From be1e21bffcd63aa2ef709acc80ef5230ff89d571 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Tue, 10 Nov 2020 13:19:18 +0000
Subject: [PATCH 1/3] Migrate API tests to GitHub workflow

---
 .github/workflows/api.yaml | 40 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 .github/workflows/api.yaml

diff --git a/.github/workflows/api.yaml b/.github/workflows/api.yaml
new file mode 100644
index 00000000000..32da03aa47a
--- /dev/null
+++ b/.github/workflows/api.yaml
@@ -0,0 +1,40 @@
+name: API tests
+on: [push, pull_request]
+env:
+  GALAXY_TEST_DBURI: 'postgres://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.7']
+    services:
+      postgres:
+        image: postgres:11
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          path: 'galaxy root'
+      - uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Cache pip dir
+        uses: actions/cache@v2
+        with:
+          path: ~/.cache/pip
+          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+      - name: Run tests
+        run: ./run_tests.sh --skip_flakey_fails -api
+        working-directory: 'galaxy root'
+      - uses: actions/upload-artifact@v2
+        if: failure()
+        with:
+          name: API test results
+          path: 'galaxy root/run_api_tests.html'

From 1e9f83b53ea8599b4414ce4dd7a63bc505603506 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Tue, 10 Nov 2020 15:33:35 +0000
Subject: [PATCH 2/3] Add missing single-quotes in tools Cheetah

---
 .../functional/tools/for_workflows/mapper.xml |  6 +--
 .../tools/for_workflows/mapper2.xml           | 44 +++++++++----------
 .../functional/tools/for_workflows/pileup.xml |  8 ++--
 tools/filters/catWrapper.xml                  | 22 +++++-----
 4 files changed, 39 insertions(+), 41 deletions(-)

diff --git a/test/functional/tools/for_workflows/mapper.xml b/test/functional/tools/for_workflows/mapper.xml
index 505e517c7db..3a6f325d475 100644
--- a/test/functional/tools/for_workflows/mapper.xml
+++ b/test/functional/tools/for_workflows/mapper.xml
@@ -1,7 +1,7 @@
 <tool id="mapper" name="Mapper" version="0.1.0">
-    <command>
-        cp $__tool_directory__/1.bam $out_file1
-    </command>
+    <command><![CDATA[
+cp '$__tool_directory__/1.bam' '$out_file1'
+    ]]></command>
     <inputs>
         <param name="input1" type="data" format="fastq" label="Fastq Input"/>
         <param name="reference" type="data" format="fasta" label="Fasta Input"/>
diff --git a/test/functional/tools/for_workflows/mapper2.xml b/test/functional/tools/for_workflows/mapper2.xml
index d3fb3b9d9a5..a800ef86616 100644
--- a/test/functional/tools/for_workflows/mapper2.xml
+++ b/test/functional/tools/for_workflows/mapper2.xml
@@ -1,29 +1,29 @@
 <tool id="mapper2" name="mapper2" version="0.1.0">
-    <command>
-        cp $__tool_directory__/1.bam $out_file1
-    </command>
+    <command><![CDATA[
+cp '$__tool_directory__/1.bam' '$out_file1'
+    ]]></command>
     <inputs>
         <!-- Conditional input block loosely based on bwa-mem. -->
         <conditional name="fastq_input">
-          <param name="fastq_input_selector" type="select" label="Single or Paired-end reads">
-            <option value="paired">Paired</option>
-            <option value="single">Single</option>
-            <option value="paired_collection">Paired Collection</option>
-            <option value="paired_iv">Paired Interleaved</option>
-          </param>
-          <when value="paired">
-            <param name="fastq_input1" type="data" format="fastq" label="Select first set of reads" />
-            <param name="fastq_input2" type="data" format="fastq" label="Select second set of reads" />
-          </when>
-          <when value="single">
-            <param name="fastq_input1" type="data" format="fastq" label="Select fastq dataset"/>
-          </when>
-          <when value="paired_collection">
-            <param name="fastq_input1" format="fastq" type="data_collection" collection_type="paired" label="Select a paired collection" />
-          </when>
-          <when value="paired_iv">
-            <param name="fastq_input1" type="data" format="fastq" label="Select fastq dataset" />
-          </when>
+            <param name="fastq_input_selector" type="select" label="Single or Paired-end reads">
+                <option value="paired">Paired</option>
+                <option value="single">Single</option>
+                <option value="paired_collection">Paired Collection</option>
+                <option value="paired_iv">Paired Interleaved</option>
+            </param>
+            <when value="paired">
+                <param name="fastq_input1" type="data" format="fastq" label="Select first set of reads" />
+                <param name="fastq_input2" type="data" format="fastq" label="Select second set of reads" />
+            </when>
+            <when value="single">
+                <param name="fastq_input1" type="data" format="fastq" label="Select fastq dataset"/>
+            </when>
+            <when value="paired_collection">
+                <param name="fastq_input1" type="data_collection" collection_type="paired" format="fastq" label="Select a paired collection" />
+            </when>
+            <when value="paired_iv">
+                <param name="fastq_input1" type="data" format="fastq" label="Select fastq dataset" />
+            </when>
         </conditional>
         <param name="reference" type="data" format="fasta" label="Fasta Input"/>
     </inputs>
diff --git a/test/functional/tools/for_workflows/pileup.xml b/test/functional/tools/for_workflows/pileup.xml
index df6c6af4149..aa17f109f03 100644
--- a/test/functional/tools/for_workflows/pileup.xml
+++ b/test/functional/tools/for_workflows/pileup.xml
@@ -1,9 +1,9 @@
 <tool id="pileup" name="Pileup" version="0.1.0">
-    <command>
-        printf "Summary" > $out_file1
-    </command>
+    <command><![CDATA[
+printf 'Summary' > '$out_file1'
+    ]]></command>
     <inputs>
-        <param name="input1" type="data" format="bam" multiple="true" label="BAM Inputs" min="1">
+        <param name="input1" type="data" format="bam" multiple="true" min="1" label="BAM Inputs">
             <validator check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" />
         </param>
         <param name="reference" type="data" format="fasta" label="Fasta Input"/>
diff --git a/tools/filters/catWrapper.xml b/tools/filters/catWrapper.xml
index 33e67e1e5a4..d4865d3c5b9 100644
--- a/tools/filters/catWrapper.xml
+++ b/tools/filters/catWrapper.xml
@@ -1,13 +1,13 @@
 <tool id="cat1" name="Concatenate datasets" version="1.0.0">
     <description>tail-to-head</description>
-    <command interpreter="python">
-        catWrapper.py
-        $out_file1
-        $input1
-        #for $q in $queries
-            ${q.input2}
-        #end for
-    </command>
+    <command interpreter="python"><![CDATA[
+catWrapper.py
+'$out_file1'
+'$input1'
+#for $q in $queries
+    '${q.input2}'
+#end for
+    ]]></command>
     <inputs>
         <param name="input1" type="data" label="Concatenate Dataset"/>
         <repeat name="queries" title="Dataset">
@@ -33,8 +33,7 @@
         </test>
         -->
     </tests>
-    <help>
-
+    <help><![CDATA[
 .. class:: warningmark
 
