- CHG: Adjusted collaborators endpoints to include projects information.

-

Author: sebastian-raubach

lib/germinate-codegen-4.7.4.jar

@@ -8,6 +8,7 @@ public class GermplasmStats
 	private String     germplasmName;
 	private Integer    traitId;
 	private String     traitName;
+	private String traitNameShort;
 	private BigDecimal min;
 	private BigDecimal avg;
 	private BigDecimal max;
@@ -92,4 +93,15 @@ public void setCount(Integer count)
 	{
 		this.count = count;
 	}
+
+	public String getTraitNameShort()
+	{
+		return traitNameShort;
+	}
+
+	public GermplasmStats setTraitNameShort(String traitNameShort)
+	{
+		this.traitNameShort = traitNameShort;
+		return this;
+	}
 }

src/main/java/jhi/germinate/resource/GermplasmStats.java

@@ -2,9 +2,21 @@
 
 public class ProjectStats
 {
-	private int publicationCount = 0;
-	private int groupCount       = 0;
-	private int datasetCount     = 0;
+	private int publicationCount  = 0;
+	private int groupCount        = 0;
+	private int datasetCount      = 0;
+	private int collaboratorCount = 0;
+
+	public int getCollaboratorCount()
+	{
+		return collaboratorCount;
+	}
+
+	public ProjectStats setCollaboratorCount(int collaboratorCount)
+	{
+		this.collaboratorCount = collaboratorCount;
+		return this;
+	}
 
 	public int getPublicationCount()
 	{

src/main/java/jhi/germinate/resource/ProjectStats.java

@@ -4,6 +4,7 @@
 import jhi.germinate.server.util.*;
 import org.jooq.*;
 import org.jooq.impl.DSL;
+import org.yaml.snakeyaml.internal.Logger;
 
 import java.util.*;
 import java.util.stream.Collectors;
@@ -201,6 +202,7 @@ default Condition filterIndividual(Filter filter, boolean jsonOperationAllowed)
 				}
 				else
 				{
+					Logger.getLogger("").warn("Trying to use a json operation, but not allowed: " + filter);
 					return null;
 				}
 			case "arrayContains":
@@ -222,6 +224,7 @@ default Condition filterIndividual(Filter filter, boolean jsonOperationAllowed)
 				}
 				else
 				{
+					Logger.getLogger("").warn("Trying to use a json operation, but not allowed: " + filter);
 					return null;
 				}
 			case "inSet":

src/main/java/jhi/germinate/server/resource/IFilteredResource.java

@@ -0,0 +1,53 @@
+package jhi.germinate.server.resource.collaborator;
+
+import jakarta.annotation.security.PermitAll;
+import jakarta.ws.rs.*;
+import jakarta.ws.rs.core.*;
+import jhi.gatekeeper.resource.PaginatedResult;
+import jhi.germinate.resource.PaginatedRequest;
+import jhi.germinate.server.Database;
+import jhi.germinate.server.database.codegen.tables.pojos.ViewTableCollaborators;
+import jhi.germinate.server.resource.BaseResource;
+import jhi.germinate.server.util.Secured;
+import org.jooq.*;
+
+import java.sql.*;
+import java.util.List;
+
+import static jhi.germinate.server.database.codegen.tables.ViewTableCollaborators.VIEW_TABLE_COLLABORATORS;
+
+@Path("collaborator/table")
+@Secured
+@PermitAll
+public class CollaboratorTableResource extends BaseResource
+{
+	@POST
+	@Consumes(MediaType.APPLICATION_JSON)
+	@Produces(MediaType.APPLICATION_JSON)
+	public Response postCollaboratorTable(PaginatedRequest request)
+			throws SQLException
+	{
+		processRequest(request);
+		try (Connection conn = Database.getConnection())
+		{
+			DSLContext context = Database.getContext(conn);
+			SelectSelectStep<Record> select = context.select();
+
+			if (previousCount == -1)
+				select.hint("SQL_CALC_FOUND_ROWS");
+
+			SelectJoinStep<Record> from = select.from(VIEW_TABLE_COLLABORATORS);
+
+			// Filter here!
+			where(from, filters, true);
+
+			List<ViewTableCollaborators> result = setPaginationAndOrderBy(from)
+					.fetch()
+					.into(ViewTableCollaborators.class);
+
+			long count = previousCount == -1 ? context.fetchOne("SELECT FOUND_ROWS()").into(Long.class) : previousCount;
+
+			return Response.ok(new PaginatedResult<>(result, count)).build();
+		}
+	}
+}

src/main/java/jhi/germinate/server/resource/collaborator/CollaboratorTableResource.java

