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Devrim Gunyel
core
Commits
0ea35cb7
Commit
0ea35cb7
authored
Nov 05, 2019
by
Piotr Gawron
Browse files
export to CellDesigner properly handles new line characters
parent
8fd36e0a
Changes
4
Hide whitespace changes
Inline
Side-by-side
CHANGELOG
View file @
0ea35cb7
...
...
@@ -5,6 +5,8 @@ minerva (15.0.0~alpha.1) stable; urgency=medium
(#
995
)
*
Bug
fix
:
clear
button
icon
,
refresh
comments
button
and
show
overview
button
icons
were
missing
(
regression
15.0.0
~
alpha
.0
)
*
Bug
fix
:
export
to
CellDesigner
names
with
new
line
is
properly
handled
(#
930
)
minerva
(
15.0.0
~
alpha
.0
)
stable
;
urgency
=
medium
*
Improvement
:
logs
provided
for
validation
data
model
are
structurized
(#
325
)
...
...
converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AbstractElementXmlParser.java
View file @
0ea35cb7
...
...
@@ -33,13 +33,13 @@ public abstract class AbstractElementXmlParser<T extends CellDesignerElement<?>,
* Default class logger.
*/
@SuppressWarnings
(
"unused"
)
private
Logger
logger
=
LogManager
.
getLogger
(
AbstractElementXmlParser
.
class
.
getName
()
);
private
Logger
logger
=
LogManager
.
getLogger
();
/**
* List of special strings in CellDesigner that should be translated into some
* UTF characters.
*/
private
List
<
Pair
<
String
,
String
>>
encodedStrings
=
new
ArrayList
<
Pair
<
String
,
String
>
>();
private
List
<
Pair
<
String
,
String
>>
encodedStrings
=
new
ArrayList
<>();
/**
* Parser of the notes that allows to extract additional structured data for the
...
...
@@ -51,61 +51,61 @@ public abstract class AbstractElementXmlParser<T extends CellDesignerElement<?>,
* Default constructor.
*/
protected
AbstractElementXmlParser
()
{
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_underscore_"
,
"_"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_
BR
_"
,
"\n"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_
br
_"
,
"\n"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_plus_"
,
"+"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_minus_"
,
"-"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_slash_"
,
"/"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_space_"
,
" "
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_Alpha_"
,
"Α"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_alpha_"
,
"α"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_Beta_"
,
"Β"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_beta_"
,
"β"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_Gamma_"
,
"Γ"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_gamma_"
,
"γ"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_Delta_"
,
"Δ"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_delta_"
,
"δ"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_Epsilon_"
,
"Ε"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_epsilon_"
,
"ε"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_Zeta_"
,
"Ζ"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_zeta_"
,
"ζ"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_Eta_"
,
"Η"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_eta_"
,
"η"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_Theta_"
,
"Θ"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_theta_"
,
"θ"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_Iota_"
,
"Ι"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_iota_"
,
"ι"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_Kappa_"
,
"Κ"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_kappa_"
,
"κ"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_Lambda_"
,
"Λ"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_lambda_"
,
"λ"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_Mu_"
,
"Μ"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_mu_"
,
"μ"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_Nu_"
,
"Ν"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_nu_"
,
"ν"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_Xi_"
,
"Ξ"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_xi_"
,
"ξ"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_Omicron_"
,
"Ο"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_omicron_"
,
"ο"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_Pi_"
,
"Π"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_pi_"
,
"π"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_Rho_"
,
"Ρ"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_rho_"
,
"ρ"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_Sigma_"
,
"Σ"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_sigma_"
,
"σ"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_Tau_"
,
"Τ"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_tau_"
,
"τ"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_Upsilon_"
,
"Υ"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_upsilon_"
,
"υ"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_Phi_"
,
"Φ"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_phi_"
,
"φ"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_Chi_"
,
"Χ"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_chi_"
,
"χ"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_Psi_"
,
"Ψ"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_psi_"
,
"ψ"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_Omega_"
,
"Ω"
));
encodedStrings
.
add
(
new
Pair
<
String
,
String
>(
"_omega_"
,
"ω"
));
encodedStrings
.
add
(
new
Pair
<>(
"_underscore_"
,
"_"
));
encodedStrings
.
add
(
new
Pair
<>(
"_
br
_"
,
"\n"
));
encodedStrings
.
add
(
new
Pair
<>(
"_
BR
_"
,
"\n"
));
encodedStrings
.
add
(
new
Pair
<>(
"_plus_"
,
"+"
));
encodedStrings
.
add
(
new
Pair
<>(
"_minus_"
,
"-"
));
encodedStrings
.
add
(
new
Pair
<>(
"_slash_"
,
"/"
));
encodedStrings
.
add
(
new
Pair
<>(
"_space_"
,
" "
));
encodedStrings
.
add
(
new
Pair
<>(
"_Alpha_"
,
"Α"
));
encodedStrings
.
add
(
new
Pair
<>(
"_alpha_"
,
"α"
));
encodedStrings
.
add
(
new
Pair
<>(
"_Beta_"
,
"Β"
));
encodedStrings
.
add
(
new
Pair
<>(
"_beta_"
,
"β"
));
encodedStrings
.
add
(
new
Pair
<>(
"_Gamma_"
,
"Γ"
));
encodedStrings
.
add
(
new
Pair
<>(
"_gamma_"
,
"γ"
));
encodedStrings
.
add
(
new
Pair
<>(
"_Delta_"
,
"Δ"
));
encodedStrings
.
add
(
new
Pair
<>(
"_delta_"
,
"δ"
));
encodedStrings
.
add
(
new
Pair
<>(
"_Epsilon_"
,
"Ε"
));
encodedStrings
.
add
(
new
Pair
<>(
"_epsilon_"
,
"ε"
));
encodedStrings
.
add
(
new
Pair
<>(
"_Zeta_"
,
"Ζ"
));
encodedStrings
.
add
(
new
Pair
<>(
"_zeta_"
,
"ζ"
));
encodedStrings
.
add
(
new
Pair
<>(
"_Eta_"
,
"Η"
));
encodedStrings
.
add
(
new
Pair
<>(
"_eta_"
,
"η"
));
encodedStrings
.
add
(
new
Pair
<>(
"_Theta_"
,
"Θ"
));
encodedStrings
.
add
(
new
Pair
<>(
"_theta_"
,
"θ"
));
encodedStrings
.
add
(
new
Pair
<>(
"_Iota_"
,
"Ι"
));
encodedStrings
.
add
(
new
Pair
<>(
"_iota_"
,
"ι"
));
encodedStrings
.
add
(
new
Pair
<>(
"_Kappa_"
,
"Κ"
));
encodedStrings
.
add
(
new
Pair
<>(
"_kappa_"
,
"κ"
));
encodedStrings
.
add
(
new
Pair
<>(
"_Lambda_"
,
"Λ"
));
encodedStrings
.
add
(
new
Pair
<>(
"_lambda_"
,
"λ"
));
encodedStrings
.
add
(
new
Pair
<>(
"_Mu_"
,
"Μ"
));
encodedStrings
.
add
(
new
Pair
<>(
"_mu_"
,
"μ"
));
encodedStrings
.
add
(
new
Pair
<>(
"_Nu_"
,
"Ν"
));
encodedStrings
.
add
(
new
Pair
<>(
"_nu_"
,
"ν"
));
encodedStrings
.
add
(
new
Pair
<>(
"_Xi_"
,
"Ξ"
));
encodedStrings
.
add
(
new
Pair
<>(
"_xi_"
,
"ξ"
));
encodedStrings
.
add
(
new
Pair
<>(
"_Omicron_"
,
"Ο"
));
encodedStrings
.
add
(
new
Pair
<>(
"_omicron_"
,
"ο"
));
encodedStrings
.
add
(
new
Pair
<>(
"_Pi_"
,
"Π"
));
encodedStrings
.
add
(
new
Pair
<>(
"_pi_"
,
"π"
));
encodedStrings
.
add
(
new
Pair
<>(
"_Rho_"
,
"Ρ"
));
encodedStrings
.
add
(
new
Pair
<>(
"_rho_"
,
"ρ"
));
encodedStrings
.
add
(
new
Pair
<>(
"_Sigma_"
,
"Σ"
));
encodedStrings
.
add
(
new
Pair
<>(
"_sigma_"
,
"σ"
));
encodedStrings
.
add
(
new
Pair
<>(
"_Tau_"
,
"Τ"
));
encodedStrings
.
add
(
new
Pair
<>(
"_tau_"
,
"τ"
));
encodedStrings
.
add
(
new
Pair
<>(
"_Upsilon_"
,
"Υ"
));
encodedStrings
.
add
(
new
Pair
<>(
"_upsilon_"
,
"υ"
));
encodedStrings
.
add
(
new
Pair
<>(
"_Phi_"
,
"Φ"
));
encodedStrings
.
add
(
new
Pair
<>(
"_phi_"
,
"φ"
));
encodedStrings
.
add
(
new
Pair
<>(
"_Chi_"
,
"Χ"
));
encodedStrings
.
add
(
new
Pair
<>(
"_chi_"
,
"χ"
));
encodedStrings
.
add
(
new
Pair
<>(
"_Psi_"
,
"Ψ"
));
encodedStrings
.
add
(
new
Pair
<>(
"_psi_"
,
"ψ"
));
encodedStrings
.
add
(
new
Pair
<>(
"_Omega_"
,
"Ω"
));
encodedStrings
.
add
(
new
Pair
<>(
"_omega_"
,
"ω"
));
}
/**
...
...
converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/AbstractElementXmlParserTest.java
0 → 100644
View file @
0ea35cb7
package
lcsb.mapviewer.converter.model.celldesigner.species
;
import
static
org
.
junit
.
Assert
.
assertTrue
;
import
org.apache.logging.log4j.LogManager
;
import
org.apache.logging.log4j.Logger
;
import
org.junit.Test
;
import
lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions
;
public
class
AbstractElementXmlParserTest
extends
CellDesignerTestFunctions
{
Logger
logger
=
LogManager
.
getLogger
();
AbstractElementXmlParser
<?,
?>
parser
=
new
ProteinXmlParser
(
null
);
@Test
public
void
testEncode
()
{
String
encoded
=
parser
.
encodeName
(
"\n"
);
assertTrue
(
encoded
.
contains
(
"_br_"
));
}
}
converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/AllSpeciesTests.java
View file @
0ea35cb7
...
...
@@ -4,7 +4,9 @@ import org.junit.runner.RunWith;
import
org.junit.runners.Suite
;
@RunWith
(
Suite
.
class
)
@Suite
.
SuiteClasses
({
AntisenseRnaXmlParserTest
.
class
,
@Suite
.
SuiteClasses
({
AbstractElementXmlParserTest
.
class
,
AntisenseRnaXmlParserTest
.
class
,
ComplexParserTest
.
class
,
GeneXmlParserTest
.
class
,
InternalModelSpeciesDataTest
.
class
,
...
...
@@ -17,6 +19,7 @@ import org.junit.runners.Suite;
SpeciesMappingTest
.
class
,
SpeciesSbmlParserTest
.
class
,
})
public
class
AllSpeciesTests
{
}
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