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BBS-report.py
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#!/usr/bin/env python3
##############################################################################
###
### This file is part of the BBS software (Bioconductor Build System).
###
### Author: Hervé Pagès <[email protected]>
### Last modification: June 16, 2021
###
import sys
import os
import time
import shutil
import re
import fnmatch
import string
import html
import bbs.fileutils
import bbs.parse
import bbs.jobs
import bbs.rdir
import BBSutils
import BBSvars
import BBSreportutils
node2aboutpage = {}
node2Rinstpkgspage = {}
node2Rinstpkgcount = {}
##############################################################################
### General stuff displayed on all pages
##############################################################################
def write_HTML_header(out, page_title=None, css_file=None, js_file=None):
report_nodes = BBSutils.getenv('BBS_REPORT_NODES')
title = BBSreportutils.make_report_title(report_nodes)
out.write('<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"')
out.write(' "http://www.w3.org/TR/html4/loose.dtd">\n')
out.write('<HTML>\n')
out.write('<HEAD>\n')
out.write('<META http-equiv="Content-Type" content="text/html; charset=UTF-8">\n')
if page_title:
title += " - " + page_title
out.write('<TITLE>%s</TITLE>\n' % title)
if css_file:
out.write('<LINK rel="stylesheet" href="%s" type="text/css">\n' % css_file)
if js_file:
out.write('<SCRIPT type="text/javascript" src="%s"></SCRIPT>\n' % js_file)
out.write('</HEAD>\n')
return
def write_abc_dispatcher(out, href="", current_letter=None,
activate_current_letter=False):
out.write('<TABLE class="abc_dispatcher"><TR>')
for i in range(65,91):
letter = chr(i)
if letter == current_letter and not activate_current_letter:
out.write('<TD style="background: inherit;">%s</TD>' % letter)
continue
html_letter = '<A href="%s#%s">%s</A>' % (href, letter, letter)
if letter == current_letter:
html_letter = '<B>[%s]</B>' % html_letter
out.write('<TD>%s</TD>' % html_letter)
out.write('</TR></TABLE>')
return
def write_goback_links(out, topdir=".", long_link=False, current_letter=None):
report_nodes = BBSutils.getenv('BBS_REPORT_NODES')
title = BBSreportutils.make_report_title(report_nodes)
TABLE_style = 'width: 100%; background: #EEE;'
out.write('<TABLE class="grid_layout" style="%s"><TR>' % TABLE_style)
TD_style = 'text-align: left; padding: 5px; vertical-align: middle;'
out.write('<TD style="%s"><I>' % TD_style)
if long_link:
out.write('Back to <B>%s</B>: ' % title)
out.write('<A href="%s/">simplified</A> ' % topdir)
out.write('<A href="%s/long-report.html">long</A>' % topdir)
else:
out.write('<A href="%s/">Back to <B>%s</B></A>' % (topdir, title))
out.write('</I></TD>')
if not no_alphabet_dispatch and current_letter != None:
out.write('<TD>')
write_abc_dispatcher(out, topdir, current_letter, True)
out.write('</TD>')
out.write('</TR></TABLE>\n')
return
def write_switch_link(out, simp_link=False, long_link=False):
if not simp_link and not long_link:
return
if simp_link:
link = '<A href="./">Switch to simplified report</A>'
else:
link = '<A href="./long-report.html">Switch to long report</A>'
out.write('<P style="margin: 0px; text-align: left">%s</P>\n' % link)
return
def write_timestamp(out):
out.write('<P class="time_stamp">\n')
date = bbs.jobs.currentDateString()
out.write('This page was generated on %s.\n' % date)
out.write('</P>\n')
return
def write_motd_asTABLE(out):
if not 'BBS_REPORT_MOTD' in os.environ:
return
motd = os.environ['BBS_REPORT_MOTD']
if motd == "":
return
out.write('<DIV class="motd">\n')
out.write('<TABLE>')
out.write('<TR><TD>%s</TD></TR>' % motd)
out.write('</TABLE>\n')
out.write('</DIV>\n')
return
def write_notes_to_developers(out, pkg, extra_note=None):
