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From 2d1416fc62016533e159f27352f17a7d97f022b1 Mon Sep 17 00:00:00 2001
From: Pavel Boldin <pboldin@cloudlinux.com>
Date: Fri, 13 Oct 2017 11:52:32 +0300
Subject: [PATCH 07/89] Toil package builder
Introduce a toil[1]-based workflow to automate patch building for
a package.
[1] https://toil.readthedocs.io/
Change-Id: I7e3a11ad95781b8989d24fbf3992dcb49e4c8dba
Signed-off-by: Pavel Boldin <pboldin@cloudlinux.com>
---
packages/rhel7/glibc/glibc-2.17-55.el7/info | 23 +-
.../glibc/glibc-2.17-55.el7/pkgfile.yaml | 5 +
scripts/pkgbuild | 28 +-
scripts/toil/README.md | 1 +
scripts/toil/build-patch.sh | 18 +
scripts/toil/pkgbuild.py | 894 ++++++++++++++++++
scripts/toil/requirements.txt | 4 +
scripts/toil/tests_pkgbuild.py | 218 +++++
8 files changed, 1175 insertions(+), 16 deletions(-)
create mode 100644 packages/rhel7/glibc/glibc-2.17-55.el7/pkgfile.yaml
create mode 100644 scripts/toil/README.md
create mode 100755 scripts/toil/build-patch.sh
create mode 100755 scripts/toil/pkgbuild.py
create mode 100644 scripts/toil/requirements.txt
create mode 100644 scripts/toil/tests_pkgbuild.py
diff --git a/packages/rhel7/glibc/glibc-2.17-55.el7/info b/packages/rhel7/glibc/glibc-2.17-55.el7/info
index 9b13a12..8cebabb 100644
--- a/packages/rhel7/glibc/glibc-2.17-55.el7/info
+++ b/packages/rhel7/glibc/glibc-2.17-55.el7/info
@@ -72,7 +72,16 @@ _install_originals() {
}
_run_tests() {
- export LD_PRELOAD=/libcare/tests/execve/execve.so
+ if test -f $LIBCARE_DIR/execve/execve.so; then
+ LD_PRELOAD=$LIBCARE_DIR/execve/execve.so
+ elif test -f $LIBCARE_DIR/tests/execve/execve.so; then
+ LD_PRELOAD=$LIBCARE_DIR/tests/execve/execve.so
+ else
+ echo "Can't find execve.so required to run tests"
+ exit 1
+ fi
+
+ export LD_PRELOAD
local ld_linux="$KP_PROJECT_BUILD_DIR/elf/ld*"
@@ -110,9 +119,11 @@ kp_patch_test() {
rm -f /var/run/libcare.sock
PATCH_ROOT=/root/${KP_PROJECT_PATCH%.*}
- /libcare/src/libcare-ctl -v server /var/run/libcare.sock $PATCH_ROOT \
- >/root/test.log 2>&1 & :
+ $KPATCH_PATH/libcare-ctl -v server /var/run/libcare.sock $PATCH_ROOT \
+ >/data/test.log 2>&1 & :
LISTENER_PID=$!
+ sleep 1
+ kill -0 $LISTENER_PID
pushd $KP_PROJECT_BUILD_DIR
@@ -123,11 +134,11 @@ kp_patch_test() {
popd
- local patched=$(awk '/kpatch_ctl targeting/ { n++ } END { print n }' /root/test.log)
+ local patched=$(awk '/kpatch_ctl targeting/ { n++ } END { print n }' /data/test.log)
test $patched -ge $executed
- grep -vq 'No patch(es) applicable to' /root/test.log
- grep 'patch hunk(s) have been successfully applied' /root/test.log \
+ grep -vq 'No patch(es) applicable to' /data/test.log
+ grep 'patch hunk(s) have been successfully applied' /data/test.log \
| wc -l
}
diff --git a/packages/rhel7/glibc/glibc-2.17-55.el7/pkgfile.yaml b/packages/rhel7/glibc/glibc-2.17-55.el7/pkgfile.yaml
new file mode 100644
index 0000000..51028ed
--- /dev/null
+++ b/packages/rhel7/glibc/glibc-2.17-55.el7/pkgfile.yaml
@@ -0,0 +1,5 @@
+image: kernelcare/centos7:gcc-4.8.2-16.el7
+prebuild: /tmp/build.orig-glibc-2.17-55.el7.x86_64.rpm.tgz
+input:
+- package: .
