import os, sys, tempfile, shutil, subprocess # ------------------------------------------------------------------------------ class DefMap(dict): def __init__(self, def_path, typed): if os.path.isfile(def_path): if os.access(def_path, os.R_OK): def_file = open(def_path) for line in def_file: if not line.startswith("#"): key, sep, value = line.strip().replace("\t", " ").partition(" ") if sep == " ": if typed: type, sep, value = value.lstrip().partition(" ") if sep == " ": value = value.lstrip() lquote = "" if value.startswith('"'): lquote = '"' elif value.startswith("'"): lquote = "'" rquote = "" if value.endswith('"'): rquote = '"' elif value.endswith("'"): rquote = "'" if lquote == rquote: self[key] = value.strip(lquote) def_file.close() def get_key(self, query): for key, value in self.items(): if query == value: return key for key, value in self.items(): if query == value.strip().replace("/", "\\"): return key def get_viewers(self): if self.has_key("EXPORT_TO_QTRVIEW") and self.has_key("RUN_COOT") and self.has_key("RUN_CCP4MG"): if self["EXPORT_TO_QTRVIEW"]: view_coot = self["RUN_COOT"] if os.path.isabs(view_coot): view_coot = os.path.abspath(view_coot) view_qtmg = self["RUN_CCP4MG"] if os.path.isabs(view_qtmg): view_qtmg = os.path.abspath(view_qtmg) return(view_coot, view_qtmg) # ------------------------------------------------------------------------------ class TmpDir: def __init__(self): self.path = os.path.abspath("report_dir") if not os.path.isdir(self.path): ccp4_scr = os.environ["CCP4_SCR"] if ccp4_scr: if not os.access(ccp4_scr, os.W_OK): ccp4_scr = None try: self.path = tempfile.mkdtemp(suffix="ccp4qtrv", dir=ccp4_scr) except: print "Cannot create or write into temporary directory. Exiting." sys.exit(1) def clear(self): try: shutil.rmtree(self.path) except: print "Cannot remove temporary directory", self.path sys.exit(1) # ------------------------------------------------------------------------------ def from_command_line(log_file_in): log_file_path = os.path.abspath(log_file_in) if not os.path.isfile(log_file_path): print log_file_path, "is not a file. Exiting." sys.exit(1) if not log_file_path.endswith(".log") and not log_file_path.endswith(".txt") : print log_file_path.endswith, "dos not have extension log. Exiting." sys.exit(1) log_dir_path, log_file_name = os.path.split(log_file_path) log_root_name = os.path.splitext(log_file_name)[0] log_root_parts = log_root_name.split("_") if sys.version_info[0] != 2 or sys.version_info[1] < 5: print "Required Python 2.5 or higher. Exiting." sys.exit(1) ccp4path = os.getenv("CCP4") if not ccp4path: print "Environement variable CCP4 is not set. Exiting." sys.exit(1) ccp4path = os.path.abspath(ccp4path) viewer = os.path.join(ccp4path, "qtrview.app", "Contents", "MacOS", "qtrview") if not os.path.isfile(viewer): viewer = os.path.join(ccp4path, "bin", "qtrview") if not os.path.isfile(viewer): viewer = viewer + ".exe" if not os.path.isfile(viewer): print "qtrview is not found at expected location. Exiting." sys.exit(1) if not os.access(viewer, os.X_OK): print viewer, "is not executable. Exiting." sys.exit(1) generator = os.path.join(ccp4path, "share", "ccp4i2", "smartie", "qtrgeneric.py") if not os.path.isfile(generator): print generator, "does not exist. Exiting." sys.exit(1) home_path = os.path.abspath(os.path.expanduser("~")) ddef_file_path = os.path.abspath("directories.def") if not os.path.isfile(ddef_file_path): ddef_file_path = os.path.join(log_dir_path, "CCP4_DATABASE", "directories.def") if not os.path.isfile(ddef_file_path): ddef_file_path = os.path.join(home_path, ".CCP4", "unix", "directories.def") if not os.path.isfile(ddef_file_path): ddef_file_path = os.path.join(home_path, "CCP4", "windows", "directories.def") if not os.path.isfile(ddef_file_path): ddef_file_path = None rep_dir = TmpDir() try: rep_rootname = os.path.join(rep_dir.path, "report") rep_inp_data = list() rep_inp_data.append("PYTHON " + sys.executable) rep_inp_data.append("XRT_GEN " + generator) rep_inp_data.append("LOGFILE " + log_file_path) rep_inp_data.append("REP_DIR " + rep_dir.path) rep_inp_data.append("REP_XRT " + rep_rootname + ".xrt") rep_inp_data.append("REP_XML " + rep_rootname + ".xml") rep_inp_data.append("CLEANUP NO") job_status = None if ddef_file_path: dir_def_map = DefMap(ddef_file_path, True) log_dir_key = dir_def_map.get_key(log_dir_path) if log_dir_key: var_name, var_sep, var_index = log_dir_key.partition(",") if var_sep == "," and var_name == "PROJECT_PATH": project = dir_def_map["PROJECT_ALIAS," + var_index] proj_db_dir = os.path.abspath(dir_def_map["PROJECT_DB," + var_index]) if proj_db_dir: if os.path.isfile(os.path.join(proj_db_dir, log_root_name + ".def")): proj_db_map = DefMap(os.path.join(proj_db_dir, "database.def"), False) if len(log_root_parts) > 1: job_id = log_root_parts[0] if log_file_name == proj_db_map["LOGFILE," + job_id]: job_status = proj_db_map["STATUS," + job_id] if job_status: rep_inp_data.append("JOB_ID " + job_id) rep_inp_data.append("PROJECT " + project) rep_inp_data.append("DIR_DEF " + ddef_file_path) rep_inp_data.append("STATUS " + job_status) if not job_status: rep_inp_data.append("STATUS RUNNING") job_title = None hkl_out_prefix = None if log_root_name == "pointandscale_sca": job_title = "Quick Scale" hkl_out_prefix = "ctruncate_" elif log_root_name == "pointandscale_sym": job_title = "Quick Symmetry" hkl_out_prefix = "pointless_" if hkl_out_prefix: log_file_unit = open(log_file_path) log_file_data = log_file_unit.read().split() log_file_unit.close() hkl_file_list = list() for word in log_file_data: if word.endswith(".mtz"): hkl_file_path = word if not os.path.isabs(word): hkl_file_path = os.path.join(log_dir_path, word) hkl_file_path = os.path.abspath(hkl_file_path) if hkl_file_path not in hkl_file_list: hkl_file_list.append(hkl_file_path) hkl_out_path = None hkl_in_name = None for hkl_file_path in hkl_file_list: hkl_file_name = os.path.split(hkl_file_path)[1] if hkl_file_name.startswith(hkl_out_prefix): hkl_out_path = hkl_file_path hkl_in_name = hkl_file_name.partition("_")[2] hkl_in_path = None for hkl_file_path in hkl_file_list: hkl_file_name = os.path.split(hkl_file_path)[1] if hkl_file_name == hkl_in_name: hkl_in_path = hkl_file_path if hkl_in_path and hkl_out_path: rep_inp_data.append("HKLIN " + hkl_in_path) rep_inp_data.append("HKLOUT " + hkl_out_path) rep_inp_data.append("TITLE " + job_title) else: rep_inp_data.append("TITLE " + log_file_name) conf_viewers = DefMap(os.path.join(log_dir_path, "CCP4_DATABASE", "configure.def"), True).get_viewers() if not conf_viewers: conf_viewers = DefMap(os.path.join(home_path, ".CCP4", "unix", "configure.def"), True).get_viewers() if not conf_viewers: conf_viewers = DefMap(os.path.join(home_path, ".CCP4", "windows", "configure.def"), True).get_viewers() if not conf_viewers: conf_viewers = DefMap(os.path.join(ccp4path, "share", "ccp4i", "etc", "UNIX", "configure.def"), True).get_viewers() if not conf_viewers: conf_viewers = DefMap(os.path.join(ccp4path, "share", "ccp4i", "etc", "WINDOWS", "configure.def"), True).get_viewers() if conf_viewers: rep_inp_data.append("RUN_COOT " + conf_viewers[0]) rep_inp_data.append("RUN_CCP4MG " + conf_viewers[1]) if os.path.exists("nograph"): print "\n".join(rep_inp_data) except: print "Cannot generate input data for QtRView. Exiting." rep_dir.clear() sys.exit(1) try: rep_inp_data.append("") rep_inp_path = rep_rootname + ".inp" rep_inp_unit = open(rep_inp_path, "w") rep_inp_unit.write("\n".join(rep_inp_data)) rep_inp_unit.close() except: print "Cannot write input file for QtRView. Exiting." rep_dir.clear() sys.exit(1) if os.path.exists("nograph"): pass else: try : subprocess.Popen([viewer, "--inp-file", rep_inp_path]).wait() except : print "Cannot launch QtRView. Exiting." rep_dir.clear() sys.exit(1) rep_dir.clear() sys.exit(0) # ------------------------------------------------------------------------------ if __name__ == '__main__': if len(sys.argv) != 2: print "Usage:", sys.argv[0], "log-file" sys.exit(1) from_command_line(sys.argv[1]) # ------------------------------------------------------------------------------