limatix 1.2.6__py3-none-any.whl

limatix/__init__.py

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+import sys
+import os
+import os.path
+
+try:
+    # py2.x
+    from urllib import pathname2url
+    pass
+except ImportError:
+    # py3.x
+    from urllib.request import pathname2url
+    pass
+
+
+class dummy(object):
+    pass
+
+
+pkgpath = sys.modules[dummy.__module__].__file__
+pkgdir=os.path.split(pkgpath)[0]
+
+def getptstepurlpath():
+
+    return [ pathname2url(os.path.join(pkgdir,"pt_steps")) ]
+
+def getchecklisturlpath():
+
+    return [ pathname2url(os.path.join(pkgdir,"limatix_checklists")) ]
+
+
+def getconfigurlpath():
+
+    return [ pathname2url(os.path.join(pkgdir,"limatix_conf")) ]
+
+
+versionpath = os.path.join(pkgdir,"version.txt")
+if os.path.exists(versionpath):
+    versionfh = open(versionpath,"r")
+    __version__=versionfh.read().strip()
+    versionfh.close()
+    pass
+else:
+    __version__="UNINSTALLED"
+    pass
+

limatix/_version.py

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+# file generated by vcs-versioning
+# don't change, don't track in version control
+from __future__ import annotations
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+version: str
+__version__: str
+__version_tuple__: tuple[int | str, ...]
+version_tuple: tuple[int | str, ...]
+commit_id: str | None
+__commit_id__: str | None
+
+__version__ = version = '1.2.6'
+__version_tuple__ = version_tuple = (1, 2, 6)
+
+__commit_id__ = commit_id = 'g986511edd'

