Mercurial > repos > geert-vandeweyer > files_to_ftp
annotate DownloadFiles.py @ 3:fe42761670f1 draft default tip
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| author | geert-vandeweyer |
|---|---|
| date | Tue, 25 Mar 2014 13:15:25 -0400 |
| parents | 837fafa672d2 |
| children |
| rev | line source |
|---|---|
| 1 | 1 #!/usr/bin/env python |
| 2 #by Geert Vandeweyer. | |
| 3 | |
| 4 #from galaxy import eggs | |
| 5 import sys, os | |
| 6 import os.path | |
| 7 import datetime | |
| 8 | |
| 9 def stop_err(msg): | |
| 10 sys.stderr.write(msg) | |
| 11 sys.exit() | |
| 12 | |
| 13 def __main__(): | |
| 14 htmloutfile = sys.argv[1] | |
| 15 useremail = sys.argv[2] | |
| 16 folder = sys.argv[3] | |
| 17 ftpdirconfig = sys.argv[4] | |
| 18 try: | |
| 19 fout = open(sys.argv[1],'w') | |
| 20 except: | |
| 21 stop_err("Output file cannot be opened for writing.") | |
| 22 | |
| 23 if len(sys.argv) < 5: | |
| 24 stop_err("No datafiles specified!"); | |
| 25 | |
| 26 # write header to outfile | |
| 27 fout.write("<html><body><h2>Files copied to your FTP account.</h2>") | |
| 28 filecounter = 5 | |
| 29 fout.write("<p><ol> ") | |
| 30 now = datetime.datetime.now() | |
| 31 date=str(now)[:10] | |
|
2
837fafa672d2
common uncompressed files are now gzipped upons transfer to the ftp directory to save space.
geert-vandeweyer
parents:
1
diff
changeset
|
32 #fout.write("<li>%s</li>" %(len(sys.argv))) |
| 1 | 33 # compose ftp storage location |
| 34 ftpdir="%s/%s/" %(ftpdirconfig,useremail) | |
| 35 if len(folder) == 0: | |
| 36 subdir = date | |
| 37 storedir="%s/%s/%s/" %(ftpdirconfig,useremail,date) | |
| 38 else: | |
| 39 storedir="%s/%s/%s/" %(ftpdirconfig,useremail,folder) | |
| 40 subdir = folder | |
| 41 if not os.path.exists(ftpdir): | |
| 3 | 42 try: |
| 43 os.makedirs(ftpdir) | |
| 44 except: | |
| 45 stop_err("User dir on FTP could not be created: %s" % (ftpdir)) | |
| 1 | 46 if not os.path.exists(storedir): |
| 3 | 47 |
| 48 try: | |
| 49 os.makedirs(storedir) | |
| 50 except: | |
| 51 stop_err("Target dir could not be created: %s" % (storedir)) | |
| 1 | 52 |
| 53 while filecounter < len(sys.argv): | |
| 54 inp = sys.argv[filecounter] | |
| 55 name = sys.argv[(filecounter+1)] | |
|
2
837fafa672d2
common uncompressed files are now gzipped upons transfer to the ftp directory to save space.
geert-vandeweyer
parents:
1
diff
changeset
|
56 name = name.replace(':','_') |
|
837fafa672d2
common uncompressed files are now gzipped upons transfer to the ftp directory to save space.
geert-vandeweyer
parents:
1
diff
changeset
|
57 name = name.replace(' ','_') |
|
837fafa672d2
common uncompressed files are now gzipped upons transfer to the ftp directory to save space.
geert-vandeweyer
parents:
1
diff
changeset
|
58 name = name.replace('@','_AT_') |
| 1 | 59 ext = sys.argv[(filecounter+2)] |
| 60 # copy files to tmp dir & filenames | |
| 3 | 61 try: |
| 62 os.system("cp '%s' '%s/%s.%s'" %(inp, storedir,name,ext)) | |
| 63 except: | |
| 64 stop_err("Copy failed for target file : %s/%s.%s. Command was\ncp '%s' '%s/%s.%s'" % (storedir,name,ext,inp,storedir,name,ext)) | |
|
2
837fafa672d2
common uncompressed files are now gzipped upons transfer to the ftp directory to save space.
geert-vandeweyer
parents:
1
diff
changeset
|
65 ## gzip if fastq/fastqsanger/vcf |
|
837fafa672d2
common uncompressed files are now gzipped upons transfer to the ftp directory to save space.
geert-vandeweyer
parents:
1
diff
changeset
|
66 if ( ext == "fastq" or ext == "fastqsanger" or ext == "vcf" or ext == "sam" or ext == "txt"): |
| 3 | 67 try: |
| 68 os.system("gzip -9 '%s/%s.%s'" %(storedir,name,ext)) | |
| 69 except: | |
| 70 stop_err("Compression of %s/%s.%s failed." % (storedir,name,ext)) | |
| 1 | 71 fout.write("<li>%s.%s</li>" %(name,ext)) |
| 72 filecounter +=3 | |
| 73 | |
| 74 fout.write("</ol></p>") | |
| 75 fout.write("<p>Info: Files written to the '%s' subdirectory in your FTP account</p></body></html>" %(subdir)) | |
| 76 # close file | |
| 77 fout.close | |
| 78 | |
| 79 | |
| 80 if __name__ == "__main__": __main__() | |
| 81 |