Table of content

The GEODESC applications and user documentation are in development. They will go live on the JR on 11 October 2022. 

Data Capture sign in

The GEODESC Data Capture application is a spreadsheet tool used to capture core description and micropaleontological observations. The spreadsheet looks and feels similar to generic spreadsheet programs, however, is is highly customized for effective and efficient workflows on the scientific ocean drilling vessel JOIDES Resolution. Functionality is in many ways enhanced with special features specific to the workflow requirements, and it is also in many ways restricted in regard to generic spreadsheet functions to ensure data integrity.

In Data Capture, you work with worksheet templates that you or your assigned team member have selected, modified, and/or created using the Template Manager application. Your data entries are autosaved in real time and each time you decide to publish the worksheet to the LIMS database, an updated data file (tab-separated values format, or TSV) is created and made available to your project scientists using the Data Access application.

To sign in to the Data Capture application (Fig. 1.1):

  • Enter your username in the Username entry field.
  • Enter your password in the Password entry field.
  • Select the project from the Chose your project dropdown list.
  • Click the Sign in button


Figure 1.1. Data Capture sign in page.


Once signed in, you will land on the Capture sheet dashboard page where you define your workset(s), or the template, hole and cores you want to work on. Opening one or more worksets will generate the data capture worksheet(s).

Capture sheet dashboard

The dashboard controls the creation of data capture worksheets. Worksheets are specified as worksets, which define the objective and scope of the observations to be entered in the worksheet. This level of control ensures that multiple observers can work on the same template as long as they are not working on the same core at the same time. The dashboard has three functional areas:

  • The Select template area lists all templates made available to the project in the Template Manager application.
  • The Create workset area allows you to specify the cores (including all their subsamples) you will be working on during your session.
  • The Existing worksets area shows worksets already specified and ready to be opened as worksheets as long as other users don't have them opened at the time.


Figure 2.1. Capture sheet dashboard.


To create a workset:

  • In the Select template area:
    • View a list of all available project templates
    • Optionally, filter the project template records:
      • Make a selection from the Scale dropdown menu.
      • Make a selection from the Type dropdown menu.
      • Note that all existing worksets are shown in the Existing worksets area based on your filter setting.
    • Select one or more templates you want to work with.
      • Note that this also filters the existing worksets in the Existing worksets to give you quick access to the ones you want to work with without the need to re-create them.
  • In the Create workset area:
    • View the expedition associated with your project, or select an expedition if multiples are associated with the project from the Expedition dropdown menu.
    • Select a site from the Site dropdown menu (mandatory)
    • Select a hole from the Hole dropdown menu (mandatory)
    • Note that this may further filter the existing worksets list in the Existing worksets area.
    • Optionally, specify a set of core numbers by entering core numbers in the top and/or bottom entry fields.
      • Note that the cores don't need to exist yet. 
      • Specifying a limited set of cores allows other observers to work on other cores of the same hole, using the same template, at the same time.
      • Limiting the workset also avoids downloads of huge data sets into the worksheet for a current session.
    • Click the Create button.
      • If the specified workset does not overlap with an existing workset, a new workset is created.
      • If the specified workset overlaps with an existing one, you will get a warning. Check the workset table.

To create a workbook with one or more worksheets:

  • In the Existing worksets area
    • Select the workset(s) that you want to open as a workbook.
      • Newly created worksets are already pre-selected for quick opening.
    • Click the Open button.
      • If any of the selected worksets are in use, you will get notified that you cannot open it. Talk to your team member(s) if you need access to (part of) those worksets.
      • If the selected workset(s) are available, the corresponding worksheet(s) will open in you current browser tab.
  • For worksets that already have data, all data are downloaded automatically.
    • For deep holes with thousands of description intervals, limiting the workset for your current session is a way to deal only wit the data you need at the time.
  • For a workset that has no data, no spreadsheet is displayed. Add samples to add rows.

