diff --git a/hdrl/build.gradle b/hdrl/build.gradle deleted file mode 100644 index 405ae240..00000000 --- a/hdrl/build.gradle +++ /dev/null @@ -1,3 +0,0 @@ -plugins { - id 'org.labkey.build.module' -} diff --git a/hdrl/module.properties b/hdrl/module.properties deleted file mode 100644 index 4a8d19cc..00000000 --- a/hdrl/module.properties +++ /dev/null @@ -1,2 +0,0 @@ -ModuleClass: org.labkey.hdrl.HDRLModule -ManageVersion: true diff --git a/hdrl/resources/credits/scripts.txt b/hdrl/resources/credits/scripts.txt deleted file mode 100644 index dc5de38f..00000000 --- a/hdrl/resources/credits/scripts.txt +++ /dev/null @@ -1,4 +0,0 @@ -{table} -Library|Version|Source|License|LabKey Dev|Purpose -Code39Azalea| |{link:Azalea Software|http://azalea.com/web-fonts/}|{link:Creative Commons|http://creativecommons.org/licenses/by-nd/3.0/deed.en_US}|klum|Barcode Web Fonts -{table} \ No newline at end of file diff --git a/hdrl/resources/etls/labware.xml b/hdrl/resources/etls/labware.xml deleted file mode 100644 index 3d50cdd0..00000000 --- a/hdrl/resources/etls/labware.xml +++ /dev/null @@ -1,25 +0,0 @@ - - - LabWare Result Tables - Update test result data from LabWare tables to LabKey tables. - - - - - - - - - - - - - - - - - - - - - diff --git a/hdrl/resources/queries/gw_labkey/specimensWithoutReport.sql b/hdrl/resources/queries/gw_labkey/specimensWithoutReport.sql deleted file mode 100644 index 1bd49ddd..00000000 --- a/hdrl/resources/queries/gw_labkey/specimensWithoutReport.sql +++ /dev/null @@ -1,27 +0,0 @@ -/* - * Copyright (c) 2015 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -SELECT test_request_id, - batch_id, - date_received, - date_completed, - sample_integrity, - test_result, - customer_code, - hdrl_status, - date_modified, - modified_result_flag, - report_file_name -FROM x_lk_outbd_specimens; \ No newline at end of file diff --git a/hdrl/resources/queries/hdrl/InboundSpecimen/.qview.xml b/hdrl/resources/queries/hdrl/InboundSpecimen/.qview.xml deleted file mode 100644 index 4ea742b2..00000000 --- a/hdrl/resources/queries/hdrl/InboundSpecimen/.qview.xml +++ /dev/null @@ -1,18 +0,0 @@ - - - - - - - - - - - - - - - - - - diff --git a/hdrl/resources/queries/hdrl/labwareRequestResults.sql b/hdrl/resources/queries/hdrl/labwareRequestResults.sql deleted file mode 100644 index d16487c0..00000000 --- a/hdrl/resources/queries/hdrl/labwareRequestResults.sql +++ /dev/null @@ -1,23 +0,0 @@ -/* - * Copyright (c) 2015-2019 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -SELECT batch_id as RequestId, - customer_note as CustomerNote, - date_received as Received, - date_completed as Completed, - date_modified as Modified, - s.RowId as RequestStatusId - FROM labwareOutboundRequests - LEFT JOIN RequestStatus s ON s.name = hdrl_status; diff --git a/hdrl/resources/queries/hdrl/labwareSpecimenResults.sql b/hdrl/resources/queries/hdrl/labwareSpecimenResults.sql deleted file mode 100644 index 59317055..00000000 --- a/hdrl/resources/queries/hdrl/labwareSpecimenResults.sql +++ /dev/null @@ -1,28 +0,0 @@ -/* - * Copyright (c) 2015-2019 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -SELECT test_request_id AS SpecimenId, - batch_id as RequestId, - date_received AS Received, - date_completed as Completed, - sample_integrity as SampleIntegrity, - test_result as TestResult, - customer_code as CustomerCode, - date_modified as Modified, - modified_result_flag as ModifiedResultFlag, - hs.RowId AS RequestStatusId, - report_file_name as ReportFileName - FROM labwareOutboundSpecimens - LEFT JOIN RequestStatus hs ON hs.name = hdrl_status; \ No newline at end of file diff --git a/hdrl/resources/queries/hdrl/specimens.query.xml b/hdrl/resources/queries/hdrl/specimens.query.xml deleted file mode 100644 index 7fd37c84..00000000 --- a/hdrl/resources/queries/hdrl/specimens.query.xml +++ /dev/null @@ -1,74 +0,0 @@ - - - - - - - Request Id - - - Specimen Id - - - Status - - rowId - requestStatus - hdrl - - - - Result Modified - - - - - - - - Gender - - RowId - gender - hdrl - - - - - - - FMP - - RowId - familyMemberPrefix - hdrl - - - - DUC - - RowId - dutyCode - hdrl - - - - SOT - - RowId - sourceOfTesting - hdrl - - - - - - - - - - -
- - - \ No newline at end of file diff --git a/hdrl/resources/queries/hdrl/specimens.sql b/hdrl/resources/queries/hdrl/specimens.sql deleted file mode 100644 index 9ab1584a..00000000 --- a/hdrl/resources/queries/hdrl/specimens.sql +++ /dev/null @@ -1,40 +0,0 @@ -/* - * Copyright (c) 2015-2019 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -SELECT - spec.RowId AS RowId, - spec.inboundRequestId as InboundRequestId, - res.RequestStatusId AS RequestStatusId, - res.ModifiedResultFlag AS ModifiedResultFlag, - spec.CustomerBarcode AS CustomerBarcode, - spec.LastName AS LastName, - spec.FirstName AS FirstName, - spec.MiddleName AS MiddleName, - spec.Initials AS Initials, - spec.GenderId AS GenderId, - spec.BirthDate AS BirthDate, - spec.DODId AS DODId, - spec.SSN AS SSN, - spec.FMPId AS FMPId, - spec.DutyCodeId AS DutyCodeid, - spec.TestingSourceId AS TestingSourceId, - spec.DrawDate as DrawDate, - res.Received AS Received, - res.Completed AS Completed, - res.SampleIntegrity AS SampleIntegrity, - res.TestResult AS TestResult, - res.CustomerCode AS CustomerCode, - res.ReportFileName as ReportFileName -FROM hdrl.InboundSpecimen spec LEFT JOIN hdrl.SpecimenResult res ON spec.RowId = res.specimenId; \ No newline at end of file diff --git a/hdrl/resources/schemas/dbscripts/oracle/labware.sql b/hdrl/resources/schemas/dbscripts/oracle/labware.sql deleted file mode 100644 index e91fe893..00000000 --- a/hdrl/resources/schemas/dbscripts/oracle/labware.sql +++ /dev/null @@ -1,111 +0,0 @@ --- ============================================= --- Author: C. Schoening --- Create date: 24-Jun-2015 --- Description: Creates the LabKey interface tables in the GW_LABKEY schema --- This script must be run Logged in with the "gw_labkey" user previously created --- Change History: --- 01-Jul-2015 CRS Added Not Null and Foreign Key constraints --- 07-Jul-2015 CRS Added additional fields to outbound tables --- ============================================= - --------------------------------------------------------- --- DDL for Table X_LK_INBND_REQUESTS --------------------------------------------------------- -CREATE TABLE X_LK_INBND_REQUESTS -( - BATCH_ID NUMBER NOT NULL -, CARRIER VARCHAR2(40) -, TRACKING_NUMBER VARCHAR2(40) -, CUSTOMER VARCHAR2(100) NOT NULL -, CONSTRAINT X_LK_INBND_REQUESTS_PK PRIMARY KEY - ( - BATCH_ID - ) - ENABLE -); - --------------------------------------------------------- --- DDL for Table X_LK_INBND_SPECIMENS --------------------------------------------------------- -CREATE TABLE X_LK_INBND_SPECIMENS -( - TEST_REQUEST_ID NUMBER NOT NULL -, BATCH_ID NUMBER NOT NULL -, TEST_REQUESTED VARCHAR2(100) NOT NULL -, CUST_BARCODE VARCHAR2(40) -, FMP VARCHAR2(2) NOT NULL -, SSN VARCHAR2(9) NOT NULL -, DRAW_DATE DATE NOT NULL -, SPECIMEN_TYPE VARCHAR2(20) -, NUM_CONTAINERS NUMBER -, SOT VARCHAR2(1) -, DUC VARCHAR2(5) -, DOD_ID VARCHAR2(20) -, FIRST_NAME VARCHAR2(40) -, MIDDLE_NAME VARCHAR2(40) -, LAST_NAME VARCHAR2(80) -, BIRTH_DATE DATE -, GENDER VARCHAR2(20) -, INITIALS VARCHAR2(5) -, CONSTRAINT X_LK_INBND_SPECIMENS_PK PRIMARY KEY - ( - TEST_REQUEST_ID - ) - ENABLE -); - --------------------------------------------------------- --- Add Foreign Key from X_LK_INBND_SPECIMENS to X_LK_INBND_REQUESTS --------------------------------------------------------- -ALTER TABLE X_LK_INBND_REQUESTS ADD CONSTRAINT INBND_SPECIMENS_BATCH_ID_FK - FOREIGN KEY (BATCH_ID) REFERENCES X_LK_INBND_REQUESTS(BATCH_ID); - --------------------------------------------------------- --- DDL for Table X_LK_OUTBD_REQUESTS --------------------------------------------------------- -CREATE TABLE X_LK_OUTBD_REQUESTS -( - BATCH_ID NUMBER NOT NULL -, HDRL_STATUS VARCHAR2(20) NOT NULL -, CUSTOMER_NOTE VARCHAR2(254) -, DATE_RECEIVED DATE -, DATE_COMPLETED DATE -, DATE_MODIFIED DATE -, CONSTRAINT X_LK_OUTBD_REQUESTS_PK PRIMARY KEY - ( - BATCH_ID - ) - ENABLE -); - --------------------------------------------------------- --- DDL for Table X_LK_OUTBD_SPECIMENS --------------------------------------------------------- -CREATE TABLE X_LK_OUTBD_SPECIMENS -( - TEST_REQUEST_ID NUMBER NOT NULL -, BATCH_ID NUMBER NOT NULL -, DATE_RECEIVED DATE -, DATE_COMPLETED DATE -, SAMPLE_INTEGRITY VARCHAR2(80) -, TEST_RESULT VARCHAR2(254) -, CUSTOMER_CODE VARCHAR2(80) -, CLINICAL_REPORT BLOB -, HDRL_STATUS VARCHAR2(20) NOT NULL -, DATE_MODIFIED DATE -, MODIFIED_RESULT_FLAG VARCHAR2(1) -, REPORT_FILE_NAME VARCHAR2(20) -, CONSTRAINT X_LK_OUTBD_SPECIMENS_PK PRIMARY KEY - ( - TEST_REQUEST_ID - ) - ENABLE -); - --------------------------------------------------------- --- Add Foreign Key from X_LK_OUTBD_SPECIMENS to X_LK_OUTBD_REQUESTS --------------------------------------------------------- -ALTER TABLE X_LK_OUTBD_SPECIMENS ADD CONSTRAINT OUTBD_SPECIMENS_BATCH_ID_FK - FOREIGN KEY (BATCH_ID) REFERENCES X_LK_OUTBD_REQUESTS(BATCH_ID); - -commit; diff --git a/hdrl/resources/schemas/dbscripts/postgresql/hdrl-0.00-16.20.sql b/hdrl/resources/schemas/dbscripts/postgresql/hdrl-0.00-16.20.sql deleted file mode 100644 index 00bd1d79..00000000 --- a/hdrl/resources/schemas/dbscripts/postgresql/hdrl-0.00-16.20.sql +++ /dev/null @@ -1,474 +0,0 @@ -/* - * Copyright (c) 2018-2019 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ - -/* hdrl-0.00-15.30.sql */ - --- Note: Despite the version number, this script was actually added early in the 15.20 cycle. -CREATE SCHEMA hdrl; - -CREATE TABLE hdrl.RequestStatus -( - RowId SERIAL NOT NULL, - Name VARCHAR(32) NOT NULL, - Description VARCHAR(128), - - CONSTRAINT PK_RequestStatus PRIMARY KEY (RowId), - CONSTRAINT UQ_RequestStatus UNIQUE (Name) -); - -INSERT INTO hdrl.RequestStatus VALUES (DEFAULT, 'Pending', 'Not yet submitted'); -INSERT INTO hdrl.RequestStatus VALUES (DEFAULT, 'Submitted', 'User has submitted the request but no other progress has occurred'); -INSERT INTO hdrl.RequestStatus VALUES (DEFAULT, 'Received', 'All specimens in the request were successfully received by the lab and are being processed'); -INSERT INTO hdrl.RequestStatus VALUES (DEFAULT, 'Completed', 'All specimens in the request have been tested, results are available'); -INSERT INTO hdrl.RequestStatus VALUES (DEFAULT, 'Exception', 'There was some issue with one or more of the specimens in the lab'); -INSERT INTO hdrl.RequestStatus VALUES (DEFAULT, 'Archived', 'There was some issue with one or more of the specimens in the lab'); - -CREATE TABLE hdrl.TestType -( - RowId SERIAL NOT NULL, - Name VARCHAR(128) NOT NULL, - - CONSTRAINT PK_TestType PRIMARY KEY (RowId), - CONSTRAINT UQ_TestType UNIQUE (Name) -); - -INSERT INTO hdrl.TestType VALUES(DEFAULT, 'HIV Screening Algorithm'); - -CREATE TABLE hdrl.FamilyMemberPrefix -( - RowId SERIAL NOT NULL, - Code CHAR(2) NOT NULL, - Description VARCHAR(128), - - CONSTRAINT PK_FamilyMemberPrefix PRIMARY KEY (RowId), - CONSTRAINT UQ_FamilyMemberPrefix UNIQUE (Code) -); - -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '00', 'No FMP Number (MEPS)'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '01', 'Oldest child'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '02', '2nd oldest child'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '03', '3rd oldest child'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '04', '4th oldest child'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '05', '5th oldest child'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '06', '6th oldest child'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '07', '7th oldest child'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '08', '8th oldest child'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '09', '9th oldest child'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '20', 'Sponsor'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '30', 'Sponsor''s current spouse'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '31', 'Sponsor''s Eligible Former Spouse(s)'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '32', 'Sponsor''s Eligible Former Spouse(s)'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '33', 'Sponsor''s Eligible Former Spouse(s)'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '40', 'Sponsor''s Dependent Mother or Stepmother'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '45', 'Sponsor''s Dependent Father or Stepfather'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '50', 'Sponsor''s Dependent Mother-in-law'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '55', 'Sponsor''s Dependent Father-in-law'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '60', 'Other Authorized Sponsor''s Dependents'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '61', 'Other Authorized Sponsor''s Dependents'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '62', 'Other Authorized Sponsor''s Dependents'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '63', 'Other Authorized Sponsor''s Dependents'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '64', 'Other Authorized Sponsor''s Dependents'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '65', 'Other Authorized Sponsor''s Dependents'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '90', 'Children of Dependents'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '91', 'Children of Dependents'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '92', 'Children of Dependents'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '93', 'Children of Dependents'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '94', 'Children of Dependents'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '95', 'Children of Dependents'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '98', 'Civilian, Indigent and Non-Indigent'); -INSERT INTO hdrl.FamilyMemberPrefix VALUES(DEFAULT, '99', 'Other Qualified Beneficiaries'); - -CREATE TABLE hdrl.SourceOfTesting -( - RowId SERIAL NOT NULL, - Code CHARACTER(1) NOT NULL, - Description VARCHAR(128), - - CONSTRAINT PK_SourceOfTesting PRIMARY KEY (RowId), - CONSTRAINT UQ_SourceOfTesting UNIQUE (Code) -); - -INSERT INTO hdrl.SourceOfTesting VALUES(DEFAULT, 'A', 'Alcohol and Drug Rehabilitation'); -INSERT INTO hdrl.SourceOfTesting VALUES(DEFAULT, 'B', 'Blood Donor'); -INSERT INTO hdrl.SourceOfTesting VALUES(DEFAULT, 'C', 'Contact Referred HIV'); -INSERT INTO hdrl.SourceOfTesting VALUES(DEFAULT, 'D', 'Deceased (whether DOA or Dying in ER'); -INSERT INTO hdrl.SourceOfTesting VALUES(DEFAULT, 'F', 'Force Testing'); -INSERT INTO hdrl.SourceOfTesting VALUES(DEFAULT, 'H', 'Post-Deployment Serum'); -INSERT INTO hdrl.SourceOfTesting VALUES(DEFAULT, 'I', 'Indicated Clinically'); -INSERT INTO hdrl.SourceOfTesting VALUES(DEFAULT, 'J', 'Jail, Prisoners or Detained Persons'); -INSERT INTO hdrl.SourceOfTesting VALUES(DEFAULT, 'M', 'Medical Adimission (including Psychiatric)'); -INSERT INTO hdrl.SourceOfTesting VALUES(DEFAULT, 'N', 'Pre-deployment Serum'); -INSERT INTO hdrl.SourceOfTesting VALUES(DEFAULT, 'O', 'Obstetrics/Gynecology Test'); -INSERT INTO hdrl.SourceOfTesting VALUES(DEFAULT, 'P', 'Physical Examination'); -INSERT INTO hdrl.SourceOfTesting VALUES(DEFAULT, 'S', 'Surgical Admission (including invasive procedures and trauma patients in the ER)'); -INSERT INTO hdrl.SourceOfTesting VALUES(DEFAULT, 'V', 'Venereal Disease Clinic Visit/STD Clinic'); -INSERT INTO hdrl.SourceOfTesting VALUES(DEFAULT, 'W', 'Double ELISA Positive, Blood Bank Specimen'); -INSERT INTO hdrl.SourceOfTesting VALUES(DEFAULT, 'X', 'Other'); -INSERT INTO hdrl.SourceOfTesting VALUES(DEFAULT, 'Z', 'Redrawn (Double ELISA Positive) Clinical Specimen'); - -CREATE TABLE hdrl.DutyCode -( - RowId SERIAL NOT NULL, - Code CHARACTER(3), - Description VARCHAR(128), - Service VARCHAR(128), - - CONSTRAINT PK_DutyCode PRIMARY KEY (RowId), - CONSTRAINT UQ_DutyDoce UNIQUE (Code) -); - -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'A12','ACDUTRA-A','USA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'A13','RECRUITS-A','USA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'A14','CADETS - ACADEMY','USA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'A15','ACDU - NTL GUARD','USA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'A22','INACDUTRA-RESERVE','USA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'A21','RET-ACDUTRA/ROTC','USA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'A00','DECEASED SPONSOR','USA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'A11','ACDU-A','USA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'A17','Unknown','USA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'A16','Unknown','USA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'A23','INACDUTRA-NTL GUARD','USA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'A24','A24 - unknown - found in Viromed data but not defined in our paper copies','USA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'A25','A25 - unknown - found in Viromed data but not defined in our paper copies','USA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'A26','APPLICANT ENLIST','USA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'A27','EX MIL MATERNITY','USA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'A28','DEPT OF EX MILITARY','USA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'A31','RET-A-LOS','USA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'A32','RET-A-PDRL','USA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'A33','RET-A-TDRL','USA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'A41','DEP-ACDU-A','USA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'A43','DEP-RET-A','USA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'A45','DEP-ACDU-DEC','USA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'B11','ACDU-NOAA','NOAA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'A47','DEP-RET-DEC','USA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'A48','UNREMARRIED FORMER SPOUSE','USA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'A49','FAM MBR OF A48','USA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'B00','DECEASED SPONSOR','NOAA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'B31','RET-NOAA-LOS','NOAA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'B32','RET-NOAA-PDRL','NOAA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'B33','RET-NOAA-TDRL','NOAA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'B41','DEP-ACDU-NOAA','NOAA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'B43','DEP-RET-NOAA','NOAA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'B45','DEP-ACDU-DEC','NOAA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'B47','DEP-RET-DEC','NOAA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'B48','UNREMARRIED FORMER SPOUSE','NOAA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'B49','FAM MBR OF B48','NOAA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'C00','DECEASED SPONSOR','USCG'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'C13','RECRUITS-CG','USCG'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'C12','ACDUTRA-CG','USCG'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'C11','ACDU-CG','USCG'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'C21','RET-ACDUTRA/ROTC','USCG'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'C14','CADETS - ACADEMY','USCG'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'C41','DEP-ACDU-CG','USCG'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'C33','RET-CG-TDRL','USCG'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'C22','INACDUTRA-RESERVE','USCG'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'C32','RET-CG-PDRL','USCG'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'C31','RET-CG-LOS','USCG'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'C28','DEPT OF EX MILITARY','USCG'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'C27','EX MIL MATERNITY','USCG'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'C26','Applicant Enlist','NOAA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'C45','DEP-ACDU-DEC','USCG'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'C43','DEP-RET-CG','USCG'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'F12','ACDUTRA-AF','USAF'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'F13','RECRUITS-AF','USAF'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'F14','CADETS-ACADEMY','USAF'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'F00','DECEASED SPONSOR','USAF'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'C48','UNREMARRIED FORMER SPOUSE','USCG'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'C49','FAM MBR OF C48','USCG'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'C47','DEP-RET-DEC','USCG'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'F11','ACDU-AF','USAF'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'F15','ACDU-NTL GUARD','USAF'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'F21','RET-ACDUTRA/ROTC','USAF'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'F22','INACDUTRA-RESERVE','USAF'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'F23','INACDUTRA-NTL GUARD','USAF'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'F26','APPLICANT ENLIST','USAF'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'F27','EX MIL MATERNITY','USAF'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'F28','DEPT OF EX MILITARY','USAF'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'F31','RET-AF-LOS','USAF'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'F32','RET-AF-PDRL','USAF'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'F33','RET-AF-TDRL','USAF'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'F41','DEP-ACDU-AF','USAF'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'F43','DEP-RET-AF','USAF'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'F45','DEP-ACDU-DEC','USAF'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'F47','DEP-RET-DEC','USAF'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'F48','UNREMARRIED FORMER SPOUSE','USAF'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'F49','FAM MBR OF