Module: Misc
- Defined in:
- lib/rbbt/util/misc.rb
Defined Under Namespace
Classes: FieldNotFoundError
Constant Summary collapse
- COLOR_LIST =
%w(#BC80BD #CCEBC5 #FFED6F #8DD3C7 #FFFFB3 #BEBADA #FB8072 #80B1D3 #FDB462 #B3DE69 #FCCDE5 #D9D9D9)
- Log2Multiplier =
1.0 / Math.log(2.0)
- ARRAY_MAX_LENGTH =
1000
- STRING_MAX_LENGTH =
ARRAY_MAX_LENGTH * 10
- IUPAC2BASE =
{ "A" => ["A"], "C" => ["C"], "G" => ["G"], "T" => ["T"], "U" => ["U"], "R" => "A or G".split(" or "), "Y" => "C or T".split(" or "), "S" => "G or C".split(" or "), "W" => "A or T".split(" or "), "K" => "G or T".split(" or "), "M" => "A or C".split(" or "), "B" => "C or G or T".split(" or "), "D" => "A or G or T".split(" or "), "H" => "A or C or T".split(" or "), "V" => "A or C or G".split(" or "), "N" => %w(A C T G), }
- BASE2COMPLEMENT =
{ "A" => "T", "C" => "G", "G" => "C", "T" => "A", "U" => "A", }
- THREE_TO_ONE_AA_CODE =
{ "ala" => "A", "arg" => "R", "asn" => "N", "asp" => "D", "cys" => "C", "glu" => "E", "gln" => "Q", "gly" => "G", "his" => "H", "ile" => "I", "leu" => "L", "lys" => "K", "met" => "M", "phe" => "F", "pro" => "P", "ser" => "S", "thr" => "T", "trp" => "W", "tyr" => "Y", "val" => "V" }
- LOCK_REPO_SERIALIZER =
Marshal
- HASH2MD5_MAX_STRING_LENGTH =
1000
- HASH2MD5_MAX_ARRAY_LENGTH =
100
Class Method Summary collapse
- .add_defaults(options, defaults = {}) ⇒ Object
- .array2hash(array, default = nil) ⇒ Object
- .benchmark(repeats = 1) ⇒ Object
- .binary_include?(array, elem) ⇒ Boolean
-
.collapse_ranges(ranges) ⇒ Object
def self.collapse_ranges_old(ranges) processed = [] last = nil ranges.sort_by{|range| range.begin }.each do |range| rbegin = range.begin rend = range.end if last.nil? or rbegin > last processed << range last = rend else new_processed = [] processed.each do |processed_range| if processed_range.end < rbegin new_processed << processed_range else eend = [rend, processed_range.end].max new_processed << (processed_range.begin..eend) break end end processed = new_processed last = rend if rend > last end end.
- .colors_for(list) ⇒ Object
- .common_path(dir, file) ⇒ Object
- .consolidate(list) ⇒ Object
- .correct_icgc_mutation(pos, ref, mut_str) ⇒ Object
- .correct_vcf_mutation(pos, ref, mut_str) ⇒ Object
- .counts(array) ⇒ Object
- .digest(text) ⇒ Object
-
.divide(array, num) ⇒ Object
Divides the array into
num
chunks of the same size by placing one element in each chunk iteratively. - .do_once(&block) ⇒ Object
- .ensembl_server(organism) ⇒ Object
- .env_add(var, value, sep = ":", prepend = true) ⇒ Object
- .fast_align(reference, sequence) ⇒ Object
- .field_position(fields, field, quiet = false) ⇒ Object
- .filename?(string) ⇒ Boolean
- .fingerprint(obj) ⇒ Object
- .fixascii(string) ⇒ Object
- .fixutf8(string) ⇒ Object
- .GET_params2hash(string) ⇒ Object
- .google_venn(list1, list2, list3, name1 = nil, name2 = nil, name3 = nil, total = nil) ⇒ Object
- .hash2GET_params(hash) ⇒ Object
- .hash2md5(hash) ⇒ Object
- .hash2string(hash) ⇒ Object
- .hash_to_html_tag_attributes(hash) ⇒ Object
- .hostname ⇒ Object
- .html_tag(tag, content = nil, params = {}) ⇒ Object
-
.humanize(value, options = {}) ⇒ Object
source: gist.github.com/ekdevdes/2450285 author: Ethan Kramer (github.com/ekdevdes).