+- patches: ../../../../patches/
diff --git a/scripts/pkgbuild b/scripts/pkgbuild
index e2ac7c7..8803db3 100755
--- a/scripts/pkgbuild
+++ b/scripts/pkgbuild
@@ -54,8 +54,9 @@ prepare() {
# Export env vars that are needed during the build
SCRIPTS="$(cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd)"
- SPWD="$(realpath $SCRIPTS/../)"
- export KPATCH_PATH=$SPWD/src
+ LIBCARE_DIR="${LIBCARE_DIR:-$SCRIPTS/..}"
+ KPATCH_PATH="${KPATCH_PATH:-$LIBCARE_DIR/src}"
+ export LIBCARE_DIR KPATCH_PATH
export OLDPATH=$PATH
export KPATCH_PASSTHROUGH_ASM=1
CPUS=`cat /proc/cpuinfo | grep ^processor | wc -l`
@@ -130,18 +131,20 @@ kp_prepare_source_deb() {
}
kp_prepare_source() {
- echo " downloading source for $KP_PROJECT"
- kp_download_source_$KP_PROJECT_FORMAT
+ if ! test -f /kcdata/$KP_PROJECT_SOURCE; then
+ echo " downloading source for $KP_PROJECT"
+ kp_download_source_$KP_PROJECT_FORMAT
+ fi
echo " preparing source for $KP_PROJECT"
kp_prepare_source_$KP_PROJECT_FORMAT
}
kp_patch_source() {
echo " patching project"
- PATCH_DIR=$SPWD/patches
+ PATCH_DIR=$LIBCARE_DIR/patches
#patch_list_apply requires this dir
mkdir -p /tmp/build.kpatch
- $SPWD/scripts/patch_list_apply $KP_PROJECT_DIR $PDIR/plist $PATCH_DIR
+ $SCRIPTS/patch_list_apply $KP_PROJECT_DIR $PDIR/plist $PATCH_DIR
}
kp_prebuild_rpm() {
@@ -364,10 +367,10 @@ overwrite_utils() {
TMPBIN=$(mktemp -d --tmpdir)
mkdir $TMPBIN/bin
- ln -fs /libcare/src/libcare-cc $TMPBIN/gcc
- ln -fs /libcare/src/libcare-cc $TMPBIN/cc
- ln -fs /libcare/src/libcare-cc $TMPBIN/g++
- ln -fs /libcare/src/libcare-cc $TMPBIN/c++
+ ln -fs $KPATCH_PATH/libcare-cc $TMPBIN/gcc
+ ln -fs $KPATCH_PATH/libcare-cc $TMPBIN/cc
+ ln -fs $KPATCH_PATH/libcare-cc $TMPBIN/g++
+ ln -fs $KPATCH_PATH/libcare-cc $TMPBIN/c++
if ! test -x /usr/bin/g++; then
rm -f $TMPBIN/g++
fi
@@ -379,6 +382,11 @@ overwrite_utils() {
fi
export PATH=$TMPBIN:$PATH
+
+ if test "$(command -v cc)" != "$TMPBIN/cc"; then
+ echo "Can't install our wrappers, missing?"
+ exit 1
+ fi
}
kp_patch_test() {
diff --git a/scripts/toil/README.md b/scripts/toil/README.md
new file mode 100644
index 0000000..5bc77b6
--- /dev/null
+++ b/scripts/toil/README.md
@@ -0,0 +1 @@
+This is where [toil](https://toil.readthedocs.io/)-based scripts do live.
diff --git a/scripts/toil/build-patch.sh b/scripts/toil/build-patch.sh
new file mode 100755
index 0000000..0e12de4
--- /dev/null
+++ b/scripts/toil/build-patch.sh
@@ -0,0 +1,18 @@
+#!/bin/sh -e
+
+exec 1>&2
+
+ln -fs /data /kcdata
+
+ls -lR /data
+
+yum install -y rpm-build
+
+LIBCARE_DIR="/data"
+KPATCH_PATH="/data/src"
+export LIBCARE_DIR KPATCH_PATH
+make -C $KPATCH_PATH clean all
+make -C /data/execve clean all
+
+/kcdata/scripts/pkgbuild $@ /kcdata/package
+ls /kcdata -lR
diff --git a/scripts/toil/pkgbuild.py b/scripts/toil/pkgbuild.py
new file mode 100755
index 0000000..c4b009a
--- /dev/null
+++ b/scripts/toil/pkgbuild.py
@@ -0,0 +1,894 @@
+#!/usr/bin/python
+"""
+Build package patches for libcare using toil[1] workflow framework.
+The basic components are the following:
+
+#. `Storage` class that works like a filesystem directory. Changes made to it
+ are passed down the chain to all the jobs via `Promise` mechanism. The
+ `Storage` class is also responsible for importing and exporting local files.
+
+#. `FileFetcherJob` job that downloads specified files from the net and puts them in
+ the storage. Supported are AWS S3, HTTP and FTP files. This is usually the
+ first job.
+
+#. `DoBuild` checks presence of the object in the Storage and runs
+ `prebuildJob` chained with `uploadJob` and `buildJob` if the object is missing.
+ Only `buildJob` is run otherwise.
+
+ This is used to build missing parts such as an archive with the baseline
+ source code called `prebuilt` which is listed as optional for the
+ `FileFetcherJob` job.
+
+#. `DockerScriptJob` that brings up a Docker container from the specified image
+ and runs the Storage-suplied script with Storage content exposed into the
+ `/data` directory.
+
+#. `UploadJob` that uploads specified objects from the Storage.
+
+#. `DoIfMissing` checks presence of the object in the Storage and runs
+ specified job if it is missing.
+
+#. `ChainJobs` is used to chain the jobs at the runtime.
+
+
+
+All the updates to the Storage are carried from the children to the followOns
+via `Promise` mechanism. The root job returns Storage from the last followOn,
+this storage is then exported to a directory.
+
+[1] https://toil.readthedocs.io/
+"""
+
+from __future__ import print_function
+
+import boto3
+import contextlib
+import collections
+import datetime
+import dateutil
+import errno
+import logging
+import os
+import requests
+import shutil
+import tarfile
+import tempfile
+import time
+import urlparse
+import yaml
+
+from toil.common import Toil
+from toil.job import Job as toilJob
+from toil.lib.docker import dockerCall, dockerCheckOutput, STOP, RM, FORGO
+
+
+def myabspath(path_or_url, root=None):
+ """Return absolute path for an url or path."""
+ if '://' not in path_or_url or path_or_url.startswith('file://'):
+ path_or_url = path_or_url.replace('file://', '')
+ if (path_or_url[0] == '.' or '/' not in path_or_url) and root:
+ path_or_url = os.path.join(root, path_or_url)
+ path_or_url = os.path.abspath(path_or_url)
+ return path_or_url
+ return
+
+FileInfo = collections.namedtuple('FileInfo', ('fileName', 'url', 'required'))
+
+def parseFileInfo(fileInfo):
+ """Parse fileInfo which is either an URL or a dictionary of form
+ {"fileName": "url"}. When url is prefixed with '*' the file is optional.