# Renviron.bioc is expected to be found in BBS_REPORT_PATH which should
# be the current working directory.
if BBSvars.buildtype != "bioc" and not os.path.exists('Renviron.bioc'):
return
out.write('<DIV class="notes_to_developers">\n')
out.write('<TABLE><TR><TD>\n')
out.write('<B>To the developers/maintainers ')
out.write('of the %s package:</B><BR>\n' % pkg)
nnotes = int(BBSvars.buildtype == "bioc") + \
int(os.path.exists('Renviron.bioc')) * 2 + \
int(extra_note != None)
prefix = '- ' if nnotes >= 2 else ''
if BBSvars.buildtype == "bioc":
url = 'https://bioconductor.org/developers/how-to/troubleshoot-build-report/'
out.write('%sAllow up to 24 hours (and sometimes ' % prefix)
out.write('48 hours) for your latest push to ')
out.write('[email protected]:packages/%s.git ' % pkg)
out.write('to reflect on this report. ')
out.write('See <A href="%s">Troubleshooting Build Report</A> ' % url)
out.write('for more information.<BR>\n')
if os.path.exists('Renviron.bioc'):
out.write('%sUse the following ' % prefix)
out.write('<A href="../%s">Renviron settings</A> ' % 'Renviron.bioc')
out.write('to reproduce errors and warnings.<BR>\n')
out.write('%sIf \'R CMD check\' started to fail recently ' % prefix)
out.write('on the Linux builder(s) over a missing dependency, ')
out.write('add the missing dependency to \'Suggests:\' in your ')
out.write('DESCRIPTION file. See ')
out.write('<A href="../%s">Renviron.bioc</A> ' % 'Renviron.bioc')
out.write('for more information.<BR>\n')
if extra_note != None:
out.write('%s%s\n' % (prefix, extra_note))
out.write('</TD></TR></TABLE>\n')
out.write('</DIV>\n')
return
##############################################################################
### write_node_specs_table()
##############################################################################
def read_Rversion(Node_rdir):
filename = 'NodeInfo/R-version.txt'
f = Node_rdir.WOpen(filename)
Rversion = bbs.parse.bytes2str(f.readline())
f.close()
Rversion = Rversion.replace('R version ', '')
Rversion_html = Rversion.replace(' ', ' ')
return Rversion_html
def get_Rconfig_value_from_file(Node_rdir, var):
filename = 'NodeInfo/R-config.txt'
dcf = Node_rdir.WOpen(filename)
val = bbs.parse.get_next_DCF_val(dcf, var, True)
dcf.close()
if val == None:
filename = '%s/%s' % (Node_rdir.label, filename)
raise bbs.parse.DcfFieldNotFoundError(filename, var)
return val
def write_Rconfig_table_from_file(out, Node_rdir, vars):
out.write('<TABLE class="Rconfig">\n')
out.write('<TR>')
out.write('<TD style="background: #CCC; width: 150px;"><I><B>R variable</B> (VAR)</I></TD>')
out.write('<TD style="background: #CCC;"><I><B>Value</B> (\'R CMD config <VAR>\' output)</I></TD>')
out.write('</TR>\n')
for var in vars:
val = get_Rconfig_value_from_file(Node_rdir, var)
out.write('<TR><TD><B>%s</B></TD><TD>%s</TD></TR>\n' % (var, val))
out.write('<TR>')
out.write('<TD COLSPAN="2" style="font-size: smaller;">')
out.write('<I>Please refer to \'R CMD config -h\' for the meaning of these variables</I>')
out.write('</TD>')
out.write('</TR>\n')
out.write('</TABLE>\n')
return
def write_SysCommandVersion_from_file(out, Node_rdir, var, config=True):
filename = 'NodeInfo/%s-version.txt' % var
f = Node_rdir.WOpen(filename, return_None_on_error=True)
if f == None:
return
if config:
cmd = get_Rconfig_value_from_file(Node_rdir, var)
syscmd = '%s --version' % cmd
out.write('<P><B>Compiler version</B> (\'%s\' output):</P>\n' % syscmd)
else:
cmd = var.lower()
syscmd = '%s --version' % cmd
out.write('<P><B>%s version</B> (\'%s\' output):</P>\n' % (cmd, syscmd))
out.write('<PRE style="margin-left: 12px;">\n')
for line in f:
out.write(bbs.parse.bytes2str(line))
f.close()
out.write('</PRE>\n')
return
def make_aboutnode_page(Node_rdir, node, long_link=False):
page_title = 'More about %s' % node.node_id
aboutnode_page = '%s-NodeInfo.html' % node.node_id
print("BBS> [make_aboutnode_page] Write %s in %s/ ..." % \
(aboutnode_page, os.getcwd()), end=" ")
sys.stdout.flush()
out = open(aboutnode_page, 'w')
write_HTML_header(out, page_title, 'report.css')
out.write('<BODY>\n')
write_goback_links(out, long_link=long_link)
write_timestamp(out)
out.write('<H2><SPAN class="%s">%s</SPAN></H2>\n' % \
(node.hostname.replace(".", "_"), page_title))
out.write('<BR>\n')
out.write('<DIV class="%s">\n' % node.hostname.replace(".", "_"))
out.write('<TABLE>\n')
out.write('<TR><TD><B>Hostname: </B></TD><TD>%s</TD></TR>\n' % node.hostname)
out.write('<TR><TD><B>OS: </B></TD><TD>%s</TD></TR>\n' % node.os_html)
out.write('<TR><TD><B>Arch: </B></TD><TD>%s</TD></TR>\n' % node.arch)
out.write('<TR><TD><B>Platform: </B></TD><TD>%s</TD></TR>\n' % node.platform)
out.write('<TR><TD><B>R version: </B></TD><TD>%s</TD></TR>\n' % read_Rversion(Node_rdir))
out.write('<TR>')
out.write('<TD><B>R environment variables: </B></TD>')
out.write('<TD>')
