# HG changeset patch # User brenninc # Date 1458748610 14400 # Node ID 25b07ce180d47c897167039ae701c8c1b9c4e20d Uploaded first version diff -r 000000000000 -r 25b07ce180d4 README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Wed Mar 23 11:56:50 2016 -0400 @@ -0,0 +1,32 @@ +This tool will lookup files on the Galaxy server machine, including mounted directories. + +The user aspects of the tool are explained in the help section of data_reader.xml + +Only directories that are included in the white list and not in the black list are allowed. + +The white and black lists can be changed without the requirement to restart the server as these are read from the tools install directory each time the tool is run. + +==== + +The white list is tool-data/white-list.ini + +Any directory that starts with any entry from this file will be considered to have passed. + +The default file includes a single / so all absolute paths will pass. + +==== + +The black list is tool-data/black-list.ini + +Any directory that contains any of the blacklisted strings anywhere in the path are excluded. + +The default file excludes most of the standard linux systems directories where data is unlikely to be found. + +It also excludes the /galaxy/ pattern to avoid users getting access to galaxy files. + +Also .. and ~ are excluded for security reasons. + + + + + diff -r 000000000000 -r 25b07ce180d4 data_reader.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_reader.xml Wed Mar 23 11:56:50 2016 -0400 @@ -0,0 +1,424 @@ + + Reads a particular data type from a directory on the server + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (results['required'] == 'data') + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r 25b07ce180d4 directory_copier.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/directory_copier.py Wed Mar 23 11:56:50 2016 -0400 @@ -0,0 +1,138 @@ +import gzip +import optparse # using optparse as hydra still python 2.6 +import os.path +import shutil +import sys + +def report_error(*args): + sys.stderr.write(' '.join(map(str,args)) + '\n') + sys.stderr.flush() + sys.exit(1) + + +def get_tool_data(name): + root_dir = os.path.dirname((os.path.realpath(__file__))) + path = os.path.join(root_dir,"tool-data",name) + if not(os.path.isfile(path)): + report_error(name,"file not found in tool's tool-data folder. Please ask you galaxy admin to add it back") + return path + + +def check_white_list(path_to_check): + white_list = get_tool_data("white-list.ini") + with open(white_list, 'r') as white_list_file: + for line in white_list_file: + line = line.strip() + if len(line) >= 1 and path_to_check.startswith(line): + return True + report_error(path_to_check,"has not been included in the white list. Please contact the local galaxy admin to add it.") + + +def check_black_list(path_to_check): + black_list = get_tool_data("black-list.ini") + with open(black_list, 'r') as black_list_file: + for line in black_list_file: + line = line.strip() + if len(line) >= 1 and line in path_to_check: + report_error(line,"has been black list so",path_to_check,"is not allowed. Please contact the local galaxy admin to change that, or add a symlink.") + return True + + +def check_pattern_get_new_name(a_file, ending, options): + if options.start: + if not(a_file.startswith(options.start)): + return