+
+ Samples:
+ >>> parseFileInfo('http://kernel.org/index.html')
+ ... "index.html", "http://kernel.org/index.html", True
+ >>> parseFileInfo('*http://kernel.org/index.html')
+ ... "index.html", "http://kernel.org/index.html", False
+ >>> parseFileInfo({'foobar.html': '*http://kernel.org/index.html'})
+ ... "foobar.html", "http://kernel.org/index.html", False
+ """
+ if isinstance(fileInfo, basestring):
+ url = fileInfo
+ fileName = os.path.basename(url)
+ elif isinstance(fileInfo, dict):
+ items = fileInfo.items()
+ if len(items) != 1:
+ raise ValueError("only one-entry dicts are allowed as fileInfo")
+ fileName, url = items[0]
+
+ required = True
+ if url.startswith('*'):
+ url = url.lstrip('*')
+ required = False
+ return FileInfo(fileName, url, required)
+
+
+class WorkflowToFileStoreProxy(object):
+ """
+ Make File.copy and Directory.copy work with toil.common.Toil object.
+ """
+ def __init__(self, workflow):
+ self.workflow = workflow
+
+ def readGlobalFile(self, fileId):
+ tmpfile = tempfile.mktemp()
+ self.workflow.exportFile(fileId, 'file://' + tmpfile)
+ return tmpfile
+
+ def writeGlobalFile(self, path):
+ return self.workflow.importFile('file:///' + path)
+
+ def getLocalTempFile(self):
+ return tempfile.mktemp()
+
+
+class Storage(dict):
+ """Keeps files organized for the workflow.
+
+ This is a dictionary that associates fileName with a file object such
+ as `File` or `Directory` class.
+
+ Additional field `promised_updates` is used to keep track of updates
+ resulting from `Promise`s of children.
+ """
+ def __init__(self, *args, **kwargs):
+ self.promised_updates = []
+ if args:
+ self.promised_updates = list(args[0].promised_updates)
+
+ super(Storage, self).__init__(*args, **kwargs)
+
+ def update(self, other):
+ """Update this Storage with files from another."""
+ if isinstance(other, Storage):
+ self.promised_updates.extend(other.promised_updates)
+
+ if isinstance(other, dict):
+ super(Storage, self).update(other)
+ else:
+ self.promised_updates.append(other)
+
+ def __setstate__(self, state):
+ """Unfold finished promised_updates."""
+ self.promised_updates = []
+ for promise in state['promised_updates']:
+ self.update(promise)
+
+ def __repr__(self):
+ s = super(Storage, self).__repr__()
+ return s + (" %r" % self.promised_updates)
+
+ @contextlib.contextmanager
+ def expose(self, rootDir=None):
+ """Expose Storage to a directory and pick up changes from it."""
+ if rootDir is None:
+ rootDir = self.fileStore.getLocalTempDir()
+ try:
+ self.toDirectory(rootDir)
+ yield rootDir
+ finally:
+ self.cleanupDirectory(rootDir)
+ self.pickupDirectory(rootDir)
+
+ def toDirectory(self, rootDir, export=False):
+ """Copy Storage content to the specified directory."""
+ for fileObj in self.values():
+ if export and isinstance(fileObj, (ImportedFile, ImportedDirectory)):
+ continue
+ fileObj.copy(self.fileStore, rootDir)
+
+ def pickupDirectory(self, directory):
+ """Pick up content of the specified directory into the Storage."""
+ files = ((name, os.path.join(directory, name))
+ for name in os.listdir(directory))
+ return self.pickupFiles(self.fileStore, files)
+
+ def cleanupDirectory(self, rootDir):
+ """Remove storage files from the directory."""
+ return
+ for fileName in self:
+ path = os.path.join(rootDir, fileName)
+
+ if os.path.isdir(path):
+ shutil.rmtree(path)
+ else:
+ os.remove(path)
+
+ def pickupFiles(self, fileStore, files):
+ """Pick up listed files into the Storage."""
+ for fileName, path in files:
+ if fileName in self:
+ continue
+
+ if os.path.isdir(path):
+ self[fileName] = Directory.fromFiles(
+ fileStore, [(fileName, path)])
+ else:
+ self[fileName] = File.fromLocalFile(
+ fileStore, fileName, path)
+
+ def importLocalFiles(self, workflow, inputs, rootDir=None):
+ """Import local files at the start of the workflow.
+
+ This is usually a first step and is done:
+ >>> with Toil(options) as toil:
+ ... storage = Storage.importLocalFiles(
+ ... toil,
+ ... ['localfile.tar', 'secondfile', 'ascript.sh'])
+ ... rootJob = RootJob(storage)
+ """
+
+ localFiles = []
+ remoteFiles = []
+
+ for fileInfo in inputs:
+
+ fileName, url, required = parseFileInfo(fileInfo)
+
+ path = myabspath(url, rootDir)
+ if path:
+ localFiles.append((fileName, path))
+ else:
+ remoteFiles.append(fileInfo)
+
+ for fileName, path in localFiles:
+ if fileName in self:
+ continue
+
+ if os.path.isdir(path):
+ self[fileName] = ImportedDirectory.fromFiles(
+ workflow, fileName, [(fileName, path)])
+ else:
+ try:
+ self[fileName] = ImportedFile.fromLocalFile(
+ workflow, fileName, path)
+ except IOError as ioerr:
+ if ioerr.errno != errno.ENOENT:
+ raise
+
+ print("imported localFiles %s" % (", ".join(self)))
+
+ inputs[:] = remoteFiles
+
+ return self
+
+ @classmethod
+ def fromLocalFiles(cls, workflow, inputs, rootDir=None):
+ storage = cls()
+ storage.importLocalFiles(workflow, inputs, rootDir)
+ return storage
+
+ def exportLocalFiles(self, workflow, outputDir):
+ """Export local files at the end of workflow.
