comparison toolfactory/rgToolFactory2.py @ 117:b1a29d3d50d6 draft

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116:b1ea31ea3f00

        ):  # cannot do this inside galaxyxml as it expects lxml objects for tests
            part1 = exml.split("<tests>")[0]
            part2 = exml.split("</tests>")[1]
            fixed = "%s\n%s\n%s" % (part1, self.test_override, part2)
            exml = fixed
        exml = exml.replace('range="1:"', 'range="1000:"')
        xf = open("%s.xml" % self.tool_name, "w")
        xf.write(exml)
        xf.write("\n")
        xf.close()
        # ready for the tarball

        client = docker.from_env()
        tvol = client.volumes.create()
        tvolname = tvol.name
        destdir = "/toolfactory/ptest"
        imrep = os.path.join(destdir, repname)
        # need to keep the container running so keep it open with tail -f.
        # will stop and destroy it when we are done
        container = client.containers.run(
            planemoimage,
            "sleep 120m",
            detach=True,

            tout.write(f"#### error: {e} from {ptestcl}\n")
        cl = f"planemo test  --test_output {imrep} --no_cleanup --test_data {destdir}/tfout/test-data --galaxy_root /home/biodocker/galaxy-central {ptestpath}"
        try:
            prun(container, tout, cl)
        except:
            pass
        testouts = tempfile.mkdtemp(suffix=None, prefix="tftemp", dir=".")
        self.copy_from_container(destdir, testouts, container)
        src = os.path.join(testouts, "ptest")
        if os.path.isdir(src):
            shutil.copytree(src, ".", dirs_exist_ok=True)

        def exclude_function(tarinfo):
            filename = tarinfo.name
            return None if filename.endswith(excludeme) else tarinfo

        for p in self.outfiles:
            oname = p[ONAMEPOS]
            tdest = os.path.join(self.testdir, "%s_sample" % oname)
            if not os.path.isfile(tdest):
                src = os.path.join(self.testdir, oname)
                if os.path.isfile(src):
                    shutil.copyfile(src, tdest)
                    dest = os.path.join(self.repdir, "%s.sample" % (oname))
                    shutil.copyfile(src, dest)
                else:
                    print(
                        "### problem - output file %s not found in testdir %s"
                        % (tdest, self.testdir)
                    )
        tf = tarfile.open(self.newtarpath, "w:gz")
        tf.add(name=self.tooloutdir, arcname=self.tool_name, filter=exclude_function)
        tf.close()

117:b1a29d3d50d6

        ):  # cannot do this inside galaxyxml as it expects lxml objects for tests
            part1 = exml.split("<tests>")[0]
            part2 = exml.split("</tests>")[1]
            fixed = "%s\n%s\n%s" % (part1, self.test_override, part2)
            exml = fixed
        #exml = exml.replace('range="1:"', 'range="1000:"')
        xf = open("%s.xml" % self.tool_name, "w")
        xf.write(exml)
        xf.write("\n")
        xf.close()
        # ready for the tarball

        client = docker.from_env()
        tvol = client.volumes.create()
        tvolname = tvol.name
        destdir = "/toolfactory/ptest"
        imrep = os.path.join(destdir, repname)
        # need to keep the container running so keep it open with sleep
        # will stop and destroy it when we are done
        container = client.containers.run(
            planemoimage,
            "sleep 120m",
            detach=True,

            tout.write(f"#### error: {e} from {ptestcl}\n")
        cl = f"planemo test  --test_output {imrep} --no_cleanup --test_data {destdir}/tfout/test-data --galaxy_root /home/biodocker/galaxy-central {ptestpath}"
        try:
            prun(container, tout, cl)
        except:
            e = sys.exc_info()[0]
            tout.write(f"#### error: {e} from {ptestcl}\n")
        testouts = tempfile.mkdtemp(suffix=None, prefix="tftemp", dir=".")
        self.copy_from_container(destdir, testouts, container)
        src = os.path.join(testouts, "ptest")
        if os.path.isdir(src):
            shutil.copytree(src, ".", dirs_exist_ok=True)

        def exclude_function(tarinfo):
            filename = tarinfo.name
            return None if filename.endswith(excludeme) else tarinfo

        if os.path.exists(self.tlog):
            tout = open(self.tlog, "a")
        else:
            tout = open(self.tlog, "w")
        for p in self.outfiles:
            oname = p[ONAMEPOS]
            tdest = os.path.join(self.testdir, "%s_sample" % oname)
            if not os.path.isfile(tdest):
                src = os.path.join(self.testdir, oname)
                if os.path.isfile(src):
                    shutil.copyfile(src, tdest)
                    dest = os.path.join(self.repdir, "%s.sample" % (oname))
                    shutil.copyfile(src, dest)
                else:
                    tout.write(
                        "###Output file %s not found in testdir %s. This is normal during the first Planemo run that generates test outputs"
                        % (tdest, self.testdir)
                    )
        tf = tarfile.open(self.newtarpath, "w:gz")
        tf.add(name=self.tooloutdir, arcname=self.tool_name, filter=exclude_function)
        tf.close()