None + if options.last: + if ending[0] == ".": + last = options.last + ending + else: + if options.last[-1] == ".": + last = options.last + ending + else: + last = options.last + "." + ending + if not(a_file.endswith(last)): + return None + if options.new_ending: + name = a_file[:-len(ending)] + if options.new_ending[0] ==".": + if name[-1] == ".": + name = name[:-1] + return name + options.new_ending + if options.decompress: + if a_file.endswith(".gz"): + return a_file[:-3] + return a_file + + +def check_and_get_new_name(a_file, options): + for ending in options.endings: + if a_file.endswith(ending): + return check_pattern_get_new_name (a_file, ending, options) + return None + + +def link(a_file, new_name, path): + file_path = os.path.join(os.path.realpath(path), a_file) + sym_path = os.path.join(os.path.realpath("output"), new_name) + #if not(os.path.exists(sym_path)): + os.link(file_path, sym_path) + + +def decompress(a_file, new_name, path): + file_path = os.path.join(os.path.realpath(path), a_file) + target_path = os.path.join(os.path.realpath("output"), new_name) + with gzip.open(file_path, 'rb') as f_in, open(target_path, 'wb') as f_out: + shutil.copyfileobj(f_in, f_out) + + +def copy_and_link(path, options): + os.mkdir("output") + with open(options.list, 'w') as list_file: + files = os.listdir(path) + files.sort() + for a_file in files: + new_name = check_and_get_new_name(a_file, options) + if new_name: + list_file.write(new_name) + list_file.write("\n") + if options.decompress: + if a_file.endswith(".gz"): + decompress(a_file, new_name,path) + else: + link(a_file, new_name, path) + elif options.link: + link(a_file, new_name, path) + + +if __name__ == '__main__': + parser = optparse.OptionParser() + parser.add_option("--path", action="store", type="string", + help="Path of directory to check. ") + parser.add_option("--ending", action="append", type="string", dest="endings", + help="Ending that can be listed and if requested linked or decompressed. ") + parser.add_option("--start", action="store", type="string", + help="String that must be at the start of the file name ") + parser.add_option("--last", action="store", type="string", + help="String that must be the last bit of the file name before the endings") + parser.add_option("--new_ending", action="store", type="string", + help="New ending to replace any previous ending in list and if required links or decompressions. Note: If not set decompression will auto remove the compressioned part of the ending") + #parser.add_option("--regex", action="store", type="string", + # help="Regex pattern the file name (less . ending) must match before the endings") + parser.add_option("--list", action="store", type="string", + help="Path to where all files should be listed. ") + parser.add_option("--link", action="store_true", default=False, + help="If set will cause links to be added in output directory. ") + parser.add_option("--decompress", action="store_true", default=False, + help="If set will cause gz files to be decompressed or if not a supported decompression ending linked.") + (options, args) = parser.parse_args() + + + path = options.path.strip() + if path[-1] != '/': + path = path + "/" + check_white_list(path) + print path, "white listed" + check_black_list(path) + print path, "not black listed" + copy_and_link(path, options) + diff -r 000000000000 -r 25b07ce180d4 test-data/other.