-
.in_dir(dir) ⇒ Object
WARN: probably not thread safeā¦
- .insist(times = 3, sleep = nil) ⇒ Object
- .intersect_sorted_arrays(a1, a2) ⇒ Object
- .is_filename?(string) ⇒ Boolean
- .IUPAC_to_base(iupac) ⇒ Object
- .lock(file, *args) ⇒ Object
- .lock_in_repo(repo, key, *args) ⇒ Object
- .log2(x) ⇒ Object
- .max(list) ⇒ Object
- .mean(list) ⇒ Object
- .memprof ⇒ Object
- .merge_sorted_arrays(a1, a2) ⇒ Object
-
.ordered_divide(array, num) ⇒ Object
Divides the array into chunks of
num
same size by placing one element in each chunk iteratively. - .path_relative_to(basedir, path) ⇒ Object
- .pid_exists?(pid) ⇒ Boolean
- .positional2hash(keys, *values) ⇒ Object
- .prepare_entity(entity, field, options = {}) ⇒ Object
- .process_options(hash, *keys) ⇒ Object
- .process_to_hash(list) ⇒ Object
- .profile(options = {}) ⇒ Object
- .profile_graph(options = {}) ⇒ Object
- .profile_html(options = {}) ⇒ Object
- .proportions(array) ⇒ Object
- .pull_keys(hash, prefix) ⇒ Object
- .random_sample_in_range(total, size) ⇒ Object
- .remove_long_items(obj) ⇒ Object
- .reset_do_once ⇒ Object
- .sample(ary, size, replacement = false) ⇒ Object
- .sanitize_filename(filename, length = 254) ⇒ Object
- .sd(list) ⇒ Object
- .send_email(from, to, subject, message, options = {}) ⇒ Object
- .sensiblewrite(path, content = nil) ⇒ Object
- .snake_case(string) ⇒ Object
- .sorted_array_hits(a1, a2) ⇒ Object
- .string2const(string) ⇒ Object
- .string2hash(string) ⇒ Object
- .string2hash_old(string) ⇒ Object
- .sum(list) ⇒ Object
- .to_utf8(string) ⇒ Object
- .total_length(ranges) ⇒ Object
- .try3times(&block) ⇒ Object
- .zip2hash(list1, list2) ⇒ Object
- .zip_fields(array) ⇒ Object
Class Method Details
.add_defaults(options, defaults = {}) ⇒ Object
1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 |
# File 'lib/rbbt/util/misc.rb', line 1047 def self.add_defaults(, defaults = {}) case when Hash === = .dup when String === = string2hash else raise "Format of '#{.inspect}' not understood. It should be a hash" end defaults.each do |key, value| next if .include? key [key] = value end end |
.array2hash(array, default = nil) ⇒ Object
667 668 669 670 671 672 673 674 |
# File 'lib/rbbt/util/misc.rb', line 667 def self.array2hash(array, default = nil) hash = {} array.each do |key, value| value = default.dup if value.nil? and not default.nil? hash[key] = value end hash end |
.benchmark(repeats = 1) ⇒ Object
699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 |
# File 'lib/rbbt/util/misc.rb', line 699 def self.benchmark(repeats = 1) require 'benchmark' res = nil begin measure = Benchmark.measure do repeats.times do res = yield end end puts "Benchmark for #{ repeats } repeats" puts measure rescue Exception puts "Benchmark aborted" raise $! end res end |
.binary_include?(array, elem) ⇒ Boolean
640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 |
# File 'lib/rbbt/util/misc.rb', line 640 def self.binary_include?(array, elem) upper = array.size - 1 lower = 0 return -1 if upper < lower while(upper >= lower) do idx = lower + (upper - lower) / 2 value = array[idx] case elem <=> value when 0 return true when -1 upper = idx - 1 when 1 lower = idx + 1 else raise "Cannot compare #{[elem.inspect, value.inspect] * " with "}" end end return false end |
.collapse_ranges(ranges) ⇒ Object
def self.collapse_ranges_old(ranges)
processed = []
last = nil
ranges.sort_by{|range| range.begin }.each do |range|
rbegin = range.begin
rend = range.end
if last.nil? or rbegin > last
processed << range
last = rend
else
new_processed = []
processed.each do |processed_range|
if processed_range.end < rbegin
new_processed << processed_range
else
eend = [rend, processed_range.end].max
new_processed << (processed_range.begin..eend)
break
end
end
processed = new_processed
last = rend if rend > last
end
end
processed
end
116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 |
# File 'lib/rbbt/util/misc.rb', line 116 def self.collapse_ranges(ranges) processed = [] last = nil final = [] ranges.sort_by{|range| range.begin }.each do |range| rbegin = range.begin rend = range.end if last.nil? or rbegin > last processed << [rbegin, rend] last = rend else new_processed = [] processed.each do |pbegin,pend| if pend < rbegin final << [pbegin, pend] else eend = [rend, pend].max new_processed << [pbegin, eend] break end end processed = new_processed last = rend if rend > last end end final.concat processed final.collect{|b,e| (b..e)} end |
.colors_for(list) ⇒ Object
71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 |
# File 'lib/rbbt/util/misc.rb', line 71 def self.colors_for(list) unused = COLOR_LIST.dup used = {} colors = list.collect do |elem| if used.include? elem used[elem] else color = unused.shift used[elem]=color color end end [colors, used] end |
.common_path(dir, file) ⇒ Object
969 970 971 972 973 974 975 976 977 978 979 980 |
# File 'lib/rbbt/util/misc.rb', line 969 def self.common_path(dir, file) file = File. file dir = File. dir return true if file == dir while File.dirname(file) != file file = File.dirname(file) return true if file == dir end return false end |
.consolidate(list) ⇒ Object
359 360 361 362 363 364 365 366 367 368 |
# File 'lib/rbbt/util/misc.rb', line 359 def self.consolidate(list) list.inject(nil){|acc,e| if acc.nil? acc = e else acc.concat e acc end } end |
.correct_icgc_mutation(pos, ref, mut_str) ⇒ Object
26 27 28 29 30 31 |
# File 'lib/rbbt/util/misc.rb', line 26 def self.correct_icgc_mutation(pos, ref, mut_str) mut = mut_str mut = '-' * (mut_str.length - 1) if mut =~/^-[ACGT]/ mut = "+" << mut if ref == '-' [pos, [mut]] end |
.correct_vcf_mutation(pos, ref, mut_str) ⇒ Object
33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 |
# File 'lib/rbbt/util/misc.rb', line 33 def self.correct_vcf_mutation(pos, ref, mut_str) muts = mut_str.nil? ? [] : mut_str.split(',') while ref.length >= 1 and muts.reject{|m| m[0] == ref[0]}.empty? ref = ref[1..-1] pos = pos + 1 muts = muts.collect{|m| m[1..-1]} end muts = muts.collect do |m| case when ref.empty? "+" << m when (m.length < ref.length and (m.empty? or ref.index(m))) "-" * (ref.length - m.length) when (ref.length == 1 and m.length == 1) m else Log.debug{"Cannot understand: #{[ref, m]} (#{ muts })"} '-' * ref.length + m end end [pos, muts] end |
.counts(array) ⇒ Object
402 403 404 405 406 407 408 409 410 |
# File 'lib/rbbt/util/misc.rb', line 402 def self.counts(array) counts = {} array.each do |e| counts[e] ||= 0 counts[e] += 1 end counts end |
.digest(text) ⇒ Object
1066 1067 1068 |
# File 'lib/rbbt/util/misc.rb', line 1066 def self.digest(text) Digest::MD5.hexdigest(text) end |
.divide(array, num) ⇒ Object
Divides the array into num
chunks of the same size by placing one element in each chunk iteratively.