+
+ This is the last step:
+ >>> with Toil(options) as toil:
+ ... ...
+ ... storage = toil.start(rootJob)
+ ... storage.exportLocalFiles(toil, 'outputDir')
+ """
+ try:
+ self.fileStore = WorkflowToFileStoreProxy(workflow)
+ return self.toDirectory(outputDir, export=True)
+ finally:
+ del self.fileStore
+
+
+class File(object):
+ """A file in Storage."""
+ def __init__(self, fileName, fileId, mode=None):
+ super(File, self).__init__()
+ self.fileName = fileName
+ self.fileId = fileId
+ self.mode = mode
+
+ def copy(self, fileStore, dest):
+ localCopy = self.localCopy(fileStore)
+ if os.path.isdir(dest):
+ dest = os.path.join(dest, self.fileName)
+ shutil.copy(localCopy, dest)
+ if self.mode:
+ os.chmod(dest, self.mode)
+
+ def localCopy(self, fileStore):
+ return fileStore.readGlobalFile(self.fileId)
+
+ @contextlib.contextmanager
+ def open(self, fileStore):
+ localFile = self.localCopy(fileStore)
+ with open(localFile) as fh:
+ yield fh
+
+ @classmethod
+ def fromLocalFile(cls, fileStore, fileName, path):
+ return cls(fileName, fileStore.writeGlobalFile(path),
+ mode=os.stat(path).st_mode)
+
+ def __str__(self):
+ return "<File(%s, %s)>" % (self.fileName, self.fileId)
+
+ __repr__ = __str__
+
+
+class ImportedFile(object):
+ def __init__(self, fileName, mode=None):
+ super(ImportedFile, self).__init__()
+ self.fileName = fileName
+ self.mode = mode
+
+ def copy(self, fileStore, dest):
+ if os.path.isdir(dest):
+ dest = os.path.join(dest, self.fileName)
+ with self.open(fileStore) as fhin:
+ with open(dest, 'w') as fhout:
+ shutil.copyfileobj(fhin, fhout)
+ if self.mode:
+ os.chmod(dest, self.mode)
+
+ def localCopy(self, fileStore):
+ fileName = fileStore.getLocalTempFile()
+ self.copy(fileStore, fileName)
+ return fileName
+
+ @contextlib.contextmanager
+ def open(self, fileStore):
+ with fileStore.jobStore.readSharedFileStream(self.fileName) as fh:
+ yield fh
+
+ @classmethod
+ def fromLocalFile(cls, workflow, fileName, path):
+ workflow.importFile('file://' + path, sharedFileName=fileName)
+
+ return cls(
+ fileName,
+ mode=os.stat(path).st_mode)
+
+ def __str__(self):
+ return "<ImportedFile(%s)>" % self.fileName
+
+ __repr__ = __str__
+
+
+class Directory(object):
+ """A directory in Storage. Kept as an archive file."""
+ def __init__(self, fileId):
+ super(Directory, self).__init__()
+ self.fileId = fileId
+
+ def localCopy(self, fileStore, outDir=None):
+ localDir = outDir or fileStore.getLocalTempDir()
+ localFile = fileStore.readGlobalFile(self.fileId)
+
+ tar = tarfile.TarFile.taropen(localFile)
+ tar.extractall(path=localDir)
+
+ return localDir
+
+ def copy(self, fileStore, dest):
+ self.localCopy(fileStore, dest)
+
+ @classmethod
+ def fromFiles(cls, fileStore, files):
+
+ with fileStore.writeGlobalFileStream() as (fh, fileId):
+ tar = tarfile.TarFile.open(fileobj=fh, mode='w')
+
+ for fileName, path in files:
+ tar.add(path, arcname=fileName)
+
+ return cls(fileId)
+
+ def __str__(self):
+ return "<Directory(%s)>" % self.fileId
+
+ __repr__ = __str__
+
+
+class ImportedDirectory(Directory):
+
+ def localCopy(self, fileStore, outDir=None):
+ localDir = outDir or fileStore.getLocalTempDir()
+
+ with fileStore.jobStore.readSharedFileStream(self.fileId) as fh:
+ tar = tarfile.TarFile(fileobj=fh, mode='r')
+ tar.extractall(path=localDir)
+
+ return localDir
+
+ @classmethod
+ def fromFiles(cls, workflow, dirName, files):
+ tmpfile = tempfile.mktemp()
+
+ tar = tarfile.TarFile.open(tmpfile, mode='w')
+
+ for fileName, path in files:
+ tar.add(path, arcname=fileName)
+
+ tar.close()
+
+ workflow.importFile('file://' + tmpfile, sharedFileName=dirName)
+ os.unlink(tmpfile)
+
+ return cls(dirName)
+
+
+class IncorrectStorageUse(Exception):
+ message = "Child `Job`s with storage added outside of running parent " \
+ "wont influence parent's storage. If this is not required " \
+ "consider using addChildNoStorage and setting child's " \
+ "storage via `self._storage = child.resultStorage`."
+
+ def __init__(self):
+ super(IncorrectStorageUse, self).__init__(self.message)
+
+
+class Job(toilJob):
+ """Job with a Storage.
