/***********************************************************************/ /* Web application structure and content */ /***********************************************************************/ /***********************************************************************/ List of web application files for mutation screening workflow (JSP application) /***********************************************************************/ -------- placed in home/web/public/resources/limsGCS/-------------------- General structure for each database object: 1.getChoice: list the actions that can be performed on a specific database table (addition, queries...) 2.getList: list the records of a specific database tables depending on the query selected in “getChoice” 3.get: contain the forms for addition, update or deletion of records 4.add/update/delete: add, update or delete records General files: index.jsp : home page (main menus) logic.jsp : switchboard (pages correspondence) menu.jsp: main menu bar & fixed parameters for whole application choiceSequencing.jsp: menu for sequencing workflow choiceHR.jsp: menu for whole mutation screening workflow menu.css, menuindex.css & menuchoice.css : for display of menus menuBrowserdetect.js & menuDynMenu.js: scripts for enabling display of dynamic menus menu_arrow.gif Users guides: guide.jsp: user guide for whole application protocols.jsp: gives access to the SOPs (list links to the documents) Projects: getListProjects.jsp : list all projects stored in the database (with relevant features) getProjects.jsp: contain the forms for addition, update or deletion of projects addProjects.jsp: add a new project in the database updateProjects.jsp: : update a specified project record with specified information deleteProjects.jsp: delete the specified project from the database Genes getListGenes.jsp: list all genes stored in the database (with relevant features) getGenes.jsp: contain the forms for addition, update or deletion of genes addGenes.jsp: add a new gene in the database updateGenes.jsp update a specified gene record with specified information deleteGenes.jsp: delete the specified gene from the database getHRGenes.jsp show all pre-screening results for the specified gene (for each sample and each amplicon: the LightScanner calls) printGenes.jsp: show information and all sequencing results for the specified gene (for each sample and each amplicon: seq variants & genotypes) getSeqHRGenes.jsp: show information, all pre-screening and all sequencing results for the specified gene (for each sample and each amplicon: LightScanner calls + seq variants & genotypes) Known variants getChoiceSeqPols.jsp: list the actions that can be performed on the known variants' table (addition, queries...) getListSeqPols.jsp: list the known variants stored in the database depending on the query selected in getChoiceSeqPol.jsp (with relevant features) getSeqPols.jsp: contain the forms for addition, update or deletion of known variants addSeqPols.jsp: add a new known seq. variant in the database updateSeqPols.jsp: update a specified variant record with specified information deleteSeqPols.jsp: delete the specified seq. variant from the database Staff getListStaff.jsp: list all staff stored in the database (with relevant features) getStaff.jsp: contain the forms for addition, update or deletion of staff addStaff.jsp: add a new staff in the database updateStaff.jsp: update a specified staff record with specified information deleteStaff.jsp: delete the specified staff from the database Suppliers getListSuppliers.jsp: list all suppliers stored in the database (with relevant features) getSuppliers.jsp: contain the forms for addition, update or deletion of suppliers addSuppliers.jsp: add a new supplier in the database updateSuppliers.jsp: update a specified supplier record with specified information deleteSuppliers.jsp: delete the specified supplier from the database Reagents getChoiceReagents.jsp: list the actions that can be performed on the reagents' table (addition, queries...) getListReagents.jsp: list the reagents stored in the database depending on the query selected in getChoiceReagents.jsp (with relevant features) getReagents.jsp: contain the forms for addition, update or deletion of reagents addReagents.jsp: add a new reagent in the database updateReagents.jsp: update a specified reagent record with specified information (and update plates records using the specified reagent to status=bad if the reagent is set to bad) deleteReagents.jsp: delete the specified reagent from the database Primers getChoicePrimers.jsp: list the actions that can be performed on the primers' table (addition, queries...) getListPrimers.jsp: list the primers stored in the database depending on the query selected in getChoicePrimers.jsp (with relevant features) getPrimers.jsp: contain the forms for addition, update or deletion of primers addPrimers.jsp: add a new primer in the database addBatchPrimers.jsp: add several new primers in the database (from 1 to 10) updatePrimers.jsp: update a specified primer record with specified information deletePrimers.jsp: delete the specified primer from the database Amplicons getChoiceAmplicons.jsp: list the actions that can be