Python BBScorevars.getenv方法代码示例

# 需要导入模块: import BBScorevars [as 别名]
# 或者: from BBScorevars import getenv [as 别名]
def stage6_make_OUTGOING():
    ## Create working directory
    OUTGOING_dir = os.path.join(BBScorevars.Central_rdir.path, "OUTGOING")
    print "BBS> [stage6] remake_dir %s" % OUTGOING_dir
    bbs.fileutils.remake_dir(OUTGOING_dir)
    ## Loop over each element of the OUTGOING map
    OUTGOING_map = BBScorevars.getenv('BBS_OUTGOING_MAP')
    map_elts = OUTGOING_map.split(" ")
    for map_elt in map_elts:
        tmp = map_elt.split(":")
        if len(tmp) != 2:
            sys.exit("ERROR: Invalid OUTGOING map element %s" % map_elt)
        source_node = False
        if tmp[0] == "source":
            source_node = True
        OUTGOING_subdir = os.path.join(OUTGOING_dir, tmp[0])
        print "BBS> [stage6] mkdir %s" % OUTGOING_subdir
        os.mkdir(OUTGOING_subdir)
        print "BBS> [stage6] cd %s/" % OUTGOING_subdir
        os.chdir(OUTGOING_subdir)
        tmp2 = tmp[1].split("+")
        if len(tmp2) == 1:
            copy_outgoing_pkgs(tmp[1], source_node)
        elif len(tmp2) == 2:
            make_outgoing_biarch_pkgs(tmp2[0], tmp2[1])
        else:
            sys.exit("ERROR: Invalid OUTGOING map element %s" % map_elt)
    return

# 需要导入模块: import BBScorevars [as 别名]
# 或者: from BBScorevars import getenv [as 别名]
def _BiocGreaterThanOrEqualTo(x, y):
    bioc_version = BBScorevars.getenv('BBS_BIOC_VERSION', False)
    # If BBS_BIOC_VERSION is not defined, then we assume it's the latest version.
    if bioc_version == None:
        return True
    parts = bioc_version.split('.')
    x0 = int(parts[0])
    y0 = int(parts[1])
    return x0 > x or (x0 == x and y0 >= y)

# 需要导入模块: import BBScorevars [as 别名]
# 或者: from BBScorevars import getenv [as 别名]
def _getMaintainerFromDir(pkg_dir):
    desc_file = getDescFile(pkg_dir)
    FNULL = open(os.devnull, 'w')
    r_home = BBScorevars.getenv('BBS_R_HOME')
    Rscript_cmd = os.path.join(r_home, "bin", "Rscript")
    script_path = os.path.join(BBScorevars.BBS_home, "utils", "getMaintainer.R")
    cmd = [Rscript_cmd, '--vanilla', script_path, desc_file]
    maintainer = subprocess.check_output(cmd, stderr=FNULL)
    if maintainer == 'NA':
        raise DcfFieldNotFoundError(desc_file, 'Maintainer')
    return maintainer

# 需要导入模块: import BBScorevars [as 别名]
# 或者: from BBScorevars import getenv [as 别名]
def copy_outgoing_pkgs(fresh_pkgs_subdir, source_node):
    tmp = fresh_pkgs_subdir.split("/")
    if len(tmp) != 2:
        sys.exit("ERROR: Invalid relative path to fresh pkgs %s (must be of the form node/subdir)" % fresh_pkgs_subdir)
    node_id = tmp[0]
    node_hostname = node_id.split("-")[0]
    fileext = BBScorevars.getNodeSpec(node_hostname, 'pkgFileExt')
    fresh_pkgs_subdir = os.path.join(BBScorevars.nodes_rdir.path, fresh_pkgs_subdir)

