1. Load affine
Before attempting upload of an affine file using the SCORS Uploader and Manager application, ensure that it complies with the specified format (see Appendix 1, or recent examples from the LIMS database). The Correlator application will in general be generating the correct formats, but legacy files may need to be corrected. The file must be CSV format and have the prescribed number and types of columns. The uploader will perform a limited number of tests and will reject non-compliant files.
To load an affine table:
Select the Load affine tab from among the available tabs (Fig. 3-1):
Load affine (will create a new CCSF depth scale)
Load splice (requires associated affine to be loaded already)
Manage (e.g., remove redundant affine/depth scales and splices)
Figure 1. SCORS Uploader user interface, Load affine tab.
On the Select affine table file line, click the Choose File button and navigate to the file in your directory.
Click Open/Load in your navigator
On the Select expedition that created the affine line, select the expedition (project) from the choice list. It will appear in the affine name.
Click Validate Affine button.
If the validation fails, you will get an error message that should be very explicit in terms of type and location of error. The most common errors encountered in initial uploads were:
Scrambled character for negative sign, presumably generated by Excel that interpreted the value as a formula.
Commas in the comment columns – these are not allowed in a CSV file.
Commas only in the last row, which are not visible when viewing and editing the file in Excel, but easily so in a text editor.
If the validation passes, a blinking message will appear: Affine validation in progress, please wait.
During the validation, the field Name generated from content will be populated; it includes the sites(s) and hole(s) present in the file you loaded.
The Current date (YYYYMMDD) field will also be populated.
If validation fails, the message Validation failed, upload aborted, check the affine file format and content will appear. Click OK and check your file.
If validation is successful, a new blinking message appears: Affine table file upload to asset manager in progress – please wait. Once this message disappears, you can proceed.
On the line Enter optional name extension (maximum 10 characters) you can add your initials, the time of day, or any other potentially useful information you want to appear in the CCSF scale name. The number of characters is limited to 10 to avoid overly lengthy file names. When leaving the field, the display labeled Final affine and depth scale name will display the complete standard name, including the expedition number you selected.
On the line Add new alternate scale or select existing affine/scale to replace, you can make an important decision:
If you want to add a new affine and associated CCSF depth scale to the data base without replacing an existing one, keep the default Add a New Record in the choice list.
If you want to replace an existing affine and associated CCSF depth scale, select the appropriate name from the choice list. The affine table and associated depth scale will be removed from the database. This action will reduce the accumulation of outdated information, user confusion, and the need for later cleanup in the database. However, consider that in some cases, it may be desirable to keep an older version (particularly if update is provided postcruise) because investigators may have been working with it.
Add any information useful to other correlation specialists or users of the depth scales in the Affine description field. The limit is 250 characters.
To complete the process, click the Upload Affine button.
A blinking message will appear: Affine transfer and CCSF depth scale creation in progress
The program will display a message when upload is successfully completed.
To confirm successful upload, go to the LIMS reports described below.
The uploaded affine files are stored and accessible in exactly the way they were uploaded. In addition, the affine tables are converted into Oracle database tables such that the cumulative offsets can be used to compute the alternate CCSF depths for samples and results. For any report available within the LIMS Reports framework, users can select the appropriate CCSF scale from the alternate depth choice list. At that point, the CCSF depths are reported for each observation or sample in the report, provided the associated core was included in the affine table to begin with.
2. Upload splice tables
Before attempting upload of an affine file using the SCORS Uploader and Manager application, ensure that it complies with the specified format (see Appendix 1, or recent examples from the LIMS database). The Correlator application will in general be generating the correct formats, but legacy files may need to be corrected. The file must be CSV format and have the prescribed number and types of columns. The uploader will perform a limited number of tests and will reject non-compliant files.
To load a splice interval table:
Select the Load splice tab from the three tabs at your disposal (Fig. 3-2).
Follow the same procedure as described for loading an affine. The following two steps are unique to loading a splice.
On the line Select affine for this splice, select the affine that applies to the splice you are uploading. Failure to select the correct affine will certainly produce unexpected results.
On the line Select optional splice tie point table file you can optionally browse to your splice tie point table (STPT), click the Load STPT button, which will load the file along with the splice interval table file. The STPT will not be used in splice calculations.
The uploaded splice files are stored and accessible in exactly the way they were uploaded. In addition, the splice interval tables are converted into Oracle database tables such that can be used to provide data by splice.
A splice was associated with an affine table at the time of upload and the corresponding CCSF scale is automatically set when user selects a splice from a choice list in the LIMS Report interface.
Figure 2. SCORS Uploader user interface, Load splice tab.
3. Manage affine tables (CCSF scales) and splices
The Manager tab allows authorized users to delete redundant affine (and associated depth scales) and splices from the database. Unauthorized users cannot use this tab.
If a user cancels an affine table by accident, it cannot be re-instated through the tools provided. However, a developer or database administrator can still recover the original upload files if needed (for a period of at least one year after).
To cancel an affine and/or splice:
Select the Manager tab (Fig. 3-3)
Select the affine or splice you want to cancel and click the Cancel affine or the Cancel splice button.
Note: If a splice has been associated with the affine at some point, the splice has to be canceled first. This is to ensure that “orphaned splices” do not exist in the database.
If you are canceling a splice, consider if you want to cancel the associated affine/CCSF scale as well (in case it was updated). If so, select the affine you want to cancel and click the Cancel affine button.
Figure 3. SCORS Uploader user interface, Manager tab.