To manage worksets:

  • When closing a workbook, you have the option of deleting or releasing the worksets.
    • If you choose to delete, the workset(s) will disappear from the Existing worksets area. Tis is a good practice to keep the workset list lean and clean.
    • If you choose to release, the workset(s) will show as available in the Existing worksets area. This is a good practice if you are your team mate will continue work on the same workset.
  • The list of existing worksets is likely to grow as multiple users work on entering and reviewing data from multiple holes. To clean up your workset list without even opening the worksheet:
    • Select the workset to be deleted.
    • Click the Delete button.

Data capture worksheet

Worksheet functional areas

A worksheet has the following functional areas:

  • Top banner
  • Ribbon
  • Cell display bar
  • Spreadsheet
  • Worksheet tab bar
  • Bottom banner

The areas are indicated in Figures 3a and 3b, and the functions in each are described below.

Figure 3a. Worksheet functional areas marked next to the screen shot of an actual worksheet.


Figure 3b. Worksheet functional areas marked next to a schematic of the worksheet.


Top banner

The top banner has 5 functions:

  • Application menu
    • Provides access to the other GEODESC applications.
  • Workset specification
    • Displays the template, hole and core selections made on the the dashboard page.
  • User name
    • Displays the user name of the account currently working on this workset.
    • No other user can use this workset at the same time. The current user needs to close and release it for another user to open the worksheet with all existing data.
  • Sign out button
  • Help link

Ribbon functions

Add samples

Observations are made on samples registered in the Laboratory Information Management System (LIMS). Add samples is the principal method for adding rows to a worksheet. In order to maintain the chain of custody and ensure that only existing samples are described, and that all samples of a certain type are described, you cannot add empty rows to your worksheet and manually add sample identities. 

To add samples to the worksheet:

  • Click the Add samples button.
    • The Add samples window opens (Fig. 3.2.1.1)
    • The available sample list is loaded.
  • Select one or more sample types.
    • The available sample types may already have been pre-filtered based on a setting in the Template Manager application.
    • Your selection may affect the sample list.
  • If the template was configured for small sample types, select one or more test types.
  • The worksheet is already configured for a hole and a subset of (or all) the cores from that hole. You can further constrain the sample selection with a subset of cores.
  • The 'Samples available based on all selections and filters' are listed and you can select one or more of them for addition to the worksheet. 
  • Tap the Add button and the selected samples are added to the worksheet. Samples that already exist in the worksheet are not shown.

Figure 3.2.1.1. Sample selector window.

Validate

The worksheet has many validation rules: those applying to the scope of description, and others as observable attributes. Some errors are flagged immediately when the observers commits them, others are revealed when the Validate function is run. Observers cannot publish the data to LIMS as long as errors exist.

Go to error

If you have flagged errors in your capture sheet, this button will focus the cursor on the left- and uppermost error in the sheet. After you have fixed the error, clicking the button will again focus on the left- and uppermost error in the sheet. When no more errors exist, a toast appears with the message ‘No errors found’.

Publish to LIMS

Data entered in the capture sheet are automatically saved to a temporary location in the database, which is not accessible by the general user (an IT representative can access the auto-saved data in case of an emergency, the kind of which has not been encountered so far.

To make the data accessible to your project scientists (and eventually the public:

  • Click the Publish to LIMS button. save the data and create a file accessible by any authorized user (the shipboard science party during the moratorium; the public after the moratorium has expired), the data must be uploaded.

Undo and redo

You can undo a limited number of your past actions. 

You can redo the last undone action.

Resort rows

Use this button to sort the rows based on the scopes of description, in the following order: Core, then Section, then Top offset.

Column visibility

Use this button to open a modal window with a list of all columns. The columns are in the order they currently are in the worksheet. You can check or uncheck columns to show or hide them, respectively. 

Move columns

Use this button to open a modal window with a list of all columns. The columns are in the order they currently are in the capture sheet. You can select columns and toggle them up and down, which means left or right, respectively, in the worksheet.

Refresh samples

Use this button to refresh. (What?)

Alignment

Cell contents can be horizontally aligned (left-align, center, right-align) and vertically aligned (top, middle, bottom). 

  • Select a cell or range of cells.

  • Click either one of the alignment buttons.

  • The text or numbers in the cell(s) take on the selected alignment treatment.