    ## Workflow packages do not have manuals/ because we do not run 
    ## `R CMD check`.
    manuals_dir = "../manuals"
    if BBScorevars.is_workflow:
        pass
    elif (source_node):
        print "BBS> [stage6] mkdir %s" % manuals_dir
        os.mkdir(manuals_dir)
    print "BBS> [stage6] BEGIN copying outgoing packages from %s." % fresh_pkgs_subdir
    pkgType = BBScorevars.getNodeSpec(node_hostname, 'pkgType')
    meat_index_file = os.path.join(BBScorevars.Central_rdir.path, BBScorevars.meat_index_file)
    dcf = open(meat_index_file, 'r')
    pkgs = bbs.parse.readPkgsFromDCF(dcf, node_id, pkgType)
    dcf.close()
    for pkg in pkgs:
        if pkgMustBeRejected(node_hostname, node_id, pkg):
            continue
        dcf = open(meat_index_file, 'r')
        version = bbs.parse.getPkgFieldFromDCF(dcf, pkg, 'Version', BBScorevars.meat_index_file)
        dcf.close()
        ## Copy pkg from 'fresh_pkgs_subdir2'.
        pkg_file = "%s_%s.%s" % (pkg, version, fileext)
        pkg_file = os.path.join(fresh_pkgs_subdir, pkg_file)
        print "BBS> [stage6]   - copying %s to OUTGOING folder ..." % pkg_file
        if os.path.exists(pkg_file):
            shutil.copy(pkg_file, ".")
        else:
            print "BBS> [stage6]     SKIPPED (file %s doesn't exist)" % pkg_file
        ## Get reference manual from pkg.Rcheck directory.
        if BBScorevars.is_workflow:
            pass
        elif source_node:
            pdf_file = "%s/meat/%s.Rcheck/%s-manual.pdf" % \
                       (BBScorevars.getenv('BBS_WORK_TOPDIR'), pkg, pkg)
            print "BBS> [stage6]   - copying %s manual to OUTGOING/manuals folder..." % pkg
            if os.path.exists(pdf_file):
                shutil.copy(pdf_file, "%s/%s.pdf" % (manuals_dir, pkg))
            else:
                print "BBS> [stage6]     SKIPPED (file %s doesn't exist)" % pdf_file
    print "BBS> [stage6] END copying outgoing packages from %s." % fresh_pkgs_subdir
    return

# 需要导入模块: import BBScorevars [as 别名]
# 或者: from BBScorevars import getenv [as 别名]
def getSTAGE2cmd(pkg, version):
    cmd = '%s CMD INSTALL %s' % (BBSvars.r_cmd, pkg)
    if sys.platform == "win32":
        win_archs = _supportedWinArchs(pkg)
        if _mustRunSTAGE2InMultiarchMode() and len(win_archs) == 2:
            curl_cmd = BBScorevars.getenv('BBS_CURL_CMD')
            srcpkg_file = pkg + '_' + version + '.tar.gz'
            srcpkg_url = BBScorevars.Central_rdir.url + '/src/contrib/' + \
                         srcpkg_file
            cmd = '%s -O %s' % (curl_cmd, srcpkg_url) + ' && ' + \
                  '%s CMD INSTALL --merge-multiarch %s' % \
                  (BBSvars.r_cmd, srcpkg_file) + ' && ' + \
                  'rm %s' % srcpkg_file
        else:
            cmd = '%s --arch %s CMD INSTALL --no-multiarch %s' % \
                  (BBSvars.r_cmd, win_archs[0], pkg)
    return cmd

# 需要导入模块: import BBScorevars [as 别名]
# 或者: from BBScorevars import getenv [as 别名]
def getSTAGE2cmd(pkg, version):
    prepend = bbs.parse.getBBSoptionFromDir(pkg, 'INSTALLprepend')
    if sys.platform != "win32":
        cmd = '%s %s' % (_get_RINSTALL_cmd0(), pkg)
    else:
        prepend_win = bbs.parse.getBBSoptionFromDir(pkg, 'INSTALLprepend.win')
        if prepend_win != None:
            prepend = prepend_win
        win_archs = _supportedWinArchs(pkg)
        if _mustRunSTAGE2InMultiarchMode() and len(win_archs) >= 2:
            ## Here is what Dan's commit message says about why BBS uses this
            ## very long and complicated compound command to install packages
            ## in multiarch mode on Windows during STAGE2 (see
            ## 'git show 87822fb346e04b4301d0c2efd7ec1a2a8762e93a'):
            ##   Install STAGE2 target pkgs to zip+libdir first, then install
            ##   zip. This mitigates the problem where the INSTALL times out
            ##   after installing only one architecture. Now, if the install
            ##   times out, it has only failed to install a package to a
            ##   temporary libdir, and the previous installation is still
            ##   intact (or pkg is not installed at all), so dependent packages
            ##   will not complain about the timed-out package being only
            ##   available for one architecture.
            ##   We still need to figure out why mzR in particular times out
            ##   during INSTALL. When run manually (admittedly not during
            ##   peak load times) the install takes ~ 5-6 minutes, even when
            ##   done via the build system.
            curl_cmd = BBScorevars.getenv('BBS_CURL_CMD')
            srcpkg_file = pkg + '_' + version + '.tar.gz'
            srcpkg_url = BBScorevars.Central_rdir.url + '/src/contrib/' + \
                         srcpkg_file
            zip_file = srcpkg_file.replace(".tar.gz", ".zip")
            cmd = '%s -O %s' % (curl_cmd, srcpkg_url) + ' && ' + \
                  _get_BuildBinPkg_cmd(srcpkg_file, win_archs) + ' && ' + \
                  '%s %s' % (_get_RINSTALL_cmd0(), zip_file) + ' && ' + \
                  'rm %s %s' % (srcpkg_file, zip_file)
        else:
            cmd = '%s %s' % (_get_RINSTALL_cmd0(win_archs), pkg)
    if prepend != None:
        cmd = '%s %s' % (prepend, cmd)
    return cmd

