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HOW TO START WITH LABCOLLECTOR
- How does LabCollector interface look?
- How does a module generally look like?
- How to set up storage in LabCollector?
- What are fields in LabCollector?
- What are records in LabCollector & how to create them?
- How to start with Antibodies module?
- How to start with Chemical structures module?
- How to start with Document module?
- How to start with Electronic Lab Notebook (ELN)?
- How to start with Equipment module?
- How to start with Plasmids module?
- How to start with Primers module?
- How to start with Reagent & Supplies module?
- How to start with Sample module?
- How to start with Sequences module?
- How to start with Strains & Cells module?
- How to use Webinars add-on?
- How to mass update memorized records?
- How to use LabCollector for COVID-19 testing?
- Show all articles ( 4 ) Collapse Articles
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INSTALLATION
- How can I connect to LabCollector from another computer?
- LabCollector Installation Requirements for AWS
- How to install LabCollector using Docker?
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- How to move a whole installation to a new Windows server?
- How to run LabCollector server on a 64bits Windows machine?
- Install LabCollector with IIS on Windows Server
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- Clean the apache log manually to improve the speed.
- Switching to the ServerManager v2.5 (old way)
- Windows Installation Using Setup Wizard
- How to enable the soap.dll extension in LSMRemote using php file or LabCollector Server Manager (Windows)?
- How to use the LabCollector Server Manager?
- How to replicate LabCollector in real time with Windows Server Manager?
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- Apache Server/Web server doesn't run on Windows 10
- Clean the apache log manually to improve the speed.
- Clean the logs manually to improve the speed.
- ERROR in log: AH00052: child pid 3461 exit signal Segmentation fault (11)
- ERROR: Warning: mysql_connect(): Client does not support authentication protocol requested by server (…)
- How to make Java applets work again after upgrading to Java 7U51+?
- How to restore overwritten documents
- I have the message "Failed to connect to mySQL server. No Database found for this lab account". What can I do?
- My LabCollector or Add-on is very slow. Why and how to fix it?
- Unknown column “auto_name_mode” in “field list”: The error is occurring when I want to adjust existing records, make new records or import data. What can I do?
- URL issue
- When I add records or any values I have this message: "incorrect integer value: for column 'count' at row 1"
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- Give access to LabCollector to collaborators outside your network
- Can the database be separated from the system on which labcollector is installed?
- I have problems installing PHP and/or MySQL. Is there an alternative?
- Mysql Server memory usage optimization
- PHP extensions needed
- Rack scanners installation and connection with ScanServer
- System Requirements - Hosted options (FR/ENG)
- What are PHP and MySQL? Do I need to have PHP & MySQL?
- How to migrate LabCollector to new Linux Server?
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GENERAL
- What is LabCollector?
- How do I install LabCollector? Where can I find the install.exe file?
- System Requirements - Hosted options (FR/ENG)
- How does the remotely hosted version work?
- Can I use LabCollector on a single computer? Can I install it on a web server?
- If I purchase ONE license, do I need to purchase additional licenses for other computers in my lab network?
- Client Area Tutorial
- LabCollector support
- What are the FDA requirements for software to comply with GxP guidelines?
- Do I need to purchase all modules? Can I use only the primers module?
- Icons meaning (EN/FR) V.6.0
- Icons meaning (EN/FR)
- How do I search in LabCollector?
- Can I see/list all records in a module?
- How do I print records?
- How to add panels to LabColletor v6.0?
- How to create tubes with storage and mark their usage? (v6.0)
- How to create and set alerts for tubes? (v6.0)
- Label network printers and roll types
- Show all articles ( 4 ) Collapse Articles
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BASIC FEATURES
- Export and print models
- How do I add multiple records without data import
- How do I link records and for what purpose?
- How do you create or edit records? (FR/EN)
- Icons meaning (EN/FR)
- Icons meaning (EN/FR) V.6.0
- Reagents & Supplies Link what is the purpose?