F48','USAF'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K51','Civilian Employee (OCONUS)','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K52','Fam Mbr of K51','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K53','Civ Employee(Fed Other)','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K54','Fam Mbr of K53','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K55','Civ Employee(DOD Remote)','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K56','Fam Mbr of K55','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K57','Civ Employee(DOD Occ Hlth)','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K58','Civ Employee(Disb Ret Exam)','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K59','Civ Employee(Others)','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K61','Civ Employee(VA)','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K62','Office of Workers Comp','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K63','Service Home(not retired)','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K64','Social Security','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K65','Contract Employee','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K66','Federal Prisoner','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K67','PHS Beneficiary(Amer Indians, Aleu, Eskimo)','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K68','PHS Beneficiary(Micronesian, Samoan, Trust)','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K69','Other US Beneficiary(Spon & Dep)','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K71','NATO/Non-NATO(Foreign Military Sales)','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K72','NATO Active Duty','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K73','Dependent of K72','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K74','Non-NATO Active Duty','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K75','Dependent of K74','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K76','K76 - unknown - found in Viromed data but not defined in our paper copies','USA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K77','Dependent of Foreign Civilian','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K78','Foreign National POW','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K82','Secry Army Designee','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K83','Secry Navy Designee','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K84','Secry Air Force Designee','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K79','Other Foreign National','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K81','Secry Defense Designee','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K89','Childre of Dependent Daughter','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K91','Civil Humanitarian Care','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K92','Emergency Care','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'M00','DECEASED SPONSOR','USMC'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'K99','Patient NOt Elsewhere Classified','OTHER_ELIGIBLES'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'M31','RET-MC-LOS','USMC'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'M28','DEPT OF EX MILITARY','USMC'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'M27','EX MIL MATERNITY','USMC'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'M26','APPLICANT ENLIST','USMC'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'M22','INACDUTRA-RESERVE-MC','USMC'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'M13','RECRUITS-MC','USMC'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'M12','ACDUTRA-MC','USMC'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'M11','ACDU-MC','USMC'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'M33','RET-MC-TDRL','USMC'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'M32','RET-MC-PDRL','USMC'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'N00','DECEASED SPONSOR','USN'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'N11','ACDU-N','USN'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'M49','FAM MBR OF M48','USMC'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'M48','UNREMARRIED FORMER SPOUSE','USMC'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'M47','DEP-RET-DEC','USMC'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'M45','DEP-ACDU-DEC','USMC'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'M43','DEP-RET-MC','USMC'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'M41','DEP-ACDU-MC','USMC'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'N12','ACDUTRA-N','USN'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'N13','RECRUITS-N','USN'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'N14','CADETS - ACADEMY','USN'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'N21','RET-ACDUTRA/ROTC','USN'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'N22','INACDUTRA-RESERVE','USN'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'N26','APPLICANT ENLIST','USN'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'N27','EX MIL MATERNITY','USN'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'N28','DEPT OF EX MILITARY','USN'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'N31','RET-N-LOS','USN'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'N24','N24 - unknown - found in Viromed data but not defined in our paper copies','USA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'N32','RET-N-PDRL','USN'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'N33','RET-N-TDRL','USN'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'P11','ACDU-PHS','PUBLIC_HEALTH'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'P00','DECEASED SPONSOR','PUBLIC_HEALTH'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'N41','DEP-ACDU-N','USN'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'N43','DEP-RET-N','USN'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'N45','DEP-ACDU-DEC','USN'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'N47','DEP-RET-DEC','USN'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'N48','UNREMARRIED FORMER SPOUSE','USN'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'N49','FAM MBR OFN48','USN'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'P12','ACDUTRA-PHS','PUBLIC_HEALTH'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'P22','INACDUTRA-RESERVE','PUBLIC_HEALTH'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'P31','RET-PHS-LOS','PUBLIC_HEALTH'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'P32','RET-PHS-PDRL','PUBLIC_HEALTH'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'P33','RET-PHS-TDRL','PUBLIC_HEALTH'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'P41','DEP-ACDU-PHS','PUBLIC_HEALTH'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'P43','DEP-RET-PHS','PUBLIC_HEALTH'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'P45','DEP-ACDU-DEC','PUBLIC_HEALTH'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'P47','DEP-RET-DEC','PUBLIC_HEALTH'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'P26','P26 - unknown - found in Viromed data but not defined in our paper copies','USA'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'P48','UNREMARRIED FORMER SPOUSE','PUBLIC_HEALTH'); -INSERT INTO hdrl.DutyCode VALUES(DEFAULT,'P49','FAM MBR OF P48','PUBLIC_HEALTH'); - -CREATE TABLE hdrl.ShippingCarrier -( - RowId SERIAL NOT NULL, - Name VARCHAR(32), - - CONSTRAINT PK_ShippingCarrier PRIMARY KEY (RowId) -); - -INSERT INTO hdrl.ShippingCarrier VALUES(DEFAULT, 'DHL'); -INSERT INTO hdrl.ShippingCarrier VALUES(DEFAULT, 'FedEx'); -INSERT INTO hdrl.ShippingCarrier VALUES(DEFAULT, 'UPS'); -INSERT INTO hdrl.ShippingCarrier VALUES(DEFAULT, 'USPS'); - -CREATE TABLE hdrl.InboundRequest -( - RequestId SERIAL NOT NULL, - RequestStatusId INT NOT NULL, - ShippingCarrierId INT, - ShippingNumber VARCHAR(32), - SubmittedBy USERID, - Submitted TIMESTAMP, - TestTypeId INT NOT NULL, - - Container ENTITYID NOT NULL, - CreatedBy USERID, - Created TIMESTAMP, - ModifiedBy USERID, - Modified TIMESTAMP, - ArchivedRequestCount INT, - - CONSTRAINT PK_InboundRequest PRIMARY KEY (RequestId), - CONSTRAINT FK_InboundRequest_Test FOREIGN KEY (TestTypeId) REFERENCES hdrl.TestType (RowId), - CONSTRAINT FK_InboundRequest_Status FOREIGN KEY (RequestStatusId) REFERENCES hdrl.RequestStatus (RowId), - CONSTRAINT FK_InboundRequest_ShippingCarrier FOREIGN KEY (ShippingCarrierId) REFERENCES hdrl.ShippingCarrier (RowId) -); - -CREATE TABLE hdrl.InboundSpecimen -( - RowId SERIAL NOT NULL, - CustomerBarcode VARCHAR(64), - LastName VARCHAR(64), - FirstName VARCHAR(64), - BirthDate TIMESTAMP, - SSN VARCHAR(9), - InboundRequestId INT NOT NULL, - FMPId INT, - DutyCodeId INT, - TestingSourceId INT, - DrawDate TIMESTAMP, - DoDId BIGINT, - Container ENTITYID NOT NULL, - MiddleName VARCHAR(64), - Initials VARCHAR(5), - NumContainers INT DEFAULT 1, - GenderId INT, - - CreatedBy USERID, - Created TIMESTAMP, - ModifiedBy USERID, - Modified TIMESTAMP, - - CONSTRAINT PK_InboundSpecimen PRIMARY KEY (RowId), - CONSTRAINT FK_InboundSpecimen_FMP FOREIGN KEY (FMPId) REFERENCES hdrl.FamilyMemberPrefix (RowId), - CONSTRAINT FK_InboundSpecimen_DutyCode FOREIGN KEY (DutyCodeId) REFERENCES hdrl.DutyCode (RowId), - CONSTRAINT FK_InboundSpecimen_TestingSource FOREIGN KEY (TestingSourceId) REFERENCES hdrl.SourceOfTesting (RowId), - CONSTRAINT FK_InboundSpecimen_Request FOREIGN KEY (InboundRequestId) REFERENCES hdrl.InboundRequest (RequestId) ON DELETE CASCADE -); - -CREATE TABLE hdrl.Gender -( - RowId SERIAL NOT NULL, - Code VARCHAR(1) NOT NULL, - Description VARCHAR(20) NOT NULL, - - CONSTRAINT PK_Gender PRIMARY KEY (RowId), - CONSTRAINT UQ_Gender UNIQUE (Code) -); - -INSERT INTO hdrl.Gender VALUES(DEFAULT, 'A', 'Ambiguous'); -INSERT INTO hdrl.Gender VALUES(DEFAULT, 'F', 'Female'); -INSERT INTO hdrl.Gender VALUES(DEFAULT, 'M', 'Male'); -INSERT INTO hdrl.Gender VALUES(DEFAULT, 'N', 'Not applicable'); -INSERT INTO hdrl.Gender VALUES(DEFAULT, 'O', 'Other'); -INSERT INTO hdrl.Gender VALUES(DEFAULT, 'U', 'Unknown'); - -ALTER TABLE hdrl.InboundSpecimen ADD CONSTRAINT FK_InboundSpecimen_Gender FOREIGN KEY (GenderId) REFERENCES hdrl.Gender (RowId); - -CREATE TABLE hdrl.RequestResult -( - RequestId INT NOT NULL, - RequestStatusId INT NOT NULL, - CustomerNote VARCHAR(254), - Received TIMESTAMP NOT NULL, - Completed TIMESTAMP, - - Container ENTITYID NOT NULL, - CreatedBy USERID, - Created TIMESTAMP, - ModifiedBy USERID, - Modified TIMESTAMP, - - CONSTRAINT PK_RequestResult PRIMARY KEY (RequestId), - CONSTRAINT FK_RequestResult_InboundRequest FOREIGN KEY (RequestId) REFERENCES hdrl.InboundRequest(RequestId) ON DELETE CASCADE, - CONSTRAINT FK_RequestResult_Status FOREIGN KEY (RequestStatusId) REFERENCES hdrl.RequestStatus(RowId) -); - -CREATE TABLE hdrl.SpecimenResult -( - SpecimenId INT NOT NULL, - RequestStatusId INT NOT NULL, - Received TIMESTAMP NOT NULL, - Completed TIMESTAMP, - SampleIntegrity VARCHAR(80), - TestResult VARCHAR(254), - CustomerCode VARCHAR(80), - ModifiedResultFlag CHAR DEFAULT 'F', - - Container ENTITYID NOT NULL, - CreatedBy USERID, - Created TIMESTAMP, - ModifiedBy USERID, - Modified TIMESTAMP, - RequestId INT NOT NULL, - ReportFileName VARCHAR(20), - - CONSTRAINT PK_SpecimenResult PRIMARY KEY (SpecimenId), - CONSTRAINT FK_SpecimenResult_InboundSpecimen FOREIGN KEY (SpecimenId) REFERENCES hdrl.InboundSpecimen(RowId) ON DELETE CASCADE, - CONSTRAINT FK_SpecimenResult_Status FOREIGN KEY (RequestStatusId) REFERENCES hdrl.RequestStatus(RowId) - -); - -ALTER TABLE hdrl.specimenResult ADD CONSTRAINT FK_SpecimenResult_InboundRequest FOREIGN KEY (RequestId) REFERENCES hdrl.InboundRequest(RequestId) ON DELETE CASCADE; - -CREATE TABLE hdrl.labwareOutboundRequests -( - batch_id INT NOT NULL, - hdrl_status VARCHAR(20), - customer_note VARCHAR(254), - date_received DATE NOT NULL, - date_completed DATE, - date_modified DATE NOT NULL, - CONSTRAINT PK_LabwareOutboundRequests PRIMARY KEY (batch_id), - CONSTRAINT FK_LabwareOutboundRequests_InboundRequest FOREIGN KEY (batch_id) REFERENCES hdrl.InboundRequest (RequestId) ON DELETE CASCADE -); - -CREATE TABLE hdrl.labwareOutboundSpecimens -( - test_request_id INT NOT NULL, - batch_id INT NOT NULL, - date_received DATE NOT NULL, - date_completed DATE, - sample_integrity VARCHAR(80), - test_result VARCHAR(254), - customer_code VARCHAR(80), - hdrl_status VARCHAR(20), - date_modified DATE NOT NULL, - modified_result_flag VARCHAR(1), - report_file_name VARCHAR(20), - - CONSTRAINT PK_LabwareOutboundSpecimens PRIMARY KEY (test_request_id), - CONSTRAINT FK_LabwareOutboundSpecimens_LabwareOutboundRequests FOREIGN KEY (batch_id) REFERENCES hdrl.labwareOutboundRequests (batch_id) ON DELETE CASCADE, - CONSTRAINT FK_LabwareOutboundSpecimens_InboundSpecimen FOREIGN KEY (test_request_id) REFERENCES hdrl.InboundSpecimen (RowId) ON DELETE CASCADE -); - -/* hdrl-15.30-16.10.sql */ - -ALTER TABLE hdrl.labwareOutboundSpecimens DROP CONSTRAINT FK_LabwareOutboundSpecimens_LabwareOutboundRequests; - -/* hdrl-16.10-16.20.sql */ - -ALTER TABLE hdrl.requestResult DROP COLUMN Container; -ALTER TABLE hdrl.specimenResult DROP COLUMN Container; - -ALTER TABLE hdrl.labwareoutboundrequests ALTER COLUMN date_received TYPE timestamp; -ALTER TABLE hdrl.labwareoutboundrequests ALTER COLUMN date_completed TYPE timestamp; -ALTER TABLE hdrl.labwareoutboundrequests ALTER COLUMN date_modified TYPE timestamp; -ALTER TABLE hdrl.labwareoutboundspecimens ALTER COLUMN date_received TYPE timestamp; -ALTER TABLE hdrl.labwareoutboundspecimens ALTER COLUMN date_completed TYPE timestamp; -ALTER TABLE hdrl.labwareoutboundspecimens ALTER COLUMN date_modified TYPE timestamp; \ No newline at end of file diff --git a/hdrl/resources/schemas/dbscripts/postgresql/labware.gw_labkey-0.00-16.20.sql b/hdrl/resources/schemas/dbscripts/postgresql/labware.gw_labkey-0.00-16.20.sql deleted file mode 100644 index 83868075..00000000 --- a/hdrl/resources/schemas/dbscripts/postgresql/labware.gw_labkey-0.00-16.20.sql +++ /dev/null @@ -1,121 +0,0 @@ -/* - * Copyright (c) 2018-2019 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ - -/* labware.gw_labkey-15.20-15.30.sql */ - -/* - * The tables below mimic the Oracle tables used for communication with LabWare. We use them for - * automated tests only. - */ -CREATE SCHEMA gw_labkey; - -CREATE TABLE gw_labkey.X_LK_INBND_REQUESTS -( - BATCH_ID INT NOT NULL -, CARRIER VARCHAR(40) -, TRACKING_NUMBER VARCHAR(40) -, CUSTOMER VARCHAR(100) NOT NULL -, STATUS VARCHAR(20) NOT NULL -, CONSTRAINT X_LK_INBND_REQUESTS_PK PRIMARY KEY - ( - BATCH_ID - ) -); - -CREATE TABLE gw_labkey.X_LK_INBND_SPECIMENS -( - TEST_REQUEST_ID INT NOT NULL -, BATCH_ID INT NOT NULL -, TEST_REQUESTED VARCHAR(100) NOT NULL -, CUST_BARCODE VARCHAR(40) -, FMP VARCHAR(2) NOT NULL -, SSN VARCHAR(9) NOT NULL -, DRAW_DATE DATE NOT NULL -, SPECIMEN_TYPE VARCHAR(20) -, NUM_CONTAINERS INT -, SOT VARCHAR(1) -, DUC VARCHAR(5) -, DOD_ID VARCHAR(20) -, FIRST_NAME VARCHAR(40) -, MIDDLE_NAME VARCHAR(40) -, LAST_NAME VARCHAR(80) -, BIRTH_DATE DATE -, GENDER VARCHAR(20) -, INITIALS VARCHAR(5) -, CONSTRAINT X_LK_INBND_SPECIMENS_PK PRIMARY KEY - ( - TEST_REQUEST_ID - ) -); - -CREATE TABLE gw_labkey.X_LK_OUTBD_REQUESTS -( - BATCH_ID INT NOT NULL -, HDRL_STATUS VARCHAR(20) NOT NULL -, CUSTOMER_NOTE VARCHAR(254) -, DATE_RECEIVED DATE NOT NULL -, DATE_COMPLETED DATE -, CONSTRAINT X_LK_OUTBD_REQUESTS_PK PRIMARY KEY - ( - BATCH_ID - ) -); - -CREATE TABLE gw_labkey.X_LK_OUTBD_SPECIMENS -( - TEST_REQUEST_ID INT NOT NULL -, BATCH_ID INT NOT NULL -, DATE_RECEIVED DATE NOT NULL -, DATE_COMPLETED DATE -, SAMPLE_INTEGRITY VARCHAR(80) -, TEST_RESULT VARCHAR(254) -, CUSTOMER_CODE VARCHAR(80) -, CLINICAL_REPORT TEXT -, CONSTRAINT X_LK_OUTBD_SPECIMENS_PK PRIMARY KEY - ( - TEST_REQUEST_ID - ) -); - -ALTER TABLE gw_labkey.X_LK_INBND_REQUESTS ALTER COLUMN STATUS DROP NOT NULL; - -ALTER TABLE gw_labkey.X_LK_INBND_REQUESTS ADD CONSTRAINT INBND_SPECIMENS_BATCH_ID_FK - FOREIGN KEY (BATCH_ID) REFERENCES gw_labkey.X_LK_INBND_REQUESTS(BATCH_ID); - -ALTER TABLE gw_labkey.X_LK_OUTBD_REQUESTS ADD COLUMN DATE_MODIFIED DATE NOT NULL; -ALTER TABLE gw_labkey.X_LK_OUTBD_REQUESTS ALTER COLUMN HDRL_STATUS DROP NOT NULL; - -ALTER TABLE gw_labkey.X_LK_OUTBD_SPECIMENS ADD COLUMN HDRL_STATUS VARCHAR(20); -ALTER TABLE gw_labkey.X_LK_OUTBD_SPECIMENS ADD COLUMN DATE_MODIFIED DATE NOT NULL; -ALTER TABLE gw_labkey.X_LK_OUTBD_SPECIMENS ADD COLUMN MODIFIED_RESULT_FLAG VARCHAR(1); -ALTER TABLE gw_labkey.X_LK_OUTBD_SPECIMENS ADD CONSTRAINT OUTBD_SPECIMENS_BATCH_ID_FK - FOREIGN KEY (BATCH_ID) REFERENCES gw_labkey.X_LK_OUTBD_REQUESTS(BATCH_ID); - -ALTER TABLE gw_labkey.X_LK_OUTBD_SPECIMENS ALTER COLUMN clinical_report TYPE BYTEA USING NULL; -ALTER TABLE gw_labkey.X_LK_OUTBD_SPECIMENS ADD COLUMN report_file_name VARCHAR(20); - -ALTER TABLE gw_labkey.X_LK_INBND_REQUESTS DROP COLUMN status; - -/* labware.gw_labkey-16.10-16.20.sql */ - -ALTER TABLE gw_labkey.X_LK_INBND_SPECIMENS ALTER draw_date TYPE timestamp; -ALTER TABLE gw_labkey.X_LK_INBND_SPECIMENS ALTER birth_date TYPE timestamp; -ALTER TABLE gw_labkey.X_LK_OUTBD_REQUESTS ALTER date_received TYPE timestamp; -ALTER TABLE gw_labkey.X_LK_OUTBD_REQUESTS ALTER date_completed TYPE timestamp; -ALTER TABLE gw_labkey.X_LK_OUTBD_REQUESTS ALTER date_modified TYPE timestamp; -ALTER TABLE gw_labkey.X_LK_OUTBD_SPECIMENS ALTER date_received TYPE timestamp; -ALTER TABLE gw_labkey.X_LK_OUTBD_SPECIMENS ALTER date_completed TYPE timestamp; -ALTER TABLE gw_labkey.X_LK_OUTBD_SPECIMENS ALTER date_modified TYPE timestamp; \ No newline at end of file diff --git a/hdrl/resources/schemas/hdrl.xml b/hdrl/resources/schemas/hdrl.xml deleted file mode 100644 index b45b91fb..00000000 --- a/hdrl/resources/schemas/hdrl.xml +++ /dev/null @@ -1,271 +0,0 @@ - - - - - - - - - -
- - - - - - -
- - - Code - - - - - -
- - - - - - - -
- - - - - - - - -
- - - Description - - - - - -
- - - - - - -
- - - RequestId - - - - Request Status - - - Shipping Carrier - - - - - UserId - Users - core - - - - - Test Type - - - - - UserId - Users - core - - - - - - UserId - Users - core - - - - - -
- - - RowId - - - SpecimenId - - - - - - - - Gender - - - Date - - - - Request - - - FMP - - - DUC - - - SOT - - - - Date - - - - - - UserId - Users - core - - - - - - UserId - Users - core - - - - -
- - - - - - Request Status - - - - - - - UserId - Users - core - - - - - - UserId - Users - core - - - - -
- - - SpecimenId - - - - RowId - RowId - InboundSpecimen - hdrl - - - - - Request Status - - - - - - - - - UserId - Users - core - - - - - - UserId - Users - core - - - - - - - -
- - - - - - - - - - -
- - - - - - - - - - - - - - - -
- diff --git a/hdrl/resources/schemas/labware.gw_labkey.xml b/hdrl/resources/schemas/labware.gw_labkey.xml deleted file mode 100644 index 61521794..00000000 --- a/hdrl/resources/schemas/labware.gw_labkey.xml +++ /dev/null @@ -1,98 +0,0 @@ - - - - - Batch_Id - - - - - - -
- - - - Test_Request_Id - - - - - Batch_Id - X_LK_INBND_REQUESTS - gw_labkey - - - - - - - - - - - - - - - - - - - -
- - - Batch_Id - - - - - - - - -
- - - Test_Request_Id - - - - - Batch_Id - X_LK_OUTBD_REQUESTS - gw_labkey - - - - - - - - - - - - - -
