Thin Section Report User Guide and Technical Notes
Peter Blum, 7 July 2016

1. Introduction

Detailed observations on thin sections are entered in a DESClogik workbook typically named "###_microscopic" (where ### is the expedition number, i.e. 396-U1565A_microscopic). The workbook has typically multiple tabs, or worksheets, one for each set of related attributes (e.g., primary mineralogy, alteration, structures). In these worksheets, a thin section description is represented by one row, or by multiple rows if multiple domains are described. This workbook format is best suited to describe and analyze data from many thin sections. However, when reviewing all aspects of one single thin section, a form type summaries of all pertinent information on 1-3 report pages is often more convenient. We therefore created a tool set that allows trained staff members to define a form report layout based on the observation workbook, and rapid production of PDF form summaries for the thin sections.
The following is the thin section report protocol approved by JRSO management on 16 June 2015:

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Double-click the icon below to get the training workbook and save it to your disk. You need to load it in the Builder and Writer applications.
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3. TS Report Writer

Getting ready

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• In the SHIP Production environment, go to this link and download the app:
• http://web.ship.iodp.tamu.edu/tasapps/thsreport/jnlp/THSReport.jnlp
• In the SHORE Production environment, go to this link and download the app:
• http://web.iodp.tamu.edu/tasapps/thsreport/jnlp/THSReport.jnlp
• Follow your browser's instruction to install the application from the JNLP file.
• Click the Run button.
• Login as guest/guest (Fig. 3.1.).

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Figure 3.1. Writer login window

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After login, you are presented with a list of all existing report version that have a report status of open (O) or locked (L) and a version status of active (A) or released (R) (see Fig. l.3.2; more on report and version status later).

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Figure 3.2. Writer window after login.

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Figure 4.2.1. Login window to Builder application.

Two types of user roles exist: Manager and Editor. Your account is given one or both by the system administrator and the type of authorization determines what you will see and be able to do. Most of the relatively few users are authorized for both roles.Image Added

4.3. Select or create a report to work with

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After you logged in, you initially see two of the four functional areas of the Front Panel (Fig. 4.3.1.).

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• Top bar for user id and logout.
• Search area with multiple search options that combine to display a list of selected report versions.

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Report status and Versions Status each always have one of four options selected and understanding these options and their combinations is critical (see below and Table 1). If you don't make any selection and click the Search button, the default display is all Open only reports and Active only versions from any owner, in reversed alphabetical order to display the more recent expeditions farther up on the list (Fig. 4.2.3).

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Figure 4.3.2. Main screen listing selected reports.

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Table 1. Common applications of report and version status search combinations.

Editor menu

The Editor action menu is available if user is an authorized editor (Fig. 4.3.3., left-hand side).

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• Edit report
• Clone Report: This is the most commonly used way of renaming or becoming owner of an existing report version.
• Create New Report: If you really want to start a new report from scratch.
• Export Definition: Option if you want to save an existing definition for use outside your environment for some reason. Exporting report definitions typically prints the JSON type definition into a new browser page.
• Copy-paste the content into a text editor and save as text.
• If necessary, add a file name extension "txt".
• Known issue:
• Many programs or operating systems do not understand the extension "JSON". If you don't get a new browser page with export
• In Firefox Preferences, Content/Pop-Ups, uncheck "Block pop-up windows
• Import Definition: Option if you want to use an existing external definition in your environment for some reason. Browse report definition file.

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Manager menu

The Editor action menu is available if user is an authorized manager (Fig. 4.3.3., right-hand side).

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Figure 4.3.3. Manager and Editor action menus.

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4.4. Building a simple report based on one source data worksheet

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• On the main screen, click the Create New Report button from the Editor menu.
• Note that you could also select an existing report from the list and click the Clone Report button,
• Enter a name for the report.
• Don't sweat it, you can always change the name by cloning the report later!
• Click the OK button and the new report is added to the report version list on the Front Panel.
• Find your new report on the list, select it by checking the box left to it, and click the Edit button. You are now in the Report Edit window and ready to go (Fig. 4.4.1).

