Adding DataArt new developments for BioSample sync with sample lacking sequencing data #12
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…ynchronize-biosamples FIND-722 Synchronize BioSamples
…ob-error FIND-721 fix problem with model
…get-all-ids FIND-748 Save and get all ids
…samples-sync FIND-748 Fix samples sync step
…thout-sequencing-further-work Feat/biosample without sequencing further work
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* getting up to sync with current infra * adding bitbucket pipeline def * was missing empty backend conf file * Adding DataArt new developments for BioSample sync with sample lacking sequencing data (#12) * FIND-722 Synchronize BioSamples * FIND-721 fix problem with model * FIND-748 Save and get all ids * FIND-748 Fix samples sync step * Fix terraform structure * importing bucket name from parameter store, creating new policy for put object * Update README.md * Update README.md * fix typo * readme * var for CICD * starting up with a few comments * adding query to get already inserted biosample ids * removing biosample ids we have already seen before date related sync * few additional fixes * clearer biosample accession * cleaning up the insert * sql function for seq-sync * filtering on biosample ids that we already have in the db * fix table name * more loggin on progress * making sure same type of list entries * fixing bioproject retrival * fixing bioproject retrieval * also appending composite alias for biosamples w/o seq * fixed name value for insertion * comments * comments * comments * adding extra args for running only sample-sync * simplifying filtering on already inserted biosamples * removing break * comments, debug switch --------- Co-authored-by: Rostyslav Stekh <[email protected]> Co-authored-by: Rostyslav Stekh <[email protected]> Co-authored-by: Sacha Laurent <[email protected]> * passing relative date to sample sync * getting up to sync with current infra * adding bitbucket pipeline def * was missing empty backend conf file * passing relative date to sample sync --------- Co-authored-by: Sacha Laurent <[email protected]> Co-authored-by: Rostyslav Stekh <[email protected]> Co-authored-by: Rostyslav Stekh <[email protected]>
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