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- What can I do with the default fields?
- Can I add a custom module to fit my specific needs?
- Custom field types
- How do you create a custom field? (For v5.2 and below)
- How do you create a custom field? For version 5.2 onwards
- Custom field: Field category option version 5.2x
- Custom fields: Tab Analysis option
- How do I customize record options?
- How do I use a Read-only field?
- How to customize LabCollector login page colors?
- How to change the language & name of custom fields?
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- What is a CSV file?
- Import your data (v6.0)
- Import your data (5.3 version and above)
- How to delimit data csv for data import?
- What are the default fields values while importing data? v6.0
- How do I format the date value as yyyy-mm-dd or yy-mm-dd to import?
- Import your samples and associated storage in 3 steps
- Import and manage your Reagent & Supplies V5.3 and above
- Importer ma BDD EndNote dans LabCollector (FR)
- How to solve errors while importing data
- How to mass update memorized records?
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- What are user level permissions?
- How do you use versioning? v5.31 and below
- How do you use versioning? v5.4 and above
- How to manage users (v5.31 and below)
- How to manage users (v5.4 and above)
- How to use AD or LDAP for login authentication?
- What are group policies and how to use them?
- What are group policies and how to use them? v5.4 and above
- What are group policies and how to use them? v6.0 and above
- How to manage users? (v.6.032+)
- How to configure access permissions?
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MODULES
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- Articles coming soon
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- How to start with Reagent & Supplies module?
- Reagent & supplies preferences (v6.03)
- Reagent & supplies preferences
- How do I create alerts for chemical and equipment?
- How do I create alerts with lots? (v6.0)
- Manage your reagent lots (v6.0)
- Manage your reagent lots
- How to dispose of a lot?
- Risk codes
- How do I manage vendors and sellers?
- How do I print risk and safety data information?
- Import and manage your Reagent & Supplies V5.3 and above
- Manage storage for Reagent & Supplies module
- Manage storage for Reagent & Supplies module (v6.0)
- GHS Hazard Pictograms, Mandatory Safety Signs and the NFPA Hazard Rating System
- How to Use SDS Maker?
- Show all articles ( 1 ) Collapse Articles
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- Articles coming soon
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- Articles coming soon
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- How do I create alerts for chemical and equipment?
- How to activate and set different types of Equipment alerts? (v6.0)
- How to activate and set different types of Equipment alerts? (v5.4 and below)
- How to add a new category and record in equipment module? (v6.0)
- How to add a new category and record in equipment module? (v5.4 and below)
- How to add control chart for calibration maintenance of equipment?
- How to Add/Edit Maintenance for Equipment? (v6.0+)
- How to add/edit maintenance for equipment (v5.4 and below)
- How to export equipment maintenance report?
- What are the options in "display maintenance" section of equipment. (v5.4 and below)
- What are the options in "display maintenance" section of equipment. (v6.0)
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- Articles coming soon
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ADD-ONS
- What are Add-ons?
- Fly Stock Manager
- What's Weight Tracker Add-On? How To Use It?
- Custom Field File Upload
- What is e-catalog add-on? And how to use it?
- Lab Cross Search
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- How to start with LSM?
- LSM Usage Guide – From Job Request to Results Reporting
- Test the LSM API
- Insert the LSMremote application in your website
- How to Perform a Paternity/Relationship Genetic Test using LSM?
- Introduction to HL7 and how to use it in LSM
- LSM Job List Icons - What do they mean?
- LSM: How to Group Test Results by Specialty?
- Lot-Sample Linking in LSM for Quality Control
- LSM: Trending and Job Charts
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- 1st step: Create users and requesters
- How to send samples from LabCollector to a LSM job
- How to link a custom module to LSM?
- How to manage case records (patients, animals...) in LSM?
- How to re-order/re-arrange job & sample custom fields in LSM?
- How to manage ranges in LSM?
