def setup(self, work_dir=None, ccp4i2_xml=None, rvapi_document=None, show_gui=False):
if not pyrvapi or not self.generate_output:
return
title = "AMPLE Results"
logger.debug("Using Andre's Pyrvapi" if API else "COULD NOT FIND Andre's API!")
if rvapi_document:
logger.debug("Restoring document: %s", rvapi_document)
pyrvapi.rvapi_restore_document2(rvapi_document)
self.jsrview_dir = os.path.dirname(rvapi_document)
else:
# Quick hack to init with Andre's stuff - can switch out for Felix's API when done
logger.debug("Starting with xml %s", ccp4i2_xml)
self.jsrview_dir = os.path.join(work_dir, "jsrview")
if not os.path.isdir(self.jsrview_dir):
os.mkdir(self.jsrview_dir)
kwargs = dict(wintitle=title,
reportdir=self.jsrview_dir,
xml=ccp4i2_xml,
abspaths=False,
# bug in jsrview:
# layout = 4 if i1 else 7,
)
API.document.newdoc(**kwargs)
if not self.own_log_tab:
self.log_tab_id = pyrvapi.rvapi_get_meta()
if show_gui:
# We start our own browser
jsrview = os.path.join(os.environ["CCP4"], "libexec", "jsrview")
subprocess.Popen([jsrview, os.path.join(self.jsrview_dir, "index.html")])
return
def setup(self,
work_dir=None,
ccp4i2_xml=None,
rvapi_document=None,
no_gui=None,
own_gui=False):
if not pyrvapi or no_gui: return
report_dir = os.path.join(work_dir, "jsrview")
if not os.path.isdir(report_dir): os.mkdir(report_dir)
docid = "AMPLE_results"
title = "AMPLE Results"
logger.debug(
"Using Andre's Pyrvapi" if API else "COULD NOT FIND Andre's API!")
if API is None:
share_jsrview = os.path.join(os.environ["CCP4"], "share",
"jsrview")
pyrvapi.rvapi_init_document(docid, report_dir, title, 1, 7,
share_jsrview, None, None, None, None)
else:
if rvapi_document:
logger.debug("Restoring document: {0}".format(rvapi_document))
pyrvapi.rvapi_restore_document2(rvapi_document)
else:
# Quick hack to init with Andre's stuff - can switch out for Felix's API when done
logger.debug("Starting with xml {0}".format(ccp4i2_xml))
kwargs = dict(
wintitle=title,
reportdir=report_dir,
xml=ccp4i2_xml,
abspaths=False,
# bug in jsrview:
# layout = 4 if i1 else 7,
)
API.document.newdoc(**kwargs)
if own_gui:
# We start our own browser
jsrview = os.path.join(os.environ["CCP4"], "libexec", "jsrview")
subprocess.Popen([jsrview, os.path.join(report_dir, "index.html")])
return
def restoreReportDocument(self):
#if not os.path.isfile(self.rvapi_doc_path):
# print " *** NO PATH TO RVAPI DOCUMENT"
pyrvapi.rvapi_restore_document2(self.rvapi_doc_path)
return pyrvapi.rvapi_get_meta()
def __init__(self, args=None):
# args = optional replacement for sys.argv to allow this class to be
# called from within other Python programs (such as tests)
rvapi_v = "...................."
pyrvapi.rvapi_version(rvapi_v)
rvapi_v = rvapi_v.split(".")
self.rvapi_version[0] = int(rvapi_v[0])
self.rvapi_version[1] = int(rvapi_v[1])
self.rvapi_version[2] = int(rvapi_v[2].replace("\x00", ""))
self.workdir = os.getcwd()
self.output_meta["retcode"] = ""
self.output_meta["report_row"] = 0
self.output_meta["results"] = {}
self.output_meta["resorder"] = []
self.file_stdout = sys.stdout
self.file_stderr = sys.stderr
# first parse command-line parameters
if args is None:
args = sys.argv[1:]
narg = 0
while narg < len(args):
key = args[narg]
narg += 1
if key == "--sge" or key == "--mp": self.exeType = key
elif key == "--no-simbad12": self.trySimbad12 = False
elif key == "--no-morda": self.tryMoRDa = False
elif key == "--no-crank2": self.tryCrank2 = False
elif key == "--no-fitligands": self.tryFitLigands = False
elif narg < len(args):
value = args[narg]
if key == "--wkdir": self.workdir = value
elif key == "--rdir": self.reportdir = value
elif key == "--outdir": self.outputdir = value
elif key == "--rvapi-prefix": self.rvapi_prefix = value
elif key == "--rvapi-document": self.rvapi_doc_path = value
elif key == "--jobid": self.jobId = value
elif key == "--qname": self.queueName = value
elif key == "--njobs": self.nSubJobs = int(value)
else:
self.output_meta[
"retcode"] = "[01-001] unknown command line parameter"
self.stderr(" *** unrecognised command line parameter " +
key)
narg += 1
# read data from standard input
self.stdout("\n INPUT DATA:" +