# Renviron.bioc is expected to be found in BBS_REPORT_PATH which should
# be the current working directory.
if os.path.exists('Renviron.bioc'):
out.write('<A href="%s">%s</A>' % ('Renviron.bioc', 'Renviron.bioc'))
else:
out.write('none')
out.write('</TD>')
out.write('</TR>\n')
out.write('</TABLE>\n')
out.write('</DIV>\n')
out.write('<HR>\n')
out.write('<H2>C compiler</H2>\n')
out.write('<DIV class="%s">\n' % node.hostname.replace(".", "_"))
C_vars = ['CC', 'CFLAGS', 'CPICFLAGS']
write_Rconfig_table_from_file(out, Node_rdir, C_vars)
write_SysCommandVersion_from_file(out, Node_rdir, 'CC')
out.write('</DIV>\n')
out.write('<HR>\n')
out.write('<H2>C++ compiler</H2>\n')
out.write('<DIV class="%s">\n' % node.hostname.replace(".", "_"))
Cplusplus_vars = ['CXX', 'CXXFLAGS', 'CXXPICFLAGS']
write_Rconfig_table_from_file(out, Node_rdir, Cplusplus_vars)
write_SysCommandVersion_from_file(out, Node_rdir, 'CXX')
out.write('</DIV>\n')
out.write('<HR>\n')
#out.write('<H2>C++98 compiler</H2>\n')
#out.write('<DIV class="%s">\n' % node.hostname.replace(".", "_"))
#Cplusplus98_vars = ['CXX98', 'CXX98FLAGS', 'CXX98PICFLAGS', 'CXX98STD']
#write_Rconfig_table_from_file(out, Node_rdir, Cplusplus98_vars)
#write_SysCommandVersion_from_file(out, Node_rdir, 'CXX98')
#out.write('</DIV>\n')
#
#out.write('<HR>\n')
out.write('<H2>C++11 compiler</H2>\n')
out.write('<DIV class="%s">\n' % node.hostname.replace(".", "_"))
Cplusplus11_vars = ['CXX11', 'CXX11FLAGS', 'CXX11PICFLAGS', 'CXX11STD']
write_Rconfig_table_from_file(out, Node_rdir, Cplusplus11_vars)
write_SysCommandVersion_from_file(out, Node_rdir, 'CXX11')
out.write('</DIV>\n')
out.write('<HR>\n')
out.write('<H2>C++14 compiler</H2>\n')
out.write('<DIV class="%s">\n' % node.hostname.replace(".", "_"))
Cplusplus14_vars = ['CXX14', 'CXX14FLAGS', 'CXX14PICFLAGS', 'CXX14STD']
write_Rconfig_table_from_file(out, Node_rdir, Cplusplus14_vars)
write_SysCommandVersion_from_file(out, Node_rdir, 'CXX14')
out.write('</DIV>\n')
out.write('<HR>\n')
out.write('<H2>C++17 compiler</H2>\n')
out.write('<DIV class="%s">\n' % node.hostname.replace(".", "_"))
Cplusplus17_vars = ['CXX17', 'CXX17FLAGS', 'CXX17PICFLAGS', 'CXX17STD']
write_Rconfig_table_from_file(out, Node_rdir, Cplusplus17_vars)
write_SysCommandVersion_from_file(out, Node_rdir, 'CXX17')
out.write('</DIV>\n')
out.write('<HR>\n')
out.write('<H2>Java</H2>\n')
out.write('<DIV class="%s">\n' % node.hostname.replace(".", "_"))
if node.os_html.find('Windows') == 0:
write_SysCommandVersion_from_file(out, Node_rdir, 'java', config=False)
else:
write_SysCommandVersion_from_file(out, Node_rdir, 'JAVA', config=False)
out.write('</DIV>\n')
out.write('<HR>\n')
out.write('<H2>Pandoc</H2>\n')
out.write('<DIV class="%s">\n' % node.hostname.replace(".", "_"))
write_SysCommandVersion_from_file(out, Node_rdir, 'pandoc', False)
out.write('</DIV>\n')
out.write('<HR>\n')
#out.write('<H2>Fortran 77 compiler</H2>\n')
#out.write('<DIV class="%s">\n' % node.hostname.replace(".", "_"))
#Fortran77_vars = ['F77', 'FFLAGS', 'FLIBS', 'FPICFLAGS']
#write_Rconfig_table_from_file(out, Node_rdir, Fortran77_vars)
#write_SysCommandVersion_from_file(out, Node_rdir, 'F77')
#out.write('</DIV>\n')
#
#out.write('<HR>\n')
#out.write('<H2>Fortran 9x compiler</H2>\n')
#out.write('<DIV class="%s">\n' % node.hostname.replace(".", "_"))
#Fortran9x_vars = ['FC', 'FCFLAGS', 'FCPICFLAGS']
#write_Rconfig_table_from_file(out, Node_rdir, Fortran9x_vars)
#write_SysCommandVersion_from_file(out, Node_rdir, 'FC')
#out.write('</DIV>\n')
#
#out.write('<HR>\n')
out.write('<P>More information might be added in the future...</P>\n')
out.write('</BODY>\n')
out.write('</HTML>\n')
out.close()
print("OK")
return aboutnode_page
def make_all_aboutnode_pages(long_link=False):
products_in_rdir = BBSvars.products_in_rdir
for node in BBSreportutils.NODES:
if node.buildbin == None: # foreign node
continue
Node_rdir = products_in_rdir.subdir(node.node_id)
aboutnode_page = make_aboutnode_page(Node_rdir, node, long_link)