limatix/bin/__init__.py

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+

limatix/bin/datacollect2.py

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+#! /usr/bin/env python
+
+import sys
+import os
+import os.path
+import string
+import datetime
+import socket
+
+try:
+    # py2.x
+    from urllib import pathname2url
+    from urllib import url2pathname
+    from urllib import quote
+    from urllib import unquote
+    pass
+except ImportError:
+    # py3.x
+    from urllib.request import pathname2url
+    from urllib.request import url2pathname
+    from urllib.parse import quote
+    from urllib.parse import unquote
+    pass
+
+
+if "--gtk3" in sys.argv or sys.version_info[0] >= 3:  # gtk3
+    import gi
+    gi.require_version('Gtk','3.0')
+    from gi.repository import Gtk as gtk
+    from gi.repository import GObject as gobject
+    pass
+else :  # gtk2
+    import gobject
+    import gtk
+    pass
+
+import subprocess
+
+from limatix import lm_units
+lm_units.units_config("insert_basic_units")
+
+
+
+class dummy(object):
+    pass
+
+## trace symbolic link to find installed directory
+#thisfile=sys.modules[dummy.__module__].__file__
+#if os.path.islink(thisfile):
+#    installedfile=os.readlink(thisfile)
+#    if not os.path.isabs(installedfile):
+#        installedfile=os.path.join(os.path.dirname(thisfile),installedfile)
+#        pass
+#    pass
+#else:
+#    installedfile=thisfile
+#    pass
+
+#installeddir=os.path.dirname(installedfile)
+
+#if os.path.exists(os.path.join(installeddir,"../lib/checklist.py")):
+#    installeddir=os.path.join(installeddir,"../")
+#    pass
+#elif os.path.exists(os.path.join(installeddir,"../gui2/lib/checklist.py")):
+#    installeddir=os.path.join(installeddir,"../gui2")
+#    pass
+
+#installedfile='/usr/local/dataguzzler-2.0.0-beta23-devel/bin/datacollect2'
+#installeddir='/usr/local/dataguzzler-2.0.0-beta23-devel/gui2'
+
+#sys.path.append(installeddir)
+#sys.path.append(os.path.join(installeddir,"lib/"))
+#sys.path.append(os.path.join(installeddir,"steps/"))
+
+
+from limatix.dc_value import numericunitsvalue as numericunitsv
+from limatix.dc_value import stringvalue as stringv
+from limatix.dc_value import hrefvalue as hrefv
+from limatix.dc_value import integervalue as integerv
+from limatix.dc_value import photosvalue as photosv
+from limatix.dc_value import datesetvalue as datesetv
+from limatix.dc_value import accumulatingdatesetvalue as accumulatingdatesetv
+from limatix.dc_value import xmltreevalue as xmltreev
+
+from limatix.dc_dbus_barcode import dc_dbus_barcode
+
+#import dg_io 
+import limatix.paramdb2 as pdb
+from limatix import paramdbfile
+from limatix import dc2_misc
+
+from limatix import checklist
+
+from limatix.dc_gtksupp import build_from_file
+from limatix.dc_gtksupp import dc_initialize_widgets
+from limatix.dc_gtksupp import import_widgets
+from limatix.dc_gtksupp import guistate as create_guistate
+
+from limatix import explogwindow
+
+from limatix import xmldoc
+from limatix import xmlexplog
+from limatix import checklistdb
+
+# from dc_dbus_paramserver import dc_dbus_paramserver
+
+
+# Plan -- 
+# 1. Build global measnum handler, assign each checklist
+#    that either has a save measurement step or 
+#    the done_is_save_measurement flag a measnum on open.
+# 2. Build "expanding date" field to accumulate dates.
+# 3. Add nospecimen <specimen> attribute for checklists
+#    that removes the <specimen> field. 
+# 4. Add step that can be used for both vibrometer settings
+# 5. Add step that clears a set of parameters
+# 6. Make Save DGS or Save Settings turn button green after execution
+
+def main(args=None):
+    if args is None:
+        args=sys.argv
+        pass
+    
+    SingleSpecimen=None
+    positionals=[]
+    cmdline_guis=[]
+    cmdline_plans=[]
+    cmdline_checklists=[]
+    cmdline_configfiles=[]
+    dpdfiles=[]
+    explogfile=None
+    newlog=False
+    parentchecklisturl=None
+    
+    argc=1
+    
+    while argc < len(args):
+        arg=args[argc]
+        
+        if arg=="-m":
+            SingleSpecimen=False
+            pass
+        elif arg=="-s":
+            SingleSpecimen=True
+            pass
+        elif arg=="-f":
+            argc+=1
+            cmdline_configfiles.append(args[argc])
+            pass
+        elif arg=="-g":
+            argc+=1
+            cmdline_guis.append(args[argc])
+            pass
+        elif arg=="-c":
+            argc+=1
+            cmdline_checklists.append(args[argc])
+            pass
+        elif arg=="-p":
+            argc+=1
+            cmdline_plans.append(args[argc])
+            pass
+        elif arg=='-n':
+            newlog=True
+            pass
+        elif arg=="-d":
+            argc+=1
+            dpdfiles.append(args[argc])
+            pass
+        elif arg=='--gtk3':
+            # handled at imports, above
+            pass
+        elif arg=='--parent':
+            # get relative url from xlg file to parent checklist
+            argc+=1
+            parentchecklisturl=args[argc]
+            pass
+        elif arg=='-h' or arg=="--help":