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Figure 4.4.1. Report edit window.

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• On the Report Edit window, click the Browse… Browse… button to Select file to upload (Fig. 4.4.1)..1).
• When loaded, the file name will be displayed underneath the Browse… button. Watch out: The report export from Desclogik is a .xlsx-file. For Thin section report writer to accept the file, you have to open the .xlsx file, change the file format to 'Excel 97-2003 workbook/.xls', just renaming the workbook extension won't do the trickWhen loaded, the file name will be displayed underneath the Browse… button.
• On the Report Edit window, click the Declare worksheets button to open the Declare Worksheets window (Fig. 4.4.2).
• On the Declare Worksheets window, a Data source worksheet item with default name "new TAB #" will be displayed and marked in yellow because it needs to be edited. Click the Add button to add as many items as you have worksheets to declare.
• In this section you only need one (the first) worksheet in the training workbook. However, eventually you'll use three so you may as well declare them now.
• Double click the first list item(s), or select it and click the Edit button.
• Select the Source worksheet name from the drop-down list of available worksheets in the source workbook.
• Using the training workbook, select "worksheet1" from the drop down list of all worksheets in the training workbook.
• Set the Identity source column to the column in the data sheet that has the identifying "sample" information (typically the row headers in the data, i.e., the first column).
• Using the training workbook, select the first column "w1samples" from the drop down list of all columns in the worksheet.
• Is this the report control worksheet? Only one worksheet can be the control worksheet and the answer is typically "YES" for the first worksheet, and "NO" for all other worksheets.
• In our training workbook, worksheet1 is the control tab.
• Repeat for all worksheets to declare.
• Using the breadcrumbs, return to the Report Edit window.
• Save your report using the Save to Database button at the top right..

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Now you are ready to design the report layout. You could try to print the reports now using instructions in Chapter 3, and find that everything works but you don't get any report because, we'll, you haven't defined any layout items yet.
Figure 4.4.3. Footer edit window.

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Adding and configuring layout elements

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Figure 4.4.4. Report definitions are structured hierarchical.

Block element

Blocks are containers for the other layout elements (field, text, grid and table). A new block can be placed below, or nested within an existing block, but you cannot place two blocks next to each other on a report page. A block is always placed below the top of an enclosing block, or below the last written item on the page (any layout element), by a top offset (points). Nested blocks can also be positioned by a left offset (points) from their enclosing blocks.
Blocks can have a border box drawn or not. If a border box is specified, the top border is drawn where the top offset was defined, and the first item within the block is written by a fixed amount below the top border (3 points). The bottom border is drawn by a fixed amount (3 points) from the last written item. Left and right borders are drawn with left and right offsets from the enclosing block, by the amount that is set for the left offset.
Drawing borders helps the reader understand the layout and data organization in a larger report. However, printing all borders in the case of nested blocks may result in too many lines. Find the right balance.
Known issue: if you DON'T draw all the borders (boxes) around all blocks, the PDF printing routine currently gets confused and draws borders incorrectly (doesn't know where to start/stop). The program needs to be amended to cover such cases.
At the start of creating a report you must create the first top-level block, all other layout elements must be within a block. Once you have your first block defined, you can add within the block nested blocks, fields, text, grids and tables, which will all be described below. You can also add more top-level blocks below the first block.
A block can display information from one source worksheet only. However, an enclosing block can display information from multiple worksheets if that information is placed within nested blocks. This is very important to understand and will be elaborated later. In this section we only need one block element.

