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Implement the two deprecations that were planned for the 2020.09 release cycle (#3047)

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* Deprecation: planned removal of .message() and .getMessage() methods

* Deprecation: planned removal of old MolHash code

* document deprecations

* output the diffs when the psql tests fail

* remove .message() from SWIG wrappers

note that the KeyError doesn't work properly. We should clean up the the exceptions here anyway

* typo
This commit is contained in:
Greg Landrum
2020-04-01 14:30:07 +02:00
committed by GitHub
parent cf031c2f7e
commit 5712176605
126 changed files with 1172 additions and 22492 deletions
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1
Code/JavaWrappers/GenericRDKitException.h
View File

@@ -19,7 +19,6 @@ class GenericRDKitException : public std::exception {
GenericRDKitException(const std::string &i) : _value(i){};
GenericRDKitException(const char *msg) : _value(msg){};
const char *what() const noexcept override { return _value.c_str(); };
const char *message() const noexcept { return what(); };
~GenericRDKitException() noexcept {};
private:

33
Code/JavaWrappers/RDKitExceptions.i
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@@ -43,7 +43,7 @@
%typemap(throws, throws="org.RDKit.ChemicalReactionException") RDKit::ChemicalReactionException {
jclass excep = jenv->FindClass("org/RDKit/ChemicalReactionException");
if (excep)
jenv->ThrowNew(excep, $1.message());
jenv->ThrowNew(excep, $1.what());
return $null;
}
@@ -52,7 +52,7 @@
%typemap(throws, throws="org.RDKit.ChemicalReactionParserException") RDKit::ChemicalReactionParserException {
jclass excep = jenv->FindClass("org/RDKit/ChemicalReactionParserException");
if (excep)
jenv->ThrowNew(excep, $1.message());
jenv->ThrowNew(excep, $1.what());
return $null;
}
@@ -61,7 +61,7 @@
%typemap(throws, throws="org.RDKit.ConformerException") RDKit::ConformerException {
jclass excep = jenv->FindClass("org/RDKit/ConformerException");
if (excep)
jenv->ThrowNew(excep, $1.message());
jenv->ThrowNew(excep, $1.what());
return $null;
}
@@ -70,7 +70,7 @@
%typemap(throws, throws="org.RDKit.MolPicklerException") RDKit::MolPicklerException {
jclass excep = jenv->FindClass("org/RDKit/MolPicklerException");
if (excep)
jenv->ThrowNew(excep, $1.message());
jenv->ThrowNew(excep, $1.what());
return $null;
}
@@ -79,7 +79,7 @@
%typemap(throws, throws="org.RDKit.MolSanitizeException") RDKit::MolSanitizeException {
jclass excep = jenv->FindClass("org/RDKit/MolSanitizeException");
if (excep)
jenv->ThrowNew(excep, $1.message());
jenv->ThrowNew(excep, $1.what());
return $null;
}
@@ -88,7 +88,7 @@
%typemap(throws, throws="org.RDKit.SmilesParseException") RDKit::SmilesParseException {
jclass excep = jenv->FindClass("org/RDKit/SmilesParseException");
if (excep)
jenv->ThrowNew(excep, $1.message());
jenv->ThrowNew(excep, $1.what());
return $null;
}
@@ -97,21 +97,16 @@
%typemap(throws, throws="org.RDKit.KeyErrorException") KeyErrorException {
jclass excep = jenv->FindClass("org/RDKit/KeyErrorException");
if (excep)
jenv->ThrowNew(excep, $1.key());
jenv->ThrowNew(excep, $1.what());
return $null;
}
%extend KeyErrorException {
std::string message() {
return "Unknown key: " + ($self)->key();
}
}
// ===== GenericRDKitException =====
%typemap(javabase) RDKit::GenericRDKitException "java.lang.RuntimeException";
%typemap(throws, throws="org.RDKit.GenericRDKitException") RDKit::GenericRDKitException {
jclass excep = jenv->FindClass("org/RDKit/GenericRDKitException");
if (excep)
jenv->ThrowNew(excep, $1.message());
jenv->ThrowNew(excep, $1.what());
return $null;
}
@@ -124,27 +119,27 @@
$action
} catch (RDKit::ChemicalReactionException &e) {
jclass clazz = jenv->FindClass("org/RDKit/ChemicalReactionException");
jenv->ThrowNew(clazz, e.message());
jenv->ThrowNew(clazz, e.what());
return $null;
} catch (RDKit::ChemicalReactionParserException &e) {
jclass clazz = jenv->FindClass("org/RDKit/ChemicalReactionParserException");
jenv->ThrowNew(clazz, e.message());
jenv->ThrowNew(clazz, e.what());
return $null;
} catch (RDKit::ConformerException &e) {
jclass clazz = jenv->FindClass("org/RDKit/ConformerException");
jenv->ThrowNew(clazz, e.message());
jenv->ThrowNew(clazz, e.what());
return $null;
} catch (RDKit::MolPicklerException &e) {
jclass clazz = jenv->FindClass("org/RDKit/MolPicklerException");
jenv->ThrowNew(clazz, e.message());
jenv->ThrowNew(clazz, e.what());
return $null;
} catch (RDKit::MolSanitizeException &e) {
jclass clazz = jenv->FindClass("org/RDKit/MolSanitizeException");
jenv->ThrowNew(clazz, e.message());
jenv->ThrowNew(clazz, e.what());
return $null;
} catch (RDKit::SmilesParseException &e) {
jclass clazz = jenv->FindClass("org/RDKit/SmilesParseException");
jenv->ThrowNew(clazz, e.message());
jenv->ThrowNew(clazz, e.what());
return $null;
} catch (KeyErrorException &e) {
jclass clazz = jenv->FindClass("org/RDKit/KeyErrorException");

