From 16e7cdf5446949847dffad705ecce0d284607a65 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Tue, 22 Oct 2024 09:50:13 +0200
Subject: [PATCH] remove integration test

---
 .../tools/mulled_example_multi_2.xml          | 79 -------------------
 test/functional/tools/sample_tool_conf.xml    |  1 -
 test/integration/test_container_resolvers.py  | 54 -------------
 3 files changed, 134 deletions(-)
 delete mode 100644 test/functional/tools/mulled_example_multi_2.xml

diff --git a/test/functional/tools/mulled_example_multi_2.xml b/test/functional/tools/mulled_example_multi_2.xml
deleted file mode 100644
index 5347dace94b7..000000000000
--- a/test/functional/tools/mulled_example_multi_2.xml
+++ /dev/null
@@ -1,79 +0,0 @@
-<!-- same as mulled_example_multi_1, but requirements use builds
-     used to show that this does not yield the same mulled v2 hash,
-     i.e. the build is considered as part of version -->
-<tool id="mulled_example_multi_2" name="mulled_example_multi_2" version="0.1.0" license="AFL-3.0">
-    <xrefs>
-        <xref type="bio.tools">bedtools</xref>
-        <xref type="bio.tools">samtools</xref>
-    </xrefs>
-    <creator>
-        <person
-            givenName="Björn"
-            familyName="Grüning"
-            url="https://github.com/bgruening"
-            identifier="http://orcid.org/0000-0002-3079-6586" />
-        <organization
-            url="https://galaxyproject.org/iuc/"
-            name="Galaxy IUC" />
-    </creator>
-    <requirements>
-        <requirement type="package" version="1.3.1=h9071d68_10">samtools</requirement>
-        <requirement type="package" version="2.26.0=0">bedtools</requirement>
-    </requirements>
-    <command><![CDATA[
-bedtools --version > '$out_file1' &&
-echo "Moo" >> '$out_file1' &&
-samtools >> '$out_file1' 2>&1 &&
-echo "Cow" >> '$out_file1' &&
-
-touch "\${TMP:-/tmp}/job_tmp" &&
-touch "\${TEMP:-/tmp}/job_temp" &&
-touch "\${TMPDIR:-/tmp}/job_tmpdir"
-    ]]></command>
-    <inputs>
-        <param name="input1" type="data" optional="true" />
-    </inputs>
-    <outputs>
-        <data name="out_file1" format="txt" />
-    </outputs>
-    <tests>
-    </tests>
-    <help><![CDATA[
-This is an example mulled tool that combines bedtools and samtools in one
-command-line invocation.
-    ]]></help>
-    <citations>
-        <citation type="doi">10.1093/bioinformatics/btq033</citation>
-        <citation type="bibtex">
-            @misc{SAM_def,
-            title={Definition of SAM/BAM format},
-            url = {https://samtools.github.io/hts-specs/},}
-        </citation>
-        <citation type="doi">10.1093/bioinformatics/btp352</citation>
-        <citation type="doi">10.1093/bioinformatics/btr076</citation>
-        <citation type="doi">10.1093/bioinformatics/btr509</citation>
-        <citation type="bibtex">
-            @misc{Danecek_et_al,
-            Author={Danecek, P., Schiffels, S., Durbin, R.},
-            title={Multiallelic calling model in bcftools (-m)},
-            url = {http://samtools.github.io/bcftools/call-m.pdf},}
-        </citation>
-        <citation type="bibtex">
-            @misc{Durbin_VCQC,
-            Author={Durbin, R.},
-            title={Segregation based metric for variant call QC},
-            url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
-        </citation>
-        <citation type="bibtex">
-            @misc{Li_SamMath,
-            Author={Li, H.},
-            title={Mathematical Notes on SAMtools Algorithms},
-            url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
-        </citation>
-        <citation type="bibtex">
-            @misc{SamTools_github,
-            title={SAMTools GitHub page},
-            url = {https://github.com/samtools/samtools},}
-        </citation>
-    </citations>
-</tool>
diff --git a/test/functional/tools/sample_tool_conf.xml b/test/functional/tools/sample_tool_conf.xml
index 85e4e03dcc81..bb9d7568f600 100644
--- a/test/functional/tools/sample_tool_conf.xml
+++ b/test/functional/tools/sample_tool_conf.xml
@@ -279,7 +279,6 @@
   <!-- Tools for dependency and container testing. -->
   <tool file="legacy_r.xml" />
   <tool file="mulled_example_multi_1.xml" />
-  <tool file="mulled_example_multi_2.xml" />
   <tool file="mulled_example_multi_versionless.xml" />
   <tool file="mulled_example_multi_incomplete.xml" />
   <tool file="mulled_example_conflict.xml" />
diff --git a/test/integration/test_container_resolvers.py b/test/integration/test_container_resolvers.py
index 8fa94a6c2a53..1d1fda4739ea 100644
--- a/test/integration/test_container_resolvers.py
+++ b/test/integration/test_container_resolvers.py
@@ -539,60 +539,6 @@ class TestDefaultContainerResolvers(DockerContainerResolverTestCase, ContainerRe
     }
 
 
-class TestDefaultContainerResolversWithBuildInfo(
-    DockerContainerResolverTestCase, ContainerResolverTestCases, MulledTestCaseWithBuildInfo
-):
-    """
-    Same as TestDefaultContainerResolvers but with a tool using build info
-    serves to check if the mulled hashes are cumputed correctly
-    """
-
-    assumptions: Dict[str, Any] = {
-        "run": {
-            "output": [
-                "bedtools v2.26.0",
-                "samtools: error while loading shared libraries: libcrypto.so.1.0.0",
-            ],
-            "cached": True,
-            "resolver_type": "mulled",  # only used to check mulled / explicit
-            "cache_name": f"quay.io/biocontainers/{MulledTestCaseWithBuildInfo.mulled_hash}",
-            "cache_namespace": "biocontainers",
-        },
-        "list": [
-            {
-                "resolver_type": "mulled",
-                "identifier": f"quay.io/biocontainers/{MulledTestCaseWithBuildInfo.mulled_hash}",
-                "cached": False,
-                "cache_name": f"quay.io/biocontainers/{MulledTestCaseWithBuildInfo.mulled_hash}",
-                "cache_namespace": "biocontainers",
-            },
-            {
-                "resolver_type": "mulled",
-                "identifier": f"quay.io/biocontainers/{MulledTestCaseWithBuildInfo.mulled_hash}",
-                "cached": False,
-                "cache_name": f"quay.io/biocontainers/{MulledTestCaseWithBuildInfo.mulled_hash}",
-                "cache_namespace": "biocontainers",
-            },
-        ],
-        "build": [
-            {
-                "resolver_type": "mulled",
-                "identifier": f"quay.io/biocontainers/{MulledTestCaseWithBuildInfo.mulled_hash}",
-                "cached": True,
-                "cache_name": f"quay.io/biocontainers/{MulledTestCaseWithBuildInfo.mulled_hash}",
-                "cache_namespace": "biocontainers",
-            },
-            {
-                "resolver_type": "cached_mulled",
-                "identifier": f"quay.io/biocontainers/{MulledTestCaseWithBuildInfo.mulled_hash}",
-                "cached": True,
-                "cache_name": f"quay.io/biocontainers/{MulledTestCaseWithBuildInfo.mulled_hash}",
-                "cache_namespace": "biocontainers",
-            },
-        ],
-    }
-
-
 class TestDefaultSingularityContainerResolvers(
     SingularityContainerResolverTestCase, ContainerResolverTestCases, MulledTestCase
 ):