1296 1297 1298 1299 1300 1301 1302 1303 1304 |
# File 'lib/rbbt/util/misc.rb', line 1296 def self.divide(array, num) chunks = [] num.to_i.times do chunks << [] end array.each_with_index{|e, i| c = i % num chunks[c] << e } chunks end |
.do_once(&block) ⇒ Object
789 790 791 792 793 794 |
# File 'lib/rbbt/util/misc.rb', line 789 def self.do_once(&block) return nil if $__did_once $__did_once = true yield nil end |
.ensembl_server(organism) ⇒ Object
300 301 302 303 304 305 306 307 |
# File 'lib/rbbt/util/misc.rb', line 300 def self.ensembl_server(organism) date = organism.split("/")[1] if date.nil? "www.ensembl.org" else "#{ date }.archive.ensembl.org" end end |
.env_add(var, value, sep = ":", prepend = true) ⇒ Object
689 690 691 692 693 694 695 696 697 |
# File 'lib/rbbt/util/misc.rb', line 689 def self.env_add(var, value, sep = ":", prepend = true) ENV[var] ||= "" return if ENV[var] =~ /(#{sep}|^)#{Regexp.quote value}(#{sep}|$)/ if prepend ENV[var] = value + sep + ENV[var] else ENV[var] += sep + ENV[var] end end |
.fast_align(reference, sequence) ⇒ Object
480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 |
# File 'lib/rbbt/util/misc.rb', line 480 def self.fast_align(reference, sequence) init_gap = -1 gap = -2 diff = -2 same = 2 cols = sequence.length + 1 rows = reference.length + 1 a = NArray.int(cols, rows) for spos in 0..cols-1 do a[spos, 0] = spos * init_gap end for rpos in 0..rows-1 do a[0, rpos] = rpos * init_gap end spos = 1 while spos < cols do rpos = 1 while rpos < rows do match = a[spos-1,rpos-1] + (sequence[spos-1] != reference[rpos-1] ? diff : same) skip_sequence = a[spos-1,rpos] + gap skip_reference = a[spos,rpos-1] + gap a[spos,rpos] = [match, skip_sequence, skip_reference].max rpos += 1 end spos += 1 end start = Misc.max(a[-1,0..rows-1]) start_pos = a[-1,0..rows-1].to_a.index start ref = '' seq = '' rpos = start_pos spos = cols - 1 while spos > 0 and rpos > 0 score = a[spos,rpos] score_match = a[spos-1,rpos-1] score_skip_reference = a[spos,rpos-1] score_skip_sequence = a[spos-1,rpos] case when score == score_match + (sequence[spos-1] != reference[rpos-1] ? diff : same) ref << reference[rpos-1] seq << sequence[spos-1] spos -= 1 rpos -= 1 when score == score_skip_reference + gap ref << reference[rpos-1] seq << '-' rpos -= 1 when score == score_skip_sequence + gap seq << sequence[spos-1] ref << '-' spos -= 1 else raise "stop" end end while (rpos > 0) ref << reference[rpos-1] seq = seq << '-' rpos -= 1 end while (spos > 0) seq << sequence[spos-1] ref = ref + '-' spos -= 1 end [ref.reverse + reference[start_pos..-1], seq.reverse + '-' * (rows - start_pos - 1)] end |
.field_position(fields, field, quiet = false) ⇒ Object
1285 1286 1287 1288 1289 1290 1291 1292 |
# File 'lib/rbbt/util/misc.rb', line 1285 def self.field_position(fields, field, quiet = false) return field if Integer === field or Range === field raise FieldNotFoundError, "Field information missing" if fields.nil? && ! quiet fields.each_with_index{|f,i| return i if f == field} field_re = Regexp.new /^#{field}$/i fields.each_with_index{|f,i| return i if f =~ field_re} raise FieldNotFoundError, "Field #{ field.inspect } was not found" unless quiet end |
.filename?(string) ⇒ Boolean
309 310 311 |
# File 'lib/rbbt/util/misc.rb', line 309 def self.filename?(string) String === string and string.length > 0 and string.length < 250 and File.exists?(string) end |
.fingerprint(obj) ⇒ Object
239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 |
# File 'lib/rbbt/util/misc.rb', line 239 def self.fingerprint(obj) case obj when nil "nil" when Symbol ":" << obj.to_s when String if obj.length > 100 "'" << obj[0..20-1] << "<...#{obj.length}...>" << obj[-10..-1] << " " << "'" else "'" << obj << "'" end when Array if (length = obj.length) > 10 "[#{length} --" << (obj.values_at(0,1, length / 2, -2, -1).collect{|e| fingerprint(e)} * ",") << "]" else "[" << (obj.collect{|e| fingerprint(e) } * ",") << "]" end when TSV obj.with_unnamed do "TSV:{"<< fingerprint(obj.all_fields|| []).inspect << ";" << fingerprint(obj.keys).inspect << "}" end when Hash if obj.length > 10 "H:{"<< fingerprint(obj.keys) << ";" << fingerprint(obj.values) << "}" else new = "{" obj.each do |k,v| new << k.to_s << '=>' << fingerprint(v) << ' ' end new << "}" end else obj.to_s end end |
.fixascii(string) ⇒ Object
1012 1013 1014 1015 1016 1017 1018 |
# File 'lib/rbbt/util/misc.rb', line 1012 def self.fixascii(string) if string.respond_to?(:encode) self.fixutf8(string).encode("ASCII-8BIT") else string end end |
.fixutf8(string) ⇒ Object
1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 |
# File 'lib/rbbt/util/misc.rb', line 1000 def self.fixutf8(string) return string if (string.respond_to? :valid_encoding? and string.valid_encoding?) or (string.respond_to? :valid_encoding and string.valid_encoding) if string.respond_to?(:encode) string.encode("UTF-16BE", :invalid => :replace, :undef => :replace, :replace => "?").encode('UTF-8') else require 'iconv' @@ic ||= Iconv.new('UTF-8//IGNORE', 'UTF-8') @@ic.iconv(string) end end |
.GET_params2hash(string) ⇒ Object
825 826 827 828 829 830 831 832 |
