samestr DB builder: probe for the mOTUs db_mOTU directory (+galaxy4) - #8346
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samestr DB builder: probe for the mOTUs db_mOTU directory (+galaxy4)#8346mvdbeek wants to merge 1 commit into
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The motus_db_versioned 'path' is ambiguous: it can point at the db_mOTU directory itself (the mOTUs DM value_translation targets motus_database/<value>/db_mOTU, and the .loc.sample documents that) or at its parent. The motus branch hard-coded '$path/db_mOTU/...', which only works when path is the parent and fails otherwise (e.g. cp: can't stat .../db_mOTU/db_mOTU_versions when path already IS the db_mOTU dir, or when consuming a data-manager bundle where the files sit directly under path). Adopt the same robust probe the mOTUs profiler uses (bgruening/galaxytools#1869): normalize the dir to $path/db_mOTU when that subdir exists, else use $path directly, then read the markers from there. Bump to +galaxy4.
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What
The SameStr mOTUs data manager assumes
motus_db_versioned.fields.pathis the parent ofdb_mOTU(it hard-codes$path/db_mOTU/...). But thatpathis ambiguous: the mOTUs DM'svalue_translationtargets${GALAXY_DATA_MANAGER_DATA_PATH}/motus_database/${value}/db_mOTUand the.loc.sampledocumentspath = .../db_mOTU, i.e.pathis thedb_mOTUfolder itself. So the hard-coded$path/db_mOTU/...doubles and fails (cp: can't stat .../db_mOTU/db_mOTU_versions) wheneverpathalready is thedb_mOTUdir — including when consuming an mOTUs data-manager bundle in a workflow (the files sit directly underpath).Fix
Adopt the same robust probe the mOTUs profiler wrapper just added in bgruening/galaxytools#1869: normalize the dir to
$path/db_mOTUwhen that subdir exists, else use$pathdirectly, then read the markers from the normalized dir. This works for both conventions (parent-with-db_mOTU/, andpath-is-db_mOTU) and for bundle consumption. Bump to+galaxy4.The existing test fixture (
path = ${__HERE__}/with adb_mOTU/subdir) exercises the parent case and is unchanged.Context / discussion
Draft pending the convention question raised on bgruening/galaxytools#1869 (is
path = the db_mOTU folderthe canonical convention going forward?). Opening as a draft so the concrete change is visible alongside that discussion. cc @SaimMomin12 @Minamehr @bernt-matthiasFound while building an mOTUs-derived SameStr database as a reference-data bundle for idc.