+
+ This Job passes Storage down the workflow via `Promise` mechanism.
+ Updates to Storage from the children are merged and passed to the
+ followOns.
+ """
+
+ _running = False
+ def __init__(self, *args, **kwargs):
+ super(Job, self).__init__(*args, **kwargs)
+ self._storage = Storage()
+ self._childStorage = Storage()
+
+ def rv(self, *path):
+ return super(Job, self).rv('rv', *path)
+
+ @property
+ def storage(self):
+ if self._running:
+ return self._storage
+ else:
+ return super(Job, self).rv('storage')
+
+ @property
+ def resultStorage(self):
+ return super(Job, self).rv('childStorage')
+
+ def _updateStorage(self, succ, promise, ourStorage):
+ if not isinstance(succ, Job):
+ return
+
+ succ._storage = promise
+
+ if ourStorage is not None:
+ if self._running:
+ ourStorage.update(succ.storage)
+ else:
+ raise IncorrectStorageUse()
+
+ def addChild(self, child):
+ """Add a child and update storage with it's promised storage"""
+ rv = super(Job, self).addChild(child)
+ self._updateStorage(child, self.storage, self._childStorage)
+ return rv
+
+ def addFollowOn(self, followOn):
+ "Add a followOn. FollowOns receive storages with updates from children"
+ rv = super(Job, self).addFollowOn(followOn)
+ self._updateStorage(followOn, self.resultStorage, None)
+ return rv
+
+ def addChildNoStorage(self, child):
+ """Add a child that won't contribute to the Storage.
+
+ Typically used to add a child whose Storage will be used as a
+ predecessor' result.
+ """
+ rv = super(Job, self).addChild(child)
+ self._updateStorage(child, self.storage, None)
+ return rv
+
+ def _run(self, jobGraph, fileStore):
+
+ self._running = True
+
+ storage = self.storage
+ storage.fileStore = fileStore
+
+ rv = super(Job, self)._run(jobGraph, fileStore)
+
+ try:
+ del storage.fileStore
+ except AttributeError:
+ pass
+ self._running = False
+
+ self._childStorage.update(self._storage)
+
+ return {
+ 'rv': rv,
+ 'storage': self._storage,
+ 'childStorage': self._childStorage
+ }
+
+
+class NoSuchFile(Exception):
+ pass
+
+
+class FileFetcherJob(Job):
+ """Fetches files from the Web into the Storage.
+
+ Accepts a list `fileInfo`s to download. There must be no local filesystem
+ files. Instead, fetcher should be primed with a Storage having them
+ imported via `importLocalFiles`.
+ """
+ def __init__(self, files, storage=None, localRootDir=None):
+ super(FileFetcherJob, self).__init__(cores=1, memory="256M")
+
+ if storage is not None:
+ self._storage = storage
+
+ self.files = files
+ if localRootDir is None:
+ localRootDir = os.path.dirname(os.path.realpath(__file__))
+ self.localRootDir = localRootDir
+
+ remoteFiles = self.remoteFiles = []
+ localFiles = []
+
+ for fileInfo in self.files:
+
+ fileName, url, required = parseFileInfo(fileInfo)
+ if fileName in self._storage:
+ continue
+
+ path = myabspath(url, self.localRootDir)
+ if path:
+ localFiles.append((fileName, path))
+ else:
+ remoteFiles.append((fileName, url, required))
+
+ if localFiles:
+ raise Exception("Non-empty localFiles, did you forgot to importLocalFiles: %s?" % localFiles)
+
+
+ def run(self, fileStore):
+
+ for fileInfo in self.remoteFiles:
+
+ fileName, url, required = fileInfo
+ if fileName in self.storage:
+ continue
+
+ try:
+ if url.startswith('s3://'):
+ child = S3DownloadJob(fileName, url)
+ else:
+ child = DownloadJob(fileName, url)
+ self.addChild(child)
+ except NoSuchFile:
+ if required:
+ raise
+
+
+class DownloadJob(Job):
+ """Download a HTTP or FTP file."""
+ def __init__(self, fileName, url):
+ self.url = url
+
+ request = requests.get(self.url, stream=True)
+ if request.status_code != 200:
+ raise NoSuchFile(self.url)
+
+ disk = request.headers.get('Content-Length', '1G')
+ request.close()
+ self.fileName = fileName
+
+ Job.__init__(self, unitName=url, memory="128M", cores=1, disk=disk)
+
+ def run(self, fileStore):
+ r = requests.get(self.url, stream=True)
+
+ with fileStore.writeGlobalFileStream() as (fh, fileId):
+ for chunk in r.iter_content(4096):
+ fh.write(chunk)
+ self.storage[self.fileName] = File(self.fileName, fileId)
+
+
+_CLIENT = None
+class S3FileJob(Job):
+
+ def parseurl(self, desturl):
+ url = urlparse.urlparse(desturl)
+ if url.scheme != "s3":
+ raise Exception("URL %s is not S3 url" % desturl)
+
+ self.url = url
+ self.bucket = self.url.netloc
+ self.key = self.url.path[1:]
+ self.desturl = desturl
+
+ def client(cls):
+
+ global _CLIENT
+ if _CLIENT is None:
+ _CLIENT = boto3.client('s3')
+ return _CLIENT
+
+
+class S3DownloadJob(S3FileJob):
+ """Download a file from AWS S3."""