# File 'lib/rbbt/util/misc.rb', line 825 def self.GET_params2hash(string) hash = {} string.split('&').collect{|item| key, value = item.split("=").values_at 0, 1 hash[key] = value.nil? ? "" : CGI.unescape(value) } hash end |
.google_venn(list1, list2, list3, name1 = nil, name2 = nil, name3 = nil, total = nil) ⇒ Object
322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 |
# File 'lib/rbbt/util/misc.rb', line 322 def self.google_venn(list1, list2, list3, name1 = nil, name2 = nil, name3 = nil, total = nil) name1 ||= "list 1" name2 ||= "list 2" name3 ||= "list 3" sizes = [list1, list2, list3, list1 & list2, list1 & list3, list2 & list3, list1 & list2 & list3].collect{|l| l.length} total = total.length if Array === total label = "#{name1}: #{sizes[0]} (#{name2}: #{sizes[3]}, #{name3}: #{sizes[4]})" label << "|#{name2}: #{sizes[1]} (#{name1}: #{sizes[3]}, #{name3}: #{sizes[5]})" label << "|#{name3}: #{sizes[2]} (#{name1}: #{sizes[4]}, #{name2}: #{sizes[5]})" if total label << "| INTERSECTION: #{sizes[6]} TOTAL: #{total}" else label << "| INTERSECTION: #{sizes[6]}" end max = total || sizes.max sizes = sizes.collect{|v| (v.to_f/max * 100).to_i.to_f / 100} url = "https://chart.googleapis.com/chart?cht=v&chs=500x300&chd=t:#{sizes * ","}&chco=FF6342,ADDE63,63C6DE,FFFFFF&chdl=#{label}" end |
.hash2GET_params(hash) ⇒ Object
834 835 836 837 838 839 840 841 842 843 844 845 846 847 |
# File 'lib/rbbt/util/misc.rb', line 834 def self.hash2GET_params(hash) hash.sort_by{|k,v| k.to_s}.collect{|k,v| next unless %w(Symbol String Float Fixnum Integer TrueClass FalseClass Module Class Object Array).include? v.class.to_s v = case when Symbol === v v.to_s when Array === v v * "," else CGI.escape(v.to_s) end [ Symbol === k ? k.to_s : k, v] * "=" }.compact * "&" end |
.hash2md5(hash) ⇒ Object
1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 |
# File 'lib/rbbt/util/misc.rb', line 1072 def self.hash2md5(hash) str = "" keys = hash.keys keys = keys.clean_annotations if keys.respond_to? :clean_annotations keys = keys.sort_by{|k| k.to_s} if hash.respond_to? :unnamed unnamed = hash.unnamed hash.unnamed = true end keys.each do |k| next if k == :monitor or k == "monitor" or k == :in_situ_persistence or k == "in_situ_persistence" v = hash[k] case when TrueClass === v str << k.to_s << "=>true" when FalseClass === v str << k.to_s << "=>false" when Hash === v str << k.to_s << "=>" << hash2md5(v) when Symbol === v str << k.to_s << "=>" << v.to_s when (String === v and v.length > HASH2MD5_MAX_STRING_LENGTH) str << k.to_s << "=>" << v[0..HASH2MD5_MAX_STRING_LENGTH] << "; #{ v.length }" when String === v str << k.to_s << "=>" << v when (Array === v and v.length > HASH2MD5_MAX_ARRAY_LENGTH) str << k.to_s << "=>[" << v[0..HASH2MD5_MAX_ARRAY_LENGTH] * "," << "; #{ v.length }]" when Array === v str << k.to_s << "=>[" << v * "," << "]" else v_ins = v.inspect case when v_ins =~ /:0x0/ str << k.to_s << "=>" << v_ins.sub(/:0x[a-f0-9]+@/,'') else str << k.to_s << "=>" << v_ins end end str << "_" << hash2md5(v.info) if defined? Annotated and Annotated === v end hash.unnamed = unnamed if hash.respond_to? :unnamed if str.empty? "" else digest(str) end end |
.hash2string(hash) ⇒ Object
817 818 819 820 821 822 823 |
# File 'lib/rbbt/util/misc.rb', line 817 def self.hash2string(hash) hash.sort_by{|k,v| k.to_s}.collect{|k,v| next unless %w(Symbol String Float Fixnum Integer TrueClass FalseClass Module Class Object).include? v.class.to_s [ Symbol === k ? ":" << k.to_s : k, Symbol === v ? ":" << v.to_s : v] * "=" }.compact * "#" end |
.hash_to_html_tag_attributes(hash) ⇒ Object
849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 |
# File 'lib/rbbt/util/misc.rb', line 849 def self.hash_to_html_tag_attributes(hash) return "" if hash.nil? or hash.empty? hash.collect{|k,v| case when (k.nil? or v.nil? or (String === v and v.empty?)) nil when Array === v [k,"'" << v * " " << "'"] * "=" when String === v [k,"'" << v << "'"] * "=" when Symbol === v [k,"'" << v.to_s << "'"] * "=" when TrueClass === v [k,"'" << v.to_s << "'"] * "=" when (Fixnum === v or Float === v) [k,"'" << v.to_s << "'"] * "=" else nil end }.compact * " " end |
.hostname ⇒ Object
897 898 899 |
# File 'lib/rbbt/util/misc.rb', line 897 def self.hostname @hostanem ||= `hostname`.strip end |
.html_tag(tag, content = nil, params = {}) ⇒ Object
871 872 873 874 875 876 877 878 879 880 881 |
# File 'lib/rbbt/util/misc.rb', line 871 def self.html_tag(tag, content = nil, params = {}) attr_str = hash_to_html_tag_attributes(params) attr_str = " " << attr_str if String === attr_str and attr_str != "" html = if content.nil? "<#{ tag }#{attr_str}/>" else "<#{ tag }#{attr_str}>#{ content }</#{ tag }>" end html end |
.humanize(value, options = {}) ⇒ Object
source: gist.github.com/ekdevdes/2450285 author: Ethan Kramer (github.com/ekdevdes)
1337 1338 1339 1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 1352 1353 1354 1355 1356 1357 1358 1359 1360 1361 1362 1363 1364 1365 1366 1367 1368 1369 1370 1371 1372 1373 1374 1375 1376 1377 1378 |
