Some of the features in caDSR II allow you to process content from a CSV file for bulk/batch importing to create new content. To view or use these features, log in as described in Logging In. These features need specially formatted templates.
Common usage details for the templates are that due to inclusion of the following Data Validations please follow these conventions:
Form Import: "Shift" + "CMD" + "t" to transform content into the correct format for importing. If you are using a REDCap data dictionary csv file, cut and paste your content into the template starting on Row 3, Column E "Variable / Field Name".
DO NOT USE | Batch User | Batch Name | Seq ID |
The Batch Owner and Batch User columns can be any text that you provide. The system does not validate these columns.
The following table lists the latest templates.
Use Data Validation | Always start with a fresh Template with Data Validation to help avoid uncaught errors due to invalid manually entered data. We have added a lot more error handling in this release, but it's not perfect yet, in particular when invalid or retired concepts are used. |
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Required Columns | All templates require a BATCH USER, BATCH NAME, and SEQ ID on each row. |
Delete/Purge | When reimporting, it is safest to select all the rows and "Delete", then select "Purge", then select all rows and “Purge Records". For Forms, select "Delete Hierarchies", then select "Purge", then select the rows and "Purge Hierarchies". |
Unique Column Names | You may add additional columns to the template for taking/keeping notes after the last template column, but the column names must be unique. |
Invalid or Retired Concepts | Invalid VM Concepts on import are not saved in the system and can create a GAP in the concept drop down. If the invalid or missing concepts are found, the system will display and error. Curators should fix all Concept Errors reported on Import BEFORE Validating. |
Concept Formatting | Concept String should not contain commas, tabs, or or other hidden characters. Always "Paste Values" in order to avoid issues. |
CSV Files!! | Template must be saved as CSV for importing. Other file types will cause an error. |
Seq ID Rules | Seq ID must be a unique integer. |
Import Exceptions | Missing Batch User, Batch Name, or Seq ID will cause Exception. |
Selecting the "Import" Command | For imports and matching, select the type of import/match item from the "Favorites" list, then select the "Import" command. For most imports there will be a dropdown with either one or two of the following choices: "Conceptual Object Import" and "Data Object Import". For most imports choose the first choice in the list. For VM Match both choices are presented, choose the second one, "Data Object Import". |
Exception on SEQ/Row Number | Multiple missing required fields may not report the correct row number in the Exception Message. Inspect the template for empty cells. |
Save / Revalidate | If making changes through front-end, Save and Revalidate. This will refresh the messages. |
Duplicates in File | Duplicate rows within the imported file are not caught on Import, but duplicate CDEs will not be created. |
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Run Transform | CDE Match transforms the Source input into one row per column and permissible value. The command to transform the Source input details is "opt"+"cmd"+"t". |
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See Instructions | Please see the CDE Match Instructions document attached to this page. |
Validating Lots of Rows | Sometimes, the system throws an error when attempting to validate more than 4 rows at a time. If that happens, try validating a few rows at a time. |
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None at this time.
Import into Existing VD | The PV VM import is designed to import an enumeration into an existing Value Domain. PV/VMs can be created using existing VMs, or you can specify a new VM either with or without concept codes. |
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Specified VM Definition | Optional Specified VM Definition is only used if the VM Type is "TEXT". The system will not throw an error but it won't be added to the VM. |
Possible Timeout | Validate/Create will timeout if more than 5 minutes. Try batches of 100 until we can redesign the code. Watch. |
VM Reuse | In a Text VM is specified and an existing VM with the exact name is found, it will be reused, even if it has concepts. The Validation message will indicate that existing VM is being used (need to fix spacing). |
After Importing | The results after importing are displayed one row per Value Meaning. All VM Match user results are kept in one database table, and without filtering results, they are all displayed in the same grid. So, after selecting "Go to Data Manager" enter your batch name and click "Apply Filter" to see just your results. |
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User Tips | The User Tips column is used to replace the VM Name. Sometimes the VM Name from your form or data is not very representative of the its meaning, or consists of too many terms IF A "User Tip" is entered it is used Instead of the VM Name. |
"Run Match" Command | Select the rows to run the match algorithm against and select the "RUN MATCH" Command. |
Column Order | The main column in VM Match is the VM Name. The processing is designed to find matching concepts based on the name and insert the Concept Name and Concept Code into the table next to the VM NAME. This order of the columns makes it easier to populate the PV/VM Template With cut and paste. You can use "Delivery Options" command to export the VM Match results into and Excel file. This simplifies creating the list of PV/VMs to import into a Value Domain. |
Import from REDCap Data Dictionary Format | Form import uses a csv file format which is one row per Question. The template contains an Excel Macro so when opening the template to paste your content into, select "Enable Macros". |
Running the Macro | Choose "Shift" + "CMD" + "t" |
Filling the template with form data | The 1st row of headings are the REDCap DD headings. The 2nd row of headings match caDSR headings. Enter a short name in the Variable / Field Name, this can be used for matching to an existing CDE. In future release it will be added as a Question Short Name. |
Form Context | REDCap does not have a column for Context. In Sprint 41 Context for the form is selected after importing the template into caDSR. |
Consistency Checking | If AI Long Name does not match the specified AI Public ID Long Name, the system will show an error. We are requesting AI Long Name and AI Type to ensure Alt names are not inadvertently added to the wrong AI. Public IDs are very similar, typos are easy to make. If this becomes onerous, we could add a Validate Step to display the AI Long Name and AI Type for curator to see and visually verify before selecting Create. |
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