- - - diff --git a/hdrl/resources/template/specimenTemplate.xlsx b/hdrl/resources/template/specimenTemplate.xlsx deleted file mode 100644 index 72bd2cbc..00000000 Binary files a/hdrl/resources/template/specimenTemplate.xlsx and /dev/null differ diff --git a/hdrl/resources/views/HDRL.html b/hdrl/resources/views/HDRL.html deleted file mode 100644 index 1d58b659..00000000 --- a/hdrl/resources/views/HDRL.html +++ /dev/null @@ -1,4 +0,0 @@ - diff --git a/hdrl/resources/views/HDRL.webpart.xml b/hdrl/resources/views/HDRL.webpart.xml deleted file mode 100644 index 6539400f..00000000 --- a/hdrl/resources/views/HDRL.webpart.xml +++ /dev/null @@ -1,3 +0,0 @@ - - - diff --git a/hdrl/resources/web/hdrl/fonts/Code39Azalea.eot b/hdrl/resources/web/hdrl/fonts/Code39Azalea.eot deleted file mode 100644 index 03af8eb9..00000000 Binary files a/hdrl/resources/web/hdrl/fonts/Code39Azalea.eot and /dev/null differ diff --git a/hdrl/resources/web/hdrl/fonts/Code39Azalea.otf b/hdrl/resources/web/hdrl/fonts/Code39Azalea.otf deleted file mode 100644 index cf2d158b..00000000 Binary files a/hdrl/resources/web/hdrl/fonts/Code39Azalea.otf and /dev/null differ diff --git a/hdrl/resources/web/hdrl/fonts/Code39Azalea.svg b/hdrl/resources/web/hdrl/fonts/Code39Azalea.svg deleted file mode 100644 index d1293cbb..00000000 --- a/hdrl/resources/web/hdrl/fonts/Code39Azalea.svg +++ /dev/null @@ -1,75 +0,0 @@ - - - - -Created by FontForge 20090914 at Sat Dec 8 00:40:35 2012 - By www-data -Copyright (c) 2012 by Jerry Whiting. All rights reserved. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/hdrl/resources/web/hdrl/fonts/Code39Azalea.ttf b/hdrl/resources/web/hdrl/fonts/Code39Azalea.ttf deleted file mode 100644 index 113101a4..00000000 Binary files a/hdrl/resources/web/hdrl/fonts/Code39Azalea.ttf and /dev/null differ diff --git a/hdrl/resources/web/hdrl/fonts/Code39Azalea.woff b/hdrl/resources/web/hdrl/fonts/Code39Azalea.woff deleted file mode 100644 index 0af8e415..00000000 Binary files a/hdrl/resources/web/hdrl/fonts/Code39Azalea.woff and /dev/null differ diff --git a/hdrl/resources/web/hdrl/fonts/barcode.css b/hdrl/resources/web/hdrl/fonts/barcode.css deleted file mode 100644 index 9e80a3bc..00000000 --- a/hdrl/resources/web/hdrl/fonts/barcode.css +++ /dev/null @@ -1,15 +0,0 @@ -/* for custom barcode fonts */ -@font-face { - font-family: barcode; - src: url(Code39Azalea.eot) format('embedded-opentype'), - url(Code39Azalea.woff) format('woff'), - url(Code39Azalea.ttf) format('truetype'), - url(Code39Azalea.svg#Code39Azalea) format('svg'); - font-weight: normal; - font-style: normal; -} - -div.barcode { - font-family: barcode; - font-size: 36pt; -} diff --git a/hdrl/resources/web/hdrl/requests.js b/hdrl/resources/web/hdrl/requests.js deleted file mode 100644 index aa45dddb..00000000 --- a/hdrl/resources/web/hdrl/requests.js +++ /dev/null @@ -1,980 +0,0 @@ -/* - * Copyright (c) 2015-2019 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -Ext4.define('LABKEY.ext4.EditRequestPanel', { - - extend: 'Ext.panel.Panel', - - constructor : function(config) { - - Ext4.applyIf(config, { - frame : false, - border : false, - bodyStyle : {background : 'transparent'} - }); - - // map for display values to keys - this.lkMap = {}; - - this.createDataModels(); - this.callParent([config]); - }, - - createDataModels : function() { - - if (!Ext4.ModelManager.isRegistered('LABKEY.HDRL.Specimen')) { - Ext4.define('LABKEY.HDRL.Specimen', { - extend: 'Ext.data.Model', - fields : [ - {name: 'RowId', mapping : 'RowId.value'}, - {name: 'InboundRequestId', mapping : 'InboundRequestId.value'}, - {name: 'CustomerBarcode', mapping : 'CustomerBarcode.value', defaultValue : null}, - {name: 'LastName', mapping : 'LastName.value', defaultValue : null}, - {name: 'FirstName', mapping : 'FirstName.value', defaultValue : null}, - {name: 'MiddleName', mapping : 'MiddleName.value', defaultValue : null}, - {name: 'Initials', mapping: 'Initials.value', defaultValue : null}, - {name: 'GenderId', mapping: 'GenderId.displayValue', defaultValue : null}, - {name: 'BirthDate', type : 'date', mapping : 'BirthDate.value', defaultValue : null}, - {name: 'SSN', mapping : 'SSN.value', defaultValue : null}, - {name: 'DODId', mapping : 'DODId.value', defaultValue : null}, - {name: 'FMPId', mapping : 'FMPId.displayValue', defaultValue : null}, - {name: 'DutyCodeId', mapping : 'DutyCodeId.displayValue', defaultValue : null}, - {name: 'TestingSourceId', mapping : 'TestingSourceId.displayValue', defaultValue : null}, - {name: 'DrawDate', type : 'date', mapping : 'DrawDate.value', defaultValue : null}, - {name: 'status'} - ] - }); - } - - this.specimenModelMap = { - inboundrequestid : 'InboundRequestId', - customerbarcode : 'CustomerBarcode', - lastname : 'LastName', - firstname : 'FirstName', - middlename : 'MiddleName', - initials: 'Initials', - genderid: 'GenderId', - gender: 'GenderId', - birthdate : 'BirthDate', - ssn : 'SSN', - dodid : 'DODId', - fmpid : 'FMPId', - fmp : 'FMPId', - dutycodeid : 'DutyCodeId', - duc : 'DutyCodeId', - testingsourceid : 'TestingSourceId', - sot : 'TestingSourceId', - drawdate : 'DrawDate', - status : 'status' - }; - - if (!Ext4.ModelManager.isRegistered('LABKEY.HDRL.SpecimenLK')) { - Ext4.define('LABKEY.HDRL.SpecimenLK', { - extend: 'Ext.data.Model', - fields: [ - {name: 'RowId'}, - {name: 'Code'}, - {name: 'Description'}, - {name: 'Service'} - ] - }); - } - - if (!Ext4.ModelManager.isRegistered('LABKEY.HDRL.Lookup')) { - Ext4.define('LABKEY.HDRL.Lookup', { - extend: 'Ext.data.Model', - fields: [ - {name: 'rowid'}, - {name: 'name'} - ] - }); - } - }, - - initComponent : function() { - - this.items = []; - - this.northPanel = this.createNorthPanel(); - this.gridPanel = this.createGridPanel(); - this.southPanel = this.createSouthPanel(); - - this.items.push(this.northPanel); - this.items.push(this.gridPanel); - this.items.push(this.southPanel); - - this.callParent(); - window.onbeforeunload = LABKEY.beforeunload(this.beforeUnload, this); - }, - - createGridPanel : function() { - - var items = []; - - // the row editing plugin - this.roweditor = Ext4.create('Ext.grid.plugin.RowEditing', { - clicksToMoveEditor : 1, - autoCancel : false, - triggerEvent : 'cellclick', - listeners : { - beforeedit : {fn : function(editor, context){ - - // don't activate the editor for checkbox selector or status field - if (context.colIdx <= 1){ - return false; - } - }, scope : this} - } - }); - - // add the request id to the select rows filter - var params = LABKEY.Query.buildQueryParams('hdrl', 'inboundSpecimen', [LABKEY.Filter.create('InboundRequestId', this.requestId)]); - params.apiVersion = 9.1; - - this.grid = Ext4.create('Ext.grid.Panel', { - title : '', - flex : 1.2, - maxHeight : 400, - autoScroll : true, - border : false, frame : false, - selType : 'checkboxmodel', - store : { - model : 'LABKEY.HDRL.Specimen', - autoLoad: true, - pageSize: 200, - pruneModifiedRecords : true, - proxy : { - type : 'ajax', - url : LABKEY.ActionURL.buildURL('query', 'selectRows.api'), - extraParams : params, - reader: { type: 'json', root: 'rows', metaProperty : 'none' } - }, - listeners : { - load : {fn : function(cmp, records){ - this.verifyRows(records, null, function(success){ - this.resetDirty(); - }); - }, scope : this}, - update : {fn : function(cmp, rec, opt, modified){ - this.markDirty(true); - this.verifyRows([rec], modified); - }, scope : this}, - datachanged : {fn : function(){this.markDirty(true);}, scope : this} - } - }, - columns: [ - {text: 'Status', dataIndex: 'status', minWidth : 150, flex : 1}, - {text: 'Customer Barcode', dataIndex: 'CustomerBarcode', width : 150, editor: {xtype: 'textfield'}}, - {text: 'Last Name', dataIndex: 'LastName', editor: {xtype: 'textfield'}}, - {text: 'First Name', dataIndex: 'FirstName', editor: {xtype: 'textfield'}}, - {text: 'Middle Name', dataIndex: 'MiddleName', editor: {xtype: 'textfield'}}, - {text: 'Initials', dataIndex: 'Initials', editor: {xtype: 'textfield'}}, - {text: 'Gender', dataIndex: 'GenderId', - editor : { - xtype : 'combo', - store : { - model : 'LABKEY.HDRL.SpecimenLK', - autoLoad: true, - pageSize: 200, - proxy : { - type : 'ajax', - url : LABKEY.ActionURL.buildURL('query', 'selectRows.api'), - extraParams : { - schemaName : 'hdrl', - queryName : 'gender' - }, - reader : { type : 'json', root : 'rows' } - }, - listeners : { - load : {fn: function(cmp, recs){this.createDisplayValueMap('GenderId', recs, 'RowId', 'Description');}, scope : this} - } - }, - valueField : 'Description', - displayField : 'Description', - editable : false - } - }, - {text: 'Date of Birth', dataIndex: 'BirthDate', width : 150, renderer : Ext4.util.Format.dateRenderer('m/d/Y') , editor : {xtype: 'datefield'}}, - {text: 'FMP', width : 75, dataIndex: 'FMPId', - editor : { - xtype : 'combo', - store : { - model : 'LABKEY.HDRL.SpecimenLK', - autoLoad: true, - pageSize: 200, - proxy : { - type : 'ajax', - url : LABKEY.ActionURL.buildURL('query', 'selectRows.api'), - extraParams : { - schemaName : 'hdrl', - queryName : 'familyMemberPrefix' - }, - reader : { type : 'json', root : 'rows' } - }, - listeners : { - load : {fn: function(cmp, recs){this.createDisplayValueMap('FMPId', recs, 'RowId', 'Code');}, scope : this} - } - }, - valueField : 'Code', - displayField : 'Code', - editable : false - } - }, - {text: 'SSN', dataIndex: 'SSN', width : 110, editor: {xtype: 'textfield'}, renderer : this.SSNRenderer, scope : this}, - {text: 'DoD ID', width : 75, dataIndex: 'DODId', editor: {xtype: 'numberfield', hideTrigger : true}}, - {text: 'DUC', width : 50, dataIndex: 'DutyCodeId', - editor : { - xtype : 'combo', - store : { - model : 'LABKEY.HDRL.SpecimenLK', - autoLoad: true, - pageSize: 200, - proxy : { - type : 'ajax', - url : LABKEY.ActionURL.buildURL('query', 'selectRows.api'), - extraParams : { - schemaName : 'hdrl', - queryName : 'dutyCode' - }, - reader : { type : 'json', root : 'rows' } - }, - listeners : { - load : {fn: function(cmp, recs){this.createDisplayValueMap('DutyCodeId', recs, 'RowId', 'Code');}, scope : this} - } - }, - valueField : 'Code', - displayField : 'Code', - editable : false - } - }, - {text: 'SOT', width : 50, dataIndex: 'TestingSourceId', - editor : { - xtype : 'combo', - store : { - model : 'LABKEY.HDRL.SpecimenLK', - autoLoad: true, - proxy : { - type : 'ajax', - url : LABKEY.ActionURL.buildURL('query', 'selectRows.api'), - extraParams : { - schemaName : 'hdrl', - queryName : 'sourceOfTesting' - }, - reader : { type : 'json', root : 'rows' } - }, - listeners : { - load : {fn: function(cmp, recs){this.createDisplayValueMap('TestingSourceId', recs, 'RowId', 'Code');}, scope : this} - } - }, - valueField : 'Code', - displayField : 'Code', - editable : false - } - }, - {text: 'Date of Draw', dataIndex: 'DrawDate', width : 150, renderer : Ext4.util.Format.dateRenderer('m/d/Y'), editor : {xtype : 'datefield'}} - ], - dockedItems : [{ - xtype : 'toolbar', - doc : 'top', - items : [ - {xtype : 'button', text : 'delete', handler : function(){ - var sm = this.grid.getSelectionModel(); - this.roweditor.cancelEdit(); - - this.grid.getStore().remove(sm.getSelection()); - this.markDirty(true); - if (this.grid.getStore().getCount() > 0) { - sm.select(0); - } - }, scope : this}, - {xtype : 'button', text : 'add specimen', handler : function() { - this.roweditor.cancelEdit(); - - // Create a model instance - var r = Ext4.create('LABKEY.HDRL.Specimen', {InboundRequestId : this.requestId}); - - this.grid.getStore().insert(0, r); - this.roweditor.startEdit(0, 2); - }, scope : this}, - ] - }], - plugins : [this.roweditor] - }); - - items.push(this.grid); - - return Ext4.create('Ext.panel.Panel', { - border : true, - minHeight : 150, - flex : 1.2, - layout : 'fit', - items : items - }); - }, - - createNorthPanel : function() { - - var formItems = []; - - if (this.requestStatusId == 2) - { - formItems.push({ - xtype : 'displayfield', - value : 'Warning: This request has already been submitted. Changes here will not be pushed to LabWare.

' - }); - } - - formItems.push({ - xtype : 'displayfield', - value : 'Test Request
' + - 'Edit existing specimens or add specimens to this test request. Click on the "ADD SPECIMEN" button to add a new specimen record. ' + - 'You can edit existing records by clicking directly on the row in the grid to activate the row editing tool.

' - }); - - formItems.push({ - xtype : 'combo', - fieldLabel : 'Request Type', - name : 'requestType', - itemId : 'requestTypeCombo', - labelSeparator : '', - store : { - model : 'LABKEY.HDRL.Lookup', - autoLoad : true, - proxy : { - type : 'ajax', - url : LABKEY.ActionURL.buildURL('query', 'selectRows.api'), - extraParams : { - schemaName : 'hdrl', - queryName : 'testType', - sort : 'name' - }, - reader : { type : 'json', root : 'rows' } - }, - listeners : { - load : {fn: function(cmp, recs){ - if (this.testTypeId){ - this.northPanel.getComponent('requestTypeCombo').setValue(this.testTypeId); - } - }, scope : this} - } - }, - listeners : { - scope : this, - change : function(cmp, value) { - this.requestType = value; - if (this.testTypeId != value) - this.markDirty(true); - - } - }, - valueField : 'RowId', - displayField : 'Name', - allowBlank : false, - editable : false - }); - - return Ext4.create('Ext.form.Panel', { - bodyPadding : 20, - border : false, - flex : 1.2, - items : formItems, - defaults : { - width : 550, - labelWidth : 150 - }, - bodyStyle : {background : 'transparent'} - }); - }, - - createSouthPanel : function() { - - var formItems = []; - - formItems.push({xtype: 'hidden', name: 'X-LABKEY-CSRF', value: LABKEY.CSRF}); - - formItems.push({ - xtype : 'fieldcontainer', - fieldLabel : 'Upload Request Details', - width : 650, - layout : 'hbox', - items : [ - { - xtype : 'fileuploadfield', - name : 'file', - width : 300, - listeners : { - change : {fn: function(cmp, value){ - this.southPanel.getComponent('specimenUploadButton').enable(); - - }, scope : this} - } - },{ - xtype : 'button', - text : 'download template', - width : 175, - margin : '0 0 0 10', - scope : this, - handler : function(){ - var form = new Ext4.form.BasicForm(this.southPanel); - form.submit({ - url : LABKEY.ActionURL.buildURL('hdrl', 'downloadSpecimenTemplate') - }); - } - } - ] - }) - - formItems.push({ - xtype : 'button', - itemId : 'specimenUploadButton', - text : 'upload file', - width : 150, - disabled : true, - scope : this, - handler : function(){ - this.grid.getEl().mask('uploading file'); - var form = new Ext4.form.BasicForm(this.southPanel); - - var processResponse = function(form, action) { - - var fileContents = Ext4.decode(action.response.responseText); - - // unable to parse the file - if (!fileContents.sheets && fileContents.exception){ - Ext4.Msg.show({title: 'Error', msg: fileContents.exception, buttons: Ext4.MessageBox.OK, icon: Ext4.MessageBox.ERROR}); - this.grid.getEl().unmask(); - LABKEY.Utils.signalWebDriverTest('uploadFile', 'Error'); - return; - } - - var data = fileContents.sheets[0].data; - - // create the model records and load them into the store - var newRecords = []; - var cols = []; - - // need to convert the parsed column names so they match our model names (case sensitive) - Ext4.each(data[0], function(field){ - - var key = field.replace(/\s+/g, '').toLowerCase(); - if (this.specimenModelMap[key]) - cols.push(this.specimenModelMap[key]); - else - cols.push(undefined); - }, this); - - for (var i = 1; i < data.length; i++){ - - var row = data[i]; - var rec = Ext4.create('LABKEY.HDRL.Specimen'); - for (var j=0; j< cols.length; j++){ - - if (cols[j]) - rec.set(cols[j], row[j] ? '' + row[j] : row[j]); - } - newRecords.push(rec); - } - - this.verifyRows(newRecords); - this.grid.getStore().loadData(newRecords, true); - this.grid.getEl().unmask(); - LABKEY.Utils.signalWebDriverTest('uploadFile', 'Success'); - }; - - form.submit({ - url : LABKEY.ActionURL.buildURL('experiment', 'parseFile'), - method: 'POST', - scope : this, - success : processResponse, - failure : processResponse - }); - - } - }) - - formItems.push({ - xtype : 'displayfield', - value : '

Shipping Information

' - }); - - formItems.push({ - xtype : 'combo', - fieldLabel : 'Carrier', - name : 'shippingCarrier', - itemId : 'shippingCarrierCombo', - labelSeparator : '', - store : { - model : 'LABKEY.HDRL.Lookup', - autoLoad : true, - proxy : { - type : 'ajax', - url : LABKEY.ActionURL.buildURL('query', 'selectRows.api'), - extraParams : { - schemaName : 'hdrl', - queryName : 'shippingCarrier', - sort : 'name' - }, - reader : { type : 'json', root : 'rows' } - }, - listeners : { - load : {fn: function(cmp, recs){ - if (this.shippingCarrierId){ - var c = this.southPanel.getComponent('shippingCarrierCombo'); - c.setValue(this.shippingCarrierId); - } - }, scope : this} - } - }, - listeners : { - scope : this, - change : function(cmp, value) { - if (this.shippingCarrierId != value) - this.markDirty(true); - this.shippingCarrier = value; - } - }, - valueField : 'RowId', - displayField : 'Name', - editable : false - }); - - formItems.push({ - xtype : 'textfield', - fieldLabel : 'Tracking #', - name : 'trackingNumber', - labelSeparator : '', - value : this.shippingNumber, - listeners : { - scope: this, - change : function(cmp, value) { - if (this.shippingNumber != value) - this.markDirty(true); - this.shippingNumber = value; - } - } - }); - - formItems.push({ - xtype : 'button', - itemId : 'packingListButton', - text : 'Print Packing List', - scope : this, - disabled : (this.grid.getStore().getCount() == 0), - width : 150, - handler : function(){ - if (this.isDirty()) - this.saveRequestAndSpecimens(this.requestStatusId, this.showPackingList); - else - this.showPackingList(); - } - }); - - return Ext4.create('Ext.form.Panel', { - bodyPadding : 20, - border : false, - flex : 1, - items : formItems, - defaults : { - width : 550, - labelWidth : 150 - }, - bodyStyle : {background : 'transparent'}, - buttonAlign : 'left', - dockedItems : [{ - style : {background : 'transparent'}, - xtype : 'toolbar', - ui : 'footer', - dock : 'bottom', - items: [ - { - xtype: 'button', - itemId : 'submitButton', - text : 'Submit Request', - disabled : (this.isSubmitted() || this.testTypeId == null), - scope : this, - handler : function() {this.handleSave(2);} - },{ - xtype: 'button', - itemId : 'saveButton', - text : 'Save', - scope : this, - handler : function(){this.handleSave(this.requestStatusId);} - }, { - xtype: 'button', - text: 'Cancel', - scope: this, - handler: function () { - this.resetDirty(); - window.location = LABKEY.ActionURL.buildURL('hdrl', 'begin.view'); - } - } - ] - }] - }); - }, - - - showPackingList : function() { - window.open(LABKEY.ActionURL.buildURL('hdrl', 'printPackingList', null, {'requestId' : this.requestId})); - }, - - toggleButtons : function() { - var submitButton = this.down('button#submitButton'); - if (submitButton) - submitButton.setDisabled(!this.validData || this.isSubmitted() || (this.testTypeId == null && this.requestType == null) || this.grid.getStore().getCount() == 0); - var saveButton = this.down('button#saveButton'); - if (saveButton) - saveButton.setDisabled(!this.isDirty() || !this.down('form').getForm().isValid()); - var packingListButton = this.down('button#packingListButton'); - if (packingListButton) - packingListButton.setDisabled(!this.validData || this.grid.getStore().getCount() == 0 || !this.down('form').getForm().isValid()); - }, - - saveSpecimens : function(newRequestStatusId, callback) { - var extraContext = null; - if (newRequestStatusId == 1){ - extraContext = {validationMode : 'OFF'}; - } else if (newRequestStatusId == 2) { - extraContext = {validationMode : 'WITH_UQ'}; - } - - // save any specimen requests - var insertedRows = []; - var updatedRows = []; - var deletedRows = []; - - Ext4.each(this.grid.getStore().getModifiedRecords(), function(rec){ - - var row = this.prepareRow(rec.copy().data); - if (!row.RowId){ - row.RowId = null; - insertedRows.push(row); - } - else { - updatedRows.push(row); - } - }, this); - - Ext4.each(this.grid.getStore().getRemovedRecords(), function(rec){ - - var row = this.prepareRow(rec.copy().data); - if (row.RowId){ - deletedRows.push(row); - } - }, this); - - this.error = false; - var commands = []; - if (insertedRows.length > 0) { - commands.push({ - schemaName : 'hdrl', - queryName : 'inboundSpecimen', - rows : insertedRows, - extraContext: extraContext, - command : 'insert' - }); - } - if (updatedRows.length > 0) { - commands.push({ - schemaName : 'hdrl', - queryName : 'inboundSpecimen', - rows : updatedRows, - extraContext: extraContext, - command : 'update' - }); - } - if (deletedRows.length > 0) { - commands.push({ - schemaName : 'hdrl', - queryName : 'inboundSpecimen', - rows : deletedRows, - command : 'delete' - }); - } - if (commands.length > 0) - { - LABKEY.Query.saveRows( - { - commands: commands, - scope: this, - success: function (res) - { - if (!this.error) - { - this.resetDirty(); - if (callback) - { - callback.call(this); - } - else - window.location = LABKEY.ActionURL.buildURL('hdrl', 'begin.view'); - } - }, - failure: function (res) - { - this.error = true; - var message = 'An error occurred saving the specimen data. See the log for details.'; - if (res.exception) - message = res.exception; - Ext4.Msg.show({ - title: "Error", - msg: message, - buttons: Ext4.MessageBox.OK, - icon: Ext4.MessageBox.ERROR - }); - } - } - ); - } - else // no specimens to update, so our state is no longer dirty - { - this.resetDirty(); - } - }, - - submitRequest : function() - { - if (this.requestId != -1) { - - var row = {requestId : this.requestId, isNewSubmit: true, requestStatusId : 2, shippingCarrierId : this.shippingCarrier, testTypeId : this.requestType, shippingNumber : this.shippingNumber}; - - // handle inserts & updates - LABKEY.Query.updateRows({ - schemaName : 'hdrl', - queryName : 'inboundRequest', - rows : [row], - scope : this, - success : function(res) { - window.location = LABKEY.ActionURL.buildURL('hdrl', 'begin.view'); - }, - failure : function(res){ - this.error = true; - var message = 'An error occurred submitting the specimen data. See the log for details.'; - if (res.exception) - message = res.exception; - Ext4.Msg.show({ - title: "Error", - msg: message, - buttons: Ext4.MessageBox.OK, - icon: Ext4.MessageBox.ERROR, - scope: this, - fn: function(buttonId, text, opt) { - window.location = LABKEY.ActionURL.buildURL('hdrl', 'editRequest.view', null, {requestId : this.requestId}); - } - }); - } - }); - - } else { - this.error = true; - Ext4.Msg.show({title: "Error", msg: 'The request must be saved before being submitted.', buttons: Ext4.MessageBox.OK, icon: Ext4.MessageBox.ERROR}); - } - }, - - isSubmitted : function() - { - return this.requestStatusId >= 2; - }, - - handleSave : function(newRequestStatusId) { - if (this.isSubmitted()) - { - Ext4.Msg.show({ - title: "Confirmation", - msg: 'Warning: This request has already been submitted. ' + - 'Changes here will not be pushed to LabWare. Do you still want to save your changes?', - buttons: Ext4.MessageBox.YESNO, - icon: Ext4.MessageBox.WARNING, - scope: this, - fn: function (buttonId, text, opt) - { - if (buttonId == "yes") - this.saveRequestAndSpecimens(2); - } - } - ); - } - else - { - this.saveRequestAndSpecimens(newRequestStatusId); - } - }, - - // @param saveCallback is used when you want to save the data on the page before executing another function - // (e.g., saving the data before printing the packing list) - saveRequestAndSpecimens : function(newRequestStatusId, saveCallback) { - - // if saving an already-submitted request, we don't want to change the status, just update the request and/or the specimens - var changeStatus = newRequestStatusId == 2 && this.requestStatusId == 1; - var form = this.down('form').getForm(); - var fn = this.requestId != -1 ? LABKEY.Query.updateRows : LABKEY.Query.insertRows; - if (form.isValid()) { // make sure we have all the required fields - - this.roweditor.completeEdit(); // check if editing is still in progress - // save the request as pending so we can update the specimen rows - var row = { - requestStatusId : changeStatus ? 