Staging database

Staging database
The processes connecting VICKI with the Samples database

Below is a diagram showing the flow of annotated sample information, from when it is created with VICKI, extracted to populate a staging database, and finally loaded into the production Samples Database. This process is designed to be initiated either aboard ship or afterward on shore.

vicki_connect.gif (14255 bytes)

Samples are annotated with the video annotation application VICKI. After the annotations are complete, the script 'VIF2staging' is run on the annotation file (VIF file) to merge sampling events with frame grabbed images and navigation data and to create a staging database in HTML. This list can be printed out and compared with samples that successfully made it to the surface. The staging database is also an Active Server Page (ASP), whose action is to run the application 'loadcoll.asp' to load data into the shore-side database.

Example of a staging database web page
The annotated samples are in rows of the table along with frame-grabs, navigation data, and any concepts and properties that were specified with VICKI. In each row, there is a box for adding comments about the collecting event and additional information about the specimen (size, fate, etc.), and there is a check box to mark samples that should be loaded into the database. At the top are boxes for entering information common to all the samples. At the bottom is the "Load database" button that calls the "loadcoll.asp" process.

(click on the image to see a full-size view)

The staging database web pages created by the ship-board process are written to the R/V Point Lobos server 'Ariel' at: http://ariel.mbari.org/~vicki/samplesDB/. The staging database web pages created by Jenny as part of post-dive re-annotations are written to http://mww.mbari.org/~paje/stage/; they are kept locally so that post-processing could be independent of a good connection to the ship. As with any web form, information typed into the form field boxes is not retained on the web page but only is used to populate the fields when the form action is successful (e.g., when "loadcoll.asp" is initiated by the Sample Coordinator). The staging database pages are periodically deleted; they are considered temporary. They may be regenerated by running VIF2staging on the appropriate VIF files.

Post-dive re-annotation and creation of staging database
Interpretation (INT) and VIF files are copied automatically to the /users/vicki/data/interpretation/ directory on calypso from the ship every day. The calypso:/data/interpretation directory is the default directory for VICKI on calypso, and it "checks" files in and out for version control. On shore, they may be reannotated:

User instructions for re-annotation:
In VICKI, choose server calypso, login as user vicki, find the file on the server calypso, and annotate as usual. Then when done, select "File, Save As" to send the interpretation file back to the server calypso with the same filename. The file will be checked out and locked while it is being worked on, and it will be checked back in by saving it back to calypso; it can be saved to calypso only once after it has been opened, due to the way the locking process works. The VIF file must then be created manually (select Source INT to VIF, then to save the file, select Source Save(text), choose server calypso, in the "Undo extract" box, select "Interpretation", and save it to the same filename prefix as the interpretation file but use the suffix .vif, not .int. If there is already a VIF file on calypso, it must be deleted (as user vicki) first before it can be re-saved.

User instructions for post-dive creation of staging database:
VIF2staging may be run on calypso and the HTML file written on shore. This is recommended for post-dive processing so that a connection to the ship is not involved. In this example, the HTML file is written to the Sample Coordinator's internal web site (requires login as user 'paje') by typing:

/u/vicki/bin/VIF2staging <filename> /u/paje/mbari_html/stage/ .
Find the HTML file at http://mww.mbari.org/~paje/stage/.

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