performed on the amplicons' table (addition, queries...) getListAmplicons.jsp: list the amplicons stored in the database depending on the query selected in getChoiceAmplicons.jsp (with relevant features) getAmplicons.jsp: contain the forms for addition, update or deletion of amplicons addAmplicons.jsp: add a new amplicon in the database (if of type PCR also add the corresponding amplicon batch in the table tblAmpliconsBatches)) updateAmplicons.jsp update a specified amplicon record with specified information (reference chromatograms) deleteAmplicons.jsp: delete the specified amplicon from the database getSeqHRAmplicons.jsp: show information, all pre-screening and all sequencing results for the specified am (for each sample: LightScanner calls + seq variants & genotypes) getHRAmplicons.jsp: show all pre-screening results for the specified amplicon (for each sample: the LightScanner calls) printAmplicons.jsp show information and all sequencing results for the specified amplicon (for each sample and each amplicon: seq variants & genotypes + list of chromatograms & status) Batches of amplicons: getListAmpliconsBatches.jsp: list all batches of amplicons stored in the database (with relevant features) getAmpliconsBatches.jsp: contain the forms for addition, update or deletion of batches of amplicons addAmpliconsBatches.jsp: add a new batch of amplicons in the database updateAmpliconsBatches.jsp update a specified batch record with specified information deleteAmpliconsBatches.jsp: delete the specified batch of amplicon from the database Amplicons Compatibilities getListAmpliconsCompatibilities.jsp: list all amplicons compatibilities stored in the database (with relevant features) getAmpliconsCompatibilities.jsp: contain the forms for addition, update or deletion of amplicons compatibilities addAmpliconsCompatibilitites.jsp: add a new amplicon compatibility in the database updateAmpliconsCompatibilities.jsp: update a specified amplicon compatibility record with specified information deleteAmpliconsCompatibilities.jsp: delete the specified amplicon compatibility from the database DNA Samples getChoiceDNASamples.jsp: list the actions that can be performed on the DNA samples' table (addition, queries...) getListDNASamples.jsp: list the DNA samples stored in the database depending on the query selected in getChoiceDNASamples.jsp (with relevant features) getDNASamples.jsp: contain the forms for addition, update or deletion of DNA samples addDNASamples.jsp: add new samples in the database (from 1 up to 24) updateDNASamples.jsp: update a specified sample record with specified information lookDNASamples.jsp: show information about a specified sample (project, position, screening sets…) deleteDNASamples.jsp: delete the specified sample from the database printDNASamples.jsp DNA plates 96 getChoiceDNAPlates.jsp: list the actions that can be performed on the 96 DNA plates' table (addition, queries...) getListDNAPlates.jsp: list the 96 DNA plates stored in the database depending on the query selected in getChoiceDNAPlates.jsp (with relevant features) getDNAPlates.jsp: contain the forms for addition, update or deletion of 96 DNA plates addDNAPlates.jsp: add a new 96 DNA plate in the database and send a file to the barcode printer with the new barcode to print. updateDNAPlates.jsp: update a specified 96 DNA plate record with specified information getDNAPlatesWells.jsp: show content and history of a specified DNA plate (picture) deleteDNAPlates.jsp: delete the specified 96 DNA plate from the database Filling DNA plates 96 <=> DNA Wells getListDNAWells.jsp list the different ways of filling a DNA plate (selection of samples, copy of plate...) getDNAWells.jsp: contain the forms for the different ways of filling or updating content of 96 DNA plates getAllDNAWells.jsp list the DNA wells stored in the database depending on the query selected in ?.jsp (with relevant features) addDNAWells.jsp : add new DNA plate wells (fill empty plate with samples selected for each well) copyBatchDNAWells.jsp add new DNA plate wells (fill empty plate with same samples than selected template plate <=> copy wells) getUpdateBatchDNAWells.jsp contain the form as plate picture for updating the content of a specified 96 DNA plates (already partially filled) updateBatchDNAWells.jsp: update the content of a specified plate with specified samples updateDNAWells.jsp: update one specified well of one specified plate with a specified sample deleteDNAWells: delete the specified well from the database DNA plates 384 getChoiceDNAPlates384.jsp: list the actions that can be performed on the 384 DNA plates' table (addition, queries...) getListDNAPlates384.jsp: list the 384 DNA plates stored in the database depending on the query selected in getChoicePlates384.jsp (with relevant features) getDNAPlates384.jsp: contain the forms for addition, update or deletion of 384 DNA plates addDNAPlates384.jsp: add a new a new 384 DNA plate in the database and send a file to the barcode printer with the new barcode to print. updateDNAPlates384.jsp: update a specified 384 DNA plate record with specified information deleteDNAPlates384.jsp: delete the specified 384 DNA plate from the database Plates For PCR