# 需要导入模块: import BBScorevars [as 别名]
# 或者: from BBScorevars import getenv [as 别名]
def getSTAGE2cmd(pkg, version):
    cmd = '%s CMD INSTALL %s' % (BBSvars.r_cmd, pkg)
    if sys.platform == "win32":
        win_archs = _supportedWinArchs(pkg)
        if _mustRunSTAGE2InMultiarchMode() and len(win_archs) == 2:
            curl_cmd = BBScorevars.getenv('BBS_CURL_CMD')
            srcpkg_file = pkg + '_' + version + '.tar.gz'
            srcpkg_url = BBScorevars.Central_rdir.url + '/src/contrib/' + \
                         srcpkg_file
            zipfile = srcpkg_file.replace(".tar.gz", ".zip")
            cmd = 'rm -rf %s.buildbin-libdir' % pkg + ' && ' + \
                  'mkdir %s.buildbin-libdir ' % pkg + ' && ' + \
                  '%s -O %s' % (curl_cmd, srcpkg_url) + ' && ' + \
                  '%s CMD INSTALL --build --library=%s.buildbin-libdir --merge-multiarch %s' % \
                  (BBSvars.r_cmd, pkg, srcpkg_file) + ' && ' + \
                  '%s CMD INSTALL %s ' % (BBSvars.r_cmd,
                    zipfile)  + ' && ' + \
                  'rm %s %s' % (srcpkg_file, zipfile)
        else:
            cmd = '%s --arch %s CMD INSTALL --no-multiarch %s' % \
                  (BBSvars.r_cmd, win_archs[0], pkg)
    return cmd

# 需要导入模块: import BBScorevars [as 别名]
# 或者: from BBScorevars import getenv [as 别名]
import bbs.rdir
import bbs.jobs
import BBScorevars


##############################################################################
### BBS GLOBAL VARIABLES
##############################################################################


### Only needed by BBS-prerun.py and BBS-run.py

MEAT0_rdir = bbs.rdir.RemoteDir('BBS_MEAT0_RDIR',
                None,
                BBScorevars.getenv('BBS_MEAT0_RDIR'),
                BBScorevars.getenv('BBS_MEAT0_RHOST', False),
                BBScorevars.getenv('BBS_MEAT0_RUSER', False),
                BBScorevars.ssh_cmd,
                BBScorevars.rsync_cmd,
                BBScorevars.rsync_rsh_cmd)

meat_path = BBScorevars.getenv('BBS_MEAT_PATH')

work_topdir = BBScorevars.getenv('BBS_WORK_TOPDIR')

r_cmd = BBScorevars.getenv('BBS_R_CMD')


### Only needed by BBS-prerun.py

# 需要导入模块: import BBScorevars [as 别名]
# 或者: from BBScorevars import getenv [as 别名]
    return

def send_CRAN_notifications(allpkgs):
    print "BBS> [send_CRAN_notifications] BEGIN..."
    send_notifications(allpkgs)
    print "BBS> [send_CRAN_notifications] END."
    return