# File 'lib/rbbt/util/misc.rb', line 1337 def self.humanize(value, = {}) if .empty? [:format] = :sentence end values = [] values = value.split('_') values.each_index do |index| # lower case each item in array # Miguel Vazquez edit: Except for acronyms values[index].downcase! unless values[index].match(/[a-zA-Z][A-Z]/) end if [:format] == :allcaps values.each do |value| value.capitalize! end if .empty? [:seperator] = " " end return values.join " " end if [:format] == :class values.each do |value| value.capitalize! end return values.join "" end if [:format] == :sentence values[0].capitalize! unless values[0].match(/[a-zA-Z][A-Z]/) return values.join " " end if [:format] == :nocaps return values.join " " end end |
.in_dir(dir) ⇒ Object
WARN: probably not thread safeā¦
983 984 985 986 987 988 989 990 991 992 993 994 |
# File 'lib/rbbt/util/misc.rb', line 983 def self.in_dir(dir) old_pwd = FileUtils.pwd res = nil begin FileUtils.mkdir_p dir unless File.exists? dir FileUtils.cd dir res = yield ensure FileUtils.cd old_pwd end res end |
.insist(times = 3, sleep = nil) ⇒ Object
800 801 802 803 804 805 806 807 808 809 810 811 |
# File 'lib/rbbt/util/misc.rb', line 800 def self.insist(times = 3, sleep = nil) try = 0 begin yield rescue Log.warn("Insisting after exception: #{$!.}") sleep sleep if sleep try += 1 retry if try < times raise $! end end |
.intersect_sorted_arrays(a1, a2) ⇒ Object
589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 |
# File 'lib/rbbt/util/misc.rb', line 589 def self.intersect_sorted_arrays(a1, a2) e1, e2 = a1.shift, a2.shift intersect = [] while true break if e1.nil? or e2.nil? case e1 <=> e2 when 0 intersect << e1 e1, e2 = a1.shift, a2.shift when -1 e1 = a1.shift while not e1.nil? and e1 < e2 when 1 e2 = a2.shift e2 = a2.shift while not e2.nil? and e2 < e1 end end intersect end |
.is_filename?(string) ⇒ Boolean
559 560 561 562 563 |
# File 'lib/rbbt/util/misc.rb', line 559 def self.is_filename?(string) return true if string.respond_to? :exists return true if String === string and string.length < 265 and File.exists? string return false end |
.IUPAC_to_base(iupac) ⇒ Object
555 556 557 |
# File 'lib/rbbt/util/misc.rb', line 555 def self.IUPAC_to_base(iupac) IUPAC2BASE[iupac] end |
.lock(file, *args) ⇒ Object
901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 |
# File 'lib/rbbt/util/misc.rb', line 901 def self.lock(file, *args) return yield file, *args if file.nil? FileUtils.mkdir_p File.dirname(File.(file)) unless File.exists? File.dirname(File.(file)) res = nil lock_path = File.(file + '.lock') lockfile = Lockfile.new(lock_path) begin if File.exists? lockfile and Misc.hostname == (info = YAML.load_file(lockfile))["host"] and info["pid"] and not Misc.pid_exists?(info["pid"]) Log.info("Removing lockfile: #{lockfile}. This pid #{Process.pid}. Content: #{info.inspect}") FileUtils.rm lockfile end rescue Log.warn("Error checking lockfile #{lockfile}: #{$!.}. Removing. Content: #{begin Open.read(lockfile) rescue "Could not open file" end}") FileUtils.rm lockfile if File.exists?(lockfile) end begin lockfile.lock do res = yield file, *args end rescue Interrupt Log.error "Process #{Process.pid} interrupted while in lock: #{ lock_path }" raise $! end res end |
.lock_in_repo(repo, key, *args) ⇒ Object
938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 |
# File 'lib/rbbt/util/misc.rb', line 938 def self.lock_in_repo(repo, key, *args) return yield file, *args if repo.nil? or key.nil? lock_key = "lock-" << key begin if repo[lock_key] and Misc.hostname == (info = LOCK_REPO_SERIALIZER.load(repo[lock_key]))["host"] and info["pid"] and not Misc.pid_exists?(info["pid"]) Log.info("Removing lockfile: #{lock_key}. This pid #{Process.pid}. Content: #{info.inspect}") repo.out lock_key end rescue Log.warn("Error checking lockfile #{lock_key}: #{$!.}. Removing. Content: #{begin repo[lock_key] rescue "Could not open file" end}") repo.out lock_key if repo.include? lock_key end while repo[lock_key] sleep 1 end repo[lock_key] = LOCK_REPO_SERIALIZER.dump({:hostname => Misc.hostname, :pid => Process.pid}) res = yield lock_key, *args repo.delete lock_key res end |
.log2(x) ⇒ Object
192 193 194 |
# File 'lib/rbbt/util/misc.rb', line 192 def self.log2(x) Math.log(x) * Log2Multiplier end |
.max(list) ⇒ Object
313 314 315 316 317 318 319 320 |
# File 'lib/rbbt/util/misc.rb', line 313 def self.max(list) max = nil list.each do |v| next if v.nil? max = v if max.nil? or v > max end max end |
.mean(list) ⇒ Object
349 350 351 |
# File 'lib/rbbt/util/misc.rb', line 349 def self.mean(list) sum(list) / list.compact.length end |
.memprof ⇒ Object
773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 |
# File 'lib/rbbt/util/misc.rb', line 773 def self.memprof require 'memprof' Memprof.start begin res = yield rescue Exception puts "Profiling aborted" raise $! ensure Memprof.stop print Memprof.stats end res end |
.merge_sorted_arrays(a1, a2) ⇒ Object
608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 |
# File 'lib/rbbt/util/misc.rb', line 608 def self.merge_sorted_arrays(a1, a2) e1, e2 = a1.shift, a2.shift new = [] while true case when (e1 and e2) case e1 <=> e2 when 0 new << e1 e1, e2 = a1.shift, a2.shift when -1 new << e1 e1 = a1.shift when 1 new << e2 e2 = a2.shift end when e2 new << e2 new.concat a2 break when e1 new << e1 new.concat a1 break else break end end new end |
.ordered_divide(array, num) ⇒ Object
Divides the array into chunks of num
same size by placing one element in each chunk iteratively.