node2aboutpage[node.node_id] = aboutnode_page
return
### Make local copy (and rename) R-instpkgs.txt file.
### Returns the 2-string tuple containing the filename of the generated page
### and the number of installed pkgs.
def make_Rinstpkgs_page(Node_rdir, node, long_link=False):
page_title = 'R packages installed on %s' % node.node_id
Rinstpkgspage = '%s-R-instpkgs.html' % node.node_id
print("BBS> [make_Rinstpkgs_page] Write %s in %s/ ..." % \
(Rinstpkgspage, os.getcwd()), end=" ")
sys.stdout.flush()
out = open(Rinstpkgspage, 'w')
write_HTML_header(out, page_title, 'report.css')
out.write('<BODY>\n')
write_goback_links(out, long_link=long_link)
write_timestamp(out)
out.write('<H2><SPAN class="%s">%s</SPAN></H2>\n' % \
(node.hostname.replace(".", "_"), page_title))
out.write('<BR>\n')
out.write('<DIV class="%s">\n' % node.hostname.replace(".", "_"))
filename = 'NodeInfo/R-instpkgs.txt'
out.write('<PRE>\n')
f = Node_rdir.WOpen(filename)
nline = 0
for line in f:
out.write(bbs.parse.bytes2str(line))
nline += 1
f.close()
out.write('</PRE>\n')
out.write('</DIV></BODY>\n')
out.write('</HTML>\n')
out.close()
print("OK")
return (Rinstpkgspage, str(nline-1))
def make_all_Rinstpkgs_pages(long_link=False):
products_in_rdir = BBSvars.products_in_rdir
for node in BBSreportutils.NODES:
if node.buildbin == None: # foreign node
continue
Node_rdir = products_in_rdir.subdir(node.node_id)
(Rinstpkgspage, Rinstpkgcount) = make_Rinstpkgs_page(Node_rdir, node,
long_link)
node2Rinstpkgspage[node.node_id] = Rinstpkgspage
node2Rinstpkgcount[node.node_id] = Rinstpkgcount
return
def write_node_specs_table(out, aboutnode_dir='.', long_link=False):
out.write('<TABLE class="node_specs">\n')
out.write('<TR>')
out.write('<TH>Hostname</TH>')
out.write('<TH>OS</TH>')
out.write('<TH>Arch (*)</TH>')
out.write('<TH>R version</TH>')
out.write('<TH style="text-align: right;">Installed pkgs</TH>')
out.write('</TR>\n')
products_in_rdir = BBSvars.products_in_rdir
for node in BBSreportutils.NODES:
if node.buildbin == None: # foreign node
continue
Node_rdir = products_in_rdir.subdir(node.node_id)
aboutnode_page = node2aboutpage[node.node_id]
aboutnode_url = '%s/%s' % (aboutnode_dir, aboutnode_page)
Rversion_html = read_Rversion(Node_rdir)
Rinstpkgspage = node2Rinstpkgspage[node.node_id]
Rinstpkgcount = node2Rinstpkgcount[node.node_id]
Rinstpkgs_url = '%s/%s' % (aboutnode_dir, Rinstpkgspage)
out.write('<TR class="%s">' % node.hostname.replace(".", "_"))
out.write('<TD><B><A href="%s"><B>%s</B></A></B></TD>' % (aboutnode_url, node.node_id))
out.write('<TD>%s</TD>' % node.os_html)
out.write('<TD>%s</TD>' % node.arch)
out.write('<TD>%s</TD>' % Rversion_html)
out.write('<TD style="text-align: right;">')
out.write('<A href="%s">%s</A>' % (Rinstpkgs_url, Rinstpkgcount))
out.write('</TD>')
out.write('</TR>\n')
out.write('<TR>')
out.write('<TD COLSPAN="5" style="font-size: smaller;">')
out.write('<I>Click on any hostname to see more info ')
out.write('about the system (e.g. compilers)')
out.write(' ')
out.write('(*) as reported by \'uname -p\', ')
out.write('except on Windows and Mac OS X</I>')
out.write('</TD>')
out.write('</TR>\n')
out.write('</TABLE>\n')
return
##############################################################################
### write_vcs_meta_for_pkg_as_TABLE()
##############################################################################
def _make_link_with_mouseover(url, content):
onmouseover = 'add_class_mouseover(this);'
onmouseout = 'remove_class_mouseover(this);'
return '<A href="%s" onmouseover="%s" onmouseout="%s">%s</A>' % \
(url, onmouseover, onmouseout, content)
def _keyval_as_HTML(key, val, inject_nbsp_in_key=True):
if inject_nbsp_in_key:
key = key.replace(' ', ' ')
val = val.replace(' ', ' ')
return '%s: <SPAN class="svn_info">%s</SPAN>' % (key, val)
def _write_keyval_as_TD(out, key, val):
html = _keyval_as_HTML(key, val)
out.write('<TD class="svn_info">%s</TD>' % html)
return
def _write_pkg_keyval_as_TD(out, pkg, key):
val = BBSreportutils.get_vcs_meta(pkg, key)
_write_keyval_as_TD(out, key, val)
return
def _write_Date_as_TD(out, pkg, key, full_line=True):
val = BBSreportutils.get_vcs_meta(pkg, key)
if not full_line:
val = ' '.join(val.split(' ')[0:3])
