From 61e96b34c477c84991354c2bf53db16583a16880 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Tue, 1 Mar 2022 15:09:38 +0100 Subject: [PATCH 1/6] add phyloseq datatype --- lib/galaxy/config/sample/datatypes_conf.xml.sample | 1 + 1 file changed, 1 insertion(+) diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample index 992f41836e7..b2f8b586a95 100644 --- a/lib/galaxy/config/sample/datatypes_conf.xml.sample +++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample @@ -641,6 +641,7 @@ + From 2511b6492fe0737cfe2d85ee7f8d8d4fe120aa0e Mon Sep 17 00:00:00 2001 From: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com> Date: Tue, 22 Feb 2022 22:29:33 +0530 Subject: [PATCH 2/6] Initial fix for quay.io repo query issue Fixes not getting a full list of images in a repo. Without this fix some container images are not resolvable. --- lib/galaxy/tool_util/deps/mulled/util.py | 20 +++++++++++++------- 1 file changed, 13 insertions(+), 7 deletions(-) diff --git a/lib/galaxy/tool_util/deps/mulled/util.py b/lib/galaxy/tool_util/deps/mulled/util.py index 2078766b8eb..6225ea9b5ed 100644 --- a/lib/galaxy/tool_util/deps/mulled/util.py +++ b/lib/galaxy/tool_util/deps/mulled/util.py @@ -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=QUAY_IO_TIMEOUT) - - repos = repos_response.json()['repositories'] - repo_names = [r["name"] for r in repos] + next_page = None + repo_names = [] + while True: + repos_parameters = {"public": "true", "namespace": namespace, "next_page": next_page} + repos_headers = {"Accept-encoding": "gzip", "Accept": "application/json"} + repos_response = requests.get( + QUAY_REPOSITORY_API_ENDPOINT, headers=repos_headers, params=repos_parameters, timeout=QUAY_IO_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 From a9eb6691582347e5bd0184cfa0c7d1e896aafcff Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Wed, 2 Mar 2022 12:24:57 +0100 Subject: [PATCH 3/6] Add profile version to ethercalc It writes to stderr, so that fails on most job runners (why not all???). --- tools/interactive/interactivetool_ethercalc.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/interactive/interactivetool_ethercalc.xml b/tools/interactive/interactivetool_ethercalc.xml index 3b8f1c2d37d..7ae74caefde 100644 --- a/tools/interactive/interactivetool_ethercalc.xml +++ b/tools/interactive/interactivetool_ethercalc.xml @@ -1,4 +1,4 @@ - + shiltemann/ethercalc-galaxy-ie:17.05 From 831a077f50f6a4c8ff218fd2b7a69a7c402ea1d3 Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Wed, 2 Mar 2022 16:30:28 +0100 Subject: [PATCH 4/6] Move header definition out of while loop Co-authored-by: Sergey Golitsynskiy --- lib/galaxy/tool_util/deps/mulled/util.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/tool_util/deps/mulled/util.py b/lib/galaxy/tool_util/deps/mulled/util.py index 6225ea9b5ed..a99d6ddd1af 100644 --- a/lib/galaxy/tool_util/deps/mulled/util.py +++ b/lib/galaxy/tool_util/deps/mulled/util.py @@ -66,9 +66,9 @@ def _namespace_has_repo_name(namespace, repo_name, resolution_cache): else: 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_headers = {"Accept-encoding": "gzip", "Accept": "application/json"} + 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=QUAY_IO_TIMEOUT) repos_response_json = repos_response.json() From 16cb094489bba0c005f5b4eeaf11738c26f29e91 Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Wed, 2 Mar 2022 16:57:42 +0100 Subject: [PATCH 5/6] Fix trailing whitespace --- lib/galaxy/tool_util/deps/mulled/util.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/tool_util/deps/mulled/util.py b/lib/galaxy/tool_util/deps/mulled/util.py index a99d6ddd1af..18f479f82c4 100644 --- a/lib/galaxy/tool_util/deps/mulled/util.py +++ b/lib/galaxy/tool_util/deps/mulled/util.py @@ -68,7 +68,7 @@ def _namespace_has_repo_name(namespace, repo_name, resolution_cache): repo_names = [] repos_headers = {"Accept-encoding": "gzip", "Accept": "application/json"} while True: - repos_parameters = {"public": "true", "namespace": namespace, "next_page": next_page} + 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=QUAY_IO_TIMEOUT) repos_response_json = repos_response.json() From f164d6c70822aae0d80b503e1091952b83a8b89c Mon Sep 17 00:00:00 2001 From: M Bernt Date: Wed, 2 Mar 2022 17:27:11 +0100 Subject: [PATCH 6/6] do subclass Co-authored-by: Nicola Soranzo --- lib/galaxy/config/sample/datatypes_conf.xml.sample | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample index b2f8b586a95..fc6d040467b 100644 --- a/lib/galaxy/config/sample/datatypes_conf.xml.sample +++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample @@ -641,7 +641,7 @@ - +