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/other.csv Wed Mar 23 11:56:50 2016 -0400 @@ -0,0 +1,18 @@ +A,top,line,with,fluff,across,many,columns +more,,,,,,, +stuff,,,,,,, +in,,,,,,, +several,,,,,,, +lines,,,,,,, +then blanks,,,,,,, +,,,,,,, +,,,,,,, +An,the,the,more,the,more,, +unimportant,x,y,unimportant,value,more,, +column,axis,axis,stuff,column,fluff,, +asas,alpha,foo,23,2,999,, +dad,alpha,bar,21,3,23,, +sd,beta,foo,21,999,34,, +wwd,gamma,foo,34,3,999,, +sd,gamma,bar,32,5,23,, +sdee,beta,bar,323,5,23,, diff -r 000000000000 -r 25b07ce180d4 test-data/other.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/other.fa Wed Mar 23 11:56:50 2016 -0400 @@ -0,0 +1,7 @@ +@SRR566546.970 HWUSI-EAS1673_11067_FC7070M:4:1:2299:1109 length=50 +TTGCCTGCCTATCATTTTAGTGCCTGTGAGGTGGAGATGTGAGGATCAGT +@SRR566546.971 HWUSI-EAS1673_11067_FC7070M:4:1:2374:1108 length=50 +GATTTGTATGAAAGTATACAACTAAAACTGCAGGTGGATCAGAGTAAGTC +@SRR566546.972 HWUSI-EAS1673_11067_FC7070M:4:1:2438:1109 length=50 +TGCATGATCTTCAGTGCCAGGACCTTATCAAGCGGTTTGGTCCCTTTGTT + diff -r 000000000000 -r 25b07ce180d4 test-data/other.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/other.fasta Wed Mar 23 11:56:50 2016 -0400 @@ -0,0 +1,7 @@ +@SRR566546.970 HWUSI-EAS1673_11067_FC7070M:4:1:2299:1109 length=50 +TTGCCTGCCTATCATTTTAGTGCCTGTGAGGTGGAGATGTGAGGATCAGT +@SRR566546.971 HWUSI-EAS1673_11067_FC7070M:4:1:2374:1108 length=50 +GATTTGTATGAAAGTATACAACTAAAACTGCAGGTGGATCAGAGTAAGTC +@SRR566546.972 HWUSI-EAS1673_11067_FC7070M:4:1:2438:1109 length=50 +TGCATGATCTTCAGTGCCAGGACCTTATCAAGCGGTTTGGTCCCTTTGTT + diff -r 000000000000 -r 25b07ce180d4 test-data/other.fasta.gz Binary file test-data/other.fasta.gz has changed diff -r 000000000000 -r 25b07ce180d4 test-data/sample1.bmp Binary file test-data/sample1.bmp has changed diff -r 000000000000 -r 25b07ce180d4 test-data/sample1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample1.csv Wed Mar 23 11:56:50 2016 -0400 @@ -0,0 +1,18 @@ +A,top,line,with,fluff,across,many,columns +more,,,,,,, +stuff,,,,,,, +in,,,,,,, +several,,,,,,, +lines,,,,,,, +then blanks,,,,,,, +,,,,,,, +,,,,,,, +An,the,the,more,the,more,, +unimportant,x,y,unimportant,value,more,, +column,axis,axis,stuff,column,fluff,, +asas,alpha,foo,23,2,999,, +dad,alpha,bar,21,3,23,, +sd,beta,foo,21,999,34,, +wwd,gamma,foo,34,3,999,, +sd,gamma,bar,32,5,23,, +sdee,beta,bar,323,5,23,, diff -r 000000000000 -r 25b07ce180d4 test-data/sample1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample1.fa Wed Mar 23 11:56:50 2016 -0400 @@ -0,0 +1,7 @@ +@SRR566546.970 HWUSI-EAS1673_11067_FC7070M:4:1:2299:1109 length=50 +TTGCCTGCCTATCATTTTAGTGCCTGTGAGGTGGAGATGTGAGGATCAGT +@SRR566546.971 HWUSI-EAS1673_11067_FC7070M:4:1:2374:1108 length=50 +GATTTGTATGAAAGTATACAACTAAAACTGCAGGTGGATCAGAGTAAGTC +@SRR566546.972 HWUSI-EAS1673_11067_FC7070M:4:1:2438:1109 length=50 +TGCATGATCTTCAGTGCCAGGACCTTATCAAGCGGTTTGGTCCCTTTGTT + diff -r 000000000000 -r 25b07ce180d4 test-data/sample1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample1.fasta Wed Mar 23 11:56:50 2016 -0400 @@ -0,0 +1,7 @@ +@SRR566546.970 HWUSI-EAS1673_11067_FC7070M:4:1:2299:1109 length=50 +TTGCCTGCCTATCATTTTAGTGCCTGTGAGGTGGAGATGTGAGGATCAGT +@SRR566546.971 HWUSI-EAS1673_11067_FC7070M:4:1:2374:1108 length=50 +GATTTGTATGAAAGTATACAACTAAAACTGCAGGTGGATCAGAGTAAGTC +@SRR566546.972 HWUSI-EAS1673_11067_FC7070M:4:1:2438:1109 length=50 +TGCATGATCTTCAGTGCCAGGACCTTATCAAGCGGTTTGGTCCCTTTGTT + diff -r 000000000000 -r 25b07ce180d4 test-data/sample1.fasta.gz Binary file test-data/sample1.fasta.gz has changed diff -r 000000000000 -r 25b07ce180d4 test-data/sample1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample1.fastq Wed Mar 23 11:56:50 2016 -0400 @@ -0,0 +1,12 @@ +@SRR566546.970 HWUSI-EAS1673_11067_FC7070M:4:1:2299:1109 length=50 +TTGCCTGCCTATCATTTTAGTGCCTGTGAGGTGGAGATGTGAGGATCAGT ++SRR566546.970 HWUSI-EAS1673_11067_FC7070M:4:1:2299:1109 length=50 +hhhhhhhhhhghhghhhhhfhhhhhfffffe`ee[`X]b[d[ed`[Y[^Y +@SRR566546.971 HWUSI-EAS1673_11067_FC7070M:4:1:2374:1108 length=50 +GATTTGTATGAAAGTATACAACTAAAACTGCAGGTGGATCAGAGTAAGTC ++SRR566546.971 HWUSI-EAS1673_11067_FC7070M:4:1:2374:1108 length=50 +hhhhgfhhcghghggfcffdhfehhhhcehdchhdhahehffffde`bVd +@SRR566546.972 HWUSI-EAS1673_11067_FC7070M:4:1:2438:1109 length=50 +TGCATGATCTTCAGTGCCAGGACCTTATCAAGCGGTTTGGTCCCTTTGTT ++SRR566546.972 HWUSI-EAS1673_11067_FC7070M:4:1:2438:1109 length=50 +dhhhgchhhghhhfhhhhhdhhhhehhghfhhhchfddffcffafhfghe diff -r 000000000000 -r 25b07ce180d4 test-data/sample1.fastq.gz Binary file test-data/sample1.fastq.gz has changed diff -r 000000000000 -r 25b07ce180d4 test-data/sample1.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample1.fq Wed Mar 23 11:56:50 2016 -0400 @@ -0,0 +1,12 @@ +@SRR566546.970 HWUSI-EAS1673_11067_FC7070M:4:1:2299:1109 length=50 +TTGCCTGCCTATCATTTTAGTGCCTGTGAGGTGGAGATGTGAGGATCAGT ++SRR566546.970 HWUSI-EAS1673_11067_FC7070M:4:1:2299:1109 length=50 +hhhhhhhhhhghhghhhhhfhhhhhfffffe`ee[`X]b[d[ed`[Y[^Y +@SRR566546.971 HWUSI-EAS1673_11067_FC7070M:4:1:2374:1108 length=50 +GATTTGTATGAAAGTATACAACTAAAACTGCAGGTGGATCAGAGTAAGTC ++SRR566546.971 HWUSI-EAS1673_11067_FC7070M:4:1:2374:1108 length=50 +hhhhgfhhcghghggfcffdhfehhhhcehdchhdhahehffffde`bVd +@SRR566546.972 HWUSI-EAS1673_11067_FC7070M:4:1:2438:1109 length=50 +TGCATGATCTTCAGTGCCAGGACCTTATCAAGCGGTTTGGTCCCTTTGTT ++SRR566546.972 HWUSI-EAS1673_11067_FC7070M:4:1:2438:1109 length=50 +dhhhgchhhghhhfhhhhhdhhhhehhghfhhhchfddffcffafhfghe diff -r 000000000000 -r 25b07ce180d4 test-data/sample1.jpeg Binary file test-data/sample1.jpeg has changed diff -r 000000000000 -r 25b07ce180d4 test-data/sample1.jpg Binary file test-data/sample1.jpg has changed diff -r 000000000000 -r 25b07ce180d4 test-data/sample1.png Binary file test-data/sample1.png has changed diff -r 000000000000 -r 25b07ce180d4 test-data/sample1.ps --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample1.ps Wed Mar 23 11:56:50 2016 -0400 @@ -0,0 +1,284 @@ +%!PS-Adobe-3.0 EPSF-3.0 +%%DocumentNeededResources: font Helvetica +%%+ font Helvetica-Bold +%%+ font Helvetica-Oblique +%%+ font Helvetica-BoldOblique +%%+ font Symbol +%%Title: R Graphics Output +%%Creator: R Software +%%Pages: (atend) +%%BoundingBox: 0 0 720 720 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1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * +r003 0 ref 9 30 5H6M * 0 0 AGCTAA * +r004 0 ref 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * +r003 16 ref 29 30 6H5M * 0 0 TAGGC * +r001 83 ref 37 30 9M = 7 -39 CAGCGCCAT * +x1 0 ref2 