changeset 102:c632db66f8c0 draft

Uploaded

--- a/toolfactory/rgToolFactory2.py	Thu Nov 26 06:17:12 2020 +0000
+++ b/toolfactory/rgToolFactory2.py	Thu Nov 26 06:26:28 2020 +0000
@@ -766,191 +766,6 @@
         container.remove()
         shutil.rmtree(testouts)
 
-
-    def planemo_biodocker_vol_test(self):
-        """planemo currently leaks dependencies if used in the same container and gets unhappy after a
-        first successful run. https://github.com/galaxyproject/planemo/issues/1078#issuecomment-731476930
-
-        Docker biocontainer has planemo with caches filled to save repeated downloads
-        Cannot get volumes to work right in this version
-
-        """
-        if os.path.exists(self.tlog):
-            tout = open(self.tlog, "a")
-        else:
-            tout = open(self.tlog, "w")
-        planemoimage = "quay.io/fubar2/planemo-biocontainer"
-        xreal = "%s.xml" % self.tool_name
-        repname = f"{self.tool_name}_planemo_test_report.html"
-        ptestrep_path = os.path.join(self.repdir,repname)
-        tool_name = self.tool_name
-        workdir = "export"
-        aworkdir = os.path.abspath(workdir)
-        os.makedirs(workdir, exist_ok=True)
-        os.chmod(workdir,0o777)
-        imworkdir = "/export"
-        # must be mounted as a volume
-        tooldir = os.path.join(workdir,self.tool_name)
-        testdir = os.path.join(tooldir,'test-data')
-        imtooldir = os.path.join(imworkdir,self.tool_name)
-        imtestdir = os.path.join(imtooldir,'test-data')
-        for d in [tooldir,testdir]:
-            if not os.path.exists(d):
-                os.mkdir(d)
-        with os.scandir(self.testdir) as outs:
-            for entry in outs:
-                if not entry.is_file():
-                    continue
-                src = os.path.join(self.testdir, entry.name)
-                dest = os.path.join(testdir, entry.name)
-                shutil.copyfile(src, dest)
-        shutil.copyfile(xreal,os.path.join(tooldir,xreal))
-        client = docker.from_env()
-        # mnt = docker.types.Mount(source='workdir', target=imworkdir) # mounts=[mnt],)
-        atestcl = "ls -lt /export"
-        container = client.containers.run(planemoimage,atestcl,
-           volumes={aworkdir:{'bind':'/export','mode':'rw'}}, )
-        tout.write(f"## Ran {atestcl} and got {container}")
-        ptestpath = os.path.join(imtooldir,xreal)
-        ptestcll = f"planemo test --job_output_files {imtooldir} --update_test_data --test_data {imtestdir} --galaxy_root /home/biodocker/galaxy-central {ptestpath}"
-        try:
-            container = client.containers.run(planemoimage,ptestcl,
-               volumes={aworkdir:{'bind':'/export','mode':'rw'}}, )
-        except:
-            pass
-        tout.write(f"## Ran {ptestcl}")
-        with os.scandir(testdir) as outs:
-            for entry in outs:
-                if not entry.is_file():
-                    continue
-                src = os.path.join(testdir, entry.name)
-                dest = os.path.join(self.testdir, entry.name)
-                shutil.copyfile(src, dest)
-        imrep_path = os.path.join(imtooldir,repname)
-        ptestcl = f"planemo test --job_output_files {imtooldir}  --test_output {imrep_path} --test_data {imtestdir} --galaxy_root /home/biodocker/galaxy-central {ptestpath}"
-        try:
-            container = client.containers.run(planemoimage,ptestcl,
-               volumes={aworkdir:{'bind':'/export','mode':'rw'}}, )
-        except:
-            pass
-        tout.write(f"## Ran {ptestcl}")
-        if os.path.isfile(imrep_path):
-            shutil.copyfile(imrep_path,ptestrep_path)
-        else:
-            tout.write(f"## planemo_biodocker_test - no test report {imrep_path} found")
-        tout.close()
-        #shutil.rmtree(workdir)
-
-
-
-    def gal_tool_test(self):
-        """
-        On path should be a handy script writes test outputs even if they don't exist
-
-        galaxy-tool-test -u http://localhost:8080 -a 3c9afe09f1b7892449d266109639c104 -o /tmp/foo -t hello -j /tmp/foo/hello.json --verbose
-
-       leaves outputs in -o !
-        """
-        gttscript = f"""#!{self.args.galaxy_venv}/bin/python3
-# -*- coding: utf-8 -*-
-import re
-import sys
-from galaxy.tool_util.verify.script import main
-if __name__ == '__main__':
-    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
-    sys.exit(main())
-
-        """
-        galaxy_lib = os.path.join(self.args.galaxy_root,'lib')
-        fakeenv = copy.copy(os.environ)
-        fakeenv ["PATH"] = "/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
-        fakeenv ["PYTHONPATH"] = f"{galaxy_lib}"
-        if os.path.exists(self.tlog):
-            tout = open(self.tlog, "a")
-        else:
-            tout = open(self.tlog, "w")
-        testouts = tempfile.mkdtemp(suffix=None, prefix="tftemp",dir="/tmp")
-        tout.write(f"#### using {testouts} as tempdir\n")
-        dummy, tfile = tempfile.mkstemp()
-        gtt = 'galaxy-tool-test'
-        gttf = open(gtt,'w')
-        gttf.write(gttscript)
-        gttf.write('\n')
-        gttf.close()
-        os.chmod(gtt,0o744)
-        cll = [
-            os.path.abspath(gtt),
-            "-u",
-            self.args.galaxy_url,
-            "-k",
-            self.args.galaxy_api_key,
-            "-t",
-            self.tool_name,
-            "-o",
-            testouts,
-        ]
-        subp = subprocess.run(
-           cll, env=fakeenv, cwd=galaxy_lib, shell=True, stderr=tout, stdout=tout
-        )
-        outfiles = []
-        for p in self.outfiles:
-            oname = p[ONAMEPOS]
-            outfiles.append(oname)
-        with os.scandir(testouts) as outs:
-            for entry in outs:
-                if not entry.is_file():
-                    continue
-                dest = os.path.join(self.tooloutdir, entry.name)
-                src = os.path.join(testouts, entry.name)
-                shutil.copyfile(src, dest)
-                testdest = os.path.join(self.testdir, entry.name)
-                src = os.path.join(testouts, entry.name)
-                shutil.copyfile(src, testdest)
-                dest = os.path.join(self.repdir,f"{entry.name}_sample")
-                tout.write(f"## found and moved output {entry.name} to {dest} and {testdest}\n")
-        tout.close()
-        #shutil.rmtree(testouts)
-        return subp.returncode
-
-    def gal_test(self):
-        """
-        Uses the built in galaxy tool tester run_test.sh
-
-        export GALAXY_TEST_SAVE="./foo" && export GALAXY_TEST_NO_CLEANUP="1" \
-        && export GALAXY_TEST_TMP_DIR=./foo && sh run_tests.sh --id rgtf2 --report_file tool_tests_tool_conf.html functional.test_toolbox
-
-        """
-        testdir = tempfile.mkdtemp(suffix=None, prefix="tftemp",dir="/tmp")
-        tool_test_rep = f"{self.tool_name}_galaxy_test_report_html.html"
-        if os.path.exists(self.tlog):
-            tout = open(self.tlog, "a")
-        else:
-            tout = open(self.tlog, "w")
-
-        fakeenv  = copy.copy(os.environ)
-        fakeenv["GALAXY_TEST_SAVE"] = testdir
-        fakeenv["GALAXY_TEST_NO_CLEANUP"] = "1"
-        fakeenv["GALAXY_TEST_TMP_DIR"] = testdir
-        galaxy_lib = os.path.join(self.args.galaxy_root,'lib')
-
-        cll = [
-       "sh", f"{self.args.galaxy_root}/run_tests.sh", "--id", self.tool_name,
-       "--report_file", os.path.join(testdir,tool_test_rep), "functional.test_toolbox",
-        ]
-        subp = subprocess.run(
-            cll, env = fakeenv ,
-            shell=False, cwd=galaxy_lib, stderr=tout, stdout=tout
-        )
-        src = os.path.join(testdir, tool_test_rep)
-        if os.path.isfile(src):
-            dest = os.path.join(self.repdir, tool_test_rep)
-            shutil.copyfile(src, dest)
-        else:
-            tout.write(f"### {src} not found\n")
-        tout.close()
-        return subp.returncode
-
-
     def shedLoad(self):
         """
         {'deleted': False,
@@ -1224,66 +1039,6 @@
         tout.close()
         return subp.returncode
 
