From 24e54dd753b3ce8c649437e91db8cec42cb02827 Mon Sep 17 00:00:00 2001
From: kfilippopolitis <kostasfilippop@gmail.com>
Date: Thu, 13 Jan 2022 03:32:48 -0800
Subject: [PATCH 1/2] Small changes
---
.../models/DTOs/MIPEngineAlgorithmResultDTO.java | 11 +++++++++--
.../mip/models/DTOs/TabularVisualizationDTO.java | 16 ++++++++++++++--
2 files changed, 23 insertions(+), 4 deletions(-)
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmResultDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmResultDTO.java
index 4491ddb44..69332ed5b 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmResultDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmResultDTO.java
@@ -9,6 +9,13 @@ import java.util.List;
@AllArgsConstructor
public class MIPEngineAlgorithmResultDTO {
private final String title;
- private final List<TabularVisualizationDTO.Field> columns;
- private final List<List<Object>> data;
+ private final List<Column> columns;
+
+ @Data
+ @AllArgsConstructor
+ public static class Column {
+ private final String name;
+ private final String type;
+ private final List<Object> data;
+ }
}
\ No newline at end of file
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/TabularVisualizationDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/TabularVisualizationDTO.java
index 3e17932f7..8804c9576 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/TabularVisualizationDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/TabularVisualizationDTO.java
@@ -17,17 +17,29 @@ public class TabularVisualizationDTO {
public TabularVisualizationDTO(MIPEngineAlgorithmResultDTO mipEngineAlgorithmResultDTO) {
HashMap<String, List<TabularVisualizationDTO.Field>> schema = new HashMap<>();
- schema.put("fields", mipEngineAlgorithmResultDTO.getColumns());
+ List<Field> fields = new ArrayList<TabularVisualizationDTO.Field>();
+ List<List<Object>> data = new ArrayList<ArrayList<TabularVisualizationDTO.Field>>()
+ for (Column column : mipEngineAlgorithmResultDTO.getColumns())
+ {
+ fields.add(new Field(column));
+ data.add(column.getData());
+ }
+ schema.put("fields", fields);
this.name = mipEngineAlgorithmResultDTO.getTitle();
this.profile = "tabular-data-resource";
this.schema = schema;
- this.data = mipEngineAlgorithmResultDTO.getData();
+ this.data = data;
}
@Data
@AllArgsConstructor
public static class Field {
private final String name;
private final String type;
+ public Field(Column column)
+ {
+ this.name = column.getName();
+ this.type = column.getType();
+ }
}
}
--
GitLab
From ef064540b5615cb2fdfd14bc7f405c39c3af3999 Mon Sep 17 00:00:00 2001
From: kfilippopolitis <kostasfilippop@gmail.com>
Date: Thu, 20 Jan 2022 00:57:28 -0800
Subject: [PATCH 2/2] Now mipengine result will be more flexible
---
.../eu/hbp/mip/controllers/AlgorithmsAPI.java | 1 -
.../mip/models/DTOs/ExaremeAlgorithmDTO.java | 14 +++---
.../eu/hbp/mip/models/DTOs/ExperimentDTO.java | 4 +-
.../models/DTOs/MIPEngineAlgorithmDTO.java | 9 ++++
.../DTOs/MIPEngineAlgorithmResultDTO.java | 21 ---------
.../models/DTOs/TabularVisualizationDTO.java | 45 -------------------
.../hbp/mip/services/ExperimentService.java | 30 ++++++-------
7 files changed, 35 insertions(+), 89 deletions(-)
delete mode 100644 src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmResultDTO.java
delete mode 100644 src/main/java/eu/hbp/mip/models/DTOs/TabularVisualizationDTO.java
diff --git a/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java b/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
index a15fd37cd..2746a2b7b 100644
--- a/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
+++ b/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
@@ -151,7 +151,6 @@ public class AlgorithmsAPI {
StringBuilder response = new StringBuilder();
HTTPUtil.sendGet(mipengineAlgorithmsUrl, response);
logger.LogUserAction(response.toString());
-
mipEngineAlgorithms = gson.fromJson(
response.toString(),
new TypeToken<ArrayList<MIPEngineAlgorithmDTO>>() {
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmDTO.java
index 584ffd424..07459a27e 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmDTO.java
@@ -37,15 +37,19 @@ public class ExaremeAlgorithmDTO {
this.desc = mipEngineAlgorithm.getDesc();
this.type = "mipengine";
List<ExaremeAlgorithmRequestParamDTO> parameters = new ArrayList<>();
