Allow importing phases from XML or CTI strings

include/cantera/base/ctml.h

@@ -785,6 +785,15 @@ void ct2ctml(const char* file, const int debug = 0);
  */
 std::string ct2ctml_string(const std::string& file);
 
+//! Get a string with the ctml representation of a cti input string.
+/*!
+ *  @param   cti    String containing the cti representation
+ *  @return  String containing the xml representation of the input
+ *
+ *  @ingroup inputfiles
+ */
+std::string ct_string2ctml_string(const std::string& cti);
+
 //! Convert a Chemkin-format mechanism into a CTI file.
 /*!
  * @param in_file         input file containing species and reactions

include/cantera/base/global.h

@@ -203,6 +203,9 @@ doublereal actEnergyToSI(const std::string& unit);
 //! @copydoc Application::get_XML_File
 XML_Node* get_XML_File(const std::string& file, int debug = 0);
 
+//! @copydoc Application::get_XML_from_string
+XML_Node* get_XML_from_string(const std::string& text);
+
 //! @copydoc Application::close_XML_File
 void close_XML_File(const std::string& file);
 

interfaces/cython/cantera/_cantera.pxd

@@ -18,6 +18,7 @@ cdef extern from "cantera/base/global.h" namespace "Cantera":
     cdef size_t CxxNpos "Cantera::npos"
     cdef void CxxAppdelete "Cantera::appdelete" ()
     cdef XML_Node* CxxGetXmlFile "Cantera::get_XML_File" (string) except +
+    cdef XML_Node* CxxGetXmlFromString "Cantera::get_XML_from_string" (string) except +
 
 cdef extern from "cantera/thermo/mix_defs.h":
     cdef int thermo_type_ideal_gas "Cantera::cIdealGas"

interfaces/cython/cantera/base.pyx

@@ -1,9 +1,10 @@
 cdef class _SolutionBase:
-    def __cinit__(self, infile='', phaseid='', phases=(), source=None):
+    def __cinit__(self, infile='', phaseid='', phases=(), origin=None,
+                  source=None):
         # Shallow copy of an existing Solution (for slicing support)
         cdef _SolutionBase other
-        if source is not None:
-            other = <_SolutionBase?>source
+        if origin is not None:
+            other = <_SolutionBase?>origin
 
             # keep a reference to the parent to prevent the underlying
             # C++ objects from being deleted
@@ -18,7 +19,12 @@ cdef class _SolutionBase:
             return
 
         # Instantiate a set of new Cantera C++ objects
-        rootNode = CxxGetXmlFile(stringify(infile))
+        if infile:
+            rootNode = CxxGetXmlFile(stringify(infile))
+        elif source:
+            rootNode = CxxGetXmlFromString(stringify(source))
+        else:
+            raise ValueError('No phase definition provided')
 
         # Get XML data
         cdef XML_Node* phaseNode
@@ -58,7 +64,7 @@ cdef class _SolutionBase:
             assert self.transport is not NULL
 
     def __getitem__(self, selection):
-        copy = self.__class__(source=self)
+        copy = self.__class__(origin=self)
         if isinstance(selection, slice):
             selection = range(selection.start or 0,
                               selection.stop or self.n_species,

interfaces/cython/cantera/ctml_writer.py

@@ -2617,21 +2617,30 @@ class Lindemann(object):
 #get_atomic_wts()
 validate()
 
-def convert(filename, outName=None):
-
+def convert(filename=None, outName=None, text=None):
     import os
-    filename = os.path.expanduser(filename)
-    base = os.path.basename(filename)
-    root, _ = os.path.splitext(base)
-    dataset(root)
+    if filename is not None:
+        filename = os.path.expanduser(filename)
+        base = os.path.basename(filename)
+        root, _ = os.path.splitext(base)
+        dataset(root)
+    elif outName is None:
+        outName = 'STDOUT'
+
     try:
-        with open(filename, 'rU') as f:
-            code = compile(f.read(), filename, 'exec')
-            exec(code)
+        if filename is not None:
+            with open(filename, 'rU') as f:
+                code = compile(f.read(), filename, 'exec')
+        else:
+            code = compile(text, '<string>', 'exec')
+        exec(code)
     except SyntaxError as err:
         # Show more context than the default SyntaxError message
         # to help see problems in multi-line statements
-        text = open(filename, 'rU').readlines()
+        if filename:
+            text = open(filename, 'rU').readlines()
+        else:
+            text = text.split('\n')
         _printerr('%s in "%s" on line %i:\n' % (err.__class__.__name__,
                                                 err.filename,
                                                 err.lineno))
@@ -2646,7 +2655,11 @@ def convert(filename, outName=None):
     except Exception as err:
         import traceback
 
-        text = open(filename, 'rU').readlines()
+        if filename:
+            text = open(filename, 'rU').readlines()
+        else:
+            text = text.split('\n')
+            filename = '<string>'
         tb = traceback.extract_tb(sys.exc_info()[2])
         lineno = tb[-1][1]
         if tb[-1][0] == filename:

interfaces/cython/cantera/test/test_thermo.py

@@ -544,6 +544,39 @@ class ImportTest(utilities.CanteraTest):
         gas2 = ct.Solution('../data/air-no-reactions.xml', 'notair')
         self.check(gas2, 'notair', 900, 5*101325, 7, 2)
 