_write_keyval_as_TD(out, key, val)
return
def _write_LastChange_as_TD(out, pkg, key, with_Revision=False):
val = BBSreportutils.get_vcs_meta(pkg, key)
html = _keyval_as_HTML(key, val)
if with_Revision:
key2 = 'Revision'
val2 = BBSreportutils.get_vcs_meta(pkg, key2)
html2 = _keyval_as_HTML(key2, val2)
html = '%s / %s' % (html, html2)
out.write('<TD class="svn_info">%s</TD>' % html)
return
def _write_svn_info_for_pkg_as_TRs(out, pkg, full_info=False):
if full_info:
out.write('<TR>')
_write_Date_as_TD(out, None, 'Snapshot Date', full_info)
out.write('</TR>\n')
out.write('<TR>')
_write_pkg_keyval_as_TD(out, pkg, 'URL')
out.write('</TR>\n')
out.write('<TR>')
_write_LastChange_as_TD(out, pkg, 'Last Changed Rev', True)
out.write('</TR>\n')
out.write('<TR>')
_write_Date_as_TD(out, pkg, 'Last Changed Date', full_info)
out.write('</TR>\n')
return
def _write_git_log_for_pkg_as_TRs(out, pkg, full_info=False):
## metadata other than snapshot date exists only for individual pkg repos
if pkg == None:
out.write('<TR>')
key = 'Approx. Package Snapshot Date/Time '
key = key.replace(' ', ' ')
key += '(<SPAN style="font-family: monospace;">git pull</SPAN>)'
val = BBSreportutils.get_vcs_meta(None, 'Snapshot Date')
if not full_info:
val = ' '.join(val.split(' ')[0:3])
html = _keyval_as_HTML(key, val, inject_nbsp_in_key=False)
out.write('<TD class="svn_info">%s</TD>' % html)
out.write('</TR>\n')
else:
if full_info:
out.write('<TR>')
_write_Date_as_TD(out, None, 'Snapshot Date', full_info)
out.write('</TR>\n')
out.write('<TR>')
_write_pkg_keyval_as_TD(out, pkg, 'git_url')
out.write('</TR>\n')
out.write('<TR>')
_write_pkg_keyval_as_TD(out, pkg, 'git_branch')
out.write('</TR>\n')
out.write('<TR>')
_write_LastChange_as_TD(out, pkg, 'git_last_commit', False)
out.write('</TR>\n')
out.write('<TR>')
_write_Date_as_TD(out, pkg, 'git_last_commit_date', full_info)
out.write('</TR>\n')
return
def write_vcs_meta_for_pkg_as_TABLE(out, pkg, full_info=False):
out.write('<TABLE class="svn_info">\n')
if BBSvars.MEAT0_type == 1:
_write_svn_info_for_pkg_as_TRs(out, pkg, full_info)
else:
_write_git_log_for_pkg_as_TRs(out, pkg, full_info)
out.write('</TABLE>\n')
return
##############################################################################
### write_explain_glyph_table()
##############################################################################
def _get_stage_labels():
stage_labels = []
buildtype = BBSvars.buildtype
for stage in BBSreportutils.stages_to_display(buildtype):
stage_labels.append(BBSreportutils.stage_label(stage))
return stage_labels
## Produce a SPAN element.
def _status_as_glyph(status):
html = status
if status != 'skipped':
html = ' %s ' % html
return '<SPAN class="glyph %s">%s</SPAN>' % (status, html)
## Produce a TD element (table cell).
def _write_glyph_box(out, status, toggleable=False):
if toggleable:
toggle_id = '%s_toggle' % status.lower()
onmouseover = 'add_class_mouseover(this);'
onmouseout = 'remove_class_mouseover(this);'
onclick = 'filter_gcards(\'%s\');' % status.lower()
TD_attrs = ['class="glyph_box toggle"',
'id="%s"' % toggle_id,
'onmouseover="%s"' % onmouseover,
'onmouseout="%s"' % onmouseout,
#'onkeypress="%s"' % onclick,
'onclick="%s"' % onclick,
'style="width: 110px;"']
checkbox_id = '%s_checkbox' % status.lower()
checkbox_attrs = 'id="%s" style="margin: 0px; padding: 0px;"' % \
checkbox_id
checkbox_html = '<INPUT type="checkbox" checked %s>' % checkbox_attrs
else:
TD_attrs = ['class="glyph_box"']
checkbox_html = ''
TD1_style = 'text-align: left; padding-left: 3px; padding-right: 3px;'
TD1_html = '<TD style="%s">%s</TD>' % (TD1_style, _status_as_glyph(status))
TD2_style = 'text-align: right; padding-right: 2px;'
TD2_html = '<TD style="%s">%s</TD>' % (TD2_style, checkbox_html)
TABLE_html = '<TABLE><TR>%s%s</TR></TABLE>' % (TD1_html, TD2_html)
out.write('<TD %s>%s</TD>\n' % (' '.join(TD_attrs), TABLE_html))
return
def _write_glyph_as_TR(out, status, explain_html, toggleable=False):
out.write('<TR>\n')
_write_glyph_box(out, status, toggleable)
out.write('<TD class="glyph_explain">%s</TD>\n' % explain_html)
out.write('</TR>\n')
return
def _explain_TIMEOUT_in_HTML(stage_labels):
labels = []
times = []
if 'INSTALL' in stage_labels:
labels.append('INSTALL')
