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Merge pull request #1009 from PhenoApps/v5_548_repeated_values_brapi_…
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…sync

v5 repeated values compatibility with brapi field sync
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@trife
trife authored Nov 27, 2024
2 parents 9b2962d + 4b63c7e commit cd67256
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Showing 4 changed files with 82 additions and 51 deletions.
9 changes: 9 additions & 0 deletions app/src/main/java/com/fieldbook/tracker/brapi/model/Observation.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@ public class Observation extends BrapiObservation {
private String collector;
private String season;
private String studyId;
private String internalVariableDbId;
private String value;
private String rep;

Expand Down Expand Up @@ -49,6 +50,14 @@ public void setStudyId(String studyId) {
this.studyId = studyId;
}

public String getInternalVariableDbId() {
return internalVariableDbId;
}

public void setInternalVariableDbId(String internalVariableDbId) {
this.internalVariableDbId = internalVariableDbId;
}

public String getValue() {
return value;
}
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71 changes: 42 additions & 29 deletions app/src/main/java/com/fieldbook/tracker/brapi/service/BrAPIServiceV2.java
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Original file line number Diff line number Diff line change
Expand Up @@ -86,6 +86,7 @@
import org.json.JSONArray;
import org.json.JSONException;
import org.json.JSONObject;
import org.threeten.bp.OffsetDateTime;

import java.lang.reflect.Type;
import java.util.ArrayList;
Expand Down Expand Up @@ -308,31 +309,31 @@ public void getPrograms(final BrapiPaginationManager paginationManager,
final Function<Integer, Void> failFunction) {
Integer initPage = paginationManager.getPage();
try {
BrapiV2ApiCallBack<BrAPIProgramListResponse> callback = new BrapiV2ApiCallBack<BrAPIProgramListResponse>() {
@Override
public void onSuccess(BrAPIProgramListResponse programsResponse, int i, Map<String, List<String>> map) {
// Cancel processing if the page that was processed is not the page
// that we are currently on. For Example: User taps "Next Page" before brapi call returns data
if (initPage.equals(paginationManager.getPage())) {
updatePageInfo(paginationManager, programsResponse.getMetadata());
List<BrAPIProgram> programList = programsResponse.getResult().getData();
function.apply(mapPrograms(programList));
}
}

@Override
public void onFailure(ApiException error, int i, Map<String, List<String>> map) {
failFunction.apply(error.getCode());
Log.e("BrAPIServiceV2", "API Exception", error);
}
};
ProgramQueryParams queryParams = new ProgramQueryParams();
queryParams.page(paginationManager.getPage()).pageSize(paginationManager.getPageSize());
programsApi.programsGetAsync(queryParams, callback);
} catch (ApiException error) {
failFunction.apply(error.getCode());
Log.e("BrAPIServiceV2", "API Exception", error);
}
BrapiV2ApiCallBack<BrAPIProgramListResponse> callback = new BrapiV2ApiCallBack<BrAPIProgramListResponse>() {
@Override
public void onSuccess(BrAPIProgramListResponse programsResponse, int i, Map<String, List<String>> map) {
// Cancel processing if the page that was processed is not the page
// that we are currently on. For Example: User taps "Next Page" before brapi call returns data
if (initPage.equals(paginationManager.getPage())) {
updatePageInfo(paginationManager, programsResponse.getMetadata());
List<BrAPIProgram> programList = programsResponse.getResult().getData();
function.apply(mapPrograms(programList));
}
}

@Override
public void onFailure(ApiException error, int i, Map<String, List<String>> map) {
failFunction.apply(error.getCode());
Log.e("BrAPIServiceV2", "API Exception", error);
}
};
ProgramQueryParams queryParams = new ProgramQueryParams();
queryParams.page(paginationManager.getPage()).pageSize(paginationManager.getPageSize());
programsApi.programsGetAsync(queryParams, callback);
} catch (ApiException error) {
failFunction.apply(error.getCode());
Log.e("BrAPIServiceV2", "API Exception", error);
}
}

private List<BrapiProgram> mapPrograms(List<BrAPIProgram> programList) {
Expand Down Expand Up @@ -972,6 +973,13 @@ private Observation mapToObservation(BrAPIObservation obs){
newObservation.setDbId(obs.getObservationDbId());
newObservation.setUnitDbId(obs.getObservationUnitDbId());
newObservation.setVariableDbId(obs.getObservationVariableDbId());
newObservation.setTimestamp(obs.getObservationTimeStamp().toString());

newObservation.setTimestamp(
OffsetDateTime.parse(
obs.getObservationTimeStamp().toString()
)
);

//search imported obs references for first field book id
List<BrAPIExternalReference> references = obs.getExternalReferences();
Expand Down Expand Up @@ -1012,6 +1020,11 @@ private List<Observation> mapObservations(List<BrAPIObservation> brapiObservatio
String internalVarId = extVariableDbIdMap.get(brapiObservation.getObservationVariableDbId());
newObservation.setVariableDbId(internalVarId);
newObservation.setValue(brapiObservation.getValue());
newObservation.setTimestamp(
OffsetDateTime.parse(
brapiObservation.getObservationTimeStamp().toString()
)
);

