Loading existing projects and save options
Quit the current Analysis session, saving the extant project as you see fit. Next we will look at a pre-existing project.
Now at the Linux/Mac shell command line type:
-> ls
And press 'Return'. You will see that we have a directory called TutorialProject in your current directory. This directory contains all the user data for the project that we are about to open. The data are spread over many directories and files. It is worth noting that the various XML files, which we shall see in a moment, are only loaded when required, when we access the data. In this way Analysis only loads the files it needs. Conversely, when a project is saved, only the files corresponding to modified data packages will be written. The application will automatically search its data directories for files, so the data available will mirror exactly what is in the directories.
Assuming you are starting inside the directory containing the downloaded tutorial data. At the command line now type:
-> tree TutorialProject/
Or if the "tree" command is not available:
-> ls -R TutorialProject/
This command will list all of the contents of the project directory:
You will see that there are several layers of directories with XML files within the directory structure. Each bottom directory contains files with a different type of data that may be loaded into the project. The rather cryptic file names are generated automatically, using the key attributes of the top object in each file, the project and user name used to generate them, and a timestamp that serves to make a globally unique identifier. The names are used by the underlying CCPN implementation and can not be renamed by hand. Reference data distributed with the release (chemical compound templates, reference chemical shifts etc.) live in another location, as do user-specific profile data. Advanced users can control which data live in which directories. Each project has a file that contains all the bookkeeping information to specify which data live where; it is in the TutorialProject/memops/Implementation directory. When you copy a project to a different location, the internal file references will no longer be pointing to the right on-disk locations. In such circumstance Analysis will look for the new file locations and upgrade the directory paths automatically - as long as you are using the standard directory setup this should not be problematical.
When the CCPN XML file formats are upgraded to a new version, the new code will automatically be able to read the old formats. For rare cases where this is not possible, like the big jump between CCPN version 1 and version 2, there is an upgrade server available.
Start Analysis with the existing project by typing:
-> analysis TutorialProject
The project will take a few moments to load, and it might tell you that the directories have moved. Also, the locations of the spectrum (binary) data will most likely have changed. If so, Analysis will try to find hem in a nearby directory and will display the new locations in the "Edit Project Spectrum & Data Paths" popup for you to check. If the popup appears, red rows correspond to files that cannot be found. Double click on a red row in the |Absolute Path| column and in the file dialog navigate to the "TutorialProject/spectra" directory. When inside the "spectra" directory, click [OK] and you will hopefully note that the red colour has gone, indicating that the spectrum files have been located. Close the popup and when it is done loading several spectrum windows will appear on screen.
M: Project: Save As allows you to save the user data in a new location. M: Project: Backup allows you to make backups, and to set the auto-backup options. There is a third place to control file locations: M: Experiment: Spectra, {File Details} controls the storage location of spectrum data files. It is anticipated that your binary spectrum files will usually residue at a location somewhat separate from the CCPN XML files.
The file locations for binary spectrum data cannot be upgraded automatically and may well get out of sync when you move projects. If a spectrum file is seemingly missing at the location specified by the CCPN project then Analysis gives you the opportunity to re-point the spectrum to the correct on-disk location. Often this can be done efficiently, when spectra are all housed in the same directory, by swapping the common part of the spectrum locations in a single step (i.e. as described above).
Also, at any time should you wish to change a spectrum location, or even move the CCPN link to a differently processed binary file, you can type in the file location of a single spectrum via M: Experiment: Spectra, {File Details} - File Name or repoint a group of files by swapping directories at M: Experiment: Spectra, {Data Locations}.
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