getChoicePlatesForPCR.jsp: list the actions that can be performed on the reagent plates for PCR's table (addition, queries...) getListPlatesForPCR.jsp: list the reagent plates for PCR stored in the database depending on the query selected in getChoicePlatesForPCR.jsp (with relevant features) getPlatesForPCR.jsp: contain the forms for addition, update or deletion of reagent plates for PCR printPlatesForPCR.jsp add several new empty reagent plates for PCR in the database (from 1 to 10) and send a file to the barcode printer with the new barcodes to print addPlatesForPCR.jsp: update from 1 to 10 plates for PCR with oil reagent & send file to Tecan with barcodes of plates to process updateBatchPlatesForPCR.jsp: update from 1 to 10 plates for PCR with PCR mix reagent updatePlatesForPCR.jsp update a specified plate for PCR with specified information deletePlatesForPCR.jsp: delete the specified plate for PCR from the database Plates PCR1 getChoicePlatesPCR1.jsp: list the actions that can be performed on the plates PCR1's table (addition, queries...) getListPlatesPCR1.jsp: list the plates PCR1 stored in the database depending on the query selected in getChoicePlatesPCR1.jsp (with relevant features) getPlatesPCR1.jsp: contain the forms for addition, update or deletion of plates PCR1 addPlatesPCR1.jsp: add new plates PCR1 in the database (from 1 to 6 with the same DNA source plate) & sent a file to the Beckman Biomek with the barcodes of the plates to be processed addPlatesPCR1_2.jsp: add new plates PCR1 in the database (from 1 to 6 with the same amplicons) updatePlatesPCR1.jsp: update a specified plate PCR1 record with specified information deletePlatesPCR1.jsp: delete the specified plate PCR1 from the database searchPlatesPCR1.jsp: show a specified plate PCR1 history and picture (content) Plates PCR2 getChoicePlatesPCR2.jsp: list the actions that can be performed on the plates PCR2's table (addition, queries...) getListPlatesPCR2.jsp: list the plates PCR2 stored in the database depending on the query selected in getChoicePlatesPCR2.jsp (with relevant features) getPlatesPCR2.jsp: contain the forms for addition, update or deletion of plates PCR2 addPlatesPCR2.jsp: list the amplicons available for the PCR2 based on the previously selected plates and amplicons used for PCR1 printPlatesPCR2.jsp: add a new plate PCR2 in the database, update plate for PCR to used and send a file to the barcode printer with the intermediate dilution plate barcode to be printed and send a file to the Beckman Biomek FX with the barcodes of the plates to process updatePlatesPCR2.jsp: update a specified plate PCR2 record with specified information deletePlatesPCR2.jsp: delete the specified plate PCR2 from the database searchPlatesPCR2.jsp: show a specified plate PCR2 history and picture (content) Plates HR* getChoicePlatesHR.jsp: list the actions that can be performed on the plates HR's table (addition, queries...) getListPlatesHR.jsp: list the plates HR stored in the database depending on the query selected in getChoicePlatesHR.jsp (with relevant features) getPlatesHR.jsp: contain the forms for addition, update or deletion of plates HR addPlatesHR.jsp: add new plate HR in the database, send a file to the barcode printer with the new barcode to print and send a worksheet to the LightScanner with the plate barcode and the plate content (sample, amplicons, positions) updatePlatesHR.jsp: update a specified plate HR record and re-send updated worksheet to the LightScanner updateResultPlatesHR.jsp: update a specified plate HR record with raw data result file, parse the analysis result file and insert records in the table tblGenotypesHR (sample, plate, position, amplicon, call,…) printPlatesHR.jsp: show a specified plate HR picture (content) and mutation scanning results Plates EXO/SAP getChoicePlatesEXOSAP.jsp: list the actions that can be performed on the plates EXO/SAP's table (addition, queries...) getListPlatesEXOSAP.jsp: list the plates EXO/SAP stored in the database depending on the query selected in getChoicePlatesEXOSAP.jsp (with relevant features) getPlatesEXOSAP.jsp: contain the forms for addition, update or deletion of plates EXO/SAP addPlatesEXOSAP.jsp: add a new classic plate EXO/SAP in the database addHRPlatesEXOSAP.jsp: add a new HR plate EXO/SAP in the database and send file to barcode printer with new barcode to print + display the content of the selected source plates for sample selection together with position, amplicon and result (=>rearray on HR plate) nextHRPlatesEXOSAP.jsp: update specified new plate EXOSAP content with selected samples and send file to the BioRobot for rearraying selected samples from three 384 well updatePlatesEXOSAP.jsp: update a specified classic plate EXOSAP record with specified information printPlatesEXOSAP.jsp show a specified plate EXOSAP history and picture (content) deletePlatesEXOSAP.jsp: delete the specified plate EXOSAP from the database Plates For Seq getChoicePlatesForSeq.jsp: list the actions that can be performed on the reagent plates for sequencing's table (addition, queries...) getListPlatesForSeq.jsp: list the reagent plates for sequencing stored in the database depending on the query selected in