/importer.py#L489 Can you give me a specific sample id?

— Reply to this email directly, view it on GitHub https://github.com/BioplatformsAustralia/bpaotu/issues/241#issuecomment-1266300560, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALSSEDPCNHZXX2OCTKINYW3WBOGEZANCNFSM6AAAAAAQ3FK56E. You are receiving this because you authored the thread.

hou098 commented 1 year ago

Neither exist in the database. They would have been skipped on ingest due to the absence of lat/lon.

~/bpaotu$ psql -h localhost -U webapp webapp Password for user webapp: psql (12.12 (Ubuntu 12.12-0ubuntu0.20.04.1), server 10.7 (Debian 10.7- 1.pgdg90+1)) Type "help" for help.

webapp=# select id from otu.sample_context where id = '139599' or id = '401602'; id

(0 rows)

webapp=# \q

On Tue, 2022-10-11 at 00:42 -0700, Smithmania wrote:

Hi David

sorry for the delay the git reply goes to my non csiro email

you could look at these 2 examples

102.100.100/139599 - this id is in our sqlite DB but does not have a lat/lon (and never will as it is a control sample)

102.100.100/401602 - This ID is not yet in our DB as the submitter has not given me the metadata sheet to ingest

hou098 commented 1 year ago

Closing — no source code changes required.