+ def __init__(self, fileName, url):
+ self.parseurl(url)
+
+ try:
+ self.obj = self.client().get_object(Bucket=self.bucket, Key=self.key)
+ except self.client().exceptions.NoSuchKey:
+ raise NoSuchFile(url)
+
+ self.fileName = fileName
+ super(S3DownloadJob, self).__init__(
+ memory="1M", cores=1, unitName="download %s" % url,
+ disk=self.obj['ContentLength'])
+
+ def run(self, fileStore):
+ with fileStore.writeGlobalFileStream() as (fh, fileId):
+ self.client().download_fileobj(Bucket=self.bucket, Key=self.key,
+ Fileobj=fh)
+ self.storage[self.fileName] = File(self.fileName, fileId)
+
+
+class S3UploadJob(S3FileJob):
+ """Upload a file to AWS S3."""
+ def __init__(self, fileId, url):
+ self.parseurl(url)
+ self.fileId = fileId
+
+ super(S3UploadJob, self).__init__(memory="1M", cores=1, unitName="upload %s" % url)
+
+
+ def run(self, fileStore):
+ localFile = fileStore.readGlobalFile(self.fileId)
+ self.client().upload_file(localFile, self.bucket, self.key)
+
+
+class DockerScriptJob(Job):
+ """Run docker script on top of an exposed Storage."""
+
+ def __init__(self, script, image,
+ args=[], cores=4, disk="4G",
+ logfileName="docker-logfile"):
+ unitName = "image={image} script={script} args={args!r}".format(
+ image=image, script=script, args=args)
+ Job.__init__(self, cores=cores, disk=disk, unitName=unitName)
+
+ self.script = script
+
+ self.image = image
+ self.args = args
+ self.logfileName = logfileName
+
+ def run(self, fileStore):
+
+ e = None
+ with self.storage.expose() as dockerRoot:
+ logfilePath = os.path.join(dockerRoot, self.logfileName)
+ with open(logfilePath, "a") as logfilefh:
+ dockerDefer = fileStore.jobStore.config.dockerDefer
+
+ dockerParameters = []
+ if dockerDefer == RM:
+ dockerParameters.append('--rm')
+
+ dockerParameters += ['-t', '-v', os.path.abspath(dockerRoot) + ':/data']
+ #dockerParameters += ['--privileged']
+ dockerParameters += ['--cap-add=SYS_PTRACE']
+
+ dockerCall(self,
+ tool=self.image, workDir=dockerRoot,
+ defer=dockerDefer, outfile=logfilefh,
+ parameters=["/data/build"]
+ + self.args,
+ dockerParameters=dockerParameters)
+
+ return str(e)
+
+ def __str__(self):
+ name = "build--script=%s--image=%s" % (
+ os.path.basename(self.script), self.image)
+ return name.replace(':', '-').replace('=', '-').replace('/', '-')
+
+
+
+DEFAULT_SCRIPT = './build-patch.sh'
+DEFAULT_IMAGE = 'centos:centos7'
+
+UploadInfo = collections.namedtuple('UploadInfo', ('fileName', 'url'))
+
+class UploadJob(Job):
+ """Upload files from the Storage.
+
+ URLs passed are `uploadInfo` instances.
+ """
+ def __init__(self, urls):
+ self.urls = [UploadInfo(*url) for url in urls]
+
+ super(UploadJob, self).__init__()
+
+ def run(self, fileStore):
+ for url in self.urls:
+ fileName, url = url
+
+ fileObj = self.storage.get(fileName)
+ if fileObj is None:
+ continue
+
+ path = myabspath(url)
+ if not path:
+ self.addChild(S3UploadJob(fileObj.fileId, url))
+ else:
+ localFile = fileStore.readGlobalFile(fileObj.fileId)
+ shutil.copy(localFile, path)
+
+
+class DoBuild(Job):
+ """If prebuild archive is not in storage do a prebuild and upload it to the
+ specified location. Otherwise just do a build."""
+
+ def __init__(self, fileName, prebuildJob, uploadJob, buildJob):
+ super(DoBuild, self).__init__(memory="256M")
+
+ self.fileName = fileName
+ self.prebuildJob = prebuildJob
+ self.buildJob = buildJob
+ self.uploadJob = uploadJob
+
+ def run(self, fileStore):
+ if self.fileName not in self.storage:
+ self.addChild(self.prebuildJob)
+
+ self.prebuildJob.addChildNoStorage(self.buildJob)
+ self.prebuildJob.addChildNoStorage(self.uploadJob)
+ else:
+ self.addChild(self.buildJob)
+
+ self._storage = self.buildJob.storage
+
+
+class BuildPatchJob(toilJob):
+ """Root job for patch building. Fetches files and runs Docker jobs.
+
+ The algorithm is the following:
+ 1. FileFetcherJob(inputs + optional prebuild).
+
+ 2. If prebuild is there, just run DockerScriptJob with a build job.
+
+ 3. If prebuild is missing, run DockerScriptJob. Chain UploadJob for it.
+ Start build job DockerScriptJob it.
