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Merge branch 'release23.11-SNAPSHOT' into 23.11_fb_EnvironmentalInpur…
…tForm # Conflicts: # onprc_ehr/src/org/labkey/onprc_ehr/ONPRC_EHRModule.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,14 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <etl xmlns="http://labkey.org/etl/xml"> | ||
| <name>KinshipDataImport</name> | ||
| <description>Import PRIMe-seq Kinship Data</description> | ||
| <transforms> | ||
| <transform id="kinship" type="TaskRefTransformStep"> | ||
| <taskref ref="org.labkey.GeneticsCore.etl.ImportGeneticsCalculationsStep"> | ||
| <settings> | ||
|
|
||
| </settings> | ||
| </taskref> | ||
| </transform> | ||
| </transforms> | ||
| </etl> |
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107 changes: 107 additions & 0 deletions
107
GeneticsCore/src/org/labkey/GeneticsCore/etl/ImportGeneticsCalculationsStep.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,107 @@ | ||
| package org.labkey.GeneticsCore.etl; | ||
|
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| import org.apache.commons.lang3.StringUtils; | ||
| import org.apache.xmlbeans.XmlException; | ||
| import org.jetbrains.annotations.NotNull; | ||
| import org.labkey.GeneticsCore.GeneticsCoreModule; | ||
| import org.labkey.api.data.Container; | ||
| import org.labkey.api.data.ContainerManager; | ||
| import org.labkey.api.di.TaskRefTask; | ||
| import org.labkey.api.ehr.EHRService; | ||
| import org.labkey.api.module.Module; | ||
| import org.labkey.api.module.ModuleLoader; | ||
| import org.labkey.api.module.ModuleProperty; | ||
| import org.labkey.api.pipeline.PipelineJob; | ||
| import org.labkey.api.pipeline.PipelineJobException; | ||
| import org.labkey.api.pipeline.RecordedActionSet; | ||
| import org.labkey.api.security.permissions.UpdatePermission; | ||
| import org.labkey.api.view.UnauthorizedException; | ||
| import org.labkey.api.writer.ContainerUser; | ||
|
|
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| import java.io.File; | ||
| import java.util.Collections; | ||
| import java.util.List; | ||
| import java.util.Map; | ||
|
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| public class ImportGeneticsCalculationsStep implements TaskRefTask | ||
| { | ||
| protected ContainerUser _containerUser; | ||
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| @Override | ||
| public RecordedActionSet run(@NotNull PipelineJob job) throws PipelineJobException | ||
| { | ||
| Module ehr = ModuleLoader.getInstance().getModule("ehr"); | ||
| Module geneticsCore = ModuleLoader.getInstance().getModule(GeneticsCoreModule.class); | ||
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| ModuleProperty mp = ehr.getModuleProperties().get("EHRStudyContainer"); | ||
| String ehrContainerPath = StringUtils.trimToNull(mp.getEffectiveValue(_containerUser.getContainer())); | ||
| if (ehrContainerPath == null) | ||
| { | ||
| throw new PipelineJobException("EHRStudyContainer has not been set"); | ||
| } | ||
|
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| Container ehrContainer = ContainerManager.getForPath(ehrContainerPath); | ||
| if (ehrContainer == null) | ||
| { | ||
| throw new PipelineJobException("Invalid container: " + ehrContainerPath); | ||
| } | ||
|
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| if (!_containerUser.getContainer().equals(ehrContainer)) | ||
| { | ||
| throw new PipelineJobException("This ETL can only be run from the EHRStudyContainer"); | ||
| } | ||
|
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| // Downstream import events will get additional permissions checks | ||
| if (!ehrContainer.hasPermission(_containerUser.getUser(), UpdatePermission.class)) | ||
| { | ||
| throw new UnauthorizedException(); | ||
| } | ||
|
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| ModuleProperty mp2 = geneticsCore.getModuleProperties().get("KinshipDataPath"); | ||
| String pipeDirPath = StringUtils.trimToNull(mp2.getEffectiveValue(ehrContainer)); | ||
| if (pipeDirPath == null) | ||
| { | ||
| throw new PipelineJobException("Must provide the filepath to import data using the KinshipDataPath module property"); | ||
| } | ||
|
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| File pipeDir = new File(pipeDirPath); | ||
| if (!pipeDir.exists()) | ||
| { | ||
| throw new PipelineJobException("Path does not exist: " + pipeDir.getPath()); | ||
| } | ||
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| File kinship = new File(pipeDir, "kinship.txt"); | ||
| if (!kinship.exists()) | ||
| { | ||
| throw new PipelineJobException("File does not exist: " + kinship.getPath()); | ||
| } | ||
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| File inbreeding = new File(pipeDir, "inbreeding.txt"); | ||
| if (!inbreeding.exists()) | ||
| { | ||
| throw new PipelineJobException("File does not exist: " + inbreeding.getPath()); | ||
| } | ||
|
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| EHRService.get().standaloneProcessKinshipAndInbreeding(ehrContainer, _containerUser.getUser(), pipeDir, job.getLogger()); | ||
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| return new RecordedActionSet(); | ||
| } | ||
|
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| @Override | ||
| public List<String> getRequiredSettings() | ||
| { | ||
| return Collections.emptyList(); | ||