@@ -1,5 +1,9 @@
 package jhi.germinate.server.resource.datasets;
 
+import jakarta.annotation.security.PermitAll;
+import jakarta.servlet.http.*;
+import jakarta.ws.rs.*;
+import jakarta.ws.rs.core.MediaType;
 import jhi.gatekeeper.resource.PaginatedResult;
 import jhi.germinate.resource.PaginatedRequest;
 import jhi.germinate.server.*;
@@ -8,19 +12,15 @@
 import jhi.germinate.server.util.Secured;
 import org.jooq.*;
 
-import jakarta.annotation.security.PermitAll;
-import jakarta.servlet.http.*;
-import jakarta.ws.rs.*;
-import jakarta.ws.rs.core.MediaType;
 import java.sql.*;
 import java.util.*;
 
-import static jhi.germinate.server.database.codegen.tables.ViewTableCollaborators.*;
+import static jhi.germinate.server.database.codegen.tables.ViewTableCollaborators.VIEW_TABLE_COLLABORATORS;
 
 @Path("dataset/{datasetId}/collaborator")
 @Secured
 @PermitAll
-public class CollaboratorTableResource extends BaseResource
+public class DatasetCollaboratorTableResource extends BaseResource
 {
 	@PathParam("datasetId")
 	private Integer datasetId;

src/main/java/jhi/germinate/server/resource/datasets/CollaboratorTableResource.java renamed to src/main/java/jhi/germinate/server/resource/datasets/DatasetCollaboratorTableResource.java

@@ -461,7 +461,7 @@ private File exportIsaTab(SubsettedDatasetRequest request, DSLContext context, L
 				resultFiles.add(datasetFile);
 				inv.addStudy(study);
 
-				List<ViewTableCollaborators> collaborators = CollaboratorTableResource.getCollaboratorsForDataset(dataset.getDatasetId(), req, resp, userDetails);
+				List<ViewTableCollaborators> collaborators = DatasetCollaboratorTableResource.getCollaboratorsForDataset(dataset.getDatasetId(), req, resp, userDetails);
 
 				if (!CollectionUtils.isEmpty(collaborators))
 					collaborators.forEach(c -> study.addContact(new Person(c.getCollaboratorLastName(), c.getCollaboratorFirstName(), c.getCollaboratorEmail(), c.getInstitutionName(), c.getInstitutionAddress())));

src/main/java/jhi/germinate/server/resource/datasets/export/DatasetExportResource.java

@@ -73,6 +73,7 @@ public List<GermplasmStats> getGermplasmTraitStats(@PathParam("germplasmId") Int
 								  GERMINATEBASE.NAME.as("germplasm_name"),
 								  PHENOTYPES.ID.as("trait_id"),
 								  PHENOTYPES.NAME.as("trait_name"),
+								  PHENOTYPES.SHORT_NAME.as("trait_name_short"),
 								  min.asField("min"),
 								  DSL.avg(PHENOTYPEDATA.PHENOTYPE_VALUE.cast(SQLDataType.DECIMAL.precision(64, 10))).as("avg"),
 								  max.asField("max"),

src/main/java/jhi/germinate/server/resource/germplasm/GermplasmTraitStatsResource.java