1308 1309 1310 1311 1312 1313 1314 1315 1316 1317 1318 |
# File 'lib/rbbt/util/misc.rb', line 1308 def self.ordered_divide(array, num) last = array.length - 1 chunks = [] current = 0 while current <= last next_current = [last, current + num - 1].min chunks << array[current..next_current] current = next_current + 1 end chunks end |
.path_relative_to(basedir, path) ⇒ Object
883 884 885 886 887 888 889 890 891 892 893 894 895 |
# File 'lib/rbbt/util/misc.rb', line 883 def self.path_relative_to(basedir, path) path = File.(path) basedir = File.(basedir) case when path == basedir "." when path =~ /#{Regexp.quote basedir}\/(.*)/ return $1 else return nil end end |
.pid_exists?(pid) ⇒ Boolean
59 60 61 62 63 64 65 66 67 |
# File 'lib/rbbt/util/misc.rb', line 59 def self.pid_exists?(pid) return false if pid.nil? begin Process.getpgid(pid.to_i) true rescue Errno::ESRCH false end end |
.positional2hash(keys, *values) ⇒ Object
370 371 372 373 374 375 376 377 378 379 380 381 |
# File 'lib/rbbt/util/misc.rb', line 370 def self.positional2hash(keys, *values) if Hash === values.last extra = values.pop inputs = Misc.zip2hash(keys, values) inputs.delete_if{|k,v| v.nil? or (String === v and v.empty?)} inputs = Misc.add_defaults inputs, extra inputs.delete_if{|k,v| not keys.include?(k) and not (Symbol === k ? keys.include?(k.to_s) : keys.include?(k.to_sym))} inputs else Misc.zip2hash(keys, values) end end |
.prepare_entity(entity, field, options = {}) ⇒ Object
196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 |
# File 'lib/rbbt/util/misc.rb', line 196 def self.prepare_entity(entity, field, = {}) return entity unless defined? Entity return entity unless String === entity or Array === entity ||= {} dup_array = .delete :dup_array if Annotated === field or Entity.respond_to?(:formats) and Entity.formats.include? field params = .dup params[:format] ||= params.delete "format" params.merge!(:format => field) unless params.include?(:format) and not ((f = params[:format]).nil? or (String === f and f.empty?)) mod = Entity === field ? field : Entity.formats[field] entity = mod.setup( ((entity.frozen? and not entity.nil?) ? entity.dup : ((Array === entity and dup_array) ? entity.collect{|e| e.nil? ? e : e.dup} : entity) ), params ) end entity end |
.process_options(hash, *keys) ⇒ Object
1125 1126 1127 1128 1129 1130 1131 |
# File 'lib/rbbt/util/misc.rb', line 1125 def self.(hash, *keys) if keys.length == 1 hash.include?(keys.first.to_sym) ? hash.delete(keys.first.to_sym) : hash.delete(keys.first.to_s) else keys.collect do |key| hash.include?(key.to_sym) ? hash.delete(key.to_sym) : hash.delete(key.to_s) end end end |
.process_to_hash(list) ⇒ Object
684 685 686 687 |
# File 'lib/rbbt/util/misc.rb', line 684 def self.process_to_hash(list) result = yield list zip2hash(list, result) end |
.profile(options = {}) ⇒ Object
756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 |
# File 'lib/rbbt/util/misc.rb', line 756 def self.profile( = {}) require 'ruby-prof' RubyProf.start begin res = yield rescue Exception puts "Profiling aborted" raise $! ensure result = RubyProf.stop printer = RubyProf::FlatPrinter.new(result) printer.print(STDOUT, ) end res end |
.profile_graph(options = {}) ⇒ Object
738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 |
# File 'lib/rbbt/util/misc.rb', line 738 def self.profile_graph( = {}) require 'ruby-prof' RubyProf.start begin res = yield rescue Exception puts "Profiling aborted" raise $! ensure result = RubyProf.stop #result.eliminate_methods!([/annotated_array_clean_/]) printer = RubyProf::GraphPrinter.new(result) printer.print(STDOUT, ) end res end |
.profile_html(options = {}) ⇒ Object
717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 |
# File 'lib/rbbt/util/misc.rb', line 717 def self.profile_html( = {}) require 'ruby-prof' RubyProf.start begin res = yield rescue Exception puts "Profiling aborted" raise $! ensure result = RubyProf.stop printer = RubyProf::MultiPrinter.new(result) TmpFile.with_file do |dir| FileUtils.mkdir_p dir unless File.exists? dir printer.print(:path => dir, :profile => 'profile') CMD.cmd("firefox -no-remote '#{ dir }'") end end res end |
.proportions(array) ⇒ Object
412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 |
# File 'lib/rbbt/util/misc.rb', line 412 def self.proportions(array) total = array.length proportions = Hash.new 0 array.each do |e| proportions[e] += 1.0 / total end class << proportions; self;end.class_eval do def to_s sort{|a,b| a[1] == b[1] ? a[0] <=> b[0] : a[1] <=> b[1]}.collect{|k,c| "%3d\t%s" % [c, k]} * "\n" end end proportions end |
.pull_keys(hash, prefix) ⇒ Object
1133 1134 1135 1136 1137 1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 |