1 30 20M * 0 0 aggttttataaaacaaataa ???????????????????? +x2 0 ref2 2 30 21M * 0 0 ggttttataaaacaaataatt ????????????????????? +x3 0 ref2 6 30 9M4I13M * 0 0 ttataaaacAAATaattaagtctaca ?????????????????????????? +x4 0 ref2 10 30 25M * 0 0 CaaaTaattaagtctacagagcaac ????????????????????????? +x5 0 ref2 12 30 24M * 0 0 aaTaattaagtctacagagcaact ???????????????????????? +x6 0 ref2 14 30 23M * 0 0 Taattaagtctacagagcaacta ??????????????????????? diff -r 000000000000 -r 25b07ce180d4 test-data/sample1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample1.tabular Wed Mar 23 11:56:50 2016 -0400 @@ -0,0 +1,7 @@ +An_unimportant_column the_x_axis the_y_axis stuff the_value_column more_more_fluff +13 asas alpha foo 23 2 999 +14 dad alpha bar 21 3 23 +15 sd beta foo 21 999 34 +16 wwd gamma foo 34 3 999 +17 sd gamma bar 32 5 23 +18 sdee beta bar 323 5 23 diff -r 000000000000 -r 25b07ce180d4 test-data/sample1.text --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample1.text Wed Mar 23 11:56:50 2016 -0400 @@ -0,0 +1,1 @@ +text1 diff -r 000000000000 -r 25b07ce180d4 test-data/sample1.tiff Binary file test-data/sample1.tiff has changed diff -r 000000000000 -r 25b07ce180d4 test-data/sample1.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample1.tsv Wed Mar 23 11:56:50 2016 -0400 @@ -0,0 +1,7 @@ +An_unimportant_column the_x_axis the_y_axis stuff the_value_column more_more_fluff +13 asas alpha foo 23 2 999 +14 dad alpha bar 21 3 23 +15 sd beta foo 21 999 34 +16 wwd gamma foo 34 3 999 +17 sd gamma bar 32 5 23 +18 sdee beta bar 323 5 23 diff -r 000000000000 -r 25b07ce180d4 test-data/sample1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample1.txt Wed Mar 23 11:56:50 2016 -0400 @@ -0,0 +1,1 @@ +1 diff -r 000000000000 -r 25b07ce180d4 test-data/sample1.xls Binary file test-data/sample1.xls has changed diff -r 000000000000 -r 25b07ce180d4 test-data/sample1.xlsx Binary file test-data/sample1.xlsx has changed diff -r 000000000000 -r 25b07ce180d4 test-data/sample2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample2.txt Wed Mar 23 11:56:50 2016 -0400 @@ -0,0 +1,1 @@ +2 diff -r 000000000000 -r 25b07ce180d4 tool-data/black-list.ini --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/black-list.ini Wed Mar 23 11:56:50 2016 -0400 @@ -0,0 +1,24 @@ +# This file only works if saved as {tool}/tool-data/black_list.ini +# It may be empty but it must exists + +# Parts of paths that will be blocked even if whitelisted. +# so for example /usr/home/galaxy/ will be blocked if /galaxy/ if nlisted here + +/bin/ +/boot/ +/dev/ +/galaxy/ +/lib/ +/lib32/ +/lib64/ +/media/ +/opt/ +/root/ +/run/ +/sbin/ +/srv/ +/sys/ +/var/ +/usr/ +.. +~ diff -r 000000000000 -r 25b07ce180d4 tool-data/white-list.ini --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/white-list.ini Wed Mar 23 11:56:50 2016 -0400 @@ -0,0 +1,15 @@ +# This file only works if saved as {tool}/tool-data/white_list.ini + +# Start of paths that will be accepted by the directory reader +# No jokers including * currently supported. +# Even files listed here will be checked against the black list + +# To accept all paths just keep line with a single slash +/ + +# Add directories absolulute for example +/home/joe_blog/galaxy_data + +# relative test_data as it only make sense for planemo tests +test-data/ +