| Previous changeset 12:b9fd06875714 (2019-07-11) Next changeset 14:a7bcaf8da69b (2019-11-14) |
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Commit message:
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f" |
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modified:
chado.py macros.xml phylogeny_gene_families.xml |
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| diff -r b9fd06875714 -r 1383275a8210 chado.py --- a/chado.py Thu Jul 11 08:37:42 2019 -0400 +++ b/chado.py Wed Aug 21 05:09:45 2019 -0400 |
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| @@ -389,7 +389,8 @@ os.environ['GALAXY_CHADO_DBPASS'], os.environ['GALAXY_CHADO_DBSCHEMA'], os.environ['GALAXY_CHADO_DBPORT'], - no_reflect=True + no_reflect=True, + pool_connections=False ) @@ -474,3 +475,43 @@ for an in ci.analysis.get_analyses(): ans_data.append((an['name'], str(an['analysis_id']), False)) return ans_data + + +def list_dbs(*args, **kwargs): + + ci = _get_instance() + + # Key for cached data + cacheKey = 'dbs' + # We don't want to trust "if key in cache" because between asking and fetch + # it might through key error. + if cacheKey not in cache: + # However if it ISN'T there, we know we're safe to fetch + put in + # there.<?xml version="1.0"?> + + data = _list_dbs(ci, *args, **kwargs) + cache[cacheKey] = data + ci.session.close() + return data + try: + # The cache key may or may not be in the cache at this point, it + # /likely/ is. However we take no chances that it wasn't evicted between + # when we checked above and now, so we reference the object from the + # cache in preparation to return. + data = cache[cacheKey] + ci.session.close() + return data + except KeyError: + # If access fails due to eviction, we will fail over and can ensure that + # data is inserted. + data = _list_dbs(ci, *args, **kwargs) + cache[cacheKey] = data + ci.session.close() + return data + + +def _list_dbs(ci, *args, **kwargs): + dbs_data = [] + for db in ci.load._get_dbs(): + dbs_data.append((db['name'], str(db['db_id']), False)) + return dbs_data |
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| diff -r b9fd06875714 -r 1383275a8210 macros.xml --- a/macros.xml Thu Jul 11 08:37:42 2019 -0400 +++ b/macros.xml Wed Aug 21 05:09:45 2019 -0400 |
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| @@ -2,7 +2,7 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="2.2.6">python-chado</requirement> + <requirement type="package" version="@LIB_VERSION@">python-chado</requirement> <requirement type="package" version="1.5">jq</requirement> <requirement type="package" version="@PG_VERSION@">postgresql</requirement> <requirement type="package" version="0.1">pglite</requirement> @@ -10,6 +10,8 @@ </requirements> </xml> + <token name="@LIB_VERSION@">2.3.0</token> + <token name="@WRAPPER_VERSION@">@LIB_VERSION@</token> <token name="@PG_VERSION@">11.2</token> <xml name="stdio"> @@ -20,8 +22,6 @@ </stdio> </xml> - <token name="@WRAPPER_VERSION@">2.2.6</token> - <xml name="citation"> <citations> </citations> |
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| diff -r b9fd06875714 -r 1383275a8210 phylogeny_gene_families.xml --- a/phylogeny_gene_families.xml Thu Jul 11 08:37:42 2019 -0400 +++ b/phylogeny_gene_families.xml Wed Aug 21 05:09:45 2019 -0400 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="phylogeny_gene_families" name="Chado refresh gene families" version="@WRAPPER_VERSION@.1"> +<tool id="phylogeny_gene_families" name="Chado refresh gene families" version="@WRAPPER_VERSION@"> <description>for phylogeny module</description> <macros> <import>macros.xml</import> |