- How to restart a job in LSM?
- I’m able to add a new job with no problems but when I try to start it I can’t do it. The following error appears: Error loading XML document: data/bl/bl-job.php. What’s the problem?
- How to accept jobs in LSM?
- How to create & execute a job in LSM?
- How to create version of test in LSM?
- How to import CSV with samples and tests in LSM?
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- 5th step: Result and invoice template
- How to generate Reports in LSM?
- How to create a processing report in LSM?
- How to Generate Invoices Report Template in LSM?
- How to create a Chain Of Custody (CoC) report and use it LSM & LSMRemote?
- How to use text editor to create a report template in LSM?
- Report tags in LSM for result/invoice/CoC/batch templates?
- Correction/Amendement actions in LSM report
- How to print and follow multiple reports/CoC's in LSMRemote?
- Error loading big reports in LabCollector
- Error loading big reports in LSM
- How to configure header & footer in LSM report/CoC/invoices? (from v4.057+)
- What's the purpose of the report unique ID barcode?
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- LSMRemote (v6.0) registration, login and other options
- LSMRemote installation steps & Integration into the website ? (v4.0)
- LSMRemote configurable options (v4.0)
- How to configure new fields, submit a job in LSMRemote & view it in LSM?
- How to search in LSMRemote?
- How to create a token for report access for patient/client using LSMRemote?
- How to generate CoC Manifest with integrated labels?
- How to print and follow multiple reports/CoC's in LSMRemote?
- Patient pre-registration configuration and LSMRemote portal connection
- How to do job pre-registration from the LSMRemote portal?
- How to integrate appointments scheduling in LSMRemote?
- How to enable the soap.dll extension in LSMRemote using php file or LabCollector Server Manager (Windows)?
- How to import jobs using LSMRemote?
- How to configure kit and activate it in LSMRemote?
- How to print in bulk the barcodes using LSMRemote?
- How to enable the soap.dll extension in LSMRemote using php file on Linux?
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- OW-Server ENET manual
- OW-Server Quick start guide
- OW-Server WiFi manual
- Quick WiFi configuration for OW-Server WiFi
- Conversion method from mA reads to specific Unit for data logger probe?
- How to setup your Data Logger in LabCollector?
- How to Install Sensors on ULT Freezers?
- How to Setup Alerts in Data Logger?
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- How to create a Book, add an Experiment and a Page?
- What is inside a Book?
- What is inside an Experiment?
- Whats inside ELN Page?
- How do I print from ELN?
- ELN Workflows
- ELN templates
- TIFF Image usage
- How to electronically sign the ELN pages?
- How to add a microplate in ELN Page?
- How to add a reagents/solutions recipe in ELN?
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- ELN - Zoho Spreadsheet Help Guide
- Graph in Flat spreadsheet
- How to change the language of ZOHO excel in ELN?
- How to replicate/import your excel in ELN?
- How to use spreadsheets?
- What is Flat & Zoho Spreadsheet Editor & how to enable it?
- How to use Flat spreadsheet & formulas in it?
- How to make graph in Flat Spreadsheet?
- What can be copy pasted from excel into Flat spreadsheet?
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- Sample-receiving add-on : Project configuration settings
- How to create & process a package in Sample receiving add-on?
- How to perform pooling in sample receiving add on?
- How to process plates in sample receiving add-on?
- How to view samples created in sample receiving add-on into a module?
- How to add samples created in sample receiving into Workflow add-on?
- How to connect and send samples from 'sample receiving' to do tests in 'LSM'?
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MOBILE APPS
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- Articles coming soon
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INTEGRATION
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API
- Introduction to LabCollector API
- API for LabCollector (v5.4+)
- API for LSM (v2)
- API for ELN (v1)
- How to test the LabCollector REST API?
- API error messages
- API: How to create boxes or plates?
- Test the Lab Service Manager API
- Webservice/API Apache setup
- How to set up your Web Services API?