 **WARNING:** Be careful not to concatenate datasets of different kinds (e.g., sequences with intervals). This tool does not check if the datasets being concatenated are in the same format.
@@ -74,6 +73,5 @@ will result in the following::
     chr1  151278832  151279227  Z  0  -
     chr2  100000030  200000955  P  0  +
     chr2  100000015  200000999  Q  0  +
-
-    </help>
+    ]]></help>
 </tool>

From efa9e0fdd1d11d58f4a504a3e8242cc59f3f1416 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Tue, 10 Nov 2020 17:17:15 +0000
Subject: [PATCH 3/3] Fix command line for tools using `interpreter` when
 galaxy root contains spaces

---
 lib/galaxy/tools/evaluation.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/tools/evaluation.py b/lib/galaxy/tools/evaluation.py
index b47b4039d46..45f21a22b6b 100644
--- a/lib/galaxy/tools/evaluation.py
+++ b/lib/galaxy/tools/evaluation.py
@@ -1,6 +1,7 @@
 import json
 import logging
 import os
+import shlex
 import tempfile
 
 
@@ -494,11 +495,12 @@ class ToolEvaluator:
             raise
         if interpreter:
             # TODO: path munging for cluster/dataset server relocatability
-            executable = command_line.split()[0]
+            command_line_tokens = shlex.split(command_line)
+            executable = command_line_tokens[0]
             tool_dir = os.path.abspath(self.tool.tool_dir)
             abs_executable = os.path.join(tool_dir, executable)
-            command_line = command_line.replace(executable, abs_executable, 1)
-            command_line = interpreter + " " + command_line
+            command_line_tokens[0:1] = [interpreter, abs_executable]
+            command_line = ' '.join(map(shlex.quote, command_line_tokens))
         self.command_line = command_line
 
     def __build_config_files(self):