@@ -21,6 +21,7 @@
 import static jhi.germinate.server.database.codegen.tables.Experiments.EXPERIMENTS;
 import static jhi.germinate.server.database.codegen.tables.Images.IMAGES;
 import static jhi.germinate.server.database.codegen.tables.Imagetypes.IMAGETYPES;
+import static jhi.germinate.server.database.codegen.tables.Projectcollaborators.PROJECTCOLLABORATORS;
 import static jhi.germinate.server.database.codegen.tables.Projectgroups.PROJECTGROUPS;
 import static jhi.germinate.server.database.codegen.tables.Projectpublications.PROJECTPUBLICATIONS;
 import static jhi.germinate.server.database.codegen.tables.Projects.PROJECTS;
@@ -52,6 +53,7 @@ public Response getProjectStats(@PathParam("projectId") Integer projectId)
 			result.setGroupCount(context.selectCount().from(PROJECTGROUPS).where(PROJECTGROUPS.PROJECT_ID.eq(projectId)).fetchOneInto(Integer.class));
 			result.setDatasetCount(context.selectCount().from(DATASETS).leftJoin(EXPERIMENTS).on(EXPERIMENTS.ID.eq(DATASETS.EXPERIMENT_ID)).where(EXPERIMENTS.PROJECT_ID.eq(projectId)).fetchOneInto(Integer.class));
 			result.setPublicationCount(context.selectCount().from(PROJECTPUBLICATIONS).where(PROJECTPUBLICATIONS.PROJECT_ID.eq(projectId)).fetchOneInto(Integer.class));
+			result.setCollaboratorCount(context.selectCount().from(PROJECTCOLLABORATORS).where(PROJECTCOLLABORATORS.PROJECT_ID.eq(projectId)).fetchOneInto(Integer.class));
 
 			return Response.ok(result).build();
 		}

src/main/java/jhi/germinate/server/resource/projects/ProjectResource.java

@@ -80,7 +80,31 @@ DROP VIEW IF EXISTS `view_table_traits`;
 CREATE ALGORITHM = UNDEFINED SQL SECURITY DEFINER VIEW `view_table_traits` AS select distinct `phenotypes`.`id` AS `trait_id`,`phenotypes`.`name` AS `trait_name`,`phenotypes`.`short_name` AS `trait_name_short`,`phenotypes`.`description` AS `trait_description`,`phenotypes`.`datatype` AS `data_type`,`phenotypes`.`restrictions` AS `trait_restrictions`,`units`.`id` AS `unit_id`,`units`.`unit_name` AS `unit_name`,`units`.`unit_description` AS `unit_description`,`units`.`unit_abbreviation` AS `unit_abbreviation`,`synonyms`.`synonyms` AS `synonyms`, (SELECT CAST(CONCAT('[', (SELECT GROUP_CONCAT(DISTINCT `dataset_id`) FROM `phenotypedata` LEFT JOIN `trialsetup` ON `trialsetup`.`id` = `phenotypedata`.`trialsetup_id` WHERE `phenotypedata`.`phenotype_id` = `phenotypes`.`id`) ,']') as json)) AS `dataset_ids`, (select count(1) from `phenotypedata` where (`phenotypedata`.`phenotype_id` = `phenotypes`.`id`)) AS `count` from ((`phenotypes` left join `units` on((`units`.`id` = `phenotypes`.`unit_id`))) left join `synonyms` on(((`synonyms`.`foreign_id` = `phenotypes`.`id`) and (`synonyms`.`synonymtype_id` = 4)))) group by `phenotypes`.`id`,`synonyms`.`id`;
 