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Now you are ready add fields, text, grids and tables to the block. Note: if you are trying to print the report at this stage you will still not get anything because empty blocks are intentionally programmed not to show.
Figure 4.4.5. Block edit window_Block Left & Right offset needs to be zero or wrapped text will spill over block border._

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Field element

The Field element is used (A) to print single values from the data sheet, and (B) to print images stored in the IODP ASMAN asset management system and downloaded on your machine when you run the Writer program.
The important thing to understand about field (and text, see below) layout element is that its location is fixed relative to the enclosing block, i.e., it is not being dynamically stacked below other layout elements the way block, grid and table are. So if you are configuring multiple fields and leave the same default offsets (from enclosing block), they will print on top of each other.
You can place multiple field (and text) elements horizontally next to each other (something you cannot do with block, grid and table elements). However, you have no control in setting the width of the field (or text) element, and the content cannot wrap, which means your content may be cut off at the right margin of the page. All you can control is the top left position of each field (or text) and that, in conjunction with the expected length of the content string, is what you have to manage positioning.
For the two limitations described above, it is recommend that the field element is used sparingly to display general data values (case A), if at all. The grid element is often a better option. However, field is the only layout element that can display images (case B) and that is its principle purpose.

A. Print a simple single value from the data sheet (we use the sample name here)

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• From the Report Edit window, double-click the "block1" item to enter Block Edit. (or select the item and click the Edit button).
• From the Select element to add list, select Field, then click the Add button.
• A field item with default name "new FIELD #" will be added to the Layout Elements list.
• Double-click the new Field item to open the Field Edit window (or select the item and click the Edit button).
• For the Data source column, select the attribute column from the source worksheet to be used.
• Remember, the attributes available in this list are from the worksheet associated with the enclosing block.
• Using the training workbook, select "w1samples" here.
• Set Left offset (points) to move the field content to the right relative to the enclosingBlock Left & Right offset needs to be zero or wrapped text will spill over block border block.
• For our training report, set it to 100 points so we can add a text label in front of it.
• Set the Top offset (points) to move the field content down page from top of block.
• For our training report, set it to 0 points.
• Set the Font size (points).
• Set it to 12 for our training report since this is our report title.
• Set the Font style.
• Set it to BOLD for our training report since this is out report title.
• Set the UseMe flag. This should typically be "YES" otherwise the content will not display and unless other content exists below, the entire block will not display.
• Set to "YES" for our training report.
• Set Border. For fields, this is typically set at NONE.
• In our training report, we don't want to draw a box around the title.
• Is this an ASMAN image column? This flag is critically important. If set to "YES", the image process is triggered (see part B).
• For our training report, the answer is "NO" here.
• Therefore, the Image width (40-500 points) is irrelevant here.

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Figure 4.4.6. Block edit with first block getting a field layout element.

Figure 4.4.7. Field edit window.

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B. Print images

Printing images has some extra requirements:

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• From the Report Edit window, double-click the "block1 title" item to enter Block Edit (or select the item and click the Edit button).
• From the Select element to add choices, select Text, then click the Add button.
• An item with default name "Text: new TEXT #" will be added to the layout items list.
• Double-click the new Text item to open the Text Edit window and configure as follows for our training report (Fig. 4.4.8.):
• Text to display = "SAMPLE NAME:"
• Left offset (points) = 5 (default).
• Top offset (points) = 0 (same as sample ID field).
• Font size (points) = 12 (same as sample ID field).
• Font style = NORMAL

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Figure 4.4.8. Text edit window

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• Go back to the Report Edit window and double click the "block 3 data1" element to enter the Block Edit window.
• In the Block Edit window, select Table from the Select element to add choice list and click the Add button. A new element "Table: new TABLE #" will be added.
• Double click the new layout element in the list to open the Table Edit window (Fig. 4.4.10). Configure the general table parameters for our training report as follows:
• Table name (not for display) = "table1" (used for the layout element listing in the Block Edit window).
• Border {GRID, NONE) = GRID.
• Left offset (points) = 5 (default), shifts left margin of table 5 points to the right of the enclosing block's left margin.
• Top offset (points) = 5 (default), shifts the table 5 points down relative to the top of the enclosing block or relative to the bottom of any layout element printed above the table.
• Internal font size (pts) = 10 (default); applies to all cells in the table except the column headers, which can have a different format (see below).
• Internal font style {NORMAL, BOLD, ITALIC"} = NORMAL; applies to all cells in the table except the column headers, which can have a different format (see below).