- What's Swagger UI? How to access it & test out API endpoints?
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TOOLS
- How do you install NCBI blast executable to use in LabCollector?
- How to setup and use Recipe Manager (old version)
- How to manage memorized items?
- Purchase order management - A to Z
- Purchase order management – A to Z (v 6.0+)
- Recipe Manager (v6.0)
- Samples batch tool (Rack scanner)
- How to use Mass Record Updater?
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UTILITIES / MIDDLEWARE
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- How to download and Install File connector v2.2? (Labcollector v6.0 )
- How to install Fileconnector in Mac OS? (Labcollector v6.0 )
- Editing a file using File Connector
- How to use a specific software to open certain types of files in fileconnector? (Labcollector v6.0 )
- How to use Fileconnector in Mac OS?
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- How to setup and configure Scan Server with LabCollector?
- Samples batch tool (Rack scanner)
- The rack barcode on top or as third element in lines?
- How to open CSV in UTF8 in Excel?
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PRINTING
- How to configure printer with LabCollector?
- How to connect USB printer to LabCollector?
- Direct Printing Compatibility (All Printers Support Generic PDF Label Printing)
- Label network printers and roll types
- Barcode label generation and printing
- How do I print barcode labels?
- How do I print box maps?
- How do I print records?
- How do I print risk and safety data information?
- How do I print storage records
- How to print labels on HTTPS environment?
- How to best configure your PDA N5000 for LabCollector use
- How can I configure my barcode scanner AGB-SC1 CCD?
- How can I configure my barcode scanner HR200C ?
- How do I configure FluidX to support ScanServer?
- Barcode Printer Connection Time Out
- AGB-W8X Manual for barcode scanning
- How to set up your Printers & Labels?
- How to Increase Label Print Quality in LabCollector?
- Show all articles ( 4 ) Collapse Articles
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STORAGE
- How to set up storage in LabCollector?
- How to create boxes/drawers/racks in storage equipment?
- How to create box models for storage?
- How to replicate and duplicate boxes in storage?
- How to store and manage straws? (EN/FR)
- How Do I Add Samples to a Specific Freezer, Shelf or Other Part of the Storage System?
- How do I get out samples from a specific freezer?
- Manage storage for Reagent & Supplies module
- How to organize Storage Browser?
- How do I print box maps?
- How do I print storage records
- Storage Check-in/out System
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COMPLIANCY
- What is in the Compliancy Pack?
- How do I use a Read-only field?
- What are the FDA requirements for software to comply with GxP guidelines?
- FDA CFR21 part 11 product checklist
- ISO 17025 compliancy requirements
- How do you use versioning? v5.31 and below
- How do you use versioning? v5.4 and above
- Should I lock, archive or delete records?
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SUPPORT
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SETTINGS
- How to configure Apache to work with Office 2007 and higher?
- How to speed up your LabCollector? (EN/FR)
- PHP extensions needed
- Speed your local network
- TIFF Image usage
- Time stamp in the records showing incorrect time.
- How to configure SMTP to use OAuth 2.0 (Microsoft & Gmail)?
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- LabCollector General setup
- LabCollector General setup - v5.4
- LabCollector General Setup 5.2
- LabCollector General setup-v6.0
- Login Options & php requirements for LDAP/SSO
- How to set up your LabCollector's general settings, logo & modules' names?
- How to configure your Proxy, Task Scheduler and Email options?
- How to configure your module search & form options?
- How to configure your Homepage external links?
- How to set up your News Feed?
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- Error loading big reports in LabCollector
- Fields with scroll bar don't work with Safari, what can I do?
- I can't manage to view box scheme in Safari, why?
- I get the error: "The program can't start because MSVCR110.dll is missing from your computer. Try reinstalling the program to fix this problem" when installing or updating LabCollector for Windows
- Issue in upload file: look at your PHP configuration
- Module search fails with 404 error or request too long
- When I want to import large files, nothing happens?