1 : this.requestStatusId, - isNewSubmit : false, - shippingCarrierId : this.shippingCarrier, - testTypeId : this.requestType, - shippingNumber : this.shippingNumber}; - if (this.requestId != -1){ - row.requestId = this.requestId; - } - - // handle inserts & updates - fn({ - schemaName : 'hdrl', - queryName : 'inboundRequest', - rows : [row], - scope : this, - success : function(res) { - if (res.rows && res.rows.length === 1) - { - this.requestId = res.rows[0].requestid; - if (this.isDirty()) - this.saveSpecimens(newRequestStatusId, changeStatus ? this.submitRequest : saveCallback); // save the specimens with the request still pending - else - this.submitRequest(); - } - }, - failure : function(){ - Ext4.Msg.show({title: "Error", msg: 'An error occurred saving the test request. See the log for details.', buttons: Ext4.MessageBox.OK, icon: Ext4.MessageBox.ERROR}); - } - }); - } - else { - Ext4.Msg.show({title: "Error", msg: 'Please enter all required fields.', buttons: Ext4.MessageBox.OK, icon: Ext4.MessageBox.ERROR}); - } - }, - - /** - * Update the status field based on the server validation of the record - */ - verifyRows : function(rows, modifiedFields, callback){ - - if (modifiedFields && (modifiedFields.length == 0 || (modifiedFields.length ==1 && modifiedFields[0] == 'status'))) { - - if (callback) - callback.call(this, true); - else - return; - } - - var ret = true; - var data = []; - Ext4.each(rows, function(rec){ - data.push(this.prepareRow(rec.copy().data)); - }, this); - - LABKEY.Ajax.request({ - url : LABKEY.ActionURL.buildURL("hdrl", "verifySpecimen.api"), - method : 'POST', - scope : this, - jsonData: { - rows : data - }, - success : function(res) { - var o = Ext4.decode(res.responseText); - - this.validData = true; - for (var i=0; i < o.rows.length; i++) - { - if (o.rows[i].ValidationStatus) - this.validData = false; - rows[i].set('status', o.rows[i].ValidationStatus); - } - - if (callback) - callback.call(this, this.validData); - } - }); - }, - - /** - * Prepares the client side row for inserting or updating to the server - * @private - */ - prepareRow : function(row){ - - // convert any lookup display values back to keys - for (var key in row){ - if (row.hasOwnProperty(key)){ - - if (this.lkMap[key]){ - row[key] = this.lkMap[key][row[key]]; - } - else if ('SSN' === key && row[key]){ - // remove hyphens and whitespace from the SSN - row[key] = row[key].replace(/-|\s+/g, ''); - } - } - } - - row.InboundRequestId = this.requestId; - return row; - }, - - /** - * Need to build the map from display value to key for the combo editors so that we can translate the store records - * at insert or update time. - * @private - */ - createDisplayValueMap : function(colName, recs, keyName, valueName) { - - var map = this.lkMap[colName] || {}; - Ext4.each(recs, function(rec){ - - var data = rec.data; - if ((data[keyName] != undefined) && (data[valueName] != undefined)) { - map[data[valueName]] = data[keyName]; - } - }); - - this.lkMap[colName] = map; - }, - - markDirty : function(dirty) { - this.dirty = dirty; - this.toggleButtons(); - LABKEY.Utils.signalWebDriverTest("pageDirty", dirty); - }, - - resetDirty : function() { - this.markDirty(false); - }, - - isDirty : function() { - return this.dirty; - }, - - beforeUnload : function() { - if (this.isDirty()) { - return 'please save your changes'; - } - }, - - /** - * grid column renderer for SSN's - * @private - */ - SSNRenderer : function(value, meta, rec, idx){ - - if (value && value.indexOf('-') == -1 && value.length == 9){ - return value.substr(0,3) + '-' + value.substr(3,2) + '-' + value.substr(5,4); - } - return value; - } -}); diff --git a/hdrl/src/org/labkey/hdrl/HDRLContainerListener.java b/hdrl/src/org/labkey/hdrl/HDRLContainerListener.java deleted file mode 100644 index 3bdef70c..00000000 --- a/hdrl/src/org/labkey/hdrl/HDRLContainerListener.java +++ /dev/null @@ -1,88 +0,0 @@ -/* - * Copyright (c) 2015-2019 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ - -package org.labkey.hdrl; - -import org.jetbrains.annotations.NotNull; -import org.labkey.api.data.Container; -import org.labkey.api.data.ContainerManager.ContainerListener; -import org.labkey.api.data.DatabaseTableType; -import org.labkey.api.data.DbSchema; -import org.labkey.api.data.DbScope; -import org.labkey.api.data.SQLFragment; -import org.labkey.api.data.SchemaTableInfo; -import org.labkey.api.data.SqlExecutor; -import org.labkey.api.security.User; -import org.labkey.api.util.ContainerUtil; -import org.labkey.hdrl.query.LabWareQuerySchema; - -import java.util.Collections; -import java.util.Collection; - -import java.beans.PropertyChangeEvent; - -public class HDRLContainerListener implements ContainerListener -{ - @Override - public void containerCreated(Container c, User user) - { - } - - @Override - public void containerDeleted(Container c, User user) - { - DbSchema hdrl = HDRLSchema.getInstance().getSchema(); - DbSchema labware = new LabWareQuerySchema(user, c).getSchema(); - try (DbScope.Transaction transaction = hdrl.getScope().ensureTransaction()) - { - deleteLabWareTable(labware, "X_LK_OUTBD_SPECIMENS", c); - deleteLabWareTable(labware, "X_LK_OUTBD_REQUESTS", c); - deleteLabWareTable(labware, "X_LK_INBND_SPECIMENS", c); - deleteLabWareTable(labware, "X_LK_INBND_REQUESTS", c); - - ContainerUtil.purgeTable(hdrl.getTable("InboundRequest"), c, null); - transaction.commit(); - } - } - - private void deleteLabWareTable(DbSchema labware, String labWareTable, Container container) - { - SqlExecutor executor = new SqlExecutor(labware.getScope()); - SchemaTableInfo tableInfo = labware.getTable("X_LK_OUTBD_SPECIMENS"); - if (tableInfo != null && tableInfo.getTableType() != DatabaseTableType.NOT_IN_DB) - { - SQLFragment deleteSQL = new SQLFragment("DELETE FROM gw_labkey.").append(labWareTable).append(" WHERE batch_id in (SELECT RequestId from hdrl.InboundRequest WHERE Container = ?)"); - deleteSQL.add(container.getId()); - executor.execute(deleteSQL); - } - } - - @Override - public void propertyChange(PropertyChangeEvent evt) - { - } - - @Override - public void containerMoved(Container c, Container oldParent, User user) - { - } - - @NotNull @Override - public Collection canMove(Container c, Container newParent, User user) - { - return Collections.emptyList(); - } -} \ No newline at end of file diff --git a/hdrl/src/org/labkey/hdrl/HDRLController.java b/hdrl/src/org/labkey/hdrl/HDRLController.java deleted file mode 100644 index a707daa2..00000000 --- a/hdrl/src/org/labkey/hdrl/HDRLController.java +++ /dev/null @@ -1,810 +0,0 @@ -/* - * Copyright (c) 2015-2019 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ - -package org.labkey.hdrl; - -import jakarta.servlet.http.HttpServletResponse; -import org.apache.commons.beanutils.BeanUtils; -import org.apache.commons.io.IOUtils; -import org.json.JSONArray; -import org.json.JSONException; -import org.json.JSONObject; -import org.labkey.api.action.ApiSimpleResponse; -import org.labkey.api.action.ApiUsageException; -import org.labkey.api.action.ExportAction; -import org.labkey.api.action.FormViewAction; -import org.labkey.api.action.Marshal; -import org.labkey.api.action.Marshaller; -import org.labkey.api.action.MutatingApiAction; -import org.labkey.api.action.ReadOnlyApiAction; -import org.labkey.api.action.SimpleApiJsonForm; -import org.labkey.api.action.SimpleViewAction; -import org.labkey.api.action.SpringActionController; -import org.labkey.api.admin.AdminUrls; -import org.labkey.api.collections.CaseInsensitiveHashMap; -import org.labkey.api.data.ContainerManager; -import org.labkey.api.data.Results; -import org.labkey.api.data.SimpleFilter; -import org.labkey.api.data.TableSelector; -import org.labkey.api.module.Module; -import org.labkey.api.module.ModuleLoader; -import org.labkey.api.query.FieldKey; -import org.labkey.api.query.QueryService; -import org.labkey.api.query.QuerySettings; -import org.labkey.api.query.QueryView; -import org.labkey.api.query.UserSchema; -import org.labkey.api.query.ValidationException; -import org.labkey.api.resource.Resource; -import org.labkey.api.security.AdminConsoleAction; -import org.labkey.api.security.RequiresPermission; -import org.labkey.api.security.permissions.AdminPermission; -import org.labkey.api.security.permissions.InsertPermission; -import org.labkey.api.security.permissions.ReadPermission; -import org.labkey.api.settings.AdminConsole; -import org.labkey.api.util.HtmlString; -import org.labkey.api.util.LinkBuilder; -import org.labkey.api.util.PageFlowUtil; -import org.labkey.api.util.Path; -import org.labkey.api.util.URLHelper; -import org.labkey.api.view.ActionURL; -import org.labkey.api.view.HtmlView; -import org.labkey.api.view.JspView; -import org.labkey.api.view.NavTree; -import org.labkey.api.view.NotFoundException; -import org.labkey.api.view.VBox; -import org.labkey.api.view.template.PageConfig; -import org.labkey.hdrl.query.HDRLQuerySchema; -import org.labkey.hdrl.query.InboundSpecimenUpdateService; -import org.labkey.hdrl.query.LabWareQuerySchema; -import org.labkey.hdrl.view.InboundRequestBean; -import org.labkey.hdrl.view.InboundSpecimenBean; -import org.springframework.validation.BindException; -import org.springframework.validation.Errors; -import org.springframework.web.servlet.ModelAndView; - -import java.io.IOException; -import java.util.ArrayList; -import java.util.Collections; -import java.util.Date; -import java.util.List; -import java.util.Map; -import java.util.Objects; - -public class HDRLController extends SpringActionController -{ - private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(HDRLController.class); - public static final String NAME = "hdrl"; - - public HDRLController() - { - setActionResolver(_actionResolver); - } - - public static void registerAdminConsoleLinks() - { - AdminConsole.addLink(AdminConsole.SettingsLinkType.Management, "HDRL Sensitive Data", new ActionURL(HDRLSensitiveDataAdminAction.class, ContainerManager.getRoot()), AdminPermission.class); - } - - @RequiresPermission(ReadPermission.class) - public class BeginAction extends SimpleViewAction - { - @Override - public ModelAndView getView(Object o, BindException errors) - { - VBox vbox = new VBox(); - - HtmlView submitView = new HtmlView("New Test Request", HtmlString.of(LinkBuilder.labkeyLink("Submit new test request", new ActionURL(EditRequestAction.class, getViewContext().getContainer())))); - vbox.addView(submitView); - - UserSchema schema = QueryService.get().getUserSchema(getUser(), getContainer(), HDRLQuerySchema.NAME); - - if (schema == null) - { - throw new NotFoundException("HDRL schema not found in the current folder."); - } - - QuerySettings settings = schema.getSettings(getViewContext(), QueryView.DATAREGIONNAME_DEFAULT, HDRLQuerySchema.TABLE_INBOUND_REQUEST); - QueryView queryView = schema.createView(getViewContext(), settings, errors); - queryView.setShowInsertNewButton(false); - queryView.setShowImportDataButton(false); - vbox.addView(queryView); - return vbox; - } - - @Override - public void addNavTrail(NavTree root) - { - root.addChild("HDRL Test Request Overview"); - } - } - - - @RequiresPermission(ReadPermission.class) - public static class RequestDetailsAction extends SimpleViewAction - { - @Override - public ModelAndView getView(Object o, BindException errors) - { - try - { - int requestId = Integer.parseInt(getViewContext().getRequest().getParameter("requestId")); - InboundRequestBean bean = HDRLManager.get().getInboundRequest(getUser(), getContainer(), requestId); - JspView jsp = new JspView<>("/org/labkey/hdrl/view/requestDetails.jsp", bean); - jsp.setTitle("Test Request"); - - UserSchema schema = QueryService.get().getUserSchema(getUser(), getContainer(), HDRLQuerySchema.NAME); - QuerySettings settings = schema.getSettings(getViewContext(), QueryView.DATAREGIONNAME_DEFAULT, HDRLQuerySchema.TABLE_SPECIMENS); - QueryView queryView = schema.createView(getViewContext(), settings, errors); - - jsp.setView("queryView", queryView); - return jsp; - } - catch (NumberFormatException x) - { - throw new ApiUsageException("RequestId is required"); - } - } - - @Override - public void addNavTrail(NavTree root) - { - root.addChild("Test Request"); - } - } - - @RequiresPermission(InsertPermission.class) - public static class EditRequestAction extends SimpleViewAction - { - private String _navLabel = "Create a new Test Request"; - - @Override - public ModelAndView getView(RequestForm form, BindException errors) throws Exception - { - if (form.getRequestId() != -1) - { - TableSelector selector = new TableSelector(org.labkey.hdrl.HDRLSchema.getInstance().getTableInfoInboundRequest()); - RequestForm object = selector.getObject(form.getRequestId(), RequestForm.class); - if (object != null) - { - _navLabel = "Edit a Test Request"; - BeanUtils.copyProperties(form, object); - } - else - { - form.setTestTypeId(1); // default to first test type - errors.reject(ERROR_MSG, "Request with id " + form.getRequestId() + " not found."); - } - } - else - { - form.setTestTypeId(1); // default to first test type - } - - if (form.getRequestStatusId() >= 2 && !getContainer().hasPermission(getUser(), AdminPermission.class)) - return HtmlView.of("This request has been submitted and is locked from editing."); - else - return new JspView<>("/org/labkey/hdrl/view/editRequest.jsp", form, errors); - } - - @Override - public void addNavTrail(NavTree root) - { - root.addChild(_navLabel); - } - } - - public static class RequestForm - { - private int _requestId = -1; - private Integer _requestStatusId = 1; - private Integer _shippingCarrierId; - private String _shippingNumber; - private Integer _testTypeId; - - public int getRequestId() - { - return _requestId; - } - - public void setRequestId(int requestId) - { - _requestId = requestId; - } - - public Integer getRequestStatusId() - { - return _requestStatusId; - } - - public void setRequestStatusId(Integer requestStatusId) - { - _requestStatusId = requestStatusId; - } - - public Integer getShippingCarrierId() - { - return _shippingCarrierId; - } - - public void setShippingCarrierId(Integer shippingCarrierId) - { - _shippingCarrierId = shippingCarrierId; - } - - public String getShippingNumber() - { - return _shippingNumber; - } - - public void setShippingNumber(String shippingNumber) - { - _shippingNumber = shippingNumber; - } - - public Integer getTestTypeId() - { - return _testTypeId; - } - - public void setTestTypeId(Integer testTypeId) - { - _testTypeId = testTypeId; - } - - } - - @RequiresPermission(ReadPermission.class) - public static class VerifySpecimenAction extends ReadOnlyApiAction - { - @Override - public Object execute(VerifyForm form, BindException errors) - { - ApiSimpleResponse response = new ApiSimpleResponse(); - JSONArray rows = Objects.requireNonNullElseGet(form.getJsonObject(), JSONObject::new).optJSONArray("rows"); - if (rows == null) - { - throw new ApiUsageException("rows not provided."); - } - List> rowsToValidate = new ArrayList<>(); - - for (int idx = 0; idx < rows.length(); ++idx) - { - JSONObject jsonObj; - try - { - jsonObj = rows.getJSONObject(idx); - } - catch (JSONException x) - { - throw new ApiUsageException("rows[" + idx + "] is not an object."); - } - if (null != jsonObj) - { - Map rowMap = new CaseInsensitiveHashMap<>(); - rowMap.putAll(jsonObj.toMap()); - - rowsToValidate.add(rowMap); - } - } - - // validate the rows - response.put("rows", rowsToValidate); - for (Map row : rowsToValidate) - { - try - { - InboundSpecimenUpdateService.validate(row); - } - catch (ValidationException ignored) - { - } - } - return response; - } - } - - public static class VerifyForm extends SimpleApiJsonForm - { - } - - - @RequiresPermission(ReadPermission.class) - public static class DownloadClinicalReportAction extends ExportAction - { - @Override - public void export(SpecimenForm form, HttpServletResponse response, BindException errors) throws Exception - { - LabWareQuerySchema lwSchema = new LabWareQuerySchema(getUser(), getContainer()); - SimpleFilter filter = new SimpleFilter(FieldKey.fromParts("test_request_id"), form.getSpecimenId()); - TableSelector selector = new TableSelector(lwSchema.getSchema().getTable(LabWareQuerySchema.TABLE_OUTBOUND_SPECIMENS), filter, null); - - try (Results result = selector.getResults(false)) - { - if (!result.next()) - throw new NotFoundException("No report available for specimen " + form.getSpecimenId()); - - String contentType = "application/pdf"; - - byte[] documentBytes = IOUtils.toByteArray(result.getBinaryStream("clinical_report")); - - response.setContentType(contentType); - response.setHeader("Content-Disposition", "attachment; filename=\"" + result.getString("report_file_name") + "\""); - response.setContentLength(documentBytes.length); - response.getOutputStream().write(documentBytes); - } - } - - @Override - public void validate(SpecimenForm form, BindException errors) - { - if (form.getSpecimenId() == null) - { - errors.reject(ERROR_MSG, "SpecimenId is required"); - } - } - } - - public static class SpecimenForm - { - private Integer _specimenId; - - public Integer getSpecimenId() - { - return _specimenId; - } - - public void setSpecimenId(Integer specimenId) - { - _specimenId = specimenId; - } - } - - @RequiresPermission(ReadPermission.class) - public static class DownloadSpecimenTemplateAction extends ExportAction - { - @Override - public void export(Object o, HttpServletResponse response, BindException errors) - { - // just download the example file checked into the repository - Module module = ModuleLoader.getInstance().getModule(HDRLModule.NAME); - Path path = Path.parse("template/").append("specimenTemplate.xlsx"); - Resource r = module.getModuleResource(path); - if (r != null && r.isFile()) - { - try - { - PageFlowUtil.streamFile(response, Collections.emptyMap(), r.getName(), r.getInputStream(), false); - } - catch (IOException ioe) - { - throw new RuntimeException(ioe); - } - } - } - } - - @RequiresPermission(ReadPermission.class) - public static class PrintPackingListAction extends SimpleViewAction - { - @Override - public ModelAndView getView(PackingListBean packingListBean, BindException errors) - { - List inboundSpecimenRows = HDRLManager.get().getInboundSpecimen(packingListBean.getRequestId()); - InboundRequestBean inboundRequestBean = HDRLManager.get().getInboundRequest(getUser(), getContainer(), packingListBean.getRequestId()); - - packingListBean.setInboundSpecimens(inboundSpecimenRows); - packingListBean.setTotalSamples(inboundSpecimenRows.size()); - packingListBean.setTestType(inboundRequestBean.getTestType()); - packingListBean.setShippingNumber(inboundRequestBean.getShippingNumber()); - packingListBean.setShippingCarrier(inboundRequestBean.getShippingCarrier()); - - JspView view = new JspView<>("/org/labkey/hdrl/view/printPackingList.jsp", packingListBean, errors); - getPageConfig().setTitle("Shipping Manifest"); - getPageConfig().setTemplate(PageConfig.Template.Print); - - return view; - } - - @Override - public void addNavTrail(NavTree root) - { - } - } - - public static class PackingListBean - { - private int _requestId = -1; - private String _shippingCarrier; - private int _totalSamples; - private String _testType; - private String _shippingNumber; - private List _inboundSpecimens; - - public int getRequestId() - { - return _requestId; - } - - public void setRequestId(int requestId) - { - _requestId = requestId; - } - - public List getInboundSpecimens() - { - return _inboundSpecimens; - } - - public void setInboundSpecimens(List inboundSpecimens) - { - _inboundSpecimens = inboundSpecimens; - } - - public String getShippingCarrier() - { - return _shippingCarrier; - } - - public void setShippingCarrier(String shippingCarrier) - { - _shippingCarrier = shippingCarrier; - } - - public int getTotalSamples() - { - return _totalSamples; - } - - public void setTotalSamples(int totalSamples) - { - _totalSamples = totalSamples; - } - - public String getTestType() - { - return _testType; - } - - public void setTestType(String testType) - { - _testType = testType; - } - public String getShippingNumber() - { - return _shippingNumber; - } - - public void setShippingNumber(String shippingNumber) - { - _shippingNumber = shippingNumber; - } - } - - @AdminConsoleAction - @RequiresPermission(AdminPermission.class) - public static class HDRLSensitiveDataAdminAction extends FormViewAction - { - @Override - public void validateCommand(SensitiveDataForm target, Errors errors) - { - if (target.getTimeWindowInDays() < 0) - { - errors.reject(ERROR_MSG, "'Number of Days' cannot be negative, it should be greater than or equal to 0."); - } - } - - @Override - public ModelAndView getView(SensitiveDataForm sensitiveDataForm, boolean reshow, BindException errors) - { - return new JspView<>("/org/labkey/hdrl/view/sensitiveData.jsp", sensitiveDataForm, errors); - } - - @Override - public boolean handlePost(SensitiveDataForm sensitiveDataForm, BindException errors) - { - HDRLManager.saveProperties(sensitiveDataForm); - return true; - } - - @Override - public URLHelper getSuccessURL(SensitiveDataForm sensitiveDataForm) - { - return urlProvider(AdminUrls.class).getAdminConsoleURL(); - } - - @Override - public void addNavTrail(NavTree root) - { - urlProvider(AdminUrls.class).addAdminNavTrail(root, "HDRL Sensitive Data Time Window", getClass(), getContainer()); - } - } - - public static class SensitiveDataForm - { - private int timeWindowInDays = HDRLManager.getNumberOfDays(); - - public int getTimeWindowInDays() - { - return timeWindowInDays; - } - - public void setTimeWindowInDays(int timeWindowInDays) - { - this.timeWindowInDays = timeWindowInDays; - } - } - - @RequiresPermission(AdminPermission.class) - @Marshal(Marshaller.Jackson) - public static class AddLabWareOutboundRequestAction extends MutatingApiAction - { - @Override - public Object execute(LabWareOutboundRequestForm form, BindException errors) - { - HDRLManager.get().insertLabWareOutboundRequest(form, getUser(), getContainer()); - - return success(); - } - - @Override - public void validateForm(LabWareOutboundRequestForm form, Errors errors) - { - if (form.getBatchId() == null) - errors.rejectValue("batchId", ERROR_MSG, "batchId is required"); - if (form.getDateReceived() == null) - errors.rejectValue("dateReceived", ERROR_MSG, "dateReceived is required"); - if (form.getDateModified() == null) - errors.rejectValue("dateModified", ERROR_MSG, "dateModified is required"); - if (form.getHdrlStatus() == null) - errors.rejectValue("hdrlStatus", ERROR_MSG, "hdrlStatus is required"); - } - } - - public static class LabWareOutboundRequestForm - { - private Integer _batchId; - private String _hdrlStatus; - private String _customerNote; - private Date _dateReceived; - private Date _dateCompleted; - private Date _dateModified; - - public Integer getBatchId() - { - return _batchId; - } - - public void setBatchId(Integer batchId) - { - _batchId = batchId; - } - - public String getCustomerNote() - { - return _customerNote; - } - - public void setCustomerNote(String customerNote) - { - _customerNote = customerNote; - } - - public Date getDateCompleted() - { - return _dateCompleted; - } - - public void setDateCompleted(Date dateCompleted) - { - _dateCompleted = dateCompleted; - } - - public Date getDateReceived() - { - return _dateReceived; - } - - public void setDateReceived(Date dateReceived) - { - _dateReceived = dateReceived; - } - - public String getHdrlStatus() - { - return _hdrlStatus; - } - - public void setHdrlStatus(String hdrlStatus) - { - _hdrlStatus = hdrlStatus; - } - - public Date getDateModified() - { - return _dateModified; - } - - public void setDateModified(Date dateModified) - { - _dateModified = dateModified; - } - } - - @RequiresPermission(AdminPermission.class) - @Marshal(Marshaller.Jackson) - public static class AddLabWareOutboundSpecimenAction extends MutatingApiAction - { - @Override - public Object execute(LabWareOutboundSpecimenForm form, BindException errors) throws Exception - { - HDRLManager.get().insertLabWareOutboundSpecimen(form, getUser(), getContainer()); - - return success(); - } - - @Override - public void validateForm(LabWareOutboundSpecimenForm form, Errors errors) - { - if (form.getTestRequestId() == null) - errors.rejectValue("testRequestId", ERROR_MSG, "testRequestId is required"); - if (form.getBatchId() == null) - errors.rejectValue("batchId", ERROR_MSG, "batchId is required"); - if (form.getDateReceived() == null) - errors.rejectValue("dateReceived", ERROR_MSG, "dateReceived is required"); - if (form.getDateModified() == null) - errors.rejectValue("dateModified", ERROR_MSG, "dateModified is required"); - if (form.getHdrlStatus() == null) - errors.rejectValue("hdrlStatus", ERROR_MSG, "hdrlStatus is required"); - } - } - - public static class LabWareOutboundSpecimenForm - { - private Integer _testRequestId; - private Integer _batchId; - private Date _dateReceived; - private Date _dateCompleted; - private String _sampleIntegrity; - private String _testResult; - private String _customerCode; - private String _clinicalReportFile; - private String _hdrlStatus; - private Date _dateModified; - private String _modifiedResultFlag; - private String _reportFileName; - - public Integer getBatchId() - { - return _batchId; - } - - public void setBatchId(Integer batchId) - { - _batchId = batchId; - } - - public String getClinicalReportFile() - { - return _clinicalReportFile; - } - - public void setClinicalReportFile(String clinicalReportFile) - { - _clinicalReportFile = clinicalReportFile; - } - - public String getHdrlStatus() - { - return _hdrlStatus; - } - - public void setHdrlStatus(String hdrlStatus) - { - _hdrlStatus = hdrlStatus; - } - - public String getCustomerCode() - { - return _customerCode; - } - - public void setCustomerCode(String customerCode) - { - _customerCode = customerCode; - } - - public Date getDateCompleted() - { - return _dateCompleted; - } - - public void setDateCompleted(Date dateCompleted) - { - _dateCompleted = dateCompleted; - } - - public Date getDateModified() - { - return _dateModified; - } - - public void setDateModified(Date dateModified) - { - _dateModified = dateModified; - } - - public Date getDateReceived() - { - return _dateReceived; - } - - public void setDateReceived(Date dateReceived) - { - _dateReceived = dateReceived; - } - - public String getModifiedResultFlag() - { - return _modifiedResultFlag; - } - - public void setModifiedResultFlag(String modifiedResultFlag) - { - _modifiedResultFlag = modifiedResultFlag; - } - - public String getSampleIntegrity() - { - return _sampleIntegrity; - } - - public void setSampleIntegrity(String sampleIntegrity) - { - _sampleIntegrity = sampleIntegrity; - } - - public Integer getTestRequestId() - { - return _testRequestId; - } - - public void setTestRequestId(Integer testRequestId) - { - _testRequestId = testRequestId; - } - - public String getTestResult() - { - return _testResult; - } - - public void setTestResult(String testResult) - { - _testResult = testResult; - } - - public String getReportFileName() - { - return _reportFileName; - } - - public void setReportFileName(String reportFileName) - { - _reportFileName = reportFileName; - } - } - -} \ No newline at end of file diff --git a/hdrl/src/org/labkey/hdrl/HDRLFolderType.java b/hdrl/src/org/labkey/hdrl/HDRLFolderType.java deleted file mode 100644 index 51daed65..00000000 --- a/hdrl/src/org/labkey/hdrl/HDRLFolderType.java +++ /dev/null @@ -1,39 +0,0 @@ -/* - * Copyright (c) 2015-2016 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -package org.labkey.hdrl; - -import org.labkey.api.module.MultiPortalFolderType; -import org.labkey.api.view.Portal; - -import java.util.Arrays; -import java.util.Collections; - -/** - * Created by: jeckels - * Date: 5/10/15 - */ -public class HDRLFolderType extends MultiPortalFolderType -{ - public HDRLFolderType(HDRLModule module) - { - super("HDRL Request Portal", - "HDRL portal for submitting assay requests and receiving results.", - Collections.emptyList(), - Arrays.asList(Portal.getPortalPart("HDRL Summary").createWebPart()), - Collections.singleton(module), - module); - } -} diff --git a/hdrl/src/org/labkey/hdrl/HDRLMaintenanceTask.java b/hdrl/src/org/labkey/hdrl/HDRLMaintenanceTask.java deleted file mode 100644 index 4a7b2a2e..00000000 --- a/hdrl/src/org/labkey/hdrl/HDRLMaintenanceTask.java +++ /dev/null @@ -1,115 +0,0 @@ -/* - * Copyright (c) 2015-2016 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -package org.labkey.hdrl; - -import org.apache.logging.log4j.Logger; -import org.labkey.api.data.DbSchema; -import org.labkey.api.data.DbScope; -import org.labkey.api.data.SQLFragment; -import org.labkey.api.data.SqlExecutor; -import org.labkey.api.util.SystemMaintenance.MaintenanceTask; -import org.labkey.hdrl.query.HDRLQuerySchema; - -import java.util.Calendar; - -/** - * Created by: jeckels - * Date: 5/10/15 - */ -public class HDRLMaintenanceTask implements MaintenanceTask -{ - @Override - public String getDescription() - { - return "HDRL Request Portal PHI Deletion"; - } - - @Override - public String getName() - { - return "HdrlPhiDeletion"; - } - - @Override - public void run(Logger log) - { - // Get this from the configurable setting - int retentionDays = HDRLManager.getNumberOfDays(); - final String requestStatusStatement = HDRLQuerySchema.COL_REQUEST_STATUS_ID + " = " + "(SELECT rowid FROM hdrl.requeststatus WHERE name = ?)"; - final String submittedCondition1 = " WHERE (" + HDRLSchema.getInstance().getSchema().getSqlDialect().getDateDiff(Calendar.DATE, "NOW()", "r.Completed") + " >= ?"; - final String submittedCondition2 = " AND i." + requestStatusStatement + ")"; - - DbSchema hdrl = HDRLSchema.getInstance().getSchema(); - try (DbScope.Transaction transaction = hdrl.getScope().ensureTransaction()) - { - // Need to stash the number of specimens in the request table, prior to deleting the specimen rows - SQLFragment addToArchivedRequestCountColSQL = new SQLFragment("UPDATE "); - addToArchivedRequestCountColSQL.append(HDRLSchema.getInstance().getTableInfoInboundRequest(), "i"); - addToArchivedRequestCountColSQL.append(" SET " + HDRLQuerySchema.COL_ARCHIVED_REQUEST_COUNT + " = (SELECT COUNT(*) FROM "); - addToArchivedRequestCountColSQL.append(HDRLSchema.getInstance().getTableInfoInboundSpecimen(), "s"); - addToArchivedRequestCountColSQL.append(" WHERE s." + HDRLQuerySchema.COL_INBOUND_REQUEST_ID + " = i.RequestId)"); - addToArchivedRequestCountColSQL.append(" FROM ").append(HDRLSchema.getInstance().getTableInfoRequestResult(), "r"); - addToArchivedRequestCountColSQL.append(submittedCondition1); - addToArchivedRequestCountColSQL.add(retentionDays); - addToArchivedRequestCountColSQL.append(submittedCondition2); - addToArchivedRequestCountColSQL.add(HDRLQuerySchema.STATUS_SUBMITTED); - - // Need to stash the number of specimens in the request table, prior to deleting the specimen rows - SQLFragment updateStatusSql = new SQLFragment("UPDATE "); - updateStatusSql.append(HDRLSchema.getInstance().getTableInfoRequestResult(), "r"); - updateStatusSql.append(" SET " + requestStatusStatement); - updateStatusSql.add(HDRLQuerySchema.STATUS_ARCHIVED); - updateStatusSql.append(" FROM ").append(HDRLSchema.getInstance().getTableInfoInboundRequest(), "i"); - updateStatusSql.append(submittedCondition1); - updateStatusSql.add(retentionDays); - updateStatusSql.append(submittedCondition2); - updateStatusSql.add(HDRLQuerySchema.STATUS_SUBMITTED); - - log.info("Adding specimen count to column '" + HDRLQuerySchema.COL_ARCHIVED_REQUEST_COUNT + "' in table " + HDRLSchema.getInstance().getTableInfoInboundRequest().getName()); - - int numRequests = new SqlExecutor(HDRLSchema.getInstance().getScope()).execute(addToArchivedRequestCountColSQL); - - log.info("Finished adding specimen count to column '" + HDRLQuerySchema.COL_ARCHIVED_REQUEST_COUNT + "' in table " - + HDRLSchema.getInstance().getTableInfoInboundRequest().getName() - +". Added specimen counts to " + numRequests +" rows."); - - log.info("Updating request status in table " + HDRLSchema.getInstance().getTableInfoRequestResult().getName()); - - numRequests = new SqlExecutor(HDRLSchema.getInstance().getScope()).execute(updateStatusSql); - - log.info("Updated " + numRequests + " rows "); - - log.info("Starting to delete HDRL specimen data"); - - // Delete specimens for requests that have been archived - // specimen results are deleted via cascading - SQLFragment specimenDeleteSQL = new SQLFragment("DELETE FROM "); - specimenDeleteSQL.append(HDRLSchema.getInstance().getTableInfoInboundSpecimen(), "s"); - specimenDeleteSQL.append(" WHERE " + HDRLQuerySchema.COL_INBOUND_REQUEST_ID + " IN (SELECT r.RequestId FROM "); - specimenDeleteSQL.append(HDRLSchema.getInstance().getTableInfoRequestResult(), "r"); - specimenDeleteSQL.append(" WHERE " + requestStatusStatement); - specimenDeleteSQL.add(HDRLQuerySchema.STATUS_ARCHIVED); - specimenDeleteSQL.append(")"); - - int inboundRowCount = new SqlExecutor(HDRLSchema.getInstance().getScope()).execute(specimenDeleteSQL); - - - log.info("Deleted " + inboundRowCount + " row(s) of HDRL inbound specimen data"); - - transaction.commit(); - } - } -} diff --git a/hdrl/src/org/labkey/hdrl/HDRLManager.java b/hdrl/src/org/labkey/hdrl/HDRLManager.java deleted file mode 100644 index eea5a106..00000000 --- a/hdrl/src/org/labkey/hdrl/HDRLManager.java +++ /dev/null @@ -1,199 +0,0 @@ -/* - * Copyright (c) 2015-2019 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ - -package org.labkey.hdrl; - -import org.apache.commons.lang3.StringUtils; -import org.apache.logging.log4j.LogManager; -import org.apache.logging.log4j.Logger; -import org.labkey.api.attachments.InputStreamAttachmentFile; -import org.labkey.api.data.CompareType; -import org.labkey.api.data.Container; -import org.labkey.api.data.PropertyManager; -import org.labkey.api.data.PropertyManager.WritablePropertyMap; -import org.labkey.api.data.SQLFragment; -import org.labkey.api.data.SimpleFilter; -import org.labkey.api.data.SqlSelector; -import org.labkey.api.data.Table; -import org.labkey.api.data.TableSelector; -import org.labkey.api.query.FieldKey; -import org.labkey.api.query.QueryService; -import org.labkey.api.query.UserSchema; -import org.labkey.api.security.User; -import org.labkey.api.view.NotFoundException; -import org.labkey.hdrl.query.HDRLQuerySchema; -import org.labkey.hdrl.query.LabWareQuerySchema; -import org.labkey.hdrl.view.InboundRequestBean; -import org.labkey.hdrl.view.InboundSpecimenBean; - -import java.io.File; -import java.io.FileInputStream; -import java.io.FileNotFoundException; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -public class HDRLManager -{ - private static final Logger LOG = LogManager.getLogger(HDRLManager.class); - private static final String HDRL_SENSITIVE_DATA_TIME_WINDOW = "hdrlSensitiveDataDeletionTimeWindow"; - private static final String NUM_OF_DAYS_KEY = "HDRLSensitiveDataDeletionWindow"; - private static final int DEFAULT_NUM_OF_DAYS = 30; //default number of days after which data will be deleted - - private static final HDRLManager _instance = new HDRLManager(); - - private HDRLManager() - { - // prevent external construction with a private default constructor - } - - public static HDRLManager get() - { - return _instance; - } - - public InboundRequestBean getInboundRequest(User user, Container container, Integer requestId) - { - UserSchema schema = QueryService.get().getUserSchema(user, container, HDRLQuerySchema.NAME); - if (schema == null) - throw new NotFoundException(HDRLModule.NAME + " module is not enabled in this container."); - - SQLFragment sql = new SQLFragment("SELECT r.RequestId, r.ShippingNumber, s.Name as RequestStatus, c.Name as ShippingCarrier, t.Name as TestType FROM "); - sql.append("(SELECT * FROM hdrl.InboundRequest WHERE (Container = ?) AND (RequestId = ?)) r "); - sql.add(container); - sql.add(requestId); - sql.append("LEFT JOIN hdrl.ShippingCarrier c on r.ShippingCarrierId = c.RowId ") - .append("LEFT JOIN hdrl.TestType t on r.TestTypeId = t.RowId ") - .append("LEFT JOIN hdrl.RequestStatus s on r.RequestStatusId = s.RowId "); - - - SqlSelector sqlSelector = new SqlSelector(schema.getDbSchema(), sql); - InboundRequestBean inboundRequestBean = sqlSelector.getObject(InboundRequestBean.class); - if (inboundRequestBean == null) - throw new NotFoundException("Request %s not found.".formatted(requestId)); - return inboundRequestBean; - } - - public List getInboundSpecimen(int requestId) - { - String joinStatement = "SELECT hdrl.inboundspecimen.*, hdrl.gender.code as genderId, hdrl.familymemberprefix.code as fmpCode, hdrl.dutycode.code as ducCode, hdrl.sourceoftesting.code as sotCode" + - " FROM hdrl.inboundspecimen" + - " LEFT JOIN hdrl.gender" + - " ON hdrl.inboundspecimen.genderId=hdrl.gender.rowid" + - " LEFT JOIN hdrl.familymemberprefix" + - " ON hdrl.inboundspecimen.fmpid=hdrl.familymemberprefix.rowid" + - " LEFT JOIN hdrl.dutycode" + - " ON hdrl.inboundspecimen.dutycodeid=hdrl.dutycode.rowid" + - " LEFT JOIN hdrl.sourceoftesting" + - " ON hdrl.inboundspecimen.testingsourceid=hdrl.sourceoftesting.rowid" + - " WHERE hdrl.inboundspecimen.inboundrequestid = ?"; - - SQLFragment sql = new SQLFragment(); - sql.append(joinStatement); - sql.add(requestId); - - SqlSelector selector = new SqlSelector(HDRLSchema.getInstance().getTableInfoInboundSpecimen().getSchema(), sql); - return selector.getArrayList(InboundSpecimenBean.class); - } - - public static void saveProperties(HDRLController.SensitiveDataForm sensitiveDataForm) - { - WritablePropertyMap map = PropertyManager.getNormalStore().getWritableProperties(HDRL_SENSITIVE_DATA_TIME_WINDOW, true); - map.clear(); - map.put(NUM_OF_DAYS_KEY, String.valueOf(sensitiveDataForm.getTimeWindowInDays())); - map.save(); - } - - private static Map getProperties() - { - return PropertyManager.getNormalStore().getProperties(HDRL_SENSITIVE_DATA_TIME_WINDOW); - } - - public static int getNumberOfDays() - { - String days = getProperties().get(NUM_OF_DAYS_KEY); - - if (StringUtils.isEmpty(days)) - { - return DEFAULT_NUM_OF_DAYS; - } - - return Integer.parseInt(days); - } - - /** - * This method is used only for populating results in the Postgres Labware outbound tables for testing. - * @param resultData - the data to populate the row in the table - * @param user - current user - * @param container - current container - */ - public void insertLabWareOutboundRequest(HDRLController.LabWareOutboundRequestForm resultData, User user, Container container) - { - LabWareQuerySchema lwSchema = new LabWareQuerySchema(user, container); - // create the request data for LabWare - Map labWareData = new HashMap<>(); - labWareData.put("batch_id", resultData.getBatchId()); - labWareData.put("hdrl_status", resultData.getHdrlStatus()); - labWareData.put("customer_note", resultData.getCustomerNote()); - labWareData.put("date_received", resultData.getDateReceived()); - labWareData.put("date_completed", resultData.getDateCompleted()); - labWareData.put("date_modified", resultData.getDateModified()); - Table.insert(user, lwSchema.getDbSchema().getTable(LabWareQuerySchema.TABLE_OUTBOUND_REQUESTS), labWareData); - } - - /** - * This method is used only for populating results in the Postgres LabWare outbound tables for testing. - * If a clinical report file is provided, this will not work when the labwareDataSource is an Oracle database - * @param resultData - the data to populate the row in the table - * @param user - current user - * @param container - current container - * @throws FileNotFoundException if the name of the clinical report file supplied is not available - */ - public void insertLabWareOutboundSpecimen(HDRLController.LabWareOutboundSpecimenForm resultData, User user, Container container) throws FileNotFoundException - { - LabWareQuerySchema lwSchema = new LabWareQuerySchema(user, container); - // create the request data for LabWare - Map labWareData = new HashMap<>(); - labWareData.put("test_request_id", resultData.getTestRequestId()); - labWareData.put("hdrl_status", resultData.getHdrlStatus()); - labWareData.put("batch_id", resultData.getBatchId()); - labWareData.put("date_received", resultData.getDateReceived()); - labWareData.put("date_completed", resultData.getDateCompleted()); - labWareData.put("date_modified", resultData.getDateModified()); - labWareData.put("sample_integrity", resultData.getSampleIntegrity()); - labWareData.put("test_result", resultData.getTestResult()); - labWareData.put("customer_code", resultData.getCustomerCode()); - labWareData.put("modified_result_flag", resultData.getModifiedResultFlag()); - labWareData.put("report_file_name", resultData.getReportFileName()); - - if (resultData.getClinicalReportFile() != null) - { - FileInputStream stream = new FileInputStream(new File(resultData.getClinicalReportFile())); - InputStreamAttachmentFile attachment = new InputStreamAttachmentFile(stream, resultData.getClinicalReportFile()); - labWareData.put("clinical_report", attachment); - } - Table.insert(user, lwSchema.getDbSchema().getTable(LabWareQuerySchema.TABLE_OUTBOUND_SPECIMENS), labWareData); - } - - public boolean hasClinicalReport(int specimenId, User user, Container container) - { - LabWareQuerySchema lwSchema = new LabWareQuerySchema(user, container); - SimpleFilter filter = new SimpleFilter(FieldKey.fromParts("test_request_id"), specimenId); - filter.addCondition(FieldKey.fromParts("clinical_report"), null, CompareType.NONBLANK); - - return new TableSelector(lwSchema.getSchema().getTable(LabWareQuerySchema.TABLE_OUTBOUND_SPECIMENS), filter, null).exists(); - } -} \ No newline at end of file diff --git a/hdrl/src/org/labkey/hdrl/HDRLSchema.java b/hdrl/src/org/labkey/hdrl/HDRLSchema.java deleted file mode 100644 index db4da000..00000000 --- a/hdrl/src/org/labkey/hdrl/HDRLSchema.java +++ /dev/null @@ -1,74 +0,0 @@ -/* - * Copyright (c) 2015 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -package org.labkey.hdrl; - -import org.labkey.api.data.DbSchema; -import org.labkey.api.data.DbSchemaType; -import org.labkey.api.data.DbScope; -import org.labkey.api.data.TableInfo; - -/** - * Created by klum on 4/18/15. - */ -public class HDRLSchema -{ - private static final HDRLSchema instance = new HDRLSchema(); - private static final String SCHEMA_NAME = "hdrl"; - - public static HDRLSchema getInstance() - { - return instance; - } - - private HDRLSchema() - { - } - - public String getSchemaName() - { - return SCHEMA_NAME; - } - - public DbSchema getSchema() - { - return DbSchema.get(SCHEMA_NAME, DbSchemaType.Module); - } - - public DbScope getScope() - { - return getSchema().getScope(); - } - - public TableInfo getTableInfoInboundRequest() - { - return getSchema().getTable("InboundRequest"); - } - - public TableInfo getTableInfoInboundSpecimen() - { - return getSchema().getTable("InboundSpecimen"); - } - - public TableInfo getTableInfoRequestResult() - { - return getSchema().getTable("RequestResult"); - } - - public TableInfo getTableInfoSpecimenResult() - { - return getSchema().getTable("SpecimenResult"); - } -} diff --git a/hdrl/src/org/labkey/hdrl/query/InboundRequestTable.java b/hdrl/src/org/labkey/hdrl/query/InboundRequestTable.java deleted file mode 100644 index 0690cbb6..00000000 --- a/hdrl/src/org/labkey/hdrl/query/InboundRequestTable.java +++ /dev/null @@ -1,96 +0,0 @@ -/* - * Copyright (c) 2015-2019 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -package org.labkey.hdrl.query; - -import org.jetbrains.annotations.NotNull; -import org.jetbrains.annotations.Nullable; -import org.labkey.api.data.ContainerFilter; -import org.labkey.api.data.ContainerForeignKey; -import org.labkey.api.data.DatabaseTableType; -import org.labkey.api.data.ForeignKey; -import org.labkey.api.data.JdbcType; -import org.labkey.api.data.SQLFragment; -import org.labkey.api.data.TableInfo; -import org.labkey.api.query.ExprColumn; -import org.labkey.api.query.FilteredTable; -import org.labkey.api.query.QueryUpdateService; -import org.labkey.api.security.UserPrincipal; -import org.labkey.api.security.permissions.Permission; - -/** - * Created by susanh on 4/13/15. - */ -public class InboundRequestTable extends FilteredTable -{ - public InboundRequestTable(HDRLQuerySchema schema, ContainerFilter cf) - { - super(schema.getDbSchema().getTable(schema.TABLE_INBOUND_REQUEST), schema, cf); - - // wrap all the existing columns - wrapAllColumns(true); - - var containerCol = getMutableColumn("Container"); - ContainerForeignKey.initColumn(containerCol, schema); - containerCol.setLabel("Folder"); - - var archivedRequestCountCol = getMutableColumn("ArchivedRequestCount"); - archivedRequestCountCol.setHidden(true); - - // add column for the number of patients - addColumn(wrapColumn("Number of Patients", new PatientCountColumn(getRealTable().getColumn("RequestId")))); - addCoalescedStatusColumn(); - addResultColumn("customerNote", "Customer Note", JdbcType.VARCHAR); - addResultColumn("received", "Received", JdbcType.DATE); - addResultColumn("completed", "Completed", JdbcType.DATE); - } - - - private void addResultColumn(String fieldName, String alias, JdbcType type) - { - SQLFragment sql = new SQLFragment("(SELECT " + fieldName + " FROM " + HDRLQuerySchema.NAME + "." + HDRLQuerySchema.TABLE_REQUEST_RESULT + " R WHERE R.RequestId = " + ExprColumn.STR_TABLE_ALIAS + ".requestId)"); - ExprColumn col = new