12
Code/JavaWrappers/csharp_wrapper/GraphMolCSharp.i
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@@ -93,32 +93,32 @@
}
catch (RDKit::ChemicalReactionException &e) {
std::string err="ChemicalReactionException: ";
err+=e.message();
err+=e.what();
SWIG_CSharpSetPendingException(SWIG_CSharpApplicationException, err.c_str());
}
catch (RDKit::ChemicalReactionParserException &e) {
std::string err="ChemicalReactionParserException: ";
err+=e.message();
err+=e.what();
SWIG_CSharpSetPendingException(SWIG_CSharpApplicationException, err.c_str());
}
catch (RDKit::ConformerException &e) {
std::string err="ConformerException: ";
err+=e.message();
err+=e.what();
SWIG_CSharpSetPendingException(SWIG_CSharpApplicationException, err.c_str());
}
catch (RDKit::MolPicklerException &e) {
std::string err="MolPicklerException: ";
err+=e.message();
err+=e.what();
SWIG_CSharpSetPendingException(SWIG_CSharpApplicationException, err.c_str());
}
catch (RDKit::MolSanitizeException &e) {
std::string err="MolSanitizeException: ";
err+=e.message();
err+=e.what();
SWIG_CSharpSetPendingException(SWIG_CSharpApplicationException, err.c_str());
}
catch (RDKit::SmilesParseException e) {
std::string err="SmilesParseException: ";
err+=e.message();
err+=e.what();
SWIG_CSharpSetPendingException(SWIG_CSharpApplicationException, err.c_str());
}
catch (KeyErrorException e) {

8
Code/JavaWrappers/gmwrapper/src-test/org/RDKit/ErrorHandlingTests.java
View File

@@ -58,8 +58,8 @@ public class ErrorHandlingTests extends GraphMolTest {
e.getClass().toString());
String what = ((KeyErrorException) e).key();
assertEquals("monkey", what);
what = ((KeyErrorException) e).message();
assertEquals("Unknown key: monkey", what);
// what = ((KeyErrorException) e).what();
// assertEquals("Unknown key: monkey", what);
}
}
@@ -81,7 +81,7 @@ public class ErrorHandlingTests extends GraphMolTest {
}
catch (GenericRDKitException e)
{
String what = e.message();
String what = e.what();
assertEquals("Unknown exception", what);
String where = e.getStackTrace()[0].getMethodName();
assertEquals("ROMol_getAtomWithIdx", where);
@@ -111,7 +111,7 @@ public class ErrorHandlingTests extends GraphMolTest {
{
assertEquals("class org.RDKit.GenericRDKitException",
e.getClass().toString());
String msg = e.message();
String msg = e.what();
assertEquals("Unknown exception", msg);
StackTraceElement[] st = e.getStackTrace();
assertEquals("ErrorGenerator_badAlloc_1",