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Merge branch 'release_21.09' into release_22.01

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This commit is contained in:
Nicola Soranzo
2022-03-02 19:18:43 +00:00
parent d1f12e7a58 8a5aabf0dd
commit 856269b248
3 changed files with 15 additions and 8 deletions
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lib/galaxy/config/sample/datatypes_conf.xml.sample
+1
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@@ -647,6 +647,7 @@
<datatype extension="gpr" type="galaxy.datatypes.microarrays:Gpr" display_in_upload="true"/>
<datatype extension="gal" type="galaxy.datatypes.microarrays:Gal" display_in_upload="true"/>
<datatype extension="rds" type="galaxy.datatypes.binary:RDS" display_in_upload="true" description="Serialized R object generated with saveRDS"/>
<datatype extension="phyloseq" type="galaxy.datatypes.binary:RDS" subclass="true" display_in_upload="true" description="Serialized phyloseq object"/>
<datatype extension="rdata" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" display_in_upload="true" description="Stored data from an R session genearted with save or save.img"/>
<datatype extension="rdata.sce" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true" description="Stored RData from a SingleCellObject"/>
<datatype extension="rdata.xcms.raw" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true"/>
lib/galaxy/tool_util/deps/mulled/util.py
+13 -7
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@@ -64,13 +64,19 @@ def _namespace_has_repo_name(namespace, repo_name, resolution_cache):
if resolution_cache is not None and cache_key in resolution_cache:
repo_names = resolution_cache.get(cache_key)
else:
repos_parameters = {'public': 'true', 'namespace': namespace}
repos_headers = {'Accept-encoding': 'gzip', 'Accept': 'application/json'}
repos_response = requests.get(
QUAY_REPOSITORY_API_ENDPOINT, headers=repos_headers, params=repos_parameters, timeout=MULLED_SOCKET_TIMEOUT)
repos = repos_response.json()['repositories']
repo_names = [r["name"] for r in repos]
next_page = None
repo_names = []
repos_headers = {"Accept-encoding": "gzip", "Accept": "application/json"}
while True:
repos_parameters = {"public": "true", "namespace": namespace, "next_page": next_page}
repos_response = requests.get(
QUAY_REPOSITORY_API_ENDPOINT, headers=repos_headers, params=repos_parameters, timeout=MULLED_SOCKET_TIMEOUT)
repos_response_json = repos_response.json()
repos = repos_response_json["repositories"]
repo_names += [r["name"] for r in repos]
next_page = repos_response_json.get("next_page")
if not next_page:
break
if resolution_cache is not None:
resolution_cache[cache_key] = repo_names
return repo_name in repo_names
tools/interactive/interactivetool_ethercalc.xml
+1 -1
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@@ -1,4 +1,4 @@
<tool id="interactive_tool_ethercalc" tool_type="interactive" name="EtherCalc" version="0.1">
<tool id="interactive_tool_ethercalc" tool_type="interactive" name="EtherCalc" version="0.1" profile="20.01">
<requirements>
<container type="docker">shiltemann/ethercalc-galaxy-ie:17.05</container>
</requirements>