-    def planemo_test(self, genoutputs=True):
-        """planemo is a requirement so is available for testing but needs a different call if
-        in the biocontainer - see above
-        and for generating test outputs if command or test overrides are supplied
-        test outputs are sent to repdir for display
-        planemo test --engine docker_galaxy  --galaxy_root /galaxy-central pyrevpos/pyrevpos.xml
-
-        Planemo runs:
-python ./scripts/functional_tests.py -v --with-nosehtml --html-report-file
-/export/galaxy-central/database/job_working_directory/000/17/working/TF_run_report_tempdir/tacrev_planemo_test_report.html
---with-xunit --xunit-file /tmp/tmpt90p7f9h/xunit.xml --with-structureddata
---structured-data-file
-/export/galaxy-central/database/job_working_directory/000/17/working/tfout/tool_test_output.json functional.test_toolbox
-
-
-        for the planemo-biocontainer,
-        planemo test --conda_dependency_resolution --skip_venv --galaxy_root /galthrow/ rgToolFactory2.xml
-
-        """
-        xreal = "%s.xml" % self.tool_name
-        tool_test_path = os.path.join(self.repdir,f"{self.tool_name}_planemo_test_report.html")
-        if os.path.exists(self.tlog):
-            tout = open(self.tlog, "a")
-        else:
-            tout = open(self.tlog, "w")
-        if genoutputs:
-            dummy, tfile = tempfile.mkstemp()
-            cll = [
-                "planemo",
-                "test",
-                "--galaxy_root",
-                self.args.galaxy_root,
-                "--update_test_data",
-                xreal,
-            ]
-            subp = subprocess.run(
-                cll,
-                env=self.ourenv,
-                shell=False,
-                cwd=self.testdir,
-                stderr=dummy,
-                stdout=dummy,
-            )
-
-        else:
-            cll = [
-                "planemo",
-                "test",
-                "--test_data", self.testdir,
-                "--test_output",tool_test_path,
-                "--galaxy_root",
-                self.args.galaxy_root,
-                xreal,
-            ]
-            subp = subprocess.run(
-                cll, env=self.ourenv, shell=False, cwd=self.testdir, stderr=tout, stdout=tout
-            )
-        tout.close()
-        return subp.returncode
-
 
     def writeShedyml(self):
         """for planemo"""