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Figure 4.4.10. Table edit window.

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Figure 4.4.11. Column edit window.

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Next, define the rows for the report table whereby each row represents a set of parameter values (e.g., abundance, size, shape), for one set of data source columns (e.g., a mineral phase).

• Click the Work on Rows button to open the Table Row Edit window.
• Click the Add button to add new rows to the list, which initially have and temporary name.
• Add nine rows for our training report.
• Double-click one added row at a time to display the cell configuration options for each row in each column (Fig. 4.4.12). Configure as follows for our training report:
• Row Name (not printed): enter "row1" through "row9". This is only to tag the elements in the row list in the Table Row Edit window. You can do it quickly using copy-paste and double clicking a new row element as soon as you have entered the name.
• Double click the row again to configure each cell. For each cell, you can either enter a fixed text (typically used for row headers, such as the mineral name), or you can select a data source column, from which the value will printed if the row is triggered for printing (see column configuration above) (used for most cells). For our training report:
• For column 0 in each row, enter a text labels "Report row N text", where N is the row number {1,……,9}
• For columns 1, 2, 3 in row1, select data source columns:
• w1attr11, w1attr12, w1attr13
• For columns 1, 2, 3 in row2, select data source columns:
• w1attr21, w1attr22, w1attr23
• …..
• For columns 1, 2, 3 in row9, select data source columns:
• w1attr91, w1attr92, w1attr93
• Save regularly using Save to Database button given the tedious work involved in configuring tables.

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Figure 4.4.12. Row edit window.

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• In the Report Edit window (Fig. 4.6.1.), double click (or create, if it doesn't exist already) the "block5 data3" item to enter the Block Edit window and configure for our training workbook:
• Block name (not printed) = "block5 data3".
• Data source worksheet = "worksheet1" (change from worksheet 3!)).
• Border = "BOX"
• You should already have a Text element in that block that says something like "WORKSHEET 3 DATA". If not, add one.
• Now, add a nested domain block element under "block5 data3" that will contain all domain-specific elements and information, i.e., Grid and Table elements that repeat for each domain. Double click the "Block: new BLOCK #" element and don't be confused by the Block Edit window looking exactly the same as before – orient yourself relative to hierarchy with the breadcrumbs!). Configure as follows:
• Block name (not printed) = "domain_block_5_1"
• Data source worksheet = "worksheet3".
• Border = "BOX"
• Within this domain block, create all the other layout elements that you want to repeat for each domain.
• First add a grid that looks the same as the one created for the simple report (see above), except that the data source references selected from the drop down lists will be "w3attr1" through "w3attr6" for the six cells of columns 2 and 4.
• Then create a table that looks the same as the one created for the simple report (see above), except that in the cell configuration, the references to attribute columns (report columns 1, 2, 3) are for worksheet3, i.e.:
• w3attr11, w3attr12, w3attr13
• w3attr21, w3attr22, w3attr23
• …..
• w3attr91, w3attr92, w3attr93

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Figure 4.6.1. Report edit window showing all five top-level blocks in training report.

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Figure 4.6.2. Block edit window for top-level block, associated with worksheet 1, containing a text element for the title and a nested domain block (associated with worksheet 3, not shown here) for elements and data that repeat for each domain

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To ensure that one could reprint the reports in the future if so desired, the current proposal is that once the data source workbook and the report definition are complete (no later than 1 year postcruise), both are zipped up and loaded as DESC assets. This in addition to the regular DESC workbook uploads and the attempt to preserve the final report definitions in the Builder.

Appendix 1: Loading and referencing images

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If no error messages appear and everything else looks normal, check if the necessary "Use Me" flag was set. For example, if you create a simple table an a block with nothing else, and none of the table columns are set with "Use Me", no columns will be used, the table header will not be printed (as specified), and the block will not be printed because nothing is in it, i.e., you get nothing.

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