times.append(int(BBSvars.INSTALL_timeout / 60.0))
if 'BUILD' in stage_labels:
labels.append('BUILD')
times.append(int(BBSvars.BUILD_timeout / 60.0))
if 'CHECK' in stage_labels:
labels.append('CHECK')
times.append(int(BBSvars.CHECK_timeout / 60.0))
if 'BUILD BIN' in stage_labels:
labels.append('BUILD BIN')
times.append(int(BBSvars.BUILDBIN_timeout / 60.0))
if len(labels) == 1:
html = labels[0]
else:
html = '%s or %s' % (', '.join(labels[:-1]), labels[-1])
html += ' of package took more than '
same_times = times[:-1] == times[1:]
if same_times:
html += str(times[0])
else:
times = [str(t) for t in times]
html += '%s or %s' % (', '.join(times[:-1]), times[-1])
html += ' minutes'
if not same_times:
html += ', respectively'
return html
def _explain_ERROR_in_HTML(stage_labels):
labels = stage_labels.copy()
if len(labels) == 1 and labels[0] == 'CHECK':
html = 'CHECK of package produced errors'
else:
CHECK_in_labels = 'CHECK' in labels
if CHECK_in_labels:
labels.remove('CHECK')
if len(labels) == 1:
html = labels[0]
else:
html = '%s or %s' % (', '.join(labels[:-1]), labels[-1])
html += ' of package failed'
if CHECK_in_labels:
html += ', or CHECK produced errors'
return 'Bad DESCRIPTION file, or ' + html
def _explain_WARNINGS_in_HTML():
return 'CHECK of package produced warnings'
def _explain_OK_in_HTML(stage_labels, simple_layout=False):
if len(stage_labels) == 1:
html = stage_labels[0]
else:
conjunction = 'and' if simple_layout else 'or'
html = '%s %s %s' % \
(', '.join(stage_labels[:-1]), conjunction, stage_labels[-1])
return html + ' of package went OK'
def _explain_NotNeeded_in_HTML():
return 'INSTALL of package was not needed ' + \
'(click on glyph to see why)'
def _explain_NA_in_HTML(stage_labels):
if len(stage_labels) == 1:
html = stage_labels[0]
else:
html = '%s or %s' % (', '.join(stage_labels[:-1]), stage_labels[-1])
html += ' result is not available because' + \
' of an anomaly in the Build System'
return html
def _explain_skipped_in_HTML(stage_labels):
labels = []
if 'CHECK' in stage_labels:
labels.append('CHECK')
if 'BUILD BIN' in stage_labels:
labels.append('BUILD BIN')
if len(labels) == 1:
html = labels[0]
else:
html = '%s or %s' % (', '.join(labels[:-1]), labels[-1])
html += ' of package was skipped because the BUILD step failed'
return html
### FH: Create checkboxes to select display types
def write_explain_glyph_table(out, simple_layout=False):
buildtype = BBSvars.buildtype
wide_table = simple_layout or \
not BBSreportutils.display_propagation_status(buildtype)
out.write('<FORM action="">\n')
styles = ['width: %s' % ('800px' if wide_table else '620px'),
'border: solid black 1px',
'border-collapse: collapse']
out.write('<TABLE style="%s">\n' % ';'.join(styles))
out.write('<TR>\n')
out.write('<TD COLSPAN="2" style="font-style: italic; border-bottom: solid black 1px;">')
out.write('<B>Package status is indicated by one of the following glyphs</B>')
out.write('</TD>\n')
out.write('</TR>\n')
stage_labels = _get_stage_labels()
explain_html = _explain_TIMEOUT_in_HTML(stage_labels)
_write_glyph_as_TR(out, "TIMEOUT", explain_html, True)
explain_html = _explain_ERROR_in_HTML(stage_labels)
_write_glyph_as_TR(out, "ERROR", explain_html, True)
if 'CHECK' in stage_labels:
explain_html = _explain_WARNINGS_in_HTML()
_write_glyph_as_TR(out, "WARNINGS", explain_html, True)
explain_html = _explain_OK_in_HTML(stage_labels, simple_layout)
_write_glyph_as_TR(out, "OK", explain_html, True)
## "NotNeeded" glyph (only used when "smart STAGE2" is enabled i.e.
## when STAGE2 skips installation of target packages not needed by
## another target package for build or check).
#if buildtype not in ["workflows", "books", "bioc-longtests"]:
# _write_glyph_as_TR(out, "NotNeeded", _explain_NotNeeded_in_HTML())
explain_html = _explain_NA_in_HTML(stage_labels)
_write_glyph_as_TR(out, "NA", explain_html)
if not simple_layout and \
('CHECK' in stage_labels or 'BUILD BIN' in stage_labels):
explain_html = _explain_skipped_in_HTML(stage_labels)
_write_glyph_as_TR(out, "skipped", explain_html)
out.write('<TR>\n')
out.write('<TD COLSPAN="2" style="font-style: italic; border-top: solid black 1px;">')
out.write('Click on any glyph in the report below ')
out.write('to access the detailed report.')
