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1 #!/usr/bin/python
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2 from datetime import datetime, timedelta
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3 from io import BytesIO as BIO
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4 import logging
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5 import os
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6 import subprocess
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7 import tarfile
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8 import time
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9 from watchdog.observers import Observer
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10 from watchdog.events import FileSystemEventHandler
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11 from watchdog.events import PatternMatchingEventHandler
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12
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13 class ToolHandler(PatternMatchingEventHandler):
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14
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15 def __init__(self, watchme):
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16 PatternMatchingEventHandler.__init__(self, patterns=['*.xml'],
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17 ignore_directories=False, case_sensitive=False)
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18 self.last_modified = datetime.now()
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19 self.tool_dir = watchme
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20 self.work_dir = os.getcwd()
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21 self.galaxy_root = os.path.split(watchme)[0]
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22 logging.info(self.galaxy_root)
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23 self.tar_dir = os.path.join(self.galaxy_root, 'tooltardir')
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24 if not os.path.exists(self.tar_dir):
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25 os.mkdir(self.tar_dir)
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26
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27 def on_created(self, event):
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28 self.on_modified(event)
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29
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30 def on_modified(self, event):
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31 if datetime.now() - self.last_modified < timedelta(seconds=1):
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32 return
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33 else:
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34 if os.path.exists(event.src_path):
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35 self.last_modified = datetime.now()
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36 logging.info(f"{event.src_path} was {event.event_type}")
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37 p = self.planemo_test(event.src_path)
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38 if p:
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39 if p.returncode == 0:
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40 newtarpath = self.makeToolTar(event.src_path)
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41 logging.info('### Tested toolshed tarball %s written' % newtarpath)
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42 else:
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43 logging.debug('### planemo stdout:')
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44 logging.debug(p.stdout)
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45 logging.debug('### planemo stderr:')
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46 logging.debug(p.stderr)
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47 logging.info('### Planemo call return code =' % p.returncode)
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48 else:
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49 logging.info('Directory %s deleted' % event.src_path)
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50
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51 def planemo_test(self, xml_path):
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52 toolpath, toolfile = os.path.split(xml_path)
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53 dirlist = os.listdir(toolpath)
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54 toolname = os.path.basename(toolpath)
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55 logging.info('### test dirlist %s, path %s toolname %s' % (dirlist, xml_path, toolname))
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56 xmls = [x for x in dirlist if os.path.splitext(x)[1] == '.xml']
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57 if not len(xmls) > 0:
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58 logging.warning('Found no xml files after change to %s' % xml_path)
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59 return None
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60 tool_test_output = os.path.join(toolpath, f"{toolname}_planemo_test_report.html")
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61 cll = [
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62 "planemo",
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63 "test",
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64 "--test_output",
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65 tool_test_output,
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66 "--galaxy_root",
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67 self.galaxy_root,
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68 "--update_test_data",
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69 xml_path,
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70 ]
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71 logging.info('### calling %s' % ' '.join(cll))
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72 p = subprocess.run(
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73 cll,
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74 cwd = toolpath,
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75 shell=False,
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76 capture_output=True,
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77 encoding='utf8',
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78 )
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79 return p
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80
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81 def makeToolTar(self, xml_path):
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82 """move outputs into test-data and prepare the tarball"""
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83 excludeme = "_planemo_test_report.html"
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84
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85 def exclude_function(tarinfo):
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86 filename = tarinfo.name
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87 return None if filename.endswith(excludeme) else tarinfo
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88
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89 tooldir, xml_file = os.path.split(xml_path)
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90 os.chdir(self.tool_dir)
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91 toolname = os.path.splitext(xml_file)[0]
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92 newtarpath = os.path.join(self.tar_dir, '%s_toolshed.gz' % toolname)
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93 tf = tarfile.open(newtarpath, "w:gz")
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94 tf.add(
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95 name=toolname,
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96 arcname=toolname,
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97 filter=exclude_function,
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98 )
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99 tf.close()
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100 os.chdir(self.work_dir)
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101 return newtarpath
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102
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103
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104 if __name__ == "__main__":
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105 watchme = '/home/ross/gal21/tools'
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106 logging.basicConfig(level=logging.INFO,
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107 #filename = os.path.join(watchme,"toolwatcher.log")
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108 #filemode = "w",
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109 format='%(asctime)s - %(message)s',
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110 datefmt='%Y-%m-%d %H:%M:%S')
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111 event_handler = ToolHandler(watchme=watchme)
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112 observer = Observer()
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113 observer.schedule(event_handler, path=watchme, recursive=True)
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114 observer.start()
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115 try:
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116 while True:
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117 time.sleep(1)
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118 except KeyboardInterrupt:
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119 observer.stop()
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120 observer.join()
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121
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122
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123
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