getChoicePlatesForSeq.jsp (with relevant features) getPlatesForSeq.jsp: contain the forms for addition, update or deletion of reagent plates for sequencing printPlatesForSeq.jsp: add several new empty reagent plates for sequencing in the database (from 1 to 10) and send a file to the barcode printer with the new barcodes to print addPlatesForSeq.jsp: update from 1 to 10 plates for sequencing with oil reagent updateBatchPlatesForSeq.jsp: update from 1 to 10 plates for sequencing with sequencing mix reagent & send file to Tecan with barcodes of plates to process updatePlatesForSeq.jsp: update a specified plate for sequencing with specified information deletePlatesForSeq.jsp: delete the specified plate for sequencing from the database Plates Seq getChoicePlatesSeq.jsp: list the actions that can be performed on the sequencing plates' table (addition, queries...) getListPlatesSeq.jsp: list the sequencing plates stored in the database depending on the query selected in getChoicePlatesSeq.jsp (with relevant features) getPlatesSeq.jsp: contain the forms for addition, update or deletion of sequencing plates addPlatesSeq.jsp: add a new sequencing plate in the database and sent a file to the Beckman Biomek FX with the barcodes of the plates to process (+update plate for seq = used) updatePlatesSeq.jsp: update a specified sequencing plate record with specified information deletePlatesSeq.jsp: delete the specified sequencing plate from the database searchPlatesSeq.jsp: show a specified sequencing plate picture (content) Plates Con getChoicePlatesCon.jsp: list the actions that can be performed on the consolidation plates' table (addition, queries...) getListPlatesCon.jsp: list the consolidation plates stored in the database depending on the query selected in getChoicePlatesCon.jsp (with relevant features) getPlatesCon.jsp: contain the forms for addition, update or deletion of consolidation plates printPlatesCon.jsp: add several new empty consolidation plates in the database (from 1 to 10) and send a file to the barcode printer with the new barcodes to print updatePlatesCon.jsp: update a specified consolidation record with specified information for precipitation step + send a file to the Beckman Biomek with the barcodes of the plates to process for precipitation nextPlatesCon.jsp: update a specified consolidation record with specified information for capillary sequencer loading step + send a file to the sequencer with the barcode of the plate to process and its ontent (samples positions) searchPlatesCon.jsp: show a specified consolidation plate history and picture (content) deletePlatesCon.jsp: delete the specified consolidation plate from the database Screening Sets getChoiceScreeningSets.jsp: list the actions that can be performed on the screening sets' table (addition, queries...) getListScreeningSets.jsp: list the screening sets stored in the database depending on the query selected in getChoiceScreeningSets.jsp (with relevant features) getScreeningSets.jsp: contain the forms for addition of screening sets addScreeningSets.jsp: add a new screening set in the database and display for selection the pairs of chromatograms available for analysis printScreeningSets.jsp: add the association screening set - pairs of chromatograms in the database (update a screening set with content) getScreeningSetsFiles.jsp: show information, content and analysis results of a specific selected screening set Divers getPrintBarcode.jsp: form to enter the barcode to reprint printBarcode.jsp: send a file to the barcode printer with the barcode to reprint resultSeq.jsp: give access to excel files with all results (for each gene mutation screening and sequencing results) /***********************************************************************/ Other important files: /***********************************************************************/ home/Backup_Scripts/ ====> contains backup scripts home/mysql-connector-java-2.0.14/ ===> contains mysql-connector home/tomcat/Jakarta-tomcat-4.1.18/ ===> contains Tomcat home/web/cgi-bin/... home/web/GCS_Sequence: directory where the chromatograms are put by the users and from where they’re downloaded into the database home/web/gcsbarcodes_script/ ======> contains scripts for connection with the robots: gcsBeckman.sh gcsBioRobot.sh gcsLightScanner.sh gcsSequencer.sh gcsTecan.sh home/web/public/resources/limsGCS/barcodes/ ====> contains all files sent to the barcode printer barcode.ext home/web/public/resources/limsGCS/beckman/ worklistPCR1_pcr_a_xxx.txt worklistPCR2_pcr_a_xxx.txt SampleSheet_exo_a_xxx.csv worklistSeq_seq_a_xxx.txt SampleSheet_con_a_xxx.txt home/web/public/resources/limsGCS/tecan/ worklistPCRMix_pcr_a_xxx.txt worklistSeqMix_seq_a_xxx.txt home/web/public/resources/limsGCS/lightscanner/ hr_a_129.txt ... home/web/webapps/local/IARC/ authorizer/iarcAuthorizer.jar crypter/iarcCrypter.jar home/web/webapps/local/IARC/limsGCS/ build.xml iarcLimsGCS.jar home/web/webapps/local/IARC/limsGCS/tag/iarcTag.jar url.properties build.xml home/web/webapps/local/IARC/limsGCS/tag/src/IARC/tag/ =====> contains java and class files home/web/webapps/local/IARC/limsGCS/tag/src/IARC/tag/tld/ ====> contains tld files (error, load…) Util/iarcUtil.jar