"\n -----------------------------------------------")
ilist = sys.stdin.read().splitlines()
for i in range(len(ilist)):
s = ilist[i].strip()
if s.startswith("HKLIN"):
self.hklpath = s.replace("HKLIN", "", 1).strip()
self.stdout("\n HKLIN " + self.hklpath)
elif s.startswith("SEQIN"):
self.seqpath = s.replace("SEQIN", "", 1).strip()
self.stdout("\n SEQIN " + self.seqpath)
elif s.startswith("XYZIN"):
self.xyzpath = s.replace("XYZIN", "", 1).strip()
self.stdout("\n XYZIN " + self.xyzpath)
elif s.startswith("HATOMS"):
self.ha_type = s.replace("HATOMS", "", 1).strip()
self.stdout("\n HATOMS " + self.ha_type)
elif s.startswith("LIGAND"):
lst = filter(None, s.replace("LIGAND", "", 1).split(" "))
self.ligands.append(lst)
self.stdout("\n LIGAND " + lst[0])
if len(lst) > 1:
self.stdout(" " + lst[1])
elif s:
self.output_meta[
"retcode"] = "[01-002] unrecognised input line"
self.stderr(" *** unrecognised input line " + s + "\n")
self.stdout("\n -----------------------------------------------\n")
# initialise work directory structure
self.scriptsdir = os.path.join(self.workdir, "scripts")
if not os.path.isdir(self.scriptsdir):
os.mkdir(self.scriptsdir)
outdir = os.path.join(self.workdir, self.outputdir)
if not os.path.isdir(outdir):
os.mkdir(outdir)
# initialise RVAPI report
self.layout = 4
if self.compare_rvapi_version([1, 0, 15]) <= 0:
self.layout = 0
self.page_cursor = [self.summaryTabId, 0]
if not self.rvapi_doc_path: # initialise rvapi report document
report_type = 1 # report with tabs
if not self.rvapi_prefix or not self.reportdir:
report_type = 0x00100000 # report will not be created
rdir = self.reportdir
if not rdir:
rdir = "report"
rdir = os.path.join(self.workdir,
rdir) # has to be full path because of Crank-2
if not os.path.isdir(rdir):
os.mkdir(rdir)
# initialise HTML report document; note that we use absolute path for
# the report directory, which is necessary for passing RVAPI document
# to applications via creation of the rvapi_document file with
# pyrvapi.rvapi_store_document2(..)
pyrvapi.rvapi_init_document(
"jscofe_report", # document Id
rdir, # report directory
"Title", # title (immaterial)
report_type, # HTML report to be produced
self.layout, # Report will start with plain page
self.rvapi_prefix, # where to look for js support
None,
None,
"task.tsk",
"i2.xml")
if self.layout == 0:
# Add tree widget
pyrvapi.rvapi_add_tree_widget(
self.navTreeId, # tree widget reference (Id)
"Workflow", # tree widget title
"body", # reference to widget holder (grid)
0, # holder row
0, # holder column
1, # row span
1 # column span
)
pyrvapi.rvapi_set_tab_proxy(self.navTreeId, "")
self.page_cursor = self.addTab(self.summaryTabId, "Summary", True)
self.putMessage(
"<h2>CCP4go (Combined Automated Structure Solution)</h2>")
else: # continue rvapi document given
pyrvapi.rvapi_restore_document2(self.rvapi_doc_path)
meta = pyrvapi.rvapi_get_meta()
#self.stdout ( "\n META = " + meta )
if meta:
d = json.loads(meta)
if "jobId" in d: self.jobId = d["jobId"]
if "stageNo" in d: self.stage_no = d["stageNo"]
if "sge_q" in d: self.SGE = True
if "sge_tc" in d: self.nSubJobs = d["sge_tc"]
if "summaryTabId" in d:
self.summaryTabId = d["summaryTabId"]
self.page_cursor[0] = self.summaryTabId
if "summaryTabRow" in d:
self.summaryTabRow = d["summaryTabRow"]
self.page_cursor[1] = self.summaryTabRow
if "navTreeId" in d:
self.navTreeId = d["navTreeId"]
pyrvapi.rvapi_set_tab_proxy(self.navTreeId, "")
if "outputDir" in d: self.outputdir = d["outputDir"]
if "outputName" in d: self.outputname = d["outputName"]
#self.stdout ( "\n summaryTabId = " + self.summaryTabId )
#self.stdout ( "\n summaryTabRow = " + str(self.summaryTabRow) )
#self.stdout ( "\n layout = " + str(self.layout) )
#self.stdout ( "\n navTreeId = " + self.navTreeId + "\n" )
#self.putMessage ( "<h2>YYYYYYYYYYYYYYY</h2>" )
#self.page_cursor = self.addTab ( "new","New",True )
#self.putMessage ( "<h2>ZZZZZZZZZZZZZZZZ</h2>" )
#self.file_stdout.write ( "nSubJobs=" + str(self.nSubJobs) + "\n" )
return
def __init__(self, identifier, html_fname=None, *args, **kwargs):
self._identifier = identifier