ExprColumn(this, alias, sql, type); - addColumn(col); - } - - private void addCoalescedStatusColumn() - { - var requestStatusCol = getMutableColumn("RequestStatusId"); - requestStatusCol.setHidden(true); - ForeignKey statusColFk = requestStatusCol.getFk(); - SQLFragment sql = new SQLFragment("COALESCE((SELECT R.requestStatusId FROM " + HDRLQuerySchema.NAME + "." + HDRLQuerySchema.TABLE_REQUEST_RESULT + " R WHERE R.RequestId = " + ExprColumn.STR_TABLE_ALIAS + ".requestId), RequestStatusId)"); - - ExprColumn col = new ExprColumn(this, "Status", sql, JdbcType.INTEGER); - col.setFk(statusColFk); - addColumn(col); - } - - @Nullable - @Override - public QueryUpdateService getUpdateService() - { - TableInfo table = getRealTable(); - if (table != null && table.getTableType() == DatabaseTableType.TABLE) - return new InboundRequestUpdateService(this, table); - - return null; - } - - @Override - public boolean hasPermission(@NotNull UserPrincipal user, @NotNull Class perm) - { - return getContainer().hasPermission(user, perm); - } -} diff --git a/hdrl/src/org/labkey/hdrl/query/InboundRequestUpdateService.java b/hdrl/src/org/labkey/hdrl/query/InboundRequestUpdateService.java deleted file mode 100644 index a8085053..00000000 --- a/hdrl/src/org/labkey/hdrl/query/InboundRequestUpdateService.java +++ /dev/null @@ -1,229 +0,0 @@ -/* - * Copyright (c) 2015-2019 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -package org.labkey.hdrl.query; - -import org.apache.commons.lang3.StringUtils; -import org.jetbrains.annotations.NotNull; -import org.jetbrains.annotations.Nullable; -import org.labkey.api.data.Container; -import org.labkey.api.data.DbScope; -import org.labkey.api.data.Results; -import org.labkey.api.data.SQLFragment; -import org.labkey.api.data.SimpleFilter; -import org.labkey.api.data.SqlSelector; -import org.labkey.api.data.Table; -import org.labkey.api.data.TableInfo; -import org.labkey.api.data.TableSelector; -import org.labkey.api.query.DefaultQueryUpdateService; -import org.labkey.api.query.DuplicateKeyException; -import org.labkey.api.query.FieldKey; -import org.labkey.api.query.InvalidKeyException; -import org.labkey.api.query.QueryUpdateServiceException; -import org.labkey.api.query.ValidationException; -import org.labkey.api.security.User; -import org.labkey.api.util.PageFlowUtil; -import org.labkey.hdrl.HDRLSchema; -import org.labkey.hdrl.view.InboundSpecimenBean; - -import java.sql.SQLException; -import java.util.Date; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -/** - * Created by klum on 4/14/2015. - */ -public class InboundRequestUpdateService extends DefaultQueryUpdateService -{ - public InboundRequestUpdateService(TableInfo queryTable, TableInfo dbTable) - { - super(queryTable, dbTable); - } - - @Override - protected Map insertRow(User user, Container container, Map row) throws DuplicateKeyException, ValidationException, QueryUpdateServiceException, SQLException - { - HDRLQuerySchema lkSchema = new HDRLQuerySchema(user, container); - - try (DbScope.Transaction lkTransaction = lkSchema.getSchema().getScope().ensureTransaction()) - { - boolean isSubmit = ((int) row.get("requestStatusId")) == 2; // this is a "Submitted" status from the requestStatus lookup table - if (isSubmit) - { - row.put("SubmittedBy", user.getUserId()); - row.put("Submitted", new Date()); - } - Map insertedRow = super.insertRow(user, container, row); - if (isSubmit) - { - pushDataToLabWare(user, container, insertedRow); - } - lkTransaction.commit(); - return insertedRow; - } - - } - - @Override - protected Map updateRow(final User user, final Container container, Map row, @NotNull Map oldRow, @Nullable Map configParameters) throws InvalidKeyException, ValidationException, QueryUpdateServiceException, SQLException - { - HDRLQuerySchema lkSchema = new HDRLQuerySchema(user, container); - - try (DbScope.Transaction lkTransaction = lkSchema.getSchema().getScope().ensureTransaction()) - { - boolean isNewSubmit = (boolean) row.get("isNewSubmit"); - if (isNewSubmit) - { - validateUniqueness((Integer) row.get("requestId")); - row.put("SubmittedBy", user.getUserId()); - row.put("Submitted", new Date()); - } - final Map updatedRow = super.updateRow(user, container, row, oldRow, configParameters); - if (isNewSubmit) - { - pushDataToLabWare(user, container, updatedRow); - } - lkTransaction.commit(); - return updatedRow; - } - } - - public static void validateUniqueness(Integer requestId) throws QueryUpdateServiceException - { - // check that there are no duplicate barcodes - List duplicates = findDuplicates(requestId, "CustomerBarcode"); - StringBuilder message = new StringBuilder(); - if (!duplicates.isEmpty()) - { - message.append("Request has specimens with duplicate fields: Customer Barcode - ").append(StringUtils.join(duplicates, ", ")); - } - - // check that all existing DODId in the specimens in this request are unique - duplicates = findDuplicates(requestId, "DoDId"); - if (!duplicates.isEmpty()) - { - if (message.isEmpty()) - message.append("Request has specimens with duplicate fields: "); - else - message.append("; "); - message.append("DoDID - ").append(StringUtils.join(duplicates, ", ")); - } - // check that all the existing SSN + FMP pairs in this request are unique - duplicates = findDuplicates(requestId, "SSN, FMPId"); - if (!duplicates.isEmpty()) - { - if (message.isEmpty()) - message.append("Request has specimens with duplicate fields: "); - else - message.append("; "); - message.append("SSN + FMP - ").append(StringUtils.join(duplicates, ", ")); - } - - if (!message.isEmpty()) - throw new QueryUpdateServiceException(message.toString()); - - } - - /** - * Returns a list of duplicates for the combination of fields given where the field values are not null. - * - * @param requestId id of the test request - * @param fields comma-separated list of fields to check for unique combinations of - * @return value of the fields that are duplicates; for the case of multiple fields the value of the first field in @fields will be in the returned list - */ - private static List findDuplicates(Integer requestId, String fields) - { - SQLFragment sql = new SQLFragment("SELECT ") - .append(fields).append(" FROM hdrl.inboundspecimen WHERE inboundrequestid = ?").add(requestId); - for (String field : fields.split(", ")) - { - sql.append(" AND ").append(field).append(" IS NOT NULL "); - } - sql.append(" GROUP BY ").append(fields) - .append(" HAVING COUNT(*) > 1 "); - SqlSelector sqlSelector = new SqlSelector(HDRLSchema.getInstance().getScope(), sql); - return sqlSelector.getArrayList(String.class); - - } - - private String getLookupValue(HDRLQuerySchema schema, String tableName, Integer rowId, String fieldName) throws SQLException - { - if (rowId == null) - return null; - - SimpleFilter filter = new SimpleFilter(FieldKey.fromParts("RowId"), rowId); - TableSelector selector = new TableSelector(schema.getTable(tableName), PageFlowUtil.set(fieldName), filter, null); - try (Results results = selector.getResults()) - { - results.next(); - String value = results.getString(FieldKey.fromParts(fieldName)); - return value; - } - - } - - private void pushDataToLabWare(User user, Container container, Map labkeyTableRow) throws SQLException - { - HDRLQuerySchema lkSchema = new HDRLQuerySchema(user, container); - - // create the request data for LabWare - Map labWareData = new HashMap<>(); - labWareData.put("Batch_ID", labkeyTableRow.get("RequestId")); - labWareData.put("Carrier", getLookupValue(lkSchema, HDRLQuerySchema.TABLE_SHIPPING_CARRIER, (Integer) labkeyTableRow.get("ShippingCarrierId"), "Name")); - labWareData.put("Tracking_Number", labkeyTableRow.get("ShippingNumber")); - labWareData.put("Customer", user.getEmail()); - - // now get the specimen rows using the requestId from the labKeyTable - SimpleFilter filter = new SimpleFilter(FieldKey.fromParts("InboundRequestId"), labkeyTableRow.get("RequestId")); - TableSelector selector = new TableSelector(lkSchema.getTable(HDRLQuerySchema.TABLE_INBOUND_SPECIMEN), filter, null); - List specimens = selector.getArrayList(InboundSpecimenBean.class); - - LabWareQuerySchema lwSchema = new LabWareQuerySchema(user, container); - - try (DbScope.Transaction lwTransaction = lwSchema.getSchema().getScope().ensureTransaction()) - { - Table.insert(user, lwSchema.getDbSchema().getTable(LabWareQuerySchema.TABLE_INBOUND_REQUESTS), labWareData); - for (InboundSpecimenBean specimen : specimens) - { - Map lwSpecimen = new HashMap<>(); - lwSpecimen.put("Test_Request_ID", specimen.getRowId()); - lwSpecimen.put("Batch_ID", specimen.getInboundRequestId()); - lwSpecimen.put("Test_Requested", getLookupValue(lkSchema, HDRLQuerySchema.TABLE_TEST_TYPE, (Integer) labkeyTableRow.get("TestTypeId"), "Name")); - lwSpecimen.put("Cust_Barcode", specimen.getCustomerBarCode()); - lwSpecimen.put("FMP", getLookupValue(lkSchema, HDRLQuerySchema.TABLE_FAMILY_MEMBER_PREFIX, specimen.getFmpId(), "Code")); - lwSpecimen.put("SSN", specimen.getSsn()); - lwSpecimen.put("Draw_Date", specimen.getDrawDate()); - lwSpecimen.put("Specimen_Type", specimen.getSpecimenType()); - lwSpecimen.put("Num_Containers", specimen.getNumberOfContainers()); - lwSpecimen.put("SOT", getLookupValue(lkSchema, HDRLQuerySchema.TABLE_SOURCE_OF_TESTING, specimen.getTestingSourceId(), "Code")); - lwSpecimen.put("DUC", getLookupValue(lkSchema, HDRLQuerySchema.TABLE_DUTY_CODE, specimen.getDutyCodeId(), "Code")); - lwSpecimen.put("DOD_ID", specimen.getDodId()); - lwSpecimen.put("First_Name", specimen.getFirstName()); - lwSpecimen.put("Middle_Name", specimen.getMiddleName()); - lwSpecimen.put("Last_Name", specimen.getLastName()); - lwSpecimen.put("Birth_Date", specimen.getBirthDate()); - lwSpecimen.put("Gender", specimen.getGenderId()); - lwSpecimen.put("Initials", specimen.getInitials()); - - Table.insert(user, lwSchema.getDbSchema().getTable(LabWareQuerySchema.TABLE_INBOUND_SPECIMENS), lwSpecimen); - } - lwTransaction.commit(); - } - } - - -} diff --git a/hdrl/src/org/labkey/hdrl/query/InboundSpecimenTable.java b/hdrl/src/org/labkey/hdrl/query/InboundSpecimenTable.java deleted file mode 100644 index 488b59c5..00000000 --- a/hdrl/src/org/labkey/hdrl/query/InboundSpecimenTable.java +++ /dev/null @@ -1,62 +0,0 @@ -/* - * Copyright (c) 2015-2019 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -package org.labkey.hdrl.query; - -import org.jetbrains.annotations.NotNull; -import org.jetbrains.annotations.Nullable; -import org.labkey.api.data.ContainerFilter; -import org.labkey.api.data.ContainerForeignKey; -import org.labkey.api.data.DatabaseTableType; -import org.labkey.api.data.TableInfo; -import org.labkey.api.query.FilteredTable; -import org.labkey.api.query.QueryUpdateService; -import org.labkey.api.security.UserPrincipal; -import org.labkey.api.security.permissions.Permission; - -/** - * Created by klum on 4/15/2015. - */ -public class InboundSpecimenTable extends FilteredTable -{ - public InboundSpecimenTable(HDRLQuerySchema schema, ContainerFilter cf) - { - super(schema.getDbSchema().getTable(HDRLQuerySchema.TABLE_INBOUND_SPECIMEN), schema, cf); - - // wrap all the existing columns - wrapAllColumns(true); - var containerCol = getMutableColumn("Container"); - ContainerForeignKey.initColumn(containerCol, schema); - containerCol.setLabel("Folder"); - } - - - @Nullable - @Override - public QueryUpdateService getUpdateService() - { - TableInfo table = getRealTable(); - if (table != null && table.getTableType() == DatabaseTableType.TABLE) - return new InboundSpecimenUpdateService(this, table); - - return null; - } - - @Override - public boolean hasPermission(@NotNull UserPrincipal user, @NotNull Class perm) - { - return getContainer().hasPermission(user, perm); - } -} diff --git a/hdrl/src/org/labkey/hdrl/query/InboundSpecimenUpdateService.java b/hdrl/src/org/labkey/hdrl/query/InboundSpecimenUpdateService.java deleted file mode 100644 index 7b494203..00000000 --- a/hdrl/src/org/labkey/hdrl/query/InboundSpecimenUpdateService.java +++ /dev/null @@ -1,218 +0,0 @@ -/* - * Copyright (c) 2015 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -package org.labkey.hdrl.query; - -import org.apache.commons.lang3.StringUtils; -import org.jetbrains.annotations.Nullable; -import org.labkey.api.data.Container; -import org.labkey.api.data.TableInfo; -import org.labkey.api.query.BatchValidationException; -import org.labkey.api.query.DefaultQueryUpdateService; -import org.labkey.api.query.DuplicateKeyException; -import org.labkey.api.query.InvalidKeyException; -import org.labkey.api.query.QueryUpdateServiceException; -import org.labkey.api.query.ValidationException; -import org.labkey.api.security.User; - -import java.sql.SQLException; -import java.text.ParseException; -import java.text.SimpleDateFormat; -import java.util.ArrayList; -import java.util.Calendar; -import java.util.Date; -import java.util.List; -import java.util.Map; - -/** - * Created by susanh on 4/16/15. - */ -public class InboundSpecimenUpdateService extends DefaultQueryUpdateService -{ - public enum ValidationMode {OFF, ON, ONLY, WITH_UQ} - - private ValidationMode validationMode = ValidationMode.ON; - - public InboundSpecimenUpdateService(TableInfo queryTable, TableInfo dbTable) - { - super(queryTable, dbTable); - } - - @Override - public List> insertRows(User user, Container container, List> rows, BatchValidationException errors, @Nullable Map configParameters, Map extraScriptContext) - throws DuplicateKeyException, QueryUpdateServiceException, SQLException - { - parseValidationMode(extraScriptContext); - List> ret = super.insertRows(user, container, rows, errors, configParameters, extraScriptContext); - - if (this.validationMode == ValidationMode.WITH_UQ) - { - InboundRequestUpdateService.validateUniqueness((Integer) rows.get(0).get("InboundRequestId")); - } - - return ret; - } - - private void parseValidationMode(Map extraScriptContext) - { - if (extraScriptContext != null && extraScriptContext.containsKey("validationMode")) - { - validationMode = ValidationMode.valueOf(extraScriptContext.get("validationMode").toString().toUpperCase()); - } - } - - @Override - public List> updateRows(User user, Container container, List> rows, List> oldKeys, BatchValidationException errors, @Nullable Map configParameters, Map extraScriptContext) throws InvalidKeyException, BatchValidationException, QueryUpdateServiceException, SQLException - { - parseValidationMode(extraScriptContext); - List> ret = super.updateRows(user, container, rows, oldKeys, errors, configParameters, extraScriptContext); - - if (this.validationMode == ValidationMode.WITH_UQ) - { - InboundRequestUpdateService.validateUniqueness((Integer) rows.get(0).get("InboundRequestId")); - } - - return ret; - } - - @Override - protected Map _insert(User user, Container c, Map row) - throws SQLException, ValidationException - { - if (validationMode != ValidationMode.OFF) - validate(row); - - if (validationMode != ValidationMode.ONLY) - return super._insert(user, c, row); - else - return row; - } - - @Override - protected Map _update(User user, Container c, Map row, Map oldRow, Object[] keys) - throws SQLException, ValidationException - { - if (validationMode != ValidationMode.OFF) - validate(row); - - if (validationMode != ValidationMode.ONLY) - return super._update(user, c, row, oldRow, keys); - else - return row; - - } - - - public static void validate(Map row) throws ValidationException - { - SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd"); - Date drawDate = null; - Calendar calendar = Calendar.getInstance(); - calendar.set(Calendar.HOUR, 0); - calendar.set(Calendar.MINUTE, 0); - calendar.set(Calendar.SECOND, 0); - calendar.set(Calendar.MILLISECOND, 0); - Date today = calendar.getTime(); - List errors = new ArrayList<>(); - List missingFields = new ArrayList<>(); - if (row.get("FMPId") == null) - missingFields.add("FMP"); - if (row.get("DrawDate") == null) - missingFields.add("Draw Date"); - else - { - if (row.get("DrawDate") instanceof Date) - drawDate = (Date) row.get("DrawDate"); - else - { - try - { - drawDate = dateFormat.parse((String) row.get("DrawDate")); - if (drawDate.after(today)) - { - errors.add("Draw date cannot be in the future"); - } - } - catch (ParseException e) - { - errors.add("Invalid draw date format"); - } - } - } - Object birthDateObj = row.get("BirthDate"); - if (birthDateObj != null) - { - Date birthDate = null; - if (birthDateObj instanceof Date d) - birthDate = d; - else - { - try - { - birthDate = dateFormat.parse((String) row.get("BirthDate")); - } - catch (ParseException e) - { - errors.add("Invalid birth date format"); - } - } - if (birthDate != null) - { - if (birthDate.after(today)) - { - errors.add("Birth date cannot be in the future"); - } - else if ((drawDate != null) && (drawDate.before(birthDate))) - { - errors.add("Draw date cannot be before birth date"); - } - } - } - if (row.get("SSN") == null || StringUtils.isEmpty(String.valueOf(row.get("SSN")))) - missingFields.add("SSN"); - else - { - String ssn = String.valueOf(row.get("SSN")); - if (!ssn.matches("^\\d{9}$")) - { - errors.add("Invalid SSN"); - } - } - if (row.get("DoDId") != null) - { - String dodId = String.valueOf(row.get("DoDId")); - if (!dodId.matches("^\\d{10}$")) - { - errors.add("Invalid DoD Id"); - } - } - if (!missingFields.isEmpty()) - { - errors.add("Required field(s) missing: " + StringUtils.join(missingFields, ", ")); - } - - if (!errors.isEmpty()) - { - String message = StringUtils.join(errors, "; "); - - row.put("ValidationStatus", message); - throw new ValidationException(message); - } - else - { - row.remove("ValidationStatus"); - } - } -} diff --git a/hdrl/src/org/labkey/hdrl/query/LabWareQuerySchema.java b/hdrl/src/org/labkey/hdrl/query/LabWareQuerySchema.java deleted file mode 100644 index ddaf82c9..00000000 --- a/hdrl/src/org/labkey/hdrl/query/LabWareQuerySchema.java +++ /dev/null @@ -1,78 +0,0 @@ -/* - * Copyright (c) 2015-2017 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -package org.labkey.hdrl.query; - -import org.labkey.api.data.Container; -import org.labkey.api.data.DbSchema; -import org.labkey.api.data.DbSchemaType; -import org.labkey.api.data.DbScope; -import org.labkey.api.module.Module; -import org.labkey.api.query.DefaultSchema; -import org.labkey.api.query.QuerySchema; -import org.labkey.api.query.SimpleUserSchema; -import org.labkey.api.query.ValidationException; -import org.labkey.api.security.User; -import org.labkey.hdrl.HDRLModule; - -public class LabWareQuerySchema extends SimpleUserSchema -{ - public static final String NAME = "GW_LABKEY"; - public static final String DATA_SOURCE_NAME = "labware"; - public static final String DESCRIPTION = "LabWare tables for test requests and specimens"; - - public static final String TABLE_INBOUND_REQUESTS = "X_LK_INBND_REQUESTS"; - public static final String TABLE_INBOUND_SPECIMENS = "X_LK_INBND_SPECIMENS"; - public static final String TABLE_OUTBOUND_REQUESTS = "X_LK_OUTBD_REQUESTS"; - public static final String TABLE_OUTBOUND_SPECIMENS = "X_LK_OUTBD_SPECIMENS"; - - public LabWareQuerySchema(User user, Container container) - { - super(NAME, DESCRIPTION, user, container, DbSchema.get(getFullyQualifiedDataSource(), DbSchemaType.Module)); - _hidden = true; - } - - public static String getFullyQualifiedDataSource() - { - return DATA_SOURCE_NAME + "." + NAME; - } - - public static void register(final HDRLModule module) - { - DefaultSchema.registerProvider(NAME, new DefaultSchema.SchemaProvider(module) - { - @Override - public QuerySchema createSchema(DefaultSchema schema, Module module) - { - return new LabWareQuerySchema(schema.getUser(), schema.getContainer()); - } - }); - } - - public static void verifyLabWareDataSource() throws ValidationException - { - String name = DATA_SOURCE_NAME + "DataSource"; - DbScope scope = DbScope.getDbScope(name); - if (scope == null) - { - throw new ValidationException("Expected to find a data source with name '" + name + "'."); - } - } - - public DbSchema getSchema() - { - return DbSchema.get(getFullyQualifiedDataSource(), DbSchemaType.Module); - } -} diff --git a/hdrl/src/org/labkey/hdrl/query/PatientCountColumn.java b/hdrl/src/org/labkey/hdrl/query/PatientCountColumn.java deleted file mode 100644 index 5a069799..00000000 --- a/hdrl/src/org/labkey/hdrl/query/PatientCountColumn.java +++ /dev/null @@ -1,37 +0,0 @@ -/* - * Copyright (c) 2015-2019 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -package org.labkey.hdrl.query; - -import org.labkey.api.data.BaseColumnInfo; -import org.labkey.api.data.ColumnInfo; -import org.labkey.api.data.SQLFragment; - -/** - * Created by susanh on 4/13/15. - */ -public class PatientCountColumn extends BaseColumnInfo -{ - public PatientCountColumn(ColumnInfo columnInfo) - { - super(columnInfo); - } - - @Override - public SQLFragment getValueSql(String tableAliasName) - { - return new SQLFragment("COALESCE(" + tableAliasName + "."