# File 'lib/rbbt/util/misc.rb', line 1133 def self.pull_keys(hash, prefix) new = {} hash.keys.each do |key| if key.to_s =~ /#{ prefix }_(.*)/ case when String === key new[$1] = hash.delete key when Symbol === key new[$1.to_sym] = hash.delete key end else if key.to_s == prefix.to_s new[key] = hash.delete key end end end new end |
.random_sample_in_range(total, size) ⇒ Object
150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 |
# File 'lib/rbbt/util/misc.rb', line 150 def self.random_sample_in_range(total, size) p = Set.new if size > total / 10 template = (0..total - 1).to_a size.times do |i| pos = (rand * (total - i)).floor if pos == template.length - 1 v = template.pop else v, n = template[pos], template[-1] template.pop template[pos] = n end p << v end else size.times do pos = nil while pos.nil? pos = (rand * total).floor if p.include? pos pos = nil end end p << pos end end p end |
.remove_long_items(obj) ⇒ Object
277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 |
# File 'lib/rbbt/util/misc.rb', line 277 def self.remove_long_items(obj) case when TSV === obj remove_long_items((obj.all_fields || []) + obj.keys.sort) when (Array === obj and obj.length > ARRAY_MAX_LENGTH) remove_long_items(obj[0..ARRAY_MAX_LENGTH-2] << "TRUNCATED at #{ ARRAY_MAX_LENGTH } (#{obj.length})") when (Hash === obj and obj.length > ARRAY_MAX_LENGTH) remove_long_items(obj.collect.compact[0..ARRAY_MAX_LENGTH-2] << ["TRUNCATED", "at #{ ARRAY_MAX_LENGTH } (#{obj.length})"]) when (String === obj and obj.length > STRING_MAX_LENGTH) obj[0..STRING_MAX_LENGTH-1] << " TRUNCATED at #{STRING_MAX_LENGTH} (#{obj.length})" when Hash === obj new = {} obj.each do |k,v| new[k] = remove_long_items(v) end new when Array === obj obj.collect do |e| remove_long_items(e) end else obj end end |
.reset_do_once ⇒ Object
796 797 798 |
# File 'lib/rbbt/util/misc.rb', line 796 def self.reset_do_once $__did_once = false end |
.sample(ary, size, replacement = false) ⇒ Object
181 182 183 184 185 186 187 188 189 |
# File 'lib/rbbt/util/misc.rb', line 181 def self.sample(ary, size, replacement = false) if ary.respond_to? :sample ary.sample size else total = ary.length p = random_sample_in_range(total, size) ary.values_at *p end end |
.sanitize_filename(filename, length = 254) ⇒ Object
222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 |
# File 'lib/rbbt/util/misc.rb', line 222 def self.sanitize_filename(filename, length = 254) if filename.length > length if filename =~ /(\..{2,9})$/ extension = $1 else extension = '' end post_fix = "--#{filename.length}@#{length}_#{Misc.digest(filename)[0..4]}" + extension filename = filename[0..(length - post_fix.length - 1)] << post_fix else filename end filename end |
.sd(list) ⇒ Object
353 354 355 356 357 |
# File 'lib/rbbt/util/misc.rb', line 353 def self.sd(list) return nil if list.length < 3 mean = mean(list) Math.sqrt(list.compact.inject(0.0){|acc,e| d = e - mean; acc += d * d}) / (list.compact.length - 1) end |
.send_email(from, to, subject, message, options = {}) ⇒ Object
383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 |
# File 'lib/rbbt/util/misc.rb', line 383 def self.send_email(from, to, subject, , = {}) IndiferentHash.setup() = Misc.add_defaults , :from_alias => nil, :to_alias => nil, :server => 'localhost', :port => 25, :user => nil, :pass => nil, :auth => :login server, port, user, pass, from_alias, to_alias, auth = Misc. , :server, :port, :user, :pass, :from_alias, :to_alias, :auth msg = <<-END_OF_MESSAGE From: #{from_alias} <#{from}> To: #{to_alias} <#{to}> Subject: #{subject} #{} END_OF_MESSAGE Net::SMTP.start(server, port, server, user, pass, auth) do |smtp| smtp. msg, from, to end end |
.sensiblewrite(path, content = nil) ⇒ Object
1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 |
# File 'lib/rbbt/util/misc.rb', line 1020 def self.sensiblewrite(path, content = nil) return if File.exists? path Misc.lock path + '.sensible_write' do if not File.exists? path begin tmp_path = path + '.tmp' content = yield if block_given? case when String === content File.open(tmp_path, 'w') do |f| f.write content end when (IO === content or StringIO === content) File.open(tmp_path, 'w') do |f| while l = content.gets; f.write l; end end else File.open(tmp_path, 'w') do |f| end end FileUtils.mv tmp_path, path rescue Exception FileUtils.rm_f tmp_path if File.exists? tmp_path FileUtils.rm_f path if File.exists? path raise $! end end end end |
.snake_case(string) ⇒ Object
1325 1326 1327 1328 1329 1330 1331 1332 1333 |
# File 'lib/rbbt/util/misc.rb', line 1325 def self.snake_case(string) return nil if string.nil? string = string.to_s if Symbol === string string. gsub(/([A-Z]{2,})([A-Z][a-z])/,'\1_\2'). gsub(/([a-z])([A-Z])/,'\1_\2'). gsub(/\s/,'_').gsub(/[^\w_]/, ''). split("_").collect{|p| p.match(/[A-Z]{2,}/) ? p : p.downcase } * "_" end |
.sorted_array_hits(a1, a2) ⇒ Object