self._html_fname = html_fname
pyrvapi.rvapi_restore_document2(self._html_fname)
def __init__(self, rvapi_document, webserver_uri, display_gui, logfile, work_dir, ccp4i2_xml=None, tab_prefix=""):
self.rvapi_document = rvapi_document
self.webserver_uri = webserver_uri
self.display_gui = display_gui
self.logfile = logfile
self.work_dir = work_dir
self.ccp4i2 = bool(ccp4i2_xml)
self.tab_prefix = tab_prefix
self.jsrview_dir = None
self._webserver_start = None
self.log_tab_id = None
self.lattice_results_tab_id = None
self.lattice_df = None
self.contaminant_results_tab_id = None
self.contaminant_df = None
self.morda_db_results_tab_id = None
self.morda_db_df = None
self.summary_tab_id = None
self.summary_tab_results_sec_id = None
self.citation_tab_id = None
self.lattice_search_results_displayed = False
self.contaminant_results_displayed = False
self.morda_results_displayed = False
self.jscofe_mode = False
self.ccp4online_mode = False
self.rhs_tab_id = None
self.rvapi_meta = RvapiMetadata()
if self.display_gui or self.ccp4i2:
ccp4 = os.environ["CCP4"]
share_jsrview = os.path.join(ccp4, "share", "jsrview")
if self.rvapi_document:
pyrvapi.rvapi_restore_document2(rvapi_document)
self.rhs_tab_id = pyrvapi.rvapi_get_meta()
self.jscofe_mode = True
self.jsrview_dir = os.path.dirname(rvapi_document)
else:
self.jsrview_dir = os.path.join(work_dir, SIMBAD_PYRVAPI_SHAREDIR)
os.mkdir(self.jsrview_dir)
wintitle = "SIMBAD Results"
if ccp4i2_xml:
self.init_from_ccp4i2_xml(ccp4i2_xml, self.jsrview_dir, share_jsrview, wintitle)
else:
pyrvapi.rvapi_init_document("SIMBAD_results", self.jsrview_dir, wintitle, 1, 7, share_jsrview, None,
None, None, None)
self.rvapi_document = os.path.join(self.jsrview_dir, "index.html")
if webserver_uri:
self._webserver_start = len(self.jsrview_dir) - 7
self.ccp4online_mode = True
elif not ccp4i2_xml:
# We start our own browser
jsrview = os.path.join(ccp4, "libexec", "jsrview")
subprocess.Popen([jsrview, os.path.join(self.jsrview_dir, "index.html")])
pyrvapi.rvapi_add_header("SIMBAD Results")
if os.path.isfile(logfile) and not self.ccp4i2:
self.create_log_tab(logfile)
pyrvapi.rvapi_flush()
def __init__(self, rvapi_document, webserver_uri, display_gui, logfile, work_dir, ccp4i2_xml=None, tab_prefix=""):
self.rvapi_document = rvapi_document
self.webserver_uri = webserver_uri
self.display_gui = display_gui
self.logfile = logfile
self.work_dir = work_dir
self.ccp4i2 = bool(ccp4i2_xml)
self.tab_prefix = tab_prefix
self.jsrview_dir = None
self._webserver_start = None
self.log_tab_id = None
self.lattice_results_tab_id = None
self.lattice_df = None
self.contaminant_results_tab_id = None
self.contaminant_df = None
self.morda_db_results_tab_id = None
self.morda_db_df = None
self.summary_tab_id = None
self.summary_tab_results_sec_id = None
self.lattice_search_results_displayed = False
self.contaminant_results_displayed = False
self.morda_results_displayed = False
self.jscofe_mode = False
self.rhs_tab_id = None
self.rvapi_meta = RvapiMetadata()
if self.display_gui or self.ccp4i2:
ccp4 = os.environ["CCP4"]
share_jsrview = os.path.join(ccp4, "share", "jsrview")
if self.rvapi_document:
pyrvapi.rvapi_restore_document2(rvapi_document)
self.rhs_tab_id = pyrvapi.rvapi_get_meta()
self.jscofe_mode = True
self.jsrview_dir = os.path.dirname(rvapi_document)
else:
self.jsrview_dir = os.path.join(work_dir, SIMBAD_PYRVAPI_SHAREDIR)
os.mkdir(self.jsrview_dir)
wintitle = "SIMBAD Results"
if ccp4i2_xml:
self.init_from_ccp4i2_xml(ccp4i2_xml, self.jsrview_dir, share_jsrview, wintitle)
else:
pyrvapi.rvapi_init_document("SIMBAD_results", self.jsrview_dir, wintitle, 1, 7, share_jsrview, None,
None, None, None)
self.rvapi_document = os.path.join(self.jsrview_dir, "index.html")
if webserver_uri:
self._webserver_start = len(self.jsrview_dir) + 1
elif not ccp4i2_xml:
# We start our own browser
jsrview = os.path.join(ccp4, "libexec", "jsrview")
subprocess.Popen([jsrview, os.path.join(self.jsrview_dir, "index.html")])
pyrvapi.rvapi_add_header("SIMBAD Results")
if os.path.isfile(logfile) and not self.ccp4i2:
self.create_log_tab(logfile)
pyrvapi.rvapi_flush()