3. Experiment/Sample/Simulation entry
The Experiment/Sample/Simulation (ESS) entry is the base of the organization scheme for Open ResearchNotes. Beside the documents, this is the place you will create and first start to include data. Unlike the documentation, which is intended for general information relevant for a larger audience (like your group), the ESS entry is specific for one sample or experiment in your research.
3.1. Create a ESS entry
The first step to work with Open ResearchNotes is to define or create an ESS entry - hence define your first experiment, sample or simulation. Basically, this is your base order entity and what you will actually do with this entry will become your next PPM entries. It is good to do a little thinking in before, what you want to put there and how you wish to identify it later - the best is that the group defines some rules for this (** this is a supervisor task **).
New ESS entries are created by the new E/S/S icon that is found on the index page or the E/S/S menu page. Clicking it, will open a form that will ask for some information:
Identifier: A short group of letters and numerals to give an identification to the sample. It might depend on the project, the kind of sample (e.g. where it has been grown), the related simulation (e.g. the type of simulation) and so on. It is not a brief description of the sample, but more a tag, ID or serial number that goes onto a sample box. It is more for internal use and identification, than for publication. Special characters will be stripped from this for security reasons.
Origin: Marks the place the ESS comes from or where it is produced. It can be a vendor name, a collaborator or the machine of the group, the group name etc. This might be more important for a physical entity than for simulations or experiments.
Produced by: The name of the person who produced the ESS. The ESS entry will be owned by the person making the entry, but the ESS might have a group or a different person who produced the actual physical object.
Short description: A 50 character string providing short information about the ESS. This information will be later visible in the overview tables and so on, and might be the main search item (beside the identifier).
Long description: A detailed description of the ESS. This part will accept formatting to the text and text size is some 50 kB (long). It is the field to store detailed information that might be relevant on the ESS level. The Markdown language (see toolbar and help allows for heading, tables, list and other formations.
On submitting the form, the ESS entry is created and shown to the user. Beside the information (now formatted into HTML), the ESS view covers some possibilities.
It notes that part of the fields are sensitized to prevent security breaches like SQL and HTML injection. To form the sample identifier all non-alphanumerical characters are removed (e.g. “+”, “-”, space etc.). By default, the long description is escaped, and all HTML code will be converted to letters. Hence, HTML commands inside the long description will not work to preferred injection of JavaScript or other things.
3.2. Editing EES entry
In the ESS view that is shown after sample creation or by clicking the sample identifier in one of the tables available on the index page, the all ESS page or the ESS index page allows editing the information allocated in the original form.
Hence, information can be updated, or new information added along the sample life. Once files are uploaded - especially images are connected to the sample entry, they can be referred in the long description (see Markdown and files section).
3.3. Template icon
You can use an existing ESS to create a template by clicking on this icon. Basically, all information, except the creator, will be transferred into a template. The template can be edited in the template menu and adapted to your needs. On sample creation, there is a template bottom in the upper-left corner that lets you pre-fill the ESS form with the information of the chosen template.
3.4. Summarize (export your ESS information)
The summarize icon will create a Markdown file with all ESS, PPM and report information of this entry and make it available for preview and download. As Markdown files are text files with some formation hints, they can be easily converted into HTML, PDF or LaTeX files. Or they can be imported into a work processor.
3.5. New P/P/M
A new Procedure, processing or measurement entry can be created by the P/P/M icon. It will be attached to the current ESS entry.
3.7. E/S/S is at
Define the location the physical object (or your computer program) is found. In this way, you can keep track of the ESS location. Entries for this drop down box can only be created by a supervisor of the group.
3.8. Dropzone
At the bottom of the ESS view is a Dropzone for files. Basically, all files of interest can be attached there and will be uploaded to the server. We will do some filtering for certain file types. The maximum size of the file depends on the configuration of your web server and the Web App. The default is 100 MB. The upload does not check for existing files and will overwrite files with the same file name. File names will be sanitized against directory transversal etc.
3.9. Associated Procedures/Processing/Measurements
Once you define a Procedures/Processing/Measurements (PPM), it will show up in this table. By clicking on the title, the information of the PPM entry will be shown (also available in the all PPM view of the ESS menu).
Furthermore, in the action menu, you can directly edit the PPM entry or delta it.
There is no undelete! Once deleted, the information and attached files are gone.
3.10. Associated Files
Uploaded files will show up in the “Associated Files” table. There is a download bottom, which will create a zip of all files and offer it to download (this might time out with large directories). Individual files can be downloaded, previewed or deleted. We have previews for images, python code, Markdown files, .dat and .txt files, and .csv files.
Finally, files can be deleted and then are gone from the server.
Image files will show, in the preview, their URL. With this, they can be included in the long description by using the ! []() construction. Copy and paste the URL into the round brackets and give a description in the []-brackets.
A final code follows a pattern like: 