##############################################################################
### MAIN SECTION
##############################################################################

print "BBS> [stage9] STARTING stage9 at %s..." % time.asctime()

BBSreportutils.data_source = BBScorevars.getenv('BBS_PUBLISHED_REPORT_URL')
notify_nodes = BBScorevars.getenv('BBS_NOTIFY_NODES')

argc = len(sys.argv)
if argc > 1:
    arg1 = sys.argv[1]
else:
    arg1 = ""

if arg1 != "":
    bbs.email.mode = "do-it"
    if arg1 != "do-it":
        bbs.email.redirect_to_addr = arg1

BBSreportutils.set_NODES(notify_nodes)
if len(BBSreportutils.NODES) != 1:

# 需要导入模块: import BBScorevars [as 别名]
# 或者: from BBScorevars import getenv [as 别名]
## Report title.
if BBScorevars.subbuilds == "bioc-longtests":
    REPORT_TITLE = "Long tests"
elif BBScorevars.subbuilds == "workflows":
    REPORT_TITLE = "Workflows build"
else:
    if len(NODES) != 1:
        REPORT_TITLE = "Multiple platform build/check"
    else:
        REPORT_TITLE = "Build/check"
REPORT_TITLE += " report for "
if BBScorevars.subbuilds == "cran":
    REPORT_TITLE += "CRAN"
else:
    bioc_version = BBScorevars.getenv('BBS_BIOC_VERSION', False)
    REPORT_TITLE += "BioC %s" % bioc_version
    if BBScorevars.subbuilds == "data-experiment":
        REPORT_TITLE += " experimental data"

## Stages to display on report (as columns in HTML table).
def stages_to_display():
    if BBScorevars.subbuilds == "bioc-longtests":
        return ['checksrc']  # we run 'buildsrc' but don't display it
    if BBScorevars.subbuilds == "workflows":
        return ['install', 'buildsrc']
    return ['install', 'buildsrc', 'checksrc', 'buildbin']

def stage_label(stage):
    stage2label = {
        'install':  "INSTALL",

# 需要导入模块: import BBScorevars [as 别名]
# 或者: from BBScorevars import getenv [as 别名]
import bbs.rdir
import bbs.jobs
import BBScorevars


##############################################################################
### BBS GLOBAL VARIABLES
##############################################################################


### Only needed by BBS-prerun.py and BBS-run.py

MEAT0_rdir = bbs.rdir.RemoteDir('BBS_MEAT0_RDIR',
                None,
                BBScorevars.getenv('BBS_MEAT0_RDIR'),
                BBScorevars.getenv('BBS_MEAT0_RHOST', False),
                BBScorevars.getenv('BBS_MEAT0_RUSER', False),
                BBScorevars.ssh_cmd,
                BBScorevars.rsync_cmd,
                BBScorevars.rsync_rsh_cmd)

meat_path = BBScorevars.getenv('BBS_MEAT_PATH')

work_topdir = BBScorevars.getenv('BBS_WORK_TOPDIR')

r_cmd = BBScorevars.getenv('BBS_R_CMD')

r_home = BBScorevars.getenv('BBS_R_HOME')

### Only needed by BBS-prerun.py

# 需要导入模块: import BBScorevars [as 别名]
# 或者: from BBScorevars import getenv [as 别名]
            if BBSreportutils.is_doing_buildbin(node):
                stage = 'buildbin'
                if skipped_is_OK:
                    status = "skipped"
                else:
                    status = get_status_from_summary_file(pkg, node.id, stage)
                out.write('%s#%s#%s: %s\n' % (pkg, node.id, stage, status))
    out.close()
    print "BBS> [make_STATUS_DB] END"
    return


##############################################################################
### MAIN SECTION
##############################################################################

print "BBS> [stage7a] STARTING stage7a at %s..." % time.asctime()

central_rdir_path = BBScorevars.Central_rdir.path
if central_rdir_path != None:
    print "BBS> [stage7a] cd %s/" % central_rdir_path
    os.chdir(central_rdir_path)

report_nodes = BBScorevars.getenv('BBS_REPORT_NODES')
BBSreportutils.set_NODES(report_nodes)
allpkgs = BBSreportutils.get_pkgs_from_meat_index()
make_STATUS_DB(allpkgs)

print "BBS> [stage7a] DONE at %s." % time.asctime()