- Why do I have the error “MySQL server has gone away” on file upload?
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NEW KB OF THE MONTH
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RECORDED PRESENTATIONS
How to import CSV with samples and tests in LSM?
You are here:
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SUMMARY:
With the LSM ad-on allows you to add a job and import multiple samples and test with CSV/text file. You can update the CSV/text file with information about multiple samples and tests related to it in LSM while adding a job. However, there are some rules you must follow to import certain types of data fields, such as multiple tests, multiple choice, check boxes, etc.
1. Create a job
2. Export CSV/Text file with samples & test column headers
3. Import CSV/Text file with samples & test details
- 3a. SAMPLES
- 3b. DEFAULT PARAMAETERS
- 3c. CUSTOM PARAMTERS
4. Save & Execute the job
1. Create a job
- You can create a job in LSM by going to ADMIN -> JOB -> ADD JOB
Please read our Knowledge Base on how to create and execute a job in LSM. - You can add job details such as requester, job priority, etc.
- You can also add information about the sample name and other sample-related parameters, as well as the tests.
- However, if you want to import multiple samples and tests, you can do so by importing a CSV/text file.
- All the options in sample level are explained in the LSM manual.
2. OPTIONAL: Export CSV/Text file with samples & test column headers
- You can create your CSV/text file to import the sample and test details directly in the “Add Job” section by adding the name of the parameters.
- However, if you have many parameters or need a template to help you with the column headings, then you can use this option to export the CSV file.
- To import the CSV/text file, you can export the template with all the pattern level parameters by clicking Export CSV.
- You can use this as a template to enter all the required information.
Note
To customize the columns you wish to export, follow these simple steps:
- Navigate to the “Results” tab of your job.
- Click on the “Columns” button.
- A pop-up will appear, allowing you to select the columns you want to include in your report. To add a column, click on its corresponding name. To remove a column, simply click on it again to deselect it.
- At the bottom of the pop-up tab, you’ll find two checkboxes: a. “Hide comment fields“: Selecting this option will hide all comment fields from the exported data. b. “Hide range fields“: Choosing this option will hide the range fields from the exported data.
3. Import CSV/Text file with samples & test details
- If you want to upload the CSV/text file, you will see the following options that you can use.
- Click on “Select file option” & upload a CSV/text file.
- Use the correct delimiters: Comma (,), Semicolon (;) and Tab (|).
Please read our Knowledge Base on how to how to delimit data in CSV - Finally, click on “Load” to upload the details from the CSV/text file.
- You need to go to ADMIN -> JOB -> ADD JOB -> SAMPLE TAB
Tips/Hints
- The below section can help you to prepare better the CSV/Text file for the import.
3a. SAMPLES
- You can add the names of the samples in each row of Excel.
- Remember that you are adding the samples for one job, so it will be an order with several samples.
- Each row in the CSV/text file is a sample.
- The name of the sample can be alphanumeric.
*It is better to avoid special characters in the sample name.
- In scenario where you have choose automatic sample naming , then the sample default parameter will not be visible, nor will be exported in the CSV file.
- This is because in automatic setting the sample names are autogenerated by the LSM.
- You can do this setting by going to ADMIN -> JOB -> SETUP -> JOBS & SAMPLES NAMING
- Therefore, you can import the sample information without the sample name.
3b. DEFAULT PARAMETERS
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SAMPLES:
- In the LSM Sample tab, there are default parameters such as sample name, sample type, comments and tests.
- Some of the default parameters are mandatory and must therefore be filled in the CSV/text file.
- Mandatory default parameters are marked with a red asterisk.
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SAMPLE TYPE:
- For the sample type, it is important to remember that the type should already be present in the ADMIN -> PREFERENCES -> SAMPLE TYPE
- A new sample type that does not yet exist in the LSM will not be imported. For example, like below:
- For the sample type, it is important to remember that the type should already be present in the ADMIN -> PREFERENCES -> SAMPLE TYPE
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COMMENT:
- This field is not mandatory and can therefore be skipped if you do not wish to provide any information here.