//Make sure we are on the right experiment level.
// This will cause bugs if there have been plot and plant level traits found as the observations retrieves all of them
Expand All @@ -1024,8 +1037,8 @@ private List<Observation> mapObservations(List<BrAPIObservation> brapiObservatio
}

public void createObservations(List<Observation> observations,
final Function<List<Observation>, Void> function,
final Function<Integer, Void> failFunction) {
final Function<List<Observation>, Void> function,
final Function<Integer, Void> failFunction) {
try {
BrapiV2ApiCallBack<BrAPIObservationListResponse> callback = new BrapiV2ApiCallBack<BrAPIObservationListResponse>() {
@Override
Expand Down Expand Up @@ -1071,8 +1084,8 @@ public void onFailure(ApiException error, int statusCode, Map<String, List<Strin
}

public void updateObservations(List<Observation> observations,
final Function<List<Observation>, Void> function,
final Function<Integer, Void> failFunction) {
final Function<List<Observation>, Void> function,
final Function<Integer, Void> failFunction) {
try {

BrapiV2ApiCallBack<BrAPIObservationListResponse> callback = new BrapiV2ApiCallBack<BrAPIObservationListResponse>() {
Expand Down
10 changes: 6 additions & 4 deletions app/src/main/java/com/fieldbook/tracker/database/dao/ObservationDao.kt
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Original file line number Diff line number Diff line change
Expand Up @@ -172,6 +172,7 @@ class ObservationDao {
obs.value AS value,
obs.observation_time_stamp,
obs.observation_unit_id,
obs.observation_variable_db_id,
obs.observation_db_id,
obs.last_synced_time,
obs.collector,
Expand All @@ -197,6 +198,7 @@ class ObservationDao {
rep = getStringVal(row, "rep")
unitDbId = getStringVal(row, "uniqueName")
variableDbId = getStringVal(row, "external_db_id")
internalVariableDbId = getStringVal(row, "observation_variable_db_id")
value = CategoryJsonUtil.processValue(row)
variableName = getStringVal(row, "observation_variable_name")
fieldBookDbId = getStringVal(row, "id")
Expand Down Expand Up @@ -378,14 +380,14 @@ class ObservationDao {

fun insertObservation(studyId: Int, model: BrapiObservation, traitIdToTypeMap:Map<String,String>): Int = withDatabase { db ->

if (getObservation("$studyId", model.unitDbId, model.variableDbId, "1")?.dbId != null) {
if (getObservation("$studyId", model.unitDbId, model.variableDbId, model.rep ?: "1")?.dbId != null) {
println(
"DbId: ${
getObservation(
"$studyId",
model.unitDbId,
model.variableDbId,
"1"
model.rep ?: "1"
)?.dbId
}"
)
Expand All @@ -398,15 +400,15 @@ class ObservationDao {
"observation_variable_name" to model.variableName,
"observation_variable_field_book_format" to variableFormat,
"value" to model.value,
"observation_time_stamp" to model.timestamp,
"observation_time_stamp" to model.timestamp.toString(),
"collector" to model.collector,
// "geoCoordinates" to model.geo_coordinates,
"geoCoordinates" to null,
"last_synced_time" to model.lastSyncedTime,
// "additional_info" to model.additional_info,
"additional_info" to null,
"observation_db_id" to model.dbId,
"rep" to "1",
"rep" to model.rep,
Study.FK to studyId,
ObservationUnit.FK to model.unitDbId,
ObservationVariable.FK to model.variableDbId
Expand Down
43 changes: 25 additions & 18 deletions app/src/main/java/com/fieldbook/tracker/dialogs/BrapiSyncObsDialog.kt
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Original file line number Diff line number Diff line change
Expand Up @@ -161,9 +161,9 @@ class BrapiSyncObsDialog(context: Context, private val syncController: FieldSync

null
}) {
println("Stopped:")
null
}
println("Stopped:")
null
}

null
}) { null }
Expand Down Expand Up @@ -256,30 +256,37 @@ internal class ImportRunnableTask(
}

try {
//Sorting here to only save the most recently taken observation if it is not already in the DB
val observationList =
studyObservations.observationList.sortedByDescending { it.timestamp }
// Calculate rep numbers for new observations based on existing observations
val hostURL = BrAPIService.getHostUrl(context)
val existingObservations = dataHelper.getObservations(hostURL)

// Track the count of existing observations for each unit-variable pair
val observationRepBaseMap = mutableMapOf<Pair<String?, String?>, Int>()
for (obs in existingObservations) {
val key = Pair(obs.unitDbId, obs.internalVariableDbId)
observationRepBaseMap[key] = observationRepBaseMap.getOrDefault(key, 0) + 1
}

// Sort new observations by timestamp so rep # will ascend in order with time
val observationList = studyObservations.observationList.sortedBy { it.timestamp }

//Then sync the observations
for (obs in observationList) {
//Leaving this here for debugging purposes
// println("****************************")
// println("Saving: varName: " + obs.variableName)
// println("Saving: value: " + obs.value)
// println("Saving: studyId: " + obs.studyId)
// println("Saving: unitDBId: " + obs.unitDbId)
// println("Saving: varDbId: " + obs.variableDbId)
val key = Pair(obs.unitDbId, obs.variableDbId)
val baseRep = observationRepBaseMap.getOrDefault(key, 0)
val nextRep = baseRep + 1
obs.rep = nextRep.toString()

// Save observation to the database and update highest rep # for the pair
dataHelper.setTraitObservations(studyObservations.fieldBookStudyDbId, obs, traitIdToType)
observationRepBaseMap[key] = nextRep
}
return 0
}
catch (exc: Exception) {
} catch (exc: Exception) {
fail = true
failMessage = exc.message ?: "ERROR"
println(exc)
Log.e("ImportRunnableTask", "Exception occurred: ${exc.message}", exc)
return null
}

}


Expand Down

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