+ HDRLQuerySchema.COL_ARCHIVED_REQUEST_COUNT + ", (SELECT COUNT(DISTINCT(SSN,FMPId)) FROM hdrl.InboundSpecimen spec WHERE spec.InboundRequestId = " + tableAliasName + ".RequestId))"); - } -} diff --git a/hdrl/src/org/labkey/hdrl/query/RequestResultTable.java b/hdrl/src/org/labkey/hdrl/query/RequestResultTable.java deleted file mode 100644 index 15bd3336..00000000 --- a/hdrl/src/org/labkey/hdrl/query/RequestResultTable.java +++ /dev/null @@ -1,55 +0,0 @@ -/* - * Copyright (c) 2015-2019 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -package org.labkey.hdrl.query; - -import org.jetbrains.annotations.NotNull; -import org.labkey.api.data.ContainerFilter; -import org.labkey.api.data.SQLFragment; -import org.labkey.api.query.FieldKey; -import org.labkey.hdrl.HDRLSchema; - -/** - * Created by susanh on 4/6/16. - */ -public class RequestResultTable extends ResultTable -{ - public RequestResultTable(@NotNull HDRLQuerySchema schema, String name, ContainerFilter cf) - { - super(schema, name, cf); - } - - @Override - protected void applyContainerFilter(ContainerFilter filter) - { - FieldKey containerFieldKey = FieldKey.fromParts("Container"); - clearConditions(containerFieldKey); - SQLFragment sql = new SQLFragment(getIdField() + " IN (SELECT r.RequestId FROM "); - sql.append(HDRLSchema.getInstance().getTableInfoInboundRequest(), "r"); - sql.append(" WHERE "); - sql.append(filter.getSQLFragment(getSchema(), new SQLFragment("r.Container"))); - sql.append(")"); - addCondition(sql, containerFieldKey); - } - - private String getIdField() - { - if (_rootTable.getName().equalsIgnoreCase(HDRLQuerySchema.TABLE_REQUEST_RESULT)) - return "RequestId"; - else if (_rootTable.getName().equalsIgnoreCase(HDRLQuerySchema.TABLE_LABWARE_OUTBOUND_RESULTS)) - return "batch_id"; - return null; - } -} diff --git a/hdrl/src/org/labkey/hdrl/query/ResultTable.java b/hdrl/src/org/labkey/hdrl/query/ResultTable.java deleted file mode 100644 index 53bee293..00000000 --- a/hdrl/src/org/labkey/hdrl/query/ResultTable.java +++ /dev/null @@ -1,70 +0,0 @@ -/* - * Copyright (c) 2015-2019 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -package org.labkey.hdrl.query; - -import org.jetbrains.annotations.NotNull; -import org.jetbrains.annotations.Nullable; -import org.labkey.api.data.Container; -import org.labkey.api.data.ContainerFilter; -import org.labkey.api.data.DatabaseTableType; -import org.labkey.api.data.TableInfo; -import org.labkey.api.dataiterator.DataIteratorBuilder; -import org.labkey.api.query.BatchValidationException; -import org.labkey.api.query.DefaultQueryUpdateService; -import org.labkey.api.query.QueryUpdateService; -import org.labkey.api.query.SimpleUserSchema; -import org.labkey.api.security.User; -import org.labkey.api.security.UserPrincipal; -import org.labkey.api.security.permissions.Permission; - -import java.util.Map; - -/** - * Created by susanh on 7/7/15. - */ -public class ResultTable extends SimpleUserSchema.SimpleTable -{ - public ResultTable(@NotNull HDRLQuerySchema schema, String tableName, ContainerFilter cf) - { - super(schema, schema.getDbSchema().getTable(tableName), cf); - init(); - } - - @Override - public boolean hasPermission(@NotNull UserPrincipal user, @NotNull Class perm) - { - return getContainer().hasPermission(user, perm); - } - - @Nullable - @Override - public QueryUpdateService getUpdateService() - { - TableInfo table = getRealTable(); - if (table != null && table.getTableType() == DatabaseTableType.TABLE) - return new DefaultQueryUpdateService(this, table) { - - @Override - public int mergeRows(User user, Container container, DataIteratorBuilder rows, BatchValidationException errors, @Nullable Map configParameters, Map extraScriptContext) - { - return _importRowsUsingDIB(user, container, rows, null, getDataIteratorContext(errors, InsertOption.MERGE, configParameters), extraScriptContext); - } - }; - - return null; - } - -} diff --git a/hdrl/src/org/labkey/hdrl/query/SpecimenResultTable.java b/hdrl/src/org/labkey/hdrl/query/SpecimenResultTable.java deleted file mode 100644 index e520789c..00000000 --- a/hdrl/src/org/labkey/hdrl/query/SpecimenResultTable.java +++ /dev/null @@ -1,57 +0,0 @@ -/* - * Copyright (c) 2015-2019 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -package org.labkey.hdrl.query; - -import org.jetbrains.annotations.NotNull; -import org.labkey.api.data.ContainerFilter; -import org.labkey.api.data.SQLFragment; -import org.labkey.api.query.FieldKey; -import org.labkey.hdrl.HDRLSchema; - -/** - * Created by susanh on 4/6/16. - */ -public class SpecimenResultTable extends ResultTable -{ - - public SpecimenResultTable(@NotNull HDRLQuerySchema schema, String name, ContainerFilter cf) - { - super(schema, name, cf); - } - - @Override - protected void applyContainerFilter(ContainerFilter filter) - { - FieldKey containerFieldKey = FieldKey.fromParts("Container"); - clearConditions(containerFieldKey); - SQLFragment sql = new SQLFragment(getIdField() + " IN (SELECT s.RowId FROM "); - sql.append(HDRLSchema.getInstance().getTableInfoInboundSpecimen(), "s"); - sql.append(" WHERE "); - sql.append(filter.getSQLFragment(getSchema(), new SQLFragment("s.Container"))); - sql.append(")"); - addCondition(sql, containerFieldKey); - } - - - private String getIdField() - { - if (_rootTable.getName().equalsIgnoreCase(HDRLQuerySchema.TABLE_SPECIMEN_RESULT)) - return "SpecimenId"; - else if (_rootTable.getName().equalsIgnoreCase(HDRLQuerySchema.TABLE_LABWARE_OUTBOUND_SPECIMENS)) - return "test_request_id"; - return null; - } -} diff --git a/hdrl/src/org/labkey/hdrl/view/InboundRequestBean.java b/hdrl/src/org/labkey/hdrl/view/InboundRequestBean.java deleted file mode 100644 index e24ade23..00000000 --- a/hdrl/src/org/labkey/hdrl/view/InboundRequestBean.java +++ /dev/null @@ -1,79 +0,0 @@ -/* - * Copyright (c) 2015-2019 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -package org.labkey.hdrl.view; - -/** - * Created by susanh on 4/15/15. - */ -public class InboundRequestBean -{ - private int _requestId; - private String _shippingNumber; - private String _requestStatus; - private String _testType; - private String _shippingCarrier; - - public int getRequestId() - { - return _requestId; - } - - public void setRequestId(int requestId) - { - _requestId = requestId; - } - - public String getShippingNumber() - { - return _shippingNumber; - } - - public void setShippingNumber(String shippingNumber) - { - _shippingNumber = shippingNumber; - } - - public String getRequestStatus() - { - return _requestStatus; - } - - public void setRequestStatus(String requestStatus) - { - _requestStatus = requestStatus; - } - - public String getTestType() - { - return _testType; - } - - public void setTestType(String testType) - { - _testType = testType; - } - - public String getShippingCarrier() - { - return _shippingCarrier; - } - - public void setShippingCarrier(String shippingCarrier) - { - _shippingCarrier = shippingCarrier; - } - -} diff --git a/hdrl/src/org/labkey/hdrl/view/InboundSpecimenBean.java b/hdrl/src/org/labkey/hdrl/view/InboundSpecimenBean.java deleted file mode 100644 index 5cb757a4..00000000 --- a/hdrl/src/org/labkey/hdrl/view/InboundSpecimenBean.java +++ /dev/null @@ -1,245 +0,0 @@ -/* - * Copyright (c) 2015-2016 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -package org.labkey.hdrl.view; - -import java.util.Date; - -/** - * Created by binalpatel on 5/12/15. - */ -public class InboundSpecimenBean -{ - private Integer _rowId; - private String _customerBarCode; - private Integer _dodId; - private String _genderId; - private String _initials; - private Integer _numberOfContainers; - private String _lastName; - private String _firstName; - private String _middleName; - private Date _birthDate; - private String _ssn; - private Integer _inboundRequestId; - private String _fmpCode; - private Integer _fmpId; - private String _ducCode; - private Integer _dutyCodeId; - private String _sotCode; - private Integer _testingSourceId; - private Date _drawDate; - private String _specimenType = "Serum"; //for now. - - public String getCustomerBarCode() - { - return _customerBarCode; - } - - public void setCustomerBarCode(String customerBarCode) - { - _customerBarCode = customerBarCode; - } - - public String getLastName() - { - return _lastName; - } - - public void setLastName(String lastName) - { - _lastName = lastName; - } - - public String getFirstName() - { - return _firstName; - } - - public void setFirstName(String firstName) - { - _firstName = firstName; - } - - public String getMiddleName() - { - return _middleName; - } - - public void setMiddleName(String middleName) - { - _middleName = middleName; - } - - public Date getBirthDate() - { - return _birthDate; - } - - public void setBirthDate(Date birthDate) - { - _birthDate = birthDate; - } - - public String getSsn() - { - return _ssn; - } - - public void setSsn(String ssn) - { - _ssn = ssn; - } - - public String getFmpCode() - { - return _fmpCode; - } - - public void setFmpCode(String fmpCode) - { - _fmpCode = fmpCode; - } - - public Integer getDutyCodeId() - { - return _dutyCodeId; - } - - public void setDutyCodeId(Integer dutyCodeId) - { - _dutyCodeId = dutyCodeId; - } - - public Integer getFmpId() - { - return _fmpId; - } - - public void setFmpId(Integer fmpId) - { - _fmpId = fmpId; - } - - public Integer getTestingSourceId() - { - return _testingSourceId; - } - - public void setTestingSourceId(Integer testingSourceId) - { - _testingSourceId = testingSourceId; - } - - public String getDucCode() - { - return _ducCode; - } - - public void setDucCode(String ducCode) - { - _ducCode = ducCode; - } - - public String getSotCode() - { - return _sotCode; - } - - public void setSotCode(String sotCode) - { - _sotCode = sotCode; - } - - public Date getDrawDate() - { - return _drawDate; - } - - public void setDrawDate(Date drawDate) - { - _drawDate = drawDate; - } - - public String getSpecimenType() - { - return _specimenType; - } - - public void setSpecimenType(String specimenType) - { - _specimenType = specimenType; - } - - public Integer getInboundRequestId() - { - return _inboundRequestId; - } - - public void setInboundRequestId(Integer inboundRequestId) - { - _inboundRequestId = inboundRequestId; - } - - public Integer getRowId() - { - return _rowId; - } - - public void setRowId(Integer rowId) - { - _rowId = rowId; - } - - public Integer getDodId() - { - return _dodId; - } - - public void setDodId(Integer dodId) - { - _dodId = dodId; - } - - public String getGenderId() - { - return _genderId; - } - - public void setGenderId(String genderId) - { - _genderId = genderId; - } - - public String getInitials() - { - return _initials; - } - - public void setInitials(String initials) - { - _initials = initials; - } - - public Integer getNumberOfContainers() - { - return _numberOfContainers; - } - - public void setNumberOfContainers(Integer numberOfContainers) - { - _numberOfContainers = numberOfContainers; - } -} diff --git a/hdrl/src/org/labkey/hdrl/view/RequestResultBean.java b/hdrl/src/org/labkey/hdrl/view/RequestResultBean.java deleted file mode 100644 index b29ab45d..00000000 --- a/hdrl/src/org/labkey/hdrl/view/RequestResultBean.java +++ /dev/null @@ -1,135 +0,0 @@ -/* - * Copyright (c) 2015-2019 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -package org.labkey.hdrl.view; - -import java.util.Date; - -/** - * Created by susanh on 7/8/15. - */ -public class RequestResultBean -{ - private int _requestId; - private int _requestStatusId; - private String _customerNote; - private Date _received; - private Date _completed; - private String _container; - private int _createdBy; - private Date _created; - private int _modifiedBy; - private Date _modified; - - public Date getCompleted() - { - return _completed; - } - - public void setCompleted(Date completed) - { - _completed = completed; - } - - public String getContainer() - { - return _container; - } - - public void setContainer(String container) - { - _container = container; - } - - public Date getCreated() - { - return _created; - } - - public void setCreated(Date created) - { - _created = created; - } - - public int getCreatedBy() - { - return _createdBy; - } - - public void setCreatedBy(int createdBy) - { - _createdBy = createdBy; - } - - public String getCustomerNote() - { - return _customerNote; - } - - public void setCustomerNote(String customerNote) - { - _customerNote = customerNote; - } - - public Date getModified() - { - return _modified; - } - - public void setModified(Date modified) - { - _modified = modified; - } - - public int getModifiedBy() - { - return _modifiedBy; - } - - public void setModifiedBy(int modifiedBy) - { - _modifiedBy = modifiedBy; - } - - public Date getReceived() - { - return _received; - } - - public void setReceived(Date received) - { - _received = received; - } - - public int getRequestId() - { - return _requestId; - } - - public void setRequestId(int requestId) - { - _requestId = requestId; - } - - public int getRequestStatusId() - { - return _requestStatusId; - } - - public void setRequestStatusId(int requestStatusId) - { - _requestStatusId = requestStatusId; - } -} diff --git a/hdrl/src/org/labkey/hdrl/view/editRequest.jsp b/hdrl/src/org/labkey/hdrl/view/editRequest.jsp deleted file mode 100644 index 77ea0057..00000000 --- a/hdrl/src/org/labkey/hdrl/view/editRequest.jsp +++ /dev/null @@ -1,67 +0,0 @@ -<% -/* - * Copyright (c) 2015-2019 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -%> -<%@ page import="org.labkey.api.data.Container" %> -<%@ page import="org.labkey.api.security.User" %> -<%@ page import="org.labkey.api.view.HttpView" %> -<%@ page import="org.labkey.api.view.JspView" %> -<%@ page import="org.labkey.api.view.ViewContext" %> -<%@ page import="org.labkey.api.view.template.ClientDependencies" %> -<%@ page import="org.labkey.hdrl.HDRLController" %> -<%@ page extends="org.labkey.api.jsp.JspBase" %> -<%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> -<%! - @Override - public void addClientDependencies(ClientDependencies dependencies) - { - dependencies.add("Ext4"); - dependencies.add("hdrl/requests.js"); - dependencies.add("hdrl/fonts/barcode.css"); - } -%> -<% - JspView me = HttpView.currentView(); - ViewContext ctx = getViewContext(); - Container c = getContainer(); - User user = getUser(); - HDRLController.RequestForm bean = me.getModelBean(); - - String renderId = "requests-editor-" + getRequestScopedUID(); -%> - - - -
- - -
- <%=link("Return to test status", HDRLController.BeginAction.class)%> -
diff --git a/hdrl/src/org/labkey/hdrl/view/printPackingList.jsp b/hdrl/src/org/labkey/hdrl/view/printPackingList.jsp deleted file mode 100644 index cefe63fc..00000000 --- a/hdrl/src/org/labkey/hdrl/view/printPackingList.jsp +++ /dev/null @@ -1,135 +0,0 @@ -<% -/* - * Copyright (c) 2015-2016 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -%> -<%@ page import="org.apache.commons.lang3.StringUtils" %> -<%@ page import="org.labkey.api.util.DateUtil" %> -<%@ page import="org.labkey.api.view.HttpView" %> -<%@ page import="org.labkey.api.view.template.ClientDependencies" %> -<%@ page import="org.labkey.hdrl.HDRLController.PackingListBean" %> -<%@ page import="org.labkey.hdrl.view.InboundSpecimenBean" %> -<%@ page import="java.util.Date" %> -<%@ page import="java.util.List" %> -<%@ page extends="org.labkey.api.jsp.JspBase" %> -<%! - @Override - public void addClientDependencies(ClientDependencies dependencies) - { - dependencies.add("hdrl/fonts/barcode.css"); - } -%> -<% - HttpView httpView = HttpView.currentView(); - PackingListBean packingListBean = (PackingListBean) httpView.getModelBean(); - List inboundSpecimens = packingListBean.getInboundSpecimens(); - - Date date = new Date(); - String dateToday = DateUtil.formatDate(getContainer(), date); -%> - - - - -
-

Shipping Manifest

-
-
-

HIPAA warning message here

-
- - - - - - - - - - - - - - - -
Customer Name: Date: <%=h(dateToday)%>
Customer Address:

Shipment Information:
Courier: <%=h(packingListBean.getShippingCarrier())%>Total Samples: <%=packingListBean.getTotalSamples()%>
Tracking Number: <%=h(packingListBean.getShippingNumber())%>Test Requested (if bulk request):
-
- - - - - - - - - - - - - - - - <% - int count = 1; - for(InboundSpecimenBean isb : inboundSpecimens) - { - if(count % 2 == 0) - { - %> - - <% - } - else - { - %> - - <% - } - count++; - %> - - - - - - - - - - - - - - <% - } - %> - -
BarcodeFMP/SSNLast NameFirst NameMiddle NameDate of BirthSOTDUCDraw DateSpecimen TypeTest Requested
<%=h(isb.getCustomerBarCode())%>
<%=h(isb.getCustomerBarCode())%>
<%=h(getConcatenatedVal(isb.getFmpCode(), isb.getSsn()))%>
<%=h(getConcatenatedVal(isb.getFmpCode(), isb.getSsn()))%>
<%=h(isb.getLastName())%>
<%=h(isb.getFirstName())%>
<%=h(isb.getMiddleName())%>
<%=formatDate(isb.getBirthDate())%><%=h(isb.getSotCode())%><%=h(isb.getDucCode())%><%=formatDate(isb.getDrawDate())%><%=h(isb.getSpecimenType())%><%=h(packingListBean.getTestType())%>
- -<%! - public String getConcatenatedVal(String fmpCode, String SSN) - { - if(StringUtils.isBlank(fmpCode) || StringUtils.isBlank(SSN)) - return null; - - return fmpCode + SSN; - } -%> \ No newline at end of file diff --git a/hdrl/src/org/labkey/hdrl/view/requestDetails.jsp b/hdrl/src/org/labkey/hdrl/view/requestDetails.jsp deleted file mode 100644 index dba26300..00000000 --- a/hdrl/src/org/labkey/hdrl/view/requestDetails.jsp +++ /dev/null @@ -1,89 +0,0 @@ -<% -/* - * Copyright (c) 2015-2019 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -%> -<%@ page import="org.labkey.api.view.HttpView" %> -<%@ page import="org.labkey.api.view.template.ClientDependencies" %> -<%@ page import="org.labkey.hdrl.HDRLController" %> -<%@ page import="org.labkey.hdrl.view.InboundRequestBean" %> -<%@ page extends="org.labkey.api.jsp.JspBase" %> -<%! - @Override - public void addClientDependencies(ClientDependencies dependencies) - { - dependencies.add("Ext4"); - dependencies.add("hdrl/fonts/barcode.css"); - } -%> -<% - HttpView me = HttpView.currentView(); - InboundRequestBean bean = (InboundRequestBean) me.getModelBean(); -%> -
- Request <%= bean.getRequestId() %> - <%=h(bean.getTestType()) %> (Status: <%= h(bean.getRequestStatus()) %>) -
-
- -
- <% me.include(me.getView("queryView"),out); %> -
-<% - String renderId = "labkey-wp-"+ getRequestScopedUID(); - - if (bean.getShippingCarrier() != null) - { -%> -
- - - - - - - - - - - - -
Shipping Information
Carrier <%= h(bean.getShippingCarrier()) %>
Tracking #<%= h(bean.getShippingNumber() == null ? "unknown" : bean.getShippingNumber()) %>
-<% - } -%> - -
-
-
- - - -
- <%=link("Return to test status", HDRLController.BeginAction.class)%> -
diff --git a/hdrl/src/org/labkey/hdrl/view/sensitiveData.jsp b/hdrl/src/org/labkey/hdrl/view/sensitiveData.jsp deleted file mode 100644 index 002c7fb2..00000000 --- a/hdrl/src/org/labkey/hdrl/view/sensitiveData.jsp +++ /dev/null @@ -1,41 +0,0 @@ -<% -/* - * Copyright (c) 2015-2019 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -%> -<%@ page import="org.labkey.api.admin.AdminUrls" %> -<%@ page import="org.labkey.api.view.HttpView" %> -<%@ page import="org.labkey.api.view.JspView" %> -<%@ page import="org.labkey.hdrl.HDRLController" %> -<%@ page extends="org.labkey.api.jsp.JspBase" %> -<%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> -<% - JspView sensitiveDataFormJspView = HttpView.currentView(); - HDRLController.SensitiveDataForm bean = sensitiveDataFormJspView.getModelBean(); - String timeWindow = String.valueOf(bean.getTimeWindowInDays()); -%> - -
- - Number of Days<%=helpPopup("Number of Days", "Enter days after which sensitive data will be deleted.")%>: - min="0"> - - -
- <%= button("Save").submit(true) %> - <%= button("Cancel").href(urlProvider(AdminUrls.class).getAdminConsoleURL())%> - - - \ No newline at end of file diff --git a/hdrl/test/sampledata/hdrl/clinical_report.pdf b/hdrl/test/sampledata/hdrl/clinical_report.pdf deleted file mode 100644 index f930b7ad..00000000 Binary files a/hdrl/test/sampledata/hdrl/clinical_report.pdf and /dev/null differ diff --git a/hdrl/test/sampledata/hdrl/sample_upload_01.tsv b/hdrl/test/sampledata/hdrl/sample_upload_01.tsv deleted file mode 100644 index 5b705552..00000000 --- a/hdrl/test/sampledata/hdrl/sample_upload_01.tsv +++ /dev/null @@ -1,4 +0,0 @@ -customerBarcode lastName firstName birthDate SSN FMPId dutyCodeId testingSourceId drawDate -5555 Jones Tom 12/1/2000 222334444 A13 P 3/1/2015 -6666 Jones Jerry 3/3/1975 A14 B -7778 Jones Gracie 3/3/2015 20 A13 P 2/3/2015 diff --git a/hdrl/test/sampledata/hdrl/sample_upload_02.xlsx b/hdrl/test/sampledata/hdrl/sample_upload_02.xlsx deleted file mode 100644 index f9a10f38..00000000 Binary files a/hdrl/test/sampledata/hdrl/sample_upload_02.xlsx and /dev/null differ diff --git a/hdrl/test/src/org/labkey/test/tests/hdrl/HDRLTest.java b/hdrl/test/src/org/labkey/test/tests/hdrl/HDRLTest.java deleted file mode 100644 index de43e10a..00000000 --- a/hdrl/test/src/org/labkey/test/tests/hdrl/HDRLTest.java +++ /dev/null @@ -1,666 +0,0 @@ -/* - * Copyright (c) 2015-2019 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -package org.labkey.test.tests.hdrl; - -import org.junit.Assert; -import org.junit.Before; -import org.junit.BeforeClass; -import org.junit.Test; -import org.junit.experimental.categories.Category; -import org.labkey.remoteapi.CommandException; -import org.labkey.remoteapi.Connection; -import org.labkey.remoteapi.SimplePostCommand; -import org.labkey.test.BaseWebDriverTest; -import org.labkey.test.Locator; -import org.labkey.test.Locators; -import org.labkey.test.TestFileUtils; -import org.labkey.test.TestTimeoutException; -import org.labkey.test.WebTestHelper; -import org.labkey.test.categories.Git; -import org.labkey.test.util.DataRegionTable; -import org.labkey.test.util.LogMethod; -import org.labkey.test.util.LoggedParam; -import org.labkey.test.util.PostgresOnlyTest; -import org.labkey.test.util.di.DataIntegrationHelper; - -import java.io.File; -import java.io.IOException; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collections; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertNotEquals; -import static org.junit.Assert.assertTrue; -import static org.labkey.test.util.PermissionsHelper.READER_ROLE; - -@Category({Git.class}) // Requires dataintegration module -@BaseWebDriverTest.ClassTimeout(minutes = 8) -public class HDRLTest extends BaseWebDriverTest implements PostgresOnlyTest -{ - protected final File TEST_SPECIMEN_UPLOAD_FILE_1 = TestFileUtils.getSampleData("hdrl/sample_upload_01.tsv"); - protected final File TEST_SPECIMEN_UPLOAD_FILE_2 = TestFileUtils.getSampleData("hdrl/sample_upload_02.xlsx"); - protected final File CLINICAL_REPORT_FILE = TestFileUtils.getSampleData("hdrl/clinical_report.pdf"); - - private static final String SUBMIT_BUTTON_TEXT = "Submit Request"; - private static final String SAVE_BUTTON_TEXT = "Save"; - private static final String PRINT_PACKING_LIST_TEXT = "Print Packing List"; - private static final String CONFIRM_SAVE_TEXT = "Do you still want to save your changes?"; - - public static final Locator.XPathLocator disabledSubmit = Locator.xpath("//a[contains(normalize-space(@class),'x4-btn-disabled')]//span[text()='" + SUBMIT_BUTTON_TEXT + "']"); - public static final Locator.XPathLocator enabledSave = Locator.xpath("//a[not(contains(normalize-space(@class), 'x4-btn-disable'))]//span[text()='" + SAVE_BUTTON_TEXT + "']"); - public static final Locator.XPathLocator enabledPrintPackingList = Locator.xpath("//a[not(contains(normalize-space(@class), 'x4-btn-disable'))]//span[text()='" + PRINT_PACKING_LIST_TEXT + "']"); - - private static final int CARRIER_COLUMN_INDEX = 2; - private static final int STATUS_COLUMN_INDEX = 13; - - @Override - protected String getProjectName() - { - return "HDRL Verification"; - } - - @BeforeClass - public static void initProject() - { - HDRLTest init = getCurrentTest(); - init.setupFolder(); - } - - - @Before - public void preTest() - { - goToProjectHome(); - } - - @Override - protected void doCleanup(boolean afterTest) throws TestTimeoutException - { - super.doCleanup(afterTest); - } - - @Override - protected boolean allowTimeZoneShifting() - { - return false; // Ext forms need to be updated to handle time zones properly - } - - private void addTestResultData(Map requestData, List> specimenData) - { - addRequestResultData(requestData); - addSpecimenResultData(specimenData); - } - - private void addRequestResultData(Map data) - { - Connection connection = WebTestHelper.getRemoteApiConnection(); - SimplePostCommand command = new SimplePostCommand("hdrl", "addLabwareOutboundRequest"); - command.setParameters(data); - - try - { - command.execute(connection, getCurrentContainerPath()); - } - catch (IOException | CommandException e) - { - throw new RuntimeException("Error posting request results", e); - } - } - - private void addSpecimenResultData(List> results) - { - Connection connection = WebTestHelper.getRemoteApiConnection(); - for (Map result : results) - { - SimplePostCommand command = new SimplePostCommand("hdrl", "addLabwareOutboundSpecimen"); - command.setParameters(result); - - try - { - command.execute(connection, getCurrentContainerPath()); - } - catch (IOException | CommandException e) - { - throw new RuntimeException("Error posting specimen results", e); - } - } - } - - @Test - public void testRetrievalOfResultsAndArchiving() throws Exception - { - Assert.assertTrue("Required module is not installed: dataintegration", _containerHelper.getAllModules().contains("dataintegration")); - createTestRequest(); - uploadFile(TEST_SPECIMEN_UPLOAD_FILE_2); - log("File uploaded waiting for content"); - waitForElement(Locator.tagContainingText("div", "555-44-3333")); - log("setting tracking number"); - doAndWaitForPageSignal(() -> setFormElement(Locator.tagWithName("input", "trackingNumber"), "testRetrievalOfResults"), "pageDirty"); - log("submitting requests"); - clickButton(SUBMIT_BUTTON_TEXT); - DataRegionTable drt = new DataRegionTable("query", this); - int idx = drt.getRowIndex("ShippingNumber", "testRetrievalOfResults"); - assertNotEquals(-1, idx); - String requestId = drt.getDataAsText(idx, "RequestId"); - - Map result = new HashMap<>(); - result.put("batchId", requestId); - result.put("dateReceived", "2015-06-01"); - result.put("dateModified", "2015-06-15"); - result.put("dateCompleted", "2015-07-01"); - result.put("hdrlStatus", "Completed"); - result.put("customerNote", "Note for id " + requestId); - - List specimenIds = getSpecimenIds(requestId, "hdrl", "InboundSpecimen", "RowId"); - - List> lwSpecimens = new ArrayList<>(); - - Map specimenResult1 = new HashMap<>(); - specimenResult1.put("batchId", String.valueOf(requestId)); - specimenResult1.put("testRequestId", specimenIds.get(0)); - specimenResult1.put("dateReceived", "2015-06-01"); - specimenResult1.put("dateCompleted", "2015-06-03"); - specimenResult1.put("dateModified", "2015-06-03"); - specimenResult1.put("sampleIntegrity", "Hemolyzed"); - specimenResult1.put("testResult", "HIV Negative"); - specimenResult1.put("customerCode", "5B"); - specimenResult1.put("clinicalReportFile", CLINICAL_REPORT_FILE.getAbsolutePath()); - specimenResult1.put("reportFileName", "reportFileName.pdf"); - specimenResult1.put("hdrlStatus", "Completed"); - specimenResult1.put("modifiedResultFlag", "F"); - lwSpecimens.add(specimenResult1); - - Map specimenResult2 = new HashMap<>(); - specimenResult2.put("batchId", requestId); - specimenResult2.put("testRequestId", specimenIds.get(1)); - specimenResult2.put("dateReceived", "2015-06-01"); - specimenResult2.put("dateModified", "2015-06-03"); - specimenResult2.put("hdrlStatus", "Exception"); - specimenResult2.put("modifiedResultFlag", "F"); - lwSpecimens.add(specimenResult2); - - addTestResultData(result, lwSpecimens); // add results for this test request - - // Run the ETL to pick up the results - new DataIntegrationHelper(getProjectName()).runTransform("{HDRL}/labware"); - - Map request = new HashMap<>(); - request.put("ShippingNumber", "testRetrievalOfResults"); - result.put("requestId", requestId); - result.put("received", "2015-06-01"); - result.put("modified", "2015-06-15"); - result.put("Status", "Received"); - result.put("CustomerNote", "Note for id " + requestId); - - // add in the request data for verification - Map specimen1 = new HashMap<>(); - specimen1.put("RequestId", String.valueOf(requestId)); - specimen1.put("SpecimenId", specimenIds.get(0)); - specimen1.put("Received", "2015-06-01 00:00"); - specimen1.put("Completed", "2015-06-03 00:00"); - specimen1.put("SampleIntegrity", "Hemolyzed"); - specimen1.put("TestResult", "HIV Negative"); - specimen1.put("CustomerCode", "5B"); - specimen1.put("RequestStatusId", "Completed"); - specimen1.put("ModifiedResultFlag", "F"); - - Map specimen2 = new HashMap<>(); - - specimen2.put("RequestId", requestId); - specimen2.put("SpecimenId", specimenIds.get(1)); - specimen2.put("Received", "2015-06-01 00:00"); - specimen2.put("RequestStatusId", "Exception"); - specimen2.put("ModifiedResultFlag", "F"); - - List> specimens = new ArrayList<>(); - specimens.add(specimen1); - specimens.add(specimen2); - - // Verify results data are shown in the grid - verifyDataRegionRows("InboundRequest", Collections.singletonList(request), "ShippingNumber"); - verifyDataRegionRows("SpecimenResult", specimens, "SpecimenId"); - - // Verify download - goToProjectHome(); - impersonateRole(READER_ROLE); - click(Locator.linkContainingText("View test requests")); - drt = new DataRegionTable("query", this); - idx = drt.getRowIndex("RequestId", requestId); - assertNotEquals(-1, idx); - log("view test results"); - assertEquals("VIEW", drt.getDataAsText(idx, 0)); - clickAndWait(drt.link(idx, 0)); - - waitForElement(Locator.tagContainingText("td", specimenIds.get(0))); - drt = new DataRegionTable("query", this); - idx = drt.getRowIndex("RowId", specimenIds.get(0)); - assertEquals("Download", drt.getDataAsText(idx, 0)); - assertEquals( Arrays.asList("Completed","Exception"),drt.getColumnDataAsText("Status")); - assertEquals( Arrays.asList("F","F"),drt.getColumnDataAsText("ModifiedResultFlag")); - assertEquals( Arrays.asList("7777","8888"),drt.getColumnDataAsText("CustomerBarCode")); - assertEquals( Arrays.asList("Johnston","Johnston"),drt.getColumnDataAsText("LastName")); - assertEquals( Arrays.asList("Jack","Fred"),drt.getColumnDataAsText("FirstName")); - assertEquals( Arrays.asList("Sparrow"," "),drt.getColumnDataAsText("MiddleName")); - assertEquals( Arrays.asList("jsj"," "),drt.getColumnDataAsText("Initials")); - assertEquals( Arrays.asList("Male","Unknown"),drt.getColumnDataAsText("Gender")); - assertEquals( Arrays.asList("2000-12-01","1940-06-07"),drt.getColumnDataAsText("BirthDate")); - assertEquals( Arrays.asList("222334444","555443333"),drt.getColumnDataAsText("SSN")); - assertEquals( Arrays.asList("01","02"),drt.getColumnDataAsText("FMP")); - assertEquals( Arrays.asList("A13","A14"),drt.getColumnDataAsText("DUC")); - assertEquals( Arrays.asList("P","B"),drt.getColumnDataAsText("SOT")); - assertEquals( Arrays.asList("2015-03-01","1975-03-03"),drt.getColumnDataAsText("DrawDate")); - assertEquals( Arrays.asList("2015-06-01 00:00","2015-06-01 00:00"),drt.getColumnDataAsText("Received")); - assertEquals( Arrays.asList("2015-06-03 00:00"," "),drt.getColumnDataAsText("Completed")); - assertEquals( Arrays.asList("Hemolyzed"," "),drt.getColumnDataAsText("SampleIntegrity")); - assertEquals( Arrays.asList("HIV Negative"," "),drt.getColumnDataAsText("TestResult")); - assertEquals( Arrays.asList("5B"," "),drt.getColumnDataAsText("CustomerCode")); - assertEquals( Arrays.asList("reportFileName.pdf"," "),drt.getColumnDataAsText("ReportFileName")); - File report = clickAndWaitForDownload(Locator.linkWithSpan("Download")); - assertTrue(report.getName().contains("reportFileName")); - stopImpersonating(); - - testDataDeletion(); - } - - @Test - public void testNewRequest() - { - log("creating a new test request"); - createTestRequest(); - assertElementPresent("Submit button should not be enabled if no specimen data are available", disabledSubmit, 1); - - // add specimen through the row picker - List> rows = new ArrayList<>(); - Map r1 = new HashMap<>(); - - r1.put("CustomerBarcode", "1234"); - r1.put("LastName", "Smith"); - r1.put("FirstName", "Jon"); - r1.put("SSN", "543"); - rows.add(r1); - addSpecimenRequestRow(r1, "Invalid SSN; Required field(s) missing: FMP, Draw Date", true); - - Map r2 = new HashMap<>(); - - r2.put("CustomerBarcode", "5678"); - r2.put("LastName", "Smith"); - r2.put("FirstName", "Tommy"); - r2.put("SSN", "543221234"); - rows.add(r2); - addSpecimenRequestRow(r2, "Required field(s) missing: FMP, Draw Date", false); - - log("ensure row editor saves the currently edited row"); - clickButton(SAVE_BUTTON_TEXT); - - // verify the inserted row via the data region table - verifyDataRegionRows("InboundSpecimen", rows, "CustomerBarcode"); - } - - @Test - public void testFileUpload() - { - createTestRequest(); - uploadFile(TEST_SPECIMEN_UPLOAD_FILE_1); - - log("verify proper SSN formatting"); - waitForElement(Locator.tagContainingText("div", "222-33-4444")); - - log("verify status message update"); - waitForElement(Locator.tagContainingText("div", "Required field(s) missing: FMP, Draw Date, SSN")); - waitForElement(Locator.tagContainingText("div", "Required field(s) missing: FMP")); - waitForElement(Locator.tagContainingText("div", "Draw date cannot be before birth date; Required field(s) missing: SSN")); - - log("verify submit disabled when there are validation errors"); - assertElementPresent("Submit button should not be enabled if request has been submitted", disabledSubmit, 1); - - clickButton(SAVE_BUTTON_TEXT); - - List> rows = new ArrayList<>(); - Map r1 = new HashMap<>(); - r1.put("CustomerBarcode", "5555"); - r1.put("LastName", "Jones"); - r1.put("FirstName", "Tom"); - r1.put("SSN", "222334444"); - r1.put("DUC", "A13"); - r1.put("SOT", "P"); - rows.add(r1); - - Map r2 = new HashMap<>(); - r2.put("CustomerBarcode", "6666"); - r2.put("LastName", "Jones"); - r2.put("FirstName", "Jerry"); - r2.put("DUC", "A14"); - r2.put("SOT", "B"); - rows.add(r2); - - // verify the inserted row via the data region table - verifyDataRegionRows("InboundSpecimen", rows, "CustomerBarcode"); - } - - @Test - public void testFileUploadAndSubmit() - { - log("creating a new test request by uploading a file"); - createTestRequest(); - _ext4Helper.selectComboBoxItem("Carrier", "FedEx"); - - uploadFile(TEST_SPECIMEN_UPLOAD_FILE_2); - - log("verify proper SSN formatting"); - waitForElement(Locator.tagContainingText("div", "222-33-4444")); - waitForElement(Locator.tagContainingText("div", "555-44-3333")); - clickButton(SAVE_BUTTON_TEXT); - - List> rows = new ArrayList<>(); - Map r1 = new HashMap<>(); - r1.put("CustomerBarcode", "7777"); - r1.put("LastName", "Johnston"); - r1.put("FirstName", "Jack"); - r1.put("MiddleName", "Sparrow"); - r1.put("Initials", "jsj"); - r1.put("Gender", "Male"); - r1.put("SSN", "222334444"); - r1.put("FMP", "01"); - r1.put("DUC", "A13"); - r1.put("SOT", "P"); - rows.add(r1); - - Map r2 = new HashMap<>(); - r2.put("CustomerBarcode", "8888"); - r2.put("LastName", "Johnston"); - r2.put("FirstName", "Fred"); - r2.put("Gender", "Unknown"); - r2.put("SSN", "555443333"); - r2.put("FMP", "02"); - r2.put("DUC", "A14"); - r2.put("SOT", "B"); - rows.add(r2); - - // verify the inserted row via the data region table - verifyDataRegionRows("InboundSpecimen", rows, "CustomerBarcode"); - - log("edit an existing request"); - goToProjectHome(); - clickAndWait(Locator.linkContainingText("View test requests")); - - DataRegionTable drt = new DataRegionTable("query", this); - int idx = drt.getRowIndex("ShippingCarrierId", "FedEx"); - assertNotEquals(-1, idx); - clickAndWait(drt.link(idx, 0)); - log("submitting an existing request"); - waitForElement(Locator.tagContainingText("div", "222-33-4444")); - waitForElement(Locator.tagContainingText("div", "555-44-3333")); - clickButton(SUBMIT_BUTTON_TEXT); - - drt = new DataRegionTable("query", this); - idx = drt.getRowIndex("ShippingCarrierId", "FedEx"); - assertNotEquals(-1, idx); - Assert.assertFalse(drt.getDataAsText(idx, "Submitted By").trim().isEmpty()); // "submitted by" field should be filled in - Assert.assertFalse(drt.getDataAsText(idx, "Submitted").trim().isEmpty()); // submitted date should be filled in - - log("ensure submitted requests are still editable by admins"); - assertEquals("EDIT", drt.getDataAsText(idx, 0)); - clickAndWait(drt.link(idx, 0)); - - waitForElement(org.labkey.test.Locators.bodyTitle("Edit a Test Request")); - - testPrintPackingList("Admin", "FedEx"); - - log("verify submitted requests are readonly for non-admins"); - - impersonateRole(READER_ROLE); - goToProjectHome(); - clickAndWait(Locator.linkContainingText("View test requests")); - drt = new DataRegionTable("query", this); - idx = drt.getRowIndex("ShippingCarrierId", "FedEx"); - assertNotEquals(-1, idx); - log("ensure submitted requests are still editable by admins"); - assertEquals("VIEW", drt.getDataAsText(idx, 0)); - clickAndWait(drt.link(idx, 0)); - - waitForElement(Locator.tagContainingText("td", "Carrier")); - waitForElement(Locator.tagContainingText("td", "FedEx")); - assertElementNotPresent(org.labkey.test.Locators.bodyTitle("Edit a Test Request")); - - testPrintPackingList(READER_ROLE, "FedEx"); - - stopImpersonating(); - } - - @Test - public void testEditSubmittedRequest() - { - createTestRequest(); - setFormElement(Locator.tagWithName("input", "trackingNumber"), "testEditSubmittedRequest"); - log("upload specimen data from a .xlsx file"); - uploadFile(TEST_SPECIMEN_UPLOAD_FILE_2); - - log("submitting new test request"); - waitForElement(Locator.tagContainingText("div", "222-33-4444")); - waitForElement(Locator.tagContainingText("div", "555-44-3333")); - clickButton(SUBMIT_BUTTON_TEXT); - assertTextNotPresent("Create a new test request"); // submit should take us back to the view test requests page - - log("Edit the submitted request as admin"); - DataRegionTable drt = new DataRegionTable("query", this); - int idx = drt.getRowIndex("ShippingNumber", "testEditSubmittedRequest"); - assertNotEquals(-1, idx); - assertEquals("Submitted", drt.getDataAsText(idx, STATUS_COLUMN_INDEX)); - String submittedDate = drt.getDataAsText(idx, 6).trim(); - - log("ensure submitted requests are still editable by admins"); - assertEquals("EDIT", drt.getDataAsText(idx, 0)); - clickAndWait(drt.link(idx, 0)); - - waitForElement(org.labkey.test.Locators.bodyTitle("Edit a Test Request")); - assertTextPresent("This request has already been submitted"); - assertElementPresent("Submit button should not be enabled if request has been submitted", disabledSubmit, 1); - - log("Test edit and cancel save of a submitted request"); - _ext4Helper.selectComboBoxItem("Carrier","DHL"); - assertElementPresent("Save button should be enabled if request has been edited", enabledSave, 1); - clickButton(SAVE_BUTTON_TEXT, 0); - waitForText(CONFIRM_SAVE_TEXT); - clickButton("No", 0); - - log("Test that not saving request does not change anything"); - clickButton("Cancel", 0); // takes you back to the view test requests page - idx = drt.getRowIndex("ShippingNumber", "testEditSubmittedRequest"); - assertNotEquals(-1, idx); - assertEquals("Submitted", drt.getDataAsText(idx, STATUS_COLUMN_INDEX)); - assertNotEquals("DHL", drt.getDataAsText(idx, CARRIER_COLUMN_INDEX)); - assertEquals("EDIT", drt.getDataAsText(idx, 0)); - - log("Test edit and save of a submitted request"); - clickAndWait(drt.link(idx, 0)); - _ext4Helper.selectComboBoxItem("Carrier","DHL"); - assertElementPresent("Save button should be enabled if request has been edited", enabledSave, 1); - clickButton(SAVE_BUTTON_TEXT, 0); - waitForText(CONFIRM_SAVE_TEXT); - clickButton("Yes"); - - log("Test that saving request does not change the request status"); - idx = drt.getRowIndex("ShippingNumber", "testEditSubmittedRequest"); - assertNotEquals(-1, idx); - assertEquals("Submitted", drt.getDataAsText(idx, STATUS_COLUMN_INDEX)); - assertEquals("DHL", drt.getDataAsText(idx, CARRIER_COLUMN_INDEX)); - // submitted date should still be the same - assertEquals(submittedDate, drt.getDataAsText(idx, 6)); - } - - private void testPrintPackingList(String role, String shippingCarrier) - { - log("Begin verifying 'Print Packing List' for role: " + role); - waitForElement(enabledPrintPackingList); - clickButton(PRINT_PACKING_LIST_TEXT,0); - - switchToWindow(1); - waitForElement(Locator.tag("div").withAttributeContaining("class", "barcode")); - assertTextPresent("Total Samples: 2", shippingCarrier); - getDriver().close(); - switchToMainWindow(); - - log("Finish verifying 'Print Packing List' for role: " + role); - - } - - public void testDataDeletion() - { - goToAdminConsole() - .clickSystemMaintenance(); - waitForText("Configure System Maintenance"); - click(Locator.linkWithText("HDRL Request Portal PHI Deletion")); - switchToWindow(1); - waitForText(30000, "HDRL Request Portal PHI Deletion complete"); - getDriver().close(); - switchToMainWindow(); - goToProjectHome(); - clickAndWait(Locator.linkWithText("View test requests")); - DataRegionTable drt = new DataRegionTable("query", this); - int idx = drt.getRowIndex("ShippingNumber", "testRetrievalOfResults"); - assertNotEquals(-1, idx); - String requestId = drt.getDataAsText(idx, "RequestId"); - Assert.assertEquals("Archived", drt.getDataAsText(idx, "Status")); - List specimenIds = getSpecimenIds(requestId, "hdrl", "InboundSpecimen", "RowId"); - assertTrue("There should be no specimens associated with the archived request", specimenIds.isEmpty()); - specimenIds = getSpecimenIds(requestId, "hdrl", "SpecimenResult", "SpecimenId"); - assertTrue("There should be no specimen results associated with the archived request", specimenIds.isEmpty()); - specimenIds = getSpecimenIds(requestId, "hdrl", "labwareOutboundSpecimens", "test_request_id"); - assertTrue("There should be no specimen results in the labware transfer table associated with the archived request", specimenIds.isEmpty()); - - } - - @LogMethod(quiet = true) - private void createTestRequest() - { - log("creating a new test request by uploading a file"); - goToProjectHome(); - clickAndWait(Locator.linkContainingText("Create a new test request")); - waitForElement(Locators.pageSignal("pageDirty", "false")); - - // we select this even though there is only one option available because there may be other types in the future - // Also, this test will fail without waiting for the combo box to be populated, so this is an easy way to wait - // for that. - _ext4Helper.selectComboBoxItem("Request Type","HIV Screening Algorithm"); - } - - @LogMethod(quiet = true) - private void uploadFile(@LoggedParam File file) - { - log("upload specimen data from a file"); - setFormElement(Locator.tagWithName("input", "file"), file); - log("clicking 'upload file'"); - log(doAndWaitForPageSignal(() -> clickButton("upload file", 0), "uploadFile")); - } - - private List getSpecimenIds(String requestId, String schema, String query, String idField) - { - goToSchemaBrowser(); - selectQuery(schema, query); - waitForText("view data"); - clickAndWait(Locator.linkContainingText("view data")); - DataRegionTable drt = new DataRegionTable("query", this); - drt.ensureColumnPresent(idField); - List specimenIds = new ArrayList<>(); - List targetRows = new ArrayList<>(); - List requestIds = drt.getColumnDataAsText(2); - for(int i = 0; i < requestIds.size(); i++) - { - if (requestIds.get(i).equals(requestId)) - targetRows.add(i); - } - List requestCol = drt.getColumnDataAsText(15); - for(int i : targetRows) - { - specimenIds.add(requestCol.get(i)); - } - return specimenIds; - } - - private void verifyDataRegionRows(String tableName, List> expectedRows, String key) - { - log("verifying specimen rows in the schema browser"); - goToSchemaBrowser(); - selectQuery("hdrl", tableName); - waitForText("view data"); - clickAndWait(Locator.linkContainingText("view data")); - DataRegionTable drt = new DataRegionTable("query", this); - - // find the row to verify - for (Map expectedRow : expectedRows) - { - int idx = drt.getRowIndex(key, expectedRow.get(key)); - assertNotEquals(String.format("Didn't find row with %s = %s", key, expectedRow.get(key)), -1, idx); - - Map actualRow = new HashMap<>(); - for (Map.Entry field : expectedRow.entrySet()) - { - actualRow.put(field.getKey(), drt.getDataAsText(idx, field.getKey())); - } - assertEquals("Bad row data", expectedRow, actualRow); - } - } - - private void addSpecimenRequestRow(Map values, String statusText, boolean updateRow) - { - clickButton("add specimen", 0); - - log("adding a specimen through the row picker"); - for (Map.Entry field : values.entrySet()) - { - Locator loc = Locator.xpath("//input[contains(@class, 'form-field') and @name='" + field.getKey() + "']"); - waitForElement(loc); - log("setting " + field.getKey()); - setFormElement(loc, field.getValue()); - } - - if (updateRow) - { - clickButton("Update", 0); - waitForElement(Locator.tagWithClass("div", "x4-grid-cell-inner").withText(statusText)); - } - } - - @LogMethod - protected void setupFolder() - { - _containerHelper.createProject(getProjectName(), "HDRL Request Portal"); - } - - protected void setTimeWindow() - { - goToAdminConsole(); - clickAndWait(Locator.linkWithText("HDRL Sensitive Data")); - setFormElement(Locator.name("timeWindowInDays"), "0"); - clickAndWait(Locator.linkWithSpan("Save")); - } - - @Override - public BrowserType bestBrowser() - { - return BrowserType.CHROME; - } - - @Override - public List getAssociatedModules() - { - return Arrays.asList("HDRL"); - } -}