- If you would like to make a comment, you can simply enter the desired text in CSV/text file..
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WarningMake sure you dont use any separators like comma, semicolon or tab in the text that you write otherwise, it will create conflict and the data will not be imported correctly.
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TESTS:
- You can fill in all the details about tests.
- The tests name should match the name mentioned in ADMIN -> JOB -> PREFERENCES -> TESTS
Be Careful noteYou need to follow rules with separator when importin multiple tests. (Please read below)
- You need to follow some rules if you want to upload multiple tests for one sample.
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- RULE 1- Same separator:
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- If you use the same separator (highlighted in yellow) for columns and multiple tests, then add the test name in double quotes (highlighted in blue and arrow)
- If you use the same separator (highlighted in yellow) for columns and multiple tests, then add the test name in double quotes (highlighted in blue and arrow)
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- RULE 1- Same separator:
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- RULE 2- different separator:
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- Use a different separator (blue highlighted and arrow) for separating just the multiple tests than the one used to separate columns (yellow highlighted)
- Use a different separator (blue highlighted and arrow) for separating just the multiple tests than the one used to separate columns (yellow highlighted)
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- RULE 2- different separator:
3c. CUSTOM PARAMETERS
- These are the parameters that you create at the sample level by going to ADMIN -> PREFERENCES -> PARAMETERS
- There can be different types of custom parameters at the sample level, they are described in LSM manual
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CHECKBOX:
- Here you need to use
- 0 = to not tick mark check box
- 1 = to tick mark check box
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DATE:
- Here you must follow the LSM date format and make sure it is identical in your CSV/text file. Otherwise, the wrong format will not be imported.
- You can check the format of the date by going to LSM and creating an example.
- You can then import the date accordingly.
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DATETIME:
- Here you must follow the LSM date & time format and make sure it is identical in your CSV/text file. Otherwise, the wrong format will not be imported.
- You can check the format of the date & time by going to LSM and creating an example.
- You can then import the date & time accordingly.
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TIME:
- You can follow the same steps the date and time mentioned above.
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VALUELIST:
- You must ensure that the values match the values defined in the valuelist parameter.
- For example, if your valuelist contains the values ‘yes’ and ‘no’, you only need to add these values.
- Values that do not match the existing values are not uploaded.
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MULTIPLE CHOICE:
- You need to make sure that the values match those that already exist.
- Values that do not match the existing values are not uploaded.
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- RULE 1- Same separator:
- If you use the same separator for columns and multiple choice options, then code the name of the test in double quotes.
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- RULE 2- different separator:
- Use a different separator for separating multiple tests than for separating columns
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NUMERIC:
- You can add values in decimals as well.
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STRING & LONGTEXT:
- You can enter text here, just as you do with the default comment field described above.
WarningMake sure you dont use any separators like comma, semicolon or tab in the text that you write otherwise, it will create conflict and the data will not be imported correctly.
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IMAGE & FILE:
- You CANNOT import a file or image using CSV/Text file in LSM job, sample parameter tab.
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AVERAGE, SD (STANDARD DEVIATION) & CALCULATED
- These fields are automatically calculated based on other fields, so you do not need to fill them in when importing fields.
- However, you must upload the other fields whose values are to be calculated in these fields.
- The other fields are numeric fields as explained above.
4. Save & Execute the job
- Once the information on the job is imported and completed now you can save the job and execute it.
Please read our Knowledge Base on how to create and execute a job in LSM.
Related topics:
- Please see the KB on how to create & execute job.
- See our KB on how to create/import reagents & equipment.
- See our KB on how to create protocols & sample types.
- See our KB on how to create parameters for a test.
- See our KB on how to create results & invoice templates.
- See our KB on how to create a test.
- Read our manual on LSM.