565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 |
# File 'lib/rbbt/util/misc.rb', line 565 def self.sorted_array_hits(a1, a2) e1, e2 = a1.shift, a2.shift counter = 0 match = [] while true break if e1.nil? or e2.nil? case e1 <=> e2 when 0 match << counter e1, e2 = a1.shift, a2.shift counter += 1 when -1 while not e1.nil? and e1 < e2 e1 = a1.shift counter += 1 end when 1 e2 = a2.shift e2 = a2.shift while not e2.nil? and e2 < e1 end end match end |
.string2const(string) ⇒ Object
1153 1154 1155 1156 1157 1158 1159 1160 1161 1162 |
# File 'lib/rbbt/util/misc.rb', line 1153 def self.string2const(string) return nil if string.nil? mod = Kernel string.to_s.split('::').each do |str| mod = mod.const_get str end mod end |
.string2hash(string) ⇒ Object
1210 1211 1212 1213 1214 1215 1216 1217 1218 1219 1220 1221 1222 1223 1224 1225 1226 1227 1228 1229 1230 1231 1232 1233 1234 1235 1236 1237 1238 1239 1240 1241 1242 1243 1244 1245 1246 1247 1248 1249 1250 1251 1252 1253 1254 1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 1265 1266 1267 1268 1269 1270 1271 1272 1273 1274 1275 1276 1277 1278 1279 1280 1281 1282 1283 |
# File 'lib/rbbt/util/misc.rb', line 1210 def self.string2hash(string) = {} string.split('#').each do |str| key, sep, value = str.partition "=" key = key[1..-1].to_sym if key[0] == ":" [key] = true and next if value.empty? [key] = value[1..-1].to_sym and next if value[0] == ":" [key] = Regexp.new(/#{value[1..-2]}/) and next if value[0] == "/" and value[-1] == "/" [key] = value[1..-2] and next if value =~ /^['"].*['"]$/ [key] = value.to_i and next if value =~ /^\d+$/ [key] = value.to_f and next if value =~ /^\d*\.\d+$/ [key] = true and next if value == "true" [key] = false and next if value == "false" [key] = value and next [key] = begin saved_safe = $SAFE $SAFE = 0 eval(value) rescue Exception value ensure $SAFE = saved_safe end end return = {} string.split(/#/).each do |str| if str.match(/(.*)=(.*)/) option, value = $1, $2 else option, value = str, true end option = option.sub(":",'').to_sym if option.chars.first == ':' value = value.sub(":",'').to_sym if String === value and value.chars.first == ':' if value == true [option] = option.to_s.chars.first != '!' else [option] = Thread.start do $SAFE = 0; case when value =~ /^(?:true|T)$/i true when value =~ /^(?:false|F)$/i false when Symbol === value value when (String === value and value =~ /^\/(.*)\/$/) Regexp.new /#{$1}/ else begin Kernel.const_get value rescue begin raise if value =~ /[a-z]/ and defined? value eval(value) rescue Exception value end end end end.value end end end |
.string2hash_old(string) ⇒ Object
1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 1203 1204 1205 1206 1207 1208 |
# File 'lib/rbbt/util/misc.rb', line 1164 def self.string2hash_old(string) = {} string.split(/#/).each do |str| if str.match(/(.*)=(.*)/) option, value = $1, $2 else option, value = str, true end option = option.sub(":",'').to_sym if option.chars.first == ':' value = value.sub(":",'').to_sym if String === value and value.chars.first == ':' if value == true [option] = option.to_s.chars.first != '!' else [option] = Thread.start do $SAFE = 0; case when value =~ /^(?:true|T)$/i true when value =~ /^(?:false|F)$/i false when Symbol === value value when (String === value and value =~ /^\/(.*)\/$/) Regexp.new /#{$1}/ else begin Kernel.const_get value rescue begin raise if value =~ /[a-z]/ and defined? value eval(value) rescue Exception value end end end end.value end end end |
.sum(list) ⇒ Object
345 346 347 |
# File 'lib/rbbt/util/misc.rb', line 345 def self.sum(list) list.compact.inject(0.0){|acc,e| acc += e} end |
.to_utf8(string) ⇒ Object
996 997 998 |
# File 'lib/rbbt/util/misc.rb', line 996 def self.to_utf8(string) string.encode("UTF-16BE", :invalid => :replace, :undef => :replace, :replace => "?").encode('UTF-8') end |
.total_length(ranges) ⇒ Object
146 147 148 |
# File 'lib/rbbt/util/misc.rb', line 146 def self.total_length(ranges) Misc.collapse_ranges(ranges).inject(0) do |total,range| total += range.end - range.begin + 1 end end |
.try3times(&block) ⇒ Object
813 814 815 |
# File 'lib/rbbt/util/misc.rb', line 813 def self.try3times(&block) insist(3, &block) end |
.zip2hash(list1, list2) ⇒ Object
676 677 678 679 680 681 682 |
# File 'lib/rbbt/util/misc.rb', line 676 def self.zip2hash(list1, list2) hash = {} list1.each_with_index do |e,i| hash[e] = list2[i] end hash end |
.zip_fields(array) ⇒ Object
1320 1321 1322 1323 |
# File 'lib/rbbt/util/misc.rb', line 1320 def self.zip_fields(array) return [] if array.empty? array[0].zip(*array[1..-1]) end |