 DROP VIEW IF EXISTS `view_table_collaborators`;
-CREATE ALGORITHM = UNDEFINED SQL SECURITY DEFINER VIEW `view_table_collaborators` AS SELECT `collaborators`.`id` AS `collaborator_id`, `collaborators`.`first_name` AS `collaborator_first_name`, `collaborators`.`last_name` AS `collaborator_last_name`, `collaborators`.`external_id` AS `collaborator_external_id`, `collaborators`.`email` AS `collaborator_email`, `collaborators`.`phone` AS `collaborator_phone`, `datasetcollaborators`.`collaborator_roles` AS `collaborator_roles`, `institutions`.`id` AS `institution_id`, `institutions`.`name` AS `institution_name`, `institutions`.`address` AS `institution_address`, `datasets`.`id` AS `dataset_id`, `countries`.`id` AS `country_id`, `countries`.`country_name` AS `country_name`, `countries`.`country_code2` AS `country_code2`, `countries`.`country_code3` AS `country_code3` FROM `collaborators` LEFT JOIN `institutions` ON `institutions`.`id` = `collaborators`.`institution_id` LEFT JOIN `countries` ON `countries`.`id` = `institutions`.`country_id` LEFT JOIN `datasetcollaborators` ON `datasetcollaborators`.`collaborator_id` = `collaborators`.`id` LEFT JOIN `datasets` ON `datasets`.`id` = `datasetcollaborators`.`dataset_id`;
+CREATE ALGORITHM = UNDEFINED SQL SECURITY DEFINER VIEW `view_table_collaborators` AS
+SELECT `collaborators`.`id`                                AS `collaborator_id`,
+       `collaborators`.`first_name`                        AS `collaborator_first_name`,
+       `collaborators`.`last_name`                         AS `collaborator_last_name`,
+       `collaborators`.`external_id`                       AS `collaborator_external_id`,
+       `collaborators`.`email`                             AS `collaborator_email`,
+       `collaborators`.`phone`                             AS `collaborator_phone`,
+       `datasetcollaborators`.`collaborator_roles`         AS `collaborator_roles`,
+       `institutions`.`id`                                 AS `institution_id`,
+       `institutions`.`name`                               AS `institution_name`,
+       `institutions`.`address`                            AS `institution_address`,
+       `datasets`.`id`                                     AS `dataset_id`,
+       `countries`.`id`                                    AS `country_id`,
+       `countries`.`country_name`                          AS `country_name`,
+       `countries`.`country_code2`                         AS `country_code2`,
+       `countries`.`country_code3`                         AS `country_code3`,
+       (SELECT json_arrayagg(`projectcollaborators`.`project_id`)
+        FROM `projectcollaborators`
+        WHERE `projectcollaborators`.`collaborator_id` = `collaborators`.`id`
+        GROUP BY `projectcollaborators`.`collaborator_id`) AS `project_ids`
+FROM `collaborators`
+         LEFT JOIN `institutions` ON `institutions`.`id` = `collaborators`.`institution_id`
+         LEFT JOIN `countries` ON `countries`.`id` = `institutions`.`country_id`
+         LEFT JOIN `datasetcollaborators` ON `datasetcollaborators`.`collaborator_id` = `collaborators`.`id`
+         LEFT JOIN `datasets` ON `datasets`.`id` = `datasetcollaborators`.`dataset_id`;
 
 DROP VIEW IF EXISTS `view_table_trials_data`;
 # CREATE ALGORITHM = UNDEFINED SQL SECURITY DEFINER VIEW `view_table_trials_data` AS select `germinatebase`.`id` AS `germplasm_id`,`germinatebase`.`general_identifier` AS `germplasm_gid`,`germinatebase`.`name` AS `germplasm_name`,`synonyms`.`synonyms` AS `germplasm_synonyms`,`g`.`name` AS `entity_parent_name`,`g`.`general_identifier` AS `entity_parent_general_identifier`,`entitytypes`.`name` AS `entity_type`,`datasets`.`id` AS `dataset_id`,`datasets`.`name` AS `dataset_name`,`datasets`.`description` AS `dataset_description`,`locations`.`site_name` AS `location_name`,`countries`.`country_name` AS `country_name`,`countries`.`country_code2` AS `country_code2`,`phenotypes`.`id` AS `trait_id`,`phenotypes`.`name` AS `trait_name`,`phenotypes`.`short_name` AS `trait_name_short`,`phenotypes`.`restrictions` AS `trait_restrictions`,`units`.`unit_name` AS `unit_name`,`treatments`.`name` AS `treatment`,`phenotypedata`.`rep` AS `rep`, `phenotypedata`.`recording_date` AS `recording_date`,`phenotypedata`.`phenotype_value` AS `trait_value` from `phenotypedata` left join `germinatebase` on `germinatebase`.`id` = `phenotypedata`.`germinatebase_id` left join `germinatebase` `g` on `germinatebase`.`entityparent_id` = `g`.`id` left join `synonyms` on (`synonyms`.`synonymtype_id` = 1 AND `synonyms`.`foreign_id` = `germinatebase`.`id`) left join `entitytypes` on `entitytypes`.`id` = `germinatebase`.`entitytype_id` left join `phenotypes` on `phenotypes`.`id` = `phenotypedata`.`phenotype_id` left join `units` on `units`.`id` = `phenotypes`.`unit_id` left join `datasets` on `datasets`.`id` = `phenotypedata`.`dataset_id` left join `locations` on `phenotypedata`.`location_id` = `locations`.`id` left join `countries` on `countries`.`id` = `locations`.`country_id` left join `treatments` on `phenotypedata`.`treatment_id` = `treatments`.`id`;