Text, font, background

Cell content can be wrapped or truncated with the Word wrap button:

  • Select a cell or cell range.
  • Tap the Word wrap button.
    • If the cell content was truncated, it will be wrapped and the row height may increase if needed.
    • If the cell content was wrapped, it will be truncated and the row height may shrink if not otherwise constrained.

The cell fill color can be set with the paint bucket button:

  • Tap the down arrow next to the paint bucket button.
  • In the dropdown color editor, select the desired color in one of two ways to 'fill the paint bucket:
    • Select any color in the editor.
    • Alternatively, select an existing color in the worksheet using the paint dropper.
  • Tap outside the color editor to close it.
  • Select a cell or cell range to be colored.
  • Tap the paint bucket button to apply the color.

The font color can be set with the 'A' icon button:

  • Tap the down arrow next to the paint bucket button.
  • In the dropdown color editor, select the desired color in one of two ways to create a font color:
    • Select any color in the editor.
    • Alternatively, select an existing color in the worksheet using the paint dropper.
  • Tap outside the color editor to close it.
  • Select a cell or cell range to be colored.
  • Tap the 'A' icon button to apply the color.

The vertical orientation button rotates the cell content by -90 degrees. This is useful for headers of columns that only require a narrow width for the data. 

Zoom

This zoom function only affects the spreadsheet in the strict sense, i.e., it does not scale the surrounding area, including the ribbon. This provides an alternative to the browser's zoom, which affects the entire page.

To scale your spreadsheet area:

  • Select a percentage from the dropdown menu.
  • A 100% button resets the zoom level to the original level. 

Freeze

Freezing rows and/or columns can improve the scrolling experience. By default, DC freezes the header row and all description scope columns (the first 13 columns that will be part of all final product files). You can change the freeze configuration in four different ways:

  • Unfreeze All
  • Restore default freeze
  • Freeze rows above and columns to the left of the selected cell
  • Freeze header row only

Close

The close button closes the workbook and provides appropriate warnings regarding the data upload status and options regarding workset management. Using this button is the recommended method to close you worksheets. However, the button is not the only way for your worksheets to close:

  • You may (accidentally) use the browser tab's close button.
  • You may be auto-signed out of the application due to security protocols.
    • TAMU mandated sign out is after 15 minutes.
    • You get a warning 1 minute before auto-sign out (Fig. 3.2.14.1)

Figure 3.2.14.1. Auto-sign out warning.


The application's behavior for all these situations is explained here (also see Fig. 3.2.14.1).


Figure 3.2.14.2. Results of closing the browser tab or worksheet (workbook).

If you get signed out involuntarily, or if you use the browser tab close button:

  • You will not get any message.
  • When signing back in, you will find the worksheet(s) closed and you'll be back on the dashboard.
    • The workset will be in the Existing worksets area, bolded and marked in use.
    • If you had data that were not uploaded, the workset(s) will also be marked as not uploaded.
    • You should open the worksheet(s) again and either continue your work or close them and release the worksets.

If you close the worksheet(s) using the application's Close button, the 'normal' way, you get two options depending on the data upload status:

  • If all data were uploaded, you are asked whether you want to (Fig. 3.2.14.2)
    • Delete worksets, or
    • Make worksets available.
  • If all data were not uploaded, you are asked whether you want to (Fig. 3.2.14.2)
    • Loose the data and delete the workset, or
    • Keep the data and make the workset available.

The bottom line is that the program doesn't loose data implicitly, the autosaved data remains until you explicitly delete them in the worksheet and then upload the edit.


Figure 3.2.14.3. Close dialog if all data have been uploaded.


Figure 3.2.14.4. Close dialog if all data have not been uploaded.