+ """
+ def __init__(self, storage, packageDescription):
+ super(BuildPatchJob, self).__init__(memory="256M")
+
+ self.storage = storage
+ self.packageDescription = packageDescription
+
+ self.script = packageDescription.get('script', DEFAULT_SCRIPT)
+ self.image = packageDescription.get('image', DEFAULT_IMAGE)
+
+ self.inputs = list(packageDescription.get('input'))
+
+ def run(self, fileStore):
+
+ tail = self
+
+ fetcher = FileFetcherJob(self.inputs, storage=self.storage)
+ tail.addFollowOn(fetcher)
+ tail = fetcher
+
+ prebuildUrl = self.packageDescription['prebuild']
+ prebuildName = os.path.basename(prebuildUrl)
+
+ prebuildJob = DockerScriptJob(
+ script=self.script,
+ image=self.image,
+ args=['-p'],
+ logfileName="prebuild.log")
+ uploadJob = UploadJob([(prebuildName, prebuildUrl)])
+
+ buildJob = DockerScriptJob(
+ script=self.script,
+ image=self.image,
+ logfileName="build.log")
+
+
+ doBuild = DoBuild(fileName=prebuildName, prebuildJob=prebuildJob,
+ uploadJob=uploadJob, buildJob=buildJob)
+ tail.addFollowOn(doBuild)
+ tail = doBuild
+
+ return tail.storage
+
+
+def get_default_outputDir():
+ outputDir = os.path.join(os.getcwd(), 'libcare-output')
+ outputDir = os.path.join(outputDir, datetime.datetime.utcnow().isoformat())
+ return outputDir
+
+def readPackageDescription(packageFile):
+ with open(packageFile) as fh:
+ packageDescription = yaml.load(fh)
+
+ inputs = packageDescription['input']
+
+ cwd = os.path.dirname(os.path.realpath(__file__))
+
+ script = packageDescription.get(
+ 'script', os.path.join(cwd, DEFAULT_SCRIPT))
+
+ inputs.append({'build': script})
+ inputs.append({'scripts': os.path.join(cwd, '../../scripts')})
+ inputs.append({'src': os.path.join(cwd, '../../src/')})
+ inputs.append({'execve': os.path.join(cwd, '../../tests/execve')})
+
+ prebuildUrl = packageDescription['prebuild']
+ if not prebuildUrl.startswith('*'):
+ prebuildUrl = '*' + prebuildUrl
+ inputs.append(prebuildUrl)
+
+ return packageDescription
+
+def start(toil):
+
+ options = toil.options
+
+ packageDescription = readPackageDescription(options.packageFile)
+
+ path = myabspath(options.outputDir)
+ if path:
+ print("output directory is", path)
+ options.outputDir = path
+ else:
+ print("output url is", options.outputDir)
+
+ rootDir = os.path.realpath(os.path.dirname(options.packageFile))
+
+ storage = Storage()
+ storage.importLocalFiles(toil, packageDescription['input'], rootDir=rootDir)
+ theJob = BuildPatchJob(storage, packageDescription)
+
+ return toil.start(theJob)
+
+def restart(toil):
+ packageDescription = readPackageDescription(toil.options.packageFile)
+
+ rootDir = os.path.realpath(os.path.dirname(toil.options.packageFile))
+
+ Storage.fromLocalFiles(toil, packageDescription['input'], rootDir=rootDir)
+
+ return toil.restart()
+
+def main():
+ parser = Job.Runner.getDefaultArgumentParser()
+ parser.add_argument('packageFile')
+ parser.add_argument('--outputDir', required=False,
+ default=get_default_outputDir())
+ parser.add_argument('--dockerDefer', required=False,
+ default='RM')
+ options = parser.parse_args()
+
+ options.disableCaching = True
+
+ with Toil(options) as toil:
+ toil.config.dockerDefer = globals()[options.dockerDefer.upper()]
+ toil._jobStore.writeConfig()
+
+ if not toil.options.restart:
+ storage = start(toil)
+ else:
+ storage = restart(toil)
+
+ try:
+ os.makedirs(options.outputDir)
+ except OSError as e:
+ if e.errno != errno.EEXIST:
+ raise
+ storage.exportLocalFiles(toil, options.outputDir)
+
+if __name__ == "__main__":
+ main()
diff --git a/scripts/toil/requirements.txt b/scripts/toil/requirements.txt
new file mode 100644
index 0000000..ea481fa
--- /dev/null
+++ b/scripts/toil/requirements.txt
@@ -0,0 +1,4 @@
+toil==3.10.1
+boto3
+requests
+pyyaml
diff --git a/scripts/toil/tests_pkgbuild.py b/scripts/toil/tests_pkgbuild.py
new file mode 100644
index 0000000..f60643d
--- /dev/null
+++ b/scripts/toil/tests_pkgbuild.py
@@ -0,0 +1,218 @@
+#!/usr/bin/python
+
+import contextlib
+import functools
+import os
+import shutil
+from StringIO import StringIO
+import tempfile
+
+from toil.common import Toil
+
+import pkgbuild
+
+def test_storage_update():
+ Storage = pkgbuild.Storage
+
+ storage = Storage(**{'test.sh': 'nothing'})
+ newStorage = Storage(**{'test2.sh': 'nothing'})
+
+ storage.update('promised_value2')
+ newStorage.update('promised_value')
+
+ newStorage.update(storage)
+
+ assert newStorage == {'test.sh': 'nothing', 'test2.sh': 'nothing'}
+ assert newStorage.promised_updates == ['promised_value', 'promised_value2']
+ assert Storage(newStorage) == newStorage
+
+def test_storage_pickle():
+ import cPickle
+ Storage = pkgbuild.Storage
+
+ storage = Storage()
+ storage['abc'] = 'test'
+ storage.update('promised_value')
+
+ storage = cPickle.loads(cPickle.dumps(storage, protocol=-1))
+ assert storage['abc'] == 'test'
+ assert storage.promised_updates == ['promised_value']
