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Posted to commits@ctakes.apache.org by se...@apache.org on 2023/02/15 13:49:35 UTC
[ctakes] branch main updated: -l, -s no longer reserved for lookupXml and SubDirectory. If wanted, they should be declared such as in DictionarySubPipe which has cli LookupXml=l
This is an automated email from the ASF dual-hosted git repository.
seanfinan pushed a commit to branch main
in repository https://gitbox.apache.org/repos/asf/ctakes.git
The following commit(s) were added to refs/heads/main by this push:
new d046dd5 -l, -s no longer reserved for lookupXml and SubDirectory. If wanted, they should be declared such as in DictionarySubPipe which has cli LookupXml=l
d046dd5 is described below
commit d046dd508bea04216a230b58b058dd0233639f28
Author: Sean Finan <se...@childrens.harvard.edu>
AuthorDate: Wed Feb 15 08:49:21 2023 -0500
-l, -s no longer reserved for lookupXml and SubDirectory.
If wanted, they should be declared such as in DictionarySubPipe which has cli LookupXml=l
---
.../apache/ctakes/core/pipeline/CliOptionals.java | 20 +++++++++++++----
.../ctakes/core/pipeline/CliOptionalsHandler.java | 20 ++++++++++-------
.../ctakes/core/pipeline/StandardCliOptions.java | 25 +++++++---------------
3 files changed, 36 insertions(+), 29 deletions(-)
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/CliOptionals.java b/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/CliOptionals.java
index 6c7e325..a07e391 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/CliOptionals.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/CliOptionals.java
@@ -65,7 +65,10 @@ public interface CliOptionals extends StandardCliOptions {
defaultValue = "" )
String getOption_k();
- // -l is reserved for common parameter "LookupXml"
+ @Option(
+ shortName = "l",
+ defaultValue = "" )
+ String getOption_l();
@Option(
shortName = "m",
@@ -91,7 +94,10 @@ public interface CliOptionals extends StandardCliOptions {
defaultValue = "" )
String getOption_r();
- // -s is reserved for common parameter "SubDirectory"
+ @Option(
+ shortName = "s",
+ defaultValue = "" )
+ String getOption_s();
@Option(
shortName = "t",
@@ -230,7 +236,10 @@ public interface CliOptionals extends StandardCliOptions {
defaultValue = "" )
String getOption_K();
- // -l is reserved for common parameter "LookupXml"
+ @Option(
+ shortName = "L",
+ defaultValue = "" )
+ String getOption_L();
@Option(
shortName = "M",
@@ -256,7 +265,10 @@ public interface CliOptionals extends StandardCliOptions {
defaultValue = "" )
String getOption_R();
- // -s is reserved for common parameter "SubDirectory"
+ @Option(
+ shortName = "S",
+ defaultValue = "" )
+ String getOption_S();
@Option(
shortName = "T",
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/CliOptionalsHandler.java b/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/CliOptionalsHandler.java
index cf8abd8..81d9c6f 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/CliOptionalsHandler.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/CliOptionalsHandler.java
@@ -27,14 +27,10 @@ final public class CliOptionalsHandler {
return optionals.getInputDirectory();
case "o":
return optionals.getOutputDirectory();
- case "s":
- return optionals.getSubDirectory();
- case "l":
- return optionals.getLookupXml();
- case StandardCliOptions.UMLS_USER:
- return optionals.getUmlsUserName();
- case StandardCliOptions.UMLS_PASS:
- return optionals.getUmlsPassword();
+ case StandardCliOptions.USER_NAME:
+ return optionals.getUserName();
+ case StandardCliOptions.PASSWORD:
+ return optionals.getPassword();
case StandardCliOptions.UMLS_KEY:
return optionals.getUmlsApiKey();
case StandardCliOptions.XMI_OUT_DIR:
@@ -65,6 +61,8 @@ final public class CliOptionalsHandler {
return optionals.getOption_j();
case "k":
return optionals.getOption_k();
+ case "l":
+ return optionals.getOption_l();
case "m":
return optionals.getOption_m();
case "n":
@@ -73,6 +71,8 @@ final public class CliOptionalsHandler {
return optionals.getOption_q();
case "r":
return optionals.getOption_r();
+ case "s":
+ return optionals.getOption_s();
case "t":
return optionals.getOption_t();
case "u":
@@ -127,6 +127,8 @@ final public class CliOptionalsHandler {
return optionals.getOption_J();
case "K":
return optionals.getOption_K();
+ case "L":
+ return optionals.getOption_L();
case "M":
return optionals.getOption_M();
case "N":
@@ -135,6 +137,8 @@ final public class CliOptionalsHandler {
return optionals.getOption_Q();
case "R":
return optionals.getOption_R();
+ case "S":
+ return optionals.getOption_S();
case "T":
return optionals.getOption_T();
case "U":
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/StandardCliOptions.java b/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/StandardCliOptions.java
index f158162..a286ccd 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/StandardCliOptions.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/StandardCliOptions.java
@@ -12,9 +12,8 @@ import com.lexicalscope.jewel.cli.Option;
public interface StandardCliOptions {
static public final String UMLS_KEY = "key";
- static public final String UMLS_USER = "user";
- static public final String UMLS_PASS = "pass";
- static public final String LOOKUP_XML = "lookupXml";
+ static public final String USER_NAME = "user";
+ static public final String PASSWORD = "pass";
static public final String PIPER_FILE = "piper";
static public final String INPUT_DIR = "inputDir";
static public final String OUTPUT_DIR = "outputDir";
@@ -46,7 +45,6 @@ public interface StandardCliOptions {
String getOutputDirectory();
@Option(
- shortName = "s",
longName = SUB_DIR,
description = "path to a subdirectory for output files.",
defaultValue = "" )
@@ -65,23 +63,16 @@ public interface StandardCliOptions {
String getHtmlOutDirectory();
@Option(
- shortName = "l",
- longName = LOOKUP_XML,
- description = "path to the xml file containing information for dictionary lookup configuration.",
+ longName = USER_NAME,
+ description = "username.",
defaultValue = "" )
- String getLookupXml();
+ String getUserName();
@Option(
- longName = UMLS_USER,
- description = "UMLS username.",
+ longName = PASSWORD,
+ description = "password.",
defaultValue = "" )
- String getUmlsUserName();
-
- @Option(
- longName = UMLS_PASS,
- description = "UMLS user password.",
- defaultValue = "" )
- String getUmlsPassword();
+ String getPassword();
@Option(