out.write('</TD>\n')
out.write('</TR>\n')
out.write('</TABLE>\n')
out.write('</FORM>\n')
return
##############################################################################
### Glyph cards (gcards) and gcard lists
##############################################################################
class LeafReportReference:
def __init__(self, pkg, node_hostname, node_id, stage):
self.pkg = pkg
self.node_hostname = node_hostname
self.node_id = node_id
self.stage = stage
def _get_all_show_classes():
status_classes = ['timeout', 'error', 'warnings', 'ok']
return ['show_%s_gcards' % status for status in status_classes]
def _write_vertical_space(out):
ncol_to_display = BBSreportutils.ncol_to_display(BBSvars.buildtype)
TD_html = '<TD COLSPAN="%s"></TD>' % (ncol_to_display + 5)
out.write('<TR class="vertical_space">%s</TR>\n' % TD_html)
return
def _url_to_pkg_landing_page(pkg):
buildtype = BBSvars.buildtype
if buildtype == "cran":
return "https://cran.rstudio.com/package=%s" % pkg
bioc_version = BBSvars.bioc_version
if buildtype == "books":
return "/books/%s/%s/" % (bioc_version, pkg)
#if buildtype == "data-annotation":
# repo = "data/annotation"
#elif buildtype == "data-experiment":
# repo = "data/experiment"
#elif buildtype == "workflows":
# repo = "workflows"
#else:
# repo = "bioc"
#url = "/packages/%s/%s/html/%s.html" % (bioc_version, repo, pkg)
## Use short URL:
url = "/packages/%s/%s" % (bioc_version, pkg)
return url
def _pkgname_as_HTML(pkg, pkgdir=None):
if pkgdir == None:
return pkg
return '<A href="%s/">%s</A>' % (pkgdir, pkg)
def _pkgname_and_version_as_HTML(pkg, version, pkgdir=None, deprecated=False):
html1 = '<B>%s %s</B>' % (_pkgname_as_HTML(pkg, pkgdir), version)
if deprecated:
html1 = '<s>%s</s>' % html1
url = _url_to_pkg_landing_page(pkg)
SPANcontent = '(<A href="%s">landing page</A>)' % url
SPANstyle = 'font-size: smaller; font-style: italic;'
html2 = '<SPAN style="%s">%s</SPAN>' % (SPANstyle, SPANcontent)
return '%s %s' % (html1, html2)
def _node_OS_Arch_as_SPAN(node):
return '<SPAN style="font-size: smaller;">%s / %s</SPAN>' % \
(node.os_html, node.arch)
def _write_node_spec_as_TD(out, node, spec_html, selected=False):
TDclasses = node.hostname.replace(".", "_")
if selected:
TDclasses += ' selected'
out.write('<TD class="%s">%s</TD>' % (TDclasses, spec_html))
return
def _write_pkg_status_as_TD(out, pkg, node, stage,
topdir='.', leafreport_ref=None):
selected = leafreport_ref != None and \
pkg == leafreport_ref.pkg and \
node.node_id == leafreport_ref.node_id and \
stage == leafreport_ref.stage
TDclasses = 'status %s %s' % (node.hostname.replace(".", "_"), stage)
if selected:
TDclasses += ' selected'
status = BBSreportutils.get_pkg_status(pkg, node.node_id, stage)
if status in ["skipped", "NA"]:
TDcontent = _status_as_glyph(status)
else:
if leafreport_ref == None:
pkgdir = '%s/%s' % (topdir, pkg)
else:
pkgdir = '.'
url = BBSreportutils.get_leafreport_rel_url(pkgdir, node.node_id, stage)
TDcontent = _make_link_with_mouseover(url, _status_as_glyph(status))
out.write('<TD class="%s">%s</TD>' % (TDclasses, TDcontent))
return
def write_stagelabel_as_TD(out, stage, leafreport_ref):
selected = leafreport_ref != None and \
stage == leafreport_ref.stage
TDclasses = 'STAGE %s' % stage
if selected:
TDclasses += ' selected'
stage_label = BBSreportutils.stage_label(stage)
TD_html = '<TD class="%s">%s</TD>' % (TDclasses, stage_label)
out.write(TD_html)
return
def write_pkg_stagelabels_as_TDs(out, leafreport_ref=None):
buildtype = BBSvars.buildtype
for stage in BBSreportutils.stages_to_display(buildtype):
write_stagelabel_as_TD(out, stage, leafreport_ref)
if BBSreportutils.display_propagation_status(buildtype):
out.write('<TD style="width: 12px;"></TD>')
return
def write_pkg_propagation_status_as_TD(out, pkg, node):
status = BBSreportutils.get_propagation_status_from_db(pkg, node.hostname)
if status == None:
TDcontent = ''
else:
IMGstyle = 'border: 0px; width: 10px; height: 10px;'
if "/" in out.name:
path = "../"
else:
path = "./"
if status.startswith("YES"):
color = "Green"
elif status.startswith("NO"):
color = "Red"
else: # "UNNEEDED"
color = "Blue"
IMGsrc = '%s120px-%s_Light_Icon.svg.png' % (path, color)
TDcontent = '<IMG style="%s" alt="%s" title="%s" src="%s">' % \
(IMGstyle, status, status, IMGsrc)
out.write('<TD class="status %s">%s</TD>' % \
(node.hostname.replace(".", "_"), TDcontent))
return
def write_pkg_statuses_as_TDs(out, pkg, node,
topdir='.', leafreport_ref=None):
TDclasses = 'status %s' % node.hostname.replace(".", "_")
buildtype = BBSvars.buildtype
ncol_to_display = BBSreportutils.ncol_to_display(buildtype)
if pkg in skipped_pkgs:
TDattrs = 'COLSPAN="%s" class="%s"' % (ncol_to_display, TDclasses)
TDcontent = _status_as_glyph('ERROR')
TDcontent += ' (Bad DESCRIPTION file)'
out.write('<TD %s>%s</TD>' % (TDattrs, TDcontent))
elif not BBSreportutils.is_supported(pkg, node):
TDattrs = 'COLSPAN="%s" class="%s"' % (ncol_to_display, TDclasses)