+
+def test_parseFileInfo():
+ parseFileInfo = pkgbuild.parseFileInfo
+
+ info = parseFileInfo('http://kernel.org/index.html')
+ assert info == pkgbuild.FileInfo(
+ fileName='index.html',
+ url='http://kernel.org/index.html',
+ required=True)
+
+ info = parseFileInfo('*http://kernel.org/index.html')
+ assert info == pkgbuild.FileInfo(
+ fileName='index.html',
+ url='http://kernel.org/index.html',
+ required=False)
+
+ info = parseFileInfo({'foobar.html': 'http://kernel.org/index.html'})
+ assert info == pkgbuild.FileInfo(
+ fileName='foobar.html',
+ url='http://kernel.org/index.html',
+ required=True)
+
+ info = parseFileInfo({'foobar.html': '*http://kernel.org/index.html'})
+ assert info == pkgbuild.FileInfo(
+ fileName='foobar.html',
+ url='http://kernel.org/index.html',
+ required=False)
+
+ try:
+ info = parseFileInfo({
+ 'foobar.html': '*http://kernel.org/index.html',
+ 'other': 'things'})
+ except ValueError:
+ pass
+ else:
+ assert False
+
+class FakeJobStorage(object):
+ def __init__(self, imported):
+ self.imported = imported
+
+ @contextlib.contextmanager
+ def readSharedFileStream(self, fileId):
+ buf = fileId
+ if self.imported and fileId in self.imported:
+ buf = self.imported[fileId]
+ yield StringIO(buf)
+
+class FakeFileStorage(object):
+ def __init__(self, imported=None):
+ self.localTempDir = tempfile.mkdtemp()
+ self.jobStore = FakeJobStorage(imported)
+
+ def getLocalTempDir(self):
+ return self.localTempDir
+
+ def readGlobalFile(self, fileId):
+ fileName = tempfile.mktemp()
+ with open(fileName, "w") as fh:
+ print(fileId)
+ fh.write(fileId)
+ return fileName
+
+ def writeGlobalFile(self, path):
+ with open(path) as fh:
+ return fh.read()
+
+ @contextlib.contextmanager
+ def writeGlobalFileStream(self):
+ fh_and_fileId = StringIO()
+ yield fh_and_fileId, fh_and_fileId
+
+class FakeWorkflow(object):
+ def __init__(self):
+ self.imported = {}
+
+ def importFile(self, path, sharedFileName):
+ self.imported[sharedFileName] = slurp(path.replace('file://', ''))
+
+def slurp(fileName):
+ return open(fileName).read()
+
+def test_storage():
+ storage = pkgbuild.Storage(
+ **{
+ 'file.txt': pkgbuild.File('file.txt', 'some content'),
+ 'imported.txt': pkgbuild.ImportedFile('imported.txt')
+ }
+ )
+ storage.fileStore = FakeFileStorage()
+
+ with storage.expose() as dirname:
+
+ assert set(os.listdir(dirname)) == set(['file.txt', 'imported.txt'])
+
+ assert slurp(os.path.join(dirname, 'file.txt')) == 'some content'
+ assert slurp(os.path.join(dirname, 'imported.txt')) == 'imported.txt'
+
+ with open(os.path.join(dirname, 'newfile.txt'), 'w') as fh:
+ fh.write('and some content here')
+
+
+ assert storage['newfile.txt'].fileId == 'and some content here'
+
+ with storage.expose() as dirname:
+
+
+ newdir = os.path.join(dirname, 'testdir')
+ os.mkdir(newdir)
+ with open(os.path.join(newdir, 'subfile'), "w") as fh:
+ fh.write('foobar')
+
+ inputs = os.listdir(dirname) + ['http://somefile.com/index.html']
+ workflow = FakeWorkflow()
+ newStorage = pkgbuild.Storage.fromLocalFiles(
+ workflow, inputs, dirname)
+ assert inputs == ['http://somefile.com/index.html']
+
+
+ assert isinstance(newStorage['testdir'], pkgbuild.ImportedDirectory)
+
+ newStorage.fileStore = FakeFileStorage(workflow.imported)
+ with newStorage.expose() as dirname:
+
+ assert slurp(os.path.join(dirname, 'file.txt')) == 'some content'
+ assert slurp(os.path.join(dirname, 'imported.txt')) == 'imported.txt'
+ assert slurp(os.path.join(dirname, 'newfile.txt')) == 'and some content here'
+ assert slurp(os.path.join(dirname, 'testdir', 'subfile')) == 'foobar'
+
+
+class DummyStorageUpdate(pkgbuild.Job):
+ def __init__(self, filename):
+ super(DummyStorageUpdate, self).__init__(unitName=filename)
+ self.filename = filename
+
+ def run(self, fileStore):
+ self.storage[self.filename] = 'something'
+
+class DummyStorageAsChild(pkgbuild.Job):
+ def run(self, fileStore):
+ a = DummyStorageUpdate('bar')
+ self.addChild(a)
+
+class RootJob(pkgbuild.Job):
+ def __init__(self, storage):
+ super(RootJob, self).__init__()
+ self._storage = storage
+
+ def run(self, fileStore):
+
+ tail = self
+
+ a = DummyStorageUpdate('foo')
+ self.addChild(a)
+ tail = a
+
+ b = DummyStorageAsChild()
+ tail.addFollowOn(b)
+ tail = b
+
+ return tail.resultStorage
+
+def test_job_storage():
+ parser = pkgbuild.Job.Runner.getDefaultArgumentParser()
+ options = parser.parse_args(['test_job_storage'])
+
+ options.workDir = tempfile.mkdtemp()
+ options.jobStore = os.path.join(options.workDir, 'workdir')
+
+ storage = pkgbuild.Storage(foobar='here i go')
+ root = RootJob(storage=storage)
+
+ try:
+ with Toil(options) as toil:
+ storage = toil.start(root)
+ finally:
+ shutil.rmtree(options.workDir)
+
+ assert storage == {'foo': 'something', 'bar': 'something', 'foobar': 'here i go'}
--
2.23.0
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