Cell display bar

  • Selected cell address
  • Selected cell content

Spreadsheet

Columns

Each worksheet has two types of columns:

  • Scope columns
    • Include the sample identity, sample interval, corresponding depth intervals and domain to be described.
    • They are exactly the same for all GEODESC templates. Some may be hidden for data capture, however the final product description files will have them all.
    • They are shaded light gray and frozen as a group by default (you can change that).
    • Note the important difference for the ‘Top offset’ and ‘Bottom offset’ columns:
      • In templates set for ‘large samples’ (template type=summary or type=macroscopic), the ‘Top offset’ and ‘Bottom offset’ columns are editable entry fields.
      • In templates set for small samples (type=microscopic), the offsets (in section) were given at the time the small samples were created and cannot be edited.
  • Observable columns
    • They represent the observables as configured in the Template Manager application.
    • Templates for micropaleontology have three types of observable column, a difference relevant when configuring the templates but not explicit in the worksheet:
      • General: observable columns are representations of observables selected or defined primarily for core description needs; they are typically added to the template from the GEODESC observable catalog.
      • Taxa columns are specifically for capturing the abundance of formally defined taxa. Template makers typically add these columns to the template in large batches, using a process only available if the template is of type=micropaleontology.
      • Taxa-like columns represent general observables that were added to the template using the same process as was used for the taxa list, i.e., it is only available if the template is of type=micropaleontology.

You cannot create columns in the Data Capture application. Columns are added, deleted and configured in the Template Manager application.

When you create a worksheet from a workset for the first time, the column display settings are those pre-defined in the Template Manager application for your convenience. The column display settings include:

  • Visibility
  • Lock visibility (you cannot change the visibility in Data Capture and if hidden, will never see the column.)
  • Column width
  • Background color

You can change the visibility for your session, and perform filter and sort operations on the worksheet, using the column context menu:

  • Hide
  • Unhide
  • Column width...
  • Filter
  • Sort

You can also drag column margins to change the column width.

You can also use the Column visibility button to see and change the visibility of all columns in a simple window.

Rows

Rows represent description intervals or domains. Rows can be added in two ways:

  • Click the Add samples button.
    • Use the filters and selection options described previously for that function.
    • A row will be added to the worksheet for each sample.
  • Insert description intervals and/or domains using the row context menu.
    • The row context menu is accessible from any cell, without the need to select the row first. 
    • The row context menu is deliberately restricted to the limited but specific functions needed for efficient core description and micropaleontology data entry.

Row context menu functions

  • Add interval - Use this function to add and constrain description intervals within the samples when the template is configured for large sample types.
  • Split and insert interval - Use this function to define an interval that overlaps with an existing interval and let it split the existing interval by adjusting the offsets to those entered for the new intervals. This menu item is only enabled if the template is configured for ‘large samples’.
  • Add domain for interval - use this function to define layers, areas, patches, constituents, etc., within a sample interval. The domains can be defined by texture, composition, and/or structural features. The function duplicates the selected row and automatically assigns domain numbers to ensure the scopes of description are unique (a basic rule).
    • The menu item inserts a new row with the same sample ID and offsets as the selected row.
    • If the domain number of the selected interval is null (no number entered), this function enters '1'. The new scope added gets domain no. '2'. If the selected interval already has a domain number, the domain number of the new interval is incremented by 1 over the highest existing domain number for the sample interval.
    • Note: The Validation function will check if duplicate scopes exist, which could happen if the observer changes the domain numbers such that the same number exists for more than one row within the same sample ID and offsets.
  • Copy all observations from this row - Use this function to copy all observations from the selected row, ignoring scope and formula cells.

  • Paste all observations in this row - Use this function to paste all observations from the (custom) clipboard into the selected row, ignoring scope and formula cells.

  • Delete row - Use this function to delete the entire row, including observations and scope of description.

Cells

List validation

Numeric validation

Formulas

a) general cell context menus such as copy and paste are not allowed in this application environment (but keyboard commands work), and (b) in the context of the GEODESC data capture workflow, actions on random groups of cells are not meaningful.

Worksheet tab bar

  • If you opened multiple worksets from the workset dashboard, the workset names are shown in the tabs below the current worksheet.

  • Although you can change the worksheet tab name, your name is ephemeral, i.e., the next time you create a worksheet from that workset the name will return to the formally defined name.

  • If you close a worksheet, the entire workbook is closed.

Bottom banner

  • Locked indicator
  • Autosave indicator
  • Error count
  • Zoom slider