+    def test_import_phase_cti_text(self):
+        cti_def = """
+ideal_gas(name='spam', elements='O H',
+          species='gri30: all',
+          options='skip_undeclared_elements',
+          initial_state=state(temperature=350, pressure=2e6))
+"""
+        gas = ct.Solution(source=cti_def)
+        self.check(gas, 'spam', 350, 2e6, 8, 2)
+
+    def test_import_phase_xml_text(self):
+        xml_def = """
+<?xml version="1.0"?>
+<ctml>
+  <validate reactions="yes" species="yes"/>
+  <phase dim="3" id="spam">
+    <elementArray datasrc="elements.xml">O</elementArray>
+    <speciesArray datasrc="gri30.xml#species_data">all
+      <skip element="undeclared"/>
+    </speciesArray>
+    <state>
+      <temperature units="K">350.0</temperature>
+      <pressure units="Pa">2000000.0</pressure>
+    </state>
+    <thermo model="IdealGas"/>
+    <kinetics model="GasKinetics"/>
+    <transport model="None"/>
+  </phase>
+</ctml>"""
+        gas = ct.Solution(source=xml_def)
+        self.check(gas, 'spam', 350, 2e6, 2, 1)
+
+
     def test_checkReactionBalance(self):
         with self.assertRaises(Exception):
             ct.Solution('../data/h2o2_unbalancedReaction.xml')

src/base/application.cpp

@@ -285,6 +285,26 @@ XML_Node* Application::get_XML_File(const std::string& file, int debug)
     return x;
 }
 
+XML_Node* Application::get_XML_from_string(const std::string& text)
+{
+    ScopedLock xmlLock(xml_mutex);
+    std::pair<XML_Node*, int>& entry = xmlfiles[text];
+    if (entry.first) {
+        // Return existing cached XML tree
+        return entry.first;
+    }
+    std::stringstream s;
+    size_t start = text.find_first_not_of(" \t\r\n");
+    if (text.substr(start,5) == "<?xml") {
+        s << text;
+    } else {
+        s << ctml::ct_string2ctml_string(text);
+    }
+    entry.first = new XML_Node();
+    entry.first->build(s);
+    return entry.first;
+}
+
 void Application::close_XML_File(const std::string& file)
 {
     ScopedLock xmlLock(xml_mutex);

src/base/application.h

@@ -300,6 +300,17 @@ public:
      */
     XML_Node* get_XML_File(const std::string& file, int debug=0) ;
 
+    //! Read a CTI or CTML string and fill up an XML tree.
+    /*!
+     *  Return a pointer to the XML tree corresponding to the specified
+     *  CTI or XML string. If the given string has been processed before,
+     *  the cached XML tree will be returned. Otherwise, the XML tree
+     *  will be generated and stored in the cache.
+     *  @param text    CTI or CTML string
+     *  @return        Root of the corresponding XML tree
+     */
+    XML_Node* get_XML_from_string(const std::string& text);
+
     //! Close an XML File
     /*!
      * Close a file that is opened by this application object

src/base/ct2ctml.cpp

@@ -80,8 +80,17 @@ void ct2ctml(const char* file, const int debug)
     out << xml;
 }
 
-std::string ct2ctml_string(const std::string& file)
+static std::string call_ctml_writer(const std::string& text, bool isfile)
 {
+    std::string file, arg;
+    if (isfile) {
+        file = text;
+        arg = "r'" + text + "'";
+    } else {
+        file = "<string>";
+        arg = "text=r'''" + text + "'''";
+    }
+
 #ifdef HAS_NO_PYTHON
     /*
      *  Section to bomb out if python is not
@@ -109,7 +118,7 @@ std::string ct2ctml_string(const std::string& file)
                     "except ImportError:\n"
                     "    print('sys.path: ' + repr(sys.path) + '\\n', file=sys.stderr)\n"
                     "    raise\n"
-                    "ctml_writer.convert(r'" + file + "', 'STDOUT')\n"
+                    "ctml_writer.convert(" + arg + ", outName='STDOUT')\n"
                     "sys.exit(0)\n");
 
         python.start(pypath(), args.begin(), args.end());
@@ -170,6 +179,15 @@ std::string ct2ctml_string(const std::string& file)
     return python_output;
 }
 
+std::string ct2ctml_string(const std::string& file)
+{
+    return call_ctml_writer(file, true);
+}
+
+std::string ct_string2ctml_string(const std::string& cti)
+{
+    return call_ctml_writer(cti, false);
+}
 
 void ck2cti(const std::string& in_file, const std::string& thermo_file,
             const std::string& transport_file, const std::string& id_tag)

src/base/global.cpp

@@ -118,6 +118,11 @@ XML_Node* get_XML_File(const std::string& file, int debug)
     return xtmp;
 }
 
+XML_Node* get_XML_from_string(const std::string& text)
+{
+    return app()->get_XML_from_string(text);
+}
+
 void close_XML_File(const std::string& file)
 {
     app()->close_XML_File(file) ;