## This is only a temporary hack based on the questionable assumption
## that a software package unsupported on Linux is GPU-reliant, which
## is of course not necessarily the case in general, but it just
## happens to be true at the moment for Bioconductor software packages.
## TODO: If we decide to get rid of the dedicated GPU-enabled builds
## (buildtype == 'bioc-gpu') and to incorporate the GPU-capable
## builders to the software builds, then we can get rid of this hack.
pkgType = BBSutils.getNodeSpec(node.hostname, 'pkgType')
show_link_to_gpu_builds = buildtype == 'bioc' and pkgType == "source"
if show_link_to_gpu_builds:
url = '%s/../bioc-gpu-LATEST/' % topdir
Astyle = 'display: inline; text-decoration: underline;'
TDcontent = 'see GPU-enabled build/check report ' + \
'<A href="%s" style="%s">here</A>' % (url, Astyle)
else:
TDcontent = '... NOT SUPPORTED ...'
TDcontent = '%s' % TDcontent.replace(' ', ' ')
out.write('<TD %s>%s</TD>' % (TDattrs, TDcontent))
else:
for stage in BBSreportutils.stages_to_display(buildtype):
if stage != 'buildbin' or BBSreportutils.is_doing_buildbin(node):
_write_pkg_status_as_TD(out, pkg, node, stage,
topdir, leafreport_ref)
else:
out.write('<TD class="%s"></TD>' % TDclasses)
if BBSreportutils.display_propagation_status(buildtype):
write_pkg_propagation_status_as_TD(out, pkg, node)
return
### Produce 2 full TRs.
def write_abc_dispatcher_within_gcard_list(out, current_letter):
## FH: Need the collapsable_rows class to blend out the alphabetical
## selection when "ok" packages are unselected.
out.write('<TBODY class="abc_dispatcher collapsable_rows">\n')
_write_vertical_space(out)
out.write('<TR class="abc">')
out.write('<TD COLSPAN="2">')
out.write('<TABLE class="big_letter"><TR><TD>')
out.write('<A name="%s">%s</A>' % \
(current_letter, current_letter))
out.write('</TD></TR></TABLE>')
out.write('</TD>')
ncol_to_display = BBSreportutils.ncol_to_display(BBSvars.buildtype)
out.write('<TD COLSPAN="%s">' % (ncol_to_display + 3))
write_abc_dispatcher(out, "", current_letter)
out.write('</TD>')
out.write('</TR>\n')
out.write('</TBODY>\n')
return
def statuses2classes(statuses):
classes = []
if "TIMEOUT" in statuses:
classes.append("timeout")
if "ERROR" in statuses:
classes.append("error")
if "WARNINGS" in statuses:
classes.append("warnings")
## A package is tagged with the "ok" class if it's not tagged with any of
## the "timeout", "error" or "warnings". Note that this means that
## a package could end up being tagged with the "ok" class even if it
## doesn't have any OK in 'statuses' (e.g. if it's unsupported on all
## platforms).
if len(classes) == 0:
classes = ["ok"]
return ' '.join(classes)
def write_quickstats_TD(out, quickstats, node, stage):
stats = quickstats[node.node_id][stage]
html = '<TABLE class="quickstats"><TR>'
html += '<TD class="glyph %s">%d</TD>' % ("TIMEOUT", stats[0])
html += '<TD class="glyph %s">%d</TD>' % ("ERROR", stats[1])
if stage == 'checksrc':
html += '<TD class="glyph %s">%d</TD>' % ("WARNINGS", stats[2])
html += '<TD class="glyph %s">%d</TD>' % ("OK", stats[3])
# Only relevant when "smart STAGE2" is enabled.
#if stage == 'install':
# html += '<TD class="glyph %s">%d</TD>' % ("NotNeeded", stats[4])
html += '</TR></TABLE>'
out.write('<TD>%s</TD>' % html)
return
### The quick stats span several table rows (TRs).
def write_quickstats(out, quickstats, no_links, selected_node=None):
out.write('<THEAD class="quickstats">\n')
out.write('<TR class="header">')
TDclass = 'leftmost top_left_corner'
TDstyle = 'padding-left: 0px;'
out.write('<TD COLSPAN="3" class="%s" style="%s">QUICK STATS</TD>' % \
(TDclass, TDstyle))
out.write('<TD>OS / Arch</TD>')
write_pkg_stagelabels_as_TDs(out)
out.write('<TD class="rightmost top_right_corner"></TD>')
out.write('</TR>\n')
nb_nodes = len(BBSreportutils.NODES);
## Find index of last non foreign node.
last_non_foreign_ix = -1
for i in range(nb_nodes):
node = BBSreportutils.NODES[i]
if node.buildbin == None: # foreign node
continue
last_non_foreign_ix = i