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Generic Configuration

Caution

This