| } | ||
|
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| @Override | ||
| public void setSettings(Map<String, String> settings) throws XmlException | ||
| { | ||
|
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| } | ||
|
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| @Override | ||
| public void setContainerUser(ContainerUser containerUser) | ||
| { | ||
| _containerUser = containerUser; | ||
| } | ||
| } |
11 changes: 11 additions & 0 deletions
11
ONPRC_EHR_ComplianceDB/resources/queries/onprc_ehr_compliancedb/SciShield_Data.query.xml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| <query xmlns="http://labkey.org/data/xml/query"> | ||
| <metadata> | ||
| <tables xmlns="http://labkey.org/data/xml"> | ||
| <table tableName="SciShield_Data" tableDbType="TABLE"> | ||
| <tableTitle>SciShield Data</tableTitle> | ||
| <columns> | ||
| </columns> | ||
| </table> | ||
| </tables> | ||
| </metadata> | ||
| </query> |
20 changes: 20 additions & 0 deletions
20
ONPRC_EHR_ComplianceDB/resources/queries/onprc_ehr_compliancedb/SciShield_Data/.qview.xml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,20 @@ | ||
| <customView xmlns="http://labkey.org/data/xml/queryCustomView"> | ||
| <columns> | ||
| <column name="employeeid"/> | ||
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| <column name="requirementname"/> | ||
| <column name="date"/> | ||
| <column name="processed"/> | ||
| <column name="comment"/> | ||
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| </columns> | ||
| <sorts> | ||
| <sort column="employeeid" descending="false"/> | ||
| <sort column="requirementname" descending="false"/> | ||
| <sort column="date" descending="true"/> | ||
| <sort column="created" descending="true"/> | ||
| </sorts> | ||
| <filters> | ||
| <filter column="processed" operator="isblank"/> | ||
| </filters> | ||
| </customView> |
34 changes: 34 additions & 0 deletions
34
..._ComplianceDB/resources/queries/onprc_ehr_compliancedb/SciShield_Reference_Data.query.xml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,34 @@ | ||
| <query xmlns="http://labkey.org/data/xml/query"> | ||
| <metadata> | ||
| <tables xmlns="http://labkey.org/data/xml"> | ||
| <table tableName="SciShield_Reference_Data" tableDbType="NOT_IN_DB"> | ||
| <tableTitle>SciShield Reference Data</tableTitle> | ||
|
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| <columns> | ||
| <column columnName ="rowId"> | ||
| <isHidden>true</isHidden> | ||
| </column> | ||
| <column columnName="value"> | ||
| <columnTitle>Value</columnTitle> | ||
| </column> | ||
| <column columnName="endDate"> | ||
| <columnTitle>End Date</columnTitle> | ||
| </column> | ||
|
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| <column columnName="columnName"> | ||
| <columnTitle>Column Name</columnTitle> | ||
| </column> | ||
|
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| <column columnName="Label"> | ||
| <columnTitle>Label</columnTitle> | ||
| </column> | ||
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| <column columnName="sort_order"> | ||
| <columnTitle>Sort Order</columnTitle> | ||
| </column> | ||
| </columns> | ||
| </table> | ||
| </tables> | ||
| </metadata> | ||
| </query> | ||
|
|
43 changes: 43 additions & 0 deletions
43
...omplianceDB/resources/schemas/dbscripts/sqlserver/onprc_ehr_compliancedb-0.000-24.000.sql
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,43 @@ | ||
|
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| CREATE SCHEMA onprc_ehr_compliancedb; | ||
| GO | ||
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| CREATE TABLE onprc_ehr_compliancedb.SciShield_Data | ||
| ( | ||
| RowId INT IDENTITY(1,1) NOT NULL, | ||
| employeeId nvarchar(255) not null, | ||
| requirementname nvarchar(255) null, | ||
| Date datetime null, | ||
| Container ENTITYID NOT NULL, | ||
| comment nvarchar(2000) null, | ||
| CreatedBy USERID, | ||
| Created datetime, | ||
| ModifiedBy USERID, | ||
| Modified datetime, | ||
| processed int NULL | ||
|
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| CONSTRAINT PK_ScieShield_Data PRIMARY KEY (RowId), | ||
| CONSTRAINT FK_ONPRC_EHR_COMPLIANCE_SCISHIELD_DATA_CONTAINER FOREIGN KEY (Container) REFERENCES core.Containers (EntityId) | ||
| ); | ||
| CREATE INDEX IX_ONPRC_EHR_COMPLIANCEDB_SCISHIELD_DATA_CONTAINER ON onprc_ehr_compliancedb.SciShield_Data (Container); | ||
|
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| CREATE TABLE onprc_ehr_compliancedb.SciShield_Reference_Data | ||
| ( | ||
| rowId int identity(1,1), | ||
| label nvarchar(250) NULL, | ||
| value nvarchar(255) NOT NULL , | ||
| columnName nvarchar(255) NOT NULL, | ||
| sort_order integer null, | ||
| endDate datetime NULL, | ||
| Container ENTITYID NOT NULL, | ||
| CreatedBy USERID, | ||
| Created datetime, | ||
| ModifiedBy USERID, | ||
| Modified datetime, | ||
|
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| CONSTRAINT pk_SciShield_reference PRIMARY KEY (value), | ||
| CONSTRAINT FK_ONPRC_EHR_COMPLIANCE_REFERENCE_DATA_CONTAINER FOREIGN KEY (Container) REFERENCES core.Containers (EntityId) | ||
| ); | ||
| CREATE INDEX IX_ONPRC_EHR_COMPLIANCEDB_SCISHIELD_REFERENCE_DATA_CONTAINER ON onprc_ehr_compliancedb.SciShield_Reference_Data (Container); | ||
|
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| GO |
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