+ if (mipEngineAlgorithm.getInputdata().getY().isPresent()){
+ parameters.add(new ExaremeAlgorithmRequestParamDTO("y", mipEngineAlgorithm.getInputdata().getY().get()));
+ }
parameters.add(new ExaremeAlgorithmRequestParamDTO("x", mipEngineAlgorithm.getInputdata().getX()));
- parameters.add(new ExaremeAlgorithmRequestParamDTO("y", mipEngineAlgorithm.getInputdata().getY()));
parameters.add(new ExaremeAlgorithmRequestParamDTO("pathology", mipEngineAlgorithm.getInputdata().getPathology()));
parameters.add(new ExaremeAlgorithmRequestParamDTO("dataset", mipEngineAlgorithm.getInputdata().getDatasets()));
parameters.add(new ExaremeAlgorithmRequestParamDTO("filter", mipEngineAlgorithm.getInputdata().getFilter()));
- mipEngineAlgorithm.getParameters().forEach((name, parameterDTO) -> {
- ExaremeAlgorithmRequestParamDTO parameter = new ExaremeAlgorithmRequestParamDTO(name, parameterDTO);
- parameters.add(parameter);
- });
+ if (mipEngineAlgorithm.getParameters().isPresent()){
+ mipEngineAlgorithm.getParameters().get().forEach((name, parameterDTO) -> {
+ ExaremeAlgorithmRequestParamDTO parameter = new ExaremeAlgorithmRequestParamDTO(name, parameterDTO);
+ parameters.add(parameter);
+ });
+ }
this.setParameters(parameters);
}
@Data
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/ExperimentDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/ExperimentDTO.java
index 378bb5126..d87297591 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/ExperimentDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/ExperimentDTO.java
@@ -25,8 +25,8 @@ public class ExperimentDTO {
private Boolean shared;
private Boolean viewed;
// Result is a list of objects because there is a limitation that java has in types.
- // Exareme has result in the type of a List<HashMap<String, Object>>
- // Galaxy has result in the type of a List<HashMap<String, List<Object>>>
+ // Exareme has result in the type of List<HashMap<String, Object>>
+ // Galaxy has result in the type of List<HashMap<String, List<Object>>>
//And there is no generic type that describes either an object or a list of objects
private List<Object> result;
private ExperimentDAO.Status status;
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
index 5edfbfe77..d991fde80 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
@@ -6,6 +6,7 @@ import lombok.Data;
import java.util.Hashtable;
import java.util.List;
+import java.util.Optional;
@Data
@AllArgsConstructor
@@ -32,6 +33,9 @@ public class MIPEngineAlgorithmDTO {
@SerializedName("inputdata")
private MIPEngineAlgorithmInputdataDTO inputdata;
+ public Optional<Hashtable<String, MIPEngineAlgorithmParameterDTO>> getParameters() {
+ return Optional.ofNullable(parameters);
+ }
@Data
@AllArgsConstructor
public static class MIPEngineAlgorithmParameterDTO {
@@ -67,6 +71,7 @@ public class MIPEngineAlgorithmDTO {
@Data
@AllArgsConstructor
public static class MIPEngineAlgorithmInputdataDTO {
+
@SerializedName("x")
private MIPEngineAlgorithmInputDataDetailDTO x;
@@ -81,6 +86,10 @@ public class MIPEngineAlgorithmDTO {
@SerializedName("filter")
private MIPEngineAlgorithmInputDataDetailDTO filter;
+
+ public Optional<MIPEngineAlgorithmInputDataDetailDTO> getY() {
+ return Optional.ofNullable(y);
+ }
}
@Data
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmResultDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmResultDTO.java
deleted file mode 100644
index 69332ed5b..000000000
--- a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmResultDTO.java
+++ /dev/null
@@ -1,21 +0,0 @@
-package eu.hbp.mip.models.DTOs;
-
-import lombok.AllArgsConstructor;
-import lombok.Data;
-
-import java.util.List;
-
-@Data
-@AllArgsConstructor
-public class MIPEngineAlgorithmResultDTO {
- private final String title;
- private final List<Column> columns;
-
- @Data
- @AllArgsConstructor
- public static class Column {
- private final String name;
- private final String type;
- private final List<Object> data;
- }
-}
\ No newline at end of file
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/TabularVisualizationDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/TabularVisualizationDTO.java
deleted file mode 100644
index 8804c9576..000000000
--- a/src/main/java/eu/hbp/mip/models/DTOs/TabularVisualizationDTO.java