+            print ("""Usage: %s [-s|-m] [-f <config.dcc>]  [-a] <explog.xlg> [-g gui.glade] [-c checklist.chx] [-p plan.plx] ...
+            
+Flags:
+  -s                  Single specimen mode
+  -m                  Multiple specimen mode
+  -n                  Create new experiment log
+  -f <config.dcc>     Open this config file (multiple OK)
+  -g <gui.glade>      Open this gui (multiple OK)
+  -c <checklist.chx>  Open this checklist (multiple OK)
+  -p <plan.plx>       Open this plan (multiple OK)
+  -d <params.dpd>     Open this parameter file (multiple OK)
+  --gtk3
+""" % (args[0]))
+            sys.exit(0)
+            pass
+        elif arg[0]=='-':
+            raise ValueError("Unknown command line switch %s" % (arg))
+        else :
+            positionals.append(arg)
+            pass
+        argc+=1
+        pass
+    
+    if len(positionals) > 1:
+        raise ValueError("Too many positional parameters (see -h for command line help")
+    
+    #if len(positionals) >= 1:
+    #    if os.path.splitext(positionals[0])[1] != ".dcc":
+    #        raise ValueError("First positional parameter %s must be a .dcc file (se#e -h for command line help)" % (positionals[0]))
+    #    configfile=positionals[0]
+    #    pass
+    
+    if len(positionals) == 1:
+        if os.path.splitext(positionals[0])[1] != ".xlg":
+            raise ValueError("First positional parameter %s must be a .xlg file (see -h for command line help)" % (positionals[0]))
+        explogfile=positionals[0]
+        pass
+    
+
+
+    if "gobject" in sys.modules:  # only for GTK2
+        gobject.threads_init()
+        pass
+    
+    import_widgets()
+
+
+    # insert config from dpd files before all other configs. 
+    configfiles=[]
+    guis=[]
+    checklists=[]
+    plans=[]
+    paramupdates=[]
+    
+    for dpdfile in dpdfiles: 
+        (dpdconfigfiles,dpdguis,dpdchxfiles,dpdplans,dpdexplog,dpdparamupdates,dpdSingleSpecimen)=paramdbfile.load_params(dpdfile)
+        configfiles.extend(dpdconfigfiles)
+        guis.extend(dpdguis)
+        checklists.extend(dpdchxfiles)
+        plans.extend(dpdplans)
+        paramupdates.append(dpdparamupdates)
+        
+        if explogfile is None and dpdexplog is not None:
+            explogfile=dpdexplog
+            pass
+        elif explogfile is not None and dpdexplog is not None: 
+            raise ValueError("Multiple experiment logs specified: %s as well as %s in %s" % (explogfile,dpdexplog,dpdfile))
+        
+        if SingleSpecimen is None and dpdSingleSpecimen is not None: 
+            SingleSpecimen=dpdSingleSpecimen
+            pass
+        elif SingleSpecimen is not None and dpdSingleSpecimen is not None:
+            raise ValueError("Single/multiple specimen mode specified multiple times.")
+        
+        pass
+    
+
+    configfiles.extend(cmdline_configfiles)
+    guis.extend(cmdline_guis)
+    checklists.extend(cmdline_checklists)
+    plans.extend(cmdline_plans)
+    
+    
+
+    
+    
+    iohandlers={}   #dg_io.io()
+    
+    paramdb=pdb.paramdb(iohandlers)
+    #if SingleSpecimen is None: # not already set on command line
+    # SingleSpecimen chooser moved to explogwindow.py
+
+
+    # define parameters
+    
+    # parameters that are supposed to go in the summary need to have an adddoc() call in explogwindow.syncexplog. Also see "not synced" in paramdbfile.py
+    # The adddoc() call can also be used to supply a default value which will be 
+    # set only if not read in from the file. 
+    #  and a corresponding remdoc call in explogwindow.unsyncexplog
+
+    # paramdb.addparam("clinfo",stringv)
+    paramdb.addparam("hostname",stringv,build=lambda param: xmldoc.synced(param),non_settable=True)
+    paramdb.addparam("specimen",stringv,build=lambda param: xmldoc.synced(param)) # reset_with_meas_record=not SingleSpecimen)... MonkeyPatched later
+    paramdb.addparam("perfby",stringv,build=lambda param: xmldoc.synced(param))
+    # paramdb.addparam("date",stringv,build=lambda param: xmldoc.synced(param))
+    #paramdb.addparam("date",datesetv,build=lambda param: xmldoc.synced_accumulating_dates(param))
+    paramdb.addparam("date",accumulatingdatesetv,build=lambda param: xmldoc.synced(param))
+    paramdb.addparam("checklists",xmltreev,build=lambda param: xmldoc.synced(param,tag_index_paths_override={"{http://limatix.org/datacollect}checklist":"@{http://www.w3.org/1999/xlink}href"}),hide_from_meas=True)
+    checklistdb.register_paramdb(paramdb,"checklists",None,False)
+    
+    paramdb.addparam("plans",xmltreev,build=lambda param: xmldoc.synced(param,tag_index_paths_override={"{http://limatix.org/datacollect}checklist":"@{http://www.w3.org/1999/xlink}href"}),hide_from_meas=True)
+    checklistdb.register_paramdb(paramdb,"plans",None,True)
+    
+    
+    paramdb.addparam("expnotes",stringv,build=lambda param: xmldoc.synced(param),hide_from_meas=True)
+    paramdb.addparam("goal",stringv,build=lambda param: xmldoc.synced(param),hide_from_meas=True)
+
+    # "dest" is the contextdir for XML data and hrefs within paramdb
+    # EXCEPT when paramdb is being written out to the experiment log.
+    # Will be auto-fixedup because the dcvalue xmlrepr methods will 
+    # convert their context to that of the file they are writing.
+    paramdb.addparam("dest",hrefv,build=lambda param: xmldoc.synced(param),hide_from_meas=True)
+    paramdb.addparam("explogname",stringv,hide_from_meas=True)
+    
+    #paramdb.addparam("nextmeasnum",integerv,build=lambda param: xmldoc.synced(param),hide_from_meas=True)
+    paramdb.addparam("measnum",integerv,build=lambda param: xmldoc.synced(param),hide_from_meas=True)
+    paramdb.addparam("expphotos",photosv,build=lambda param: xmldoc.synced(param),hide_from_meas=True)
+    paramdb.addparam("measphotos",photosv,reset_with_meas_record=True)
+    paramdb.addparam("notes",stringv,build=lambda param: xmldoc.synced(param))  # notes is shared between (the measurement checklist(s) that have done_is_save_measurement set or have a save measurement step) and the experiment log (although notes is not written directly to the experiment log except in a save measurement step)
+
+    # print "Notes value: ", str(type(str(paramdb["notes"].dcvalue)))
+
+    paramdb.addparam("measchecklist",hrefv,reset_with_meas_record=True)
+    
+
+    # auto-set date 
+    if paramdb["date"].dcvalue.isblank():
+        curdate=datetime.date.today()
+        paramdb["date"].requestvalstr_sync(curdate.isoformat())
+        pass
+
+    # auto-set hostname
+    dc2_misc.set_hostname(paramdb)
+    # print str(paramdb["date"].dcvalue)
+    
+    # Connect to dbus (barcode reader)
+    dbuslink=dc_dbus_barcode(paramdb)
+    
+    
+
+    explogwin=explogwindow.explogwindow(os.path.join(os.path.split(explogwindow.__file__)[0],"explogwin.glade"),paramdb,SingleSpecimen)
+    
+    ## Create dbus paramserver
+    #paramserver=dc_dbus_paramserver(paramdb,explogwin.checklists)
+    # paramserver is now created within explogwin.createparamserver() and stored as a member of explogwin
+    
+
+    guistate=create_guistate(iohandlers,paramdb) # can add search directories as additional parameters here [os.path.split(fname)[0]])
+
+    
+    explogwin.dc_gui_init(guistate)
+    
+    confighrefs=[ hrefv(pathname2url(configfile),contexthref=hrefv("./")) for configfile in configfiles ]
+    
+    if len(confighrefs)==0:
+        confighrefs=None
+        pass
+    
+    if explogfile is not None and newlog:
+        #sys.stderr.write("new_explog(%s)\n" % (explogfile))
+        explogwin.new_explog(hrefv(pathname2url(explogfile),contexthref=hrefv("./")),parentchecklisturl=parentchecklisturl,confighrefs=confighrefs)
+        pass
+    elif explogfile is not None and not newlog:
+        #sys.stderr.write("open_explog(%s)\n" % (explogfile))
+        explogwin.open_explog(hrefv(pathname2url(explogfile),contexthref=hrefv("./")),confighrefs=confighrefs)
+        pass
+
+
+    ## load config files
+    #for configfile in configfiles: 
+    #    #sys.stderr.write("datacollect2: Loading config file %s\n" % (configfile))
+    #    confighref=hrefv(pathname2url(configfile))
+    #    explogwin.load_config(confighref)
+    #    pass
+
+
+    # update paramdb entries specified in .dpd file
+    dpdlog=[]
+    for paramupdate in paramupdates:
+        dpdlog.extend(paramdbfile.apply_paramdb_updates(paramupdate,paramdb))
+        pass
+
+    for (paramname,status,val1,val2) in dpdlog:
+        if status=="dangerous":
+            sys.stderr.write("Warning loading %s: Dangerous parameter %s ignored\n" % (dpdfile,paramname))
+            pass
+        elif status=="mismatch":
+            sys.stderr.write("Warning loading %s: Parameter %s request mismatch (requested: %s; actual: %s)\n" % (dpdfile,paramname,str(val1),str(val2)))
+            pass
+        elif status=="error":
+            sys.stderr.write("Warning loading %s: Parameter %s request error (requested: %s)\n" % (dpdfile,paramname,str(val1)))
+            pass
+        elif status!="match":
+            raise ValueError("Unknown status message loading paramdb from %s" % (dpdfile))
+        
+        pass
+    
+
+
+
+
+    if explogwin.explog is not None and explogwin.explog.filehref is not None:
+        for gui in guis:
+            guihref=hrefv(pathname2url(gui),contexthref=hrefv("./"))
+            explogwin.open_gui(guihref)
+            #explogwin.open_gui(gui)
+            pass
+        
+        for checklist in checklists:
+            checklisthref=hrefv(pathname2url(checklist),contexthref=hrefv("./"))
+            
+            explogwin.addtochecklistmenu(checklisthref)
+            explogwin.open_checklist(checklisthref)
+            pass
+    
+        for plan in plans:
+            planhref=hrefv(pathname2url(plan),contexthref=hrefv("./"))
+            explogwin.open_plan(planhref)
+            pass
+        pass
+    elif len(guis) > 0 or len(checklists) > 0 or len(plans) > 0:
+        print("Cannot auto-open gui, checklist, or plan unless experiment log opened.")
+        sys.exit(1)
+        pass
+
+    
+
+    #win=explogwin.getwindow()
+    explogwin.show_all()
+    gtk.main()
+    pass