+++ /dev/null
@@ -1,45 +0,0 @@
-package eu.hbp.mip.models.DTOs;
-
-import lombok.AllArgsConstructor;
-import lombok.Data;
-
-import java.util.HashMap;
-import java.util.List;
-
-@Data
-@AllArgsConstructor
-public class TabularVisualizationDTO {
- private final String name;
- private final String profile;
- private final HashMap<String, List<Field>> schema;
- private final List<List<Object>> data;
-
-
- public TabularVisualizationDTO(MIPEngineAlgorithmResultDTO mipEngineAlgorithmResultDTO) {
- HashMap<String, List<TabularVisualizationDTO.Field>> schema = new HashMap<>();
- List<Field> fields = new ArrayList<TabularVisualizationDTO.Field>();
- List<List<Object>> data = new ArrayList<ArrayList<TabularVisualizationDTO.Field>>()
- for (Column column : mipEngineAlgorithmResultDTO.getColumns())
- {
- fields.add(new Field(column));
- data.add(column.getData());
- }
- schema.put("fields", fields);
- this.name = mipEngineAlgorithmResultDTO.getTitle();
- this.profile = "tabular-data-resource";
- this.schema = schema;
- this.data = data;
- }
- @Data
- @AllArgsConstructor
- public static class Field {
- private final String name;
- private final String type;
- public Field(Column column)
- {
- this.name = column.getName();
- this.type = column.getType();
- }
- }
-}
-
diff --git a/src/main/java/eu/hbp/mip/services/ExperimentService.java b/src/main/java/eu/hbp/mip/services/ExperimentService.java
index 8ba133261..1a4403d76 100644
--- a/src/main/java/eu/hbp/mip/services/ExperimentService.java
+++ b/src/main/java/eu/hbp/mip/services/ExperimentService.java
@@ -390,18 +390,6 @@ public class ExperimentService {
return experimentDatasets;
}
- private List<Object> convertMIPEngineToExaremeAlgorithmResult(
- MIPEngineAlgorithmResultDTO mipEngineAlgorithmResultDTO
- ) {
- Map<String, Object> exaremeResultElement = new HashMap<>();
- exaremeResultElement.put("data", new TabularVisualizationDTO(mipEngineAlgorithmResultDTO));
- exaremeResultElement.put("type", "application/vnd.dataresource+json");
-
- List<Object> exaremeResult = new ArrayList<>();
- exaremeResult.add(exaremeResultElement);
- return exaremeResult;
- }
-
/**
* Creates an experiment and runs it on the background.
* Uses the exareme or mip-engine engine that run an experiment synchronously.
@@ -527,9 +515,9 @@ public class ExperimentService {
List<Object> exaremeAlgorithmResult = new ArrayList<>();
if (requestResponseCode == 200) {
- MIPEngineAlgorithmResultDTO mipEngineAlgorithmResultDTO =
- JsonConverters.convertJsonStringToObject(String.valueOf(requestResponseBody), MIPEngineAlgorithmResultDTO.class);
- exaremeAlgorithmResult = convertMIPEngineToExaremeAlgorithmResult(mipEngineAlgorithmResultDTO);
+ Object mipEngineResult =
+ JsonConverters.convertJsonStringToObject(String.valueOf(requestResponseBody), Object.class);
+ exaremeAlgorithmResult.add(mipEngineResult);
} else if (requestResponseCode == 400) {
Map<String, Object> exaremeAlgorithmResultElement = new HashMap<>();
@@ -543,6 +531,12 @@ public class ExperimentService {
exaremeAlgorithmResultElement.put("type", "text/plain+user_error");
exaremeAlgorithmResult.add(exaremeAlgorithmResultElement);
+ } else if (requestResponseCode == 461) {
+ Map<String, Object> exaremeAlgorithmResultElement = new HashMap<>();
+ exaremeAlgorithmResultElement.put("data", String.valueOf(requestResponseBody));
+ exaremeAlgorithmResultElement.put("type", "text/plain+error");
+ exaremeAlgorithmResult.add(exaremeAlgorithmResultElement);
+
} else if (requestResponseCode == 500) {
Map<String, Object> exaremeAlgorithmResultElement = new HashMap<>();
exaremeAlgorithmResultElement.put("data",
@@ -551,6 +545,12 @@ public class ExperimentService {
exaremeAlgorithmResultElement.put("type", "text/plain+error");
exaremeAlgorithmResult.add(exaremeAlgorithmResultElement);
+ } else if (requestResponseCode == 512) {
+ Map<String, Object> exaremeAlgorithmResultElement = new HashMap<>();
+ exaremeAlgorithmResultElement.put("data", String.valueOf(requestResponseBody));
+ exaremeAlgorithmResultElement.put("type", "text/plain+error");
+ exaremeAlgorithmResult.add(exaremeAlgorithmResultElement);
+
} else {
logger.LogUserAction(
"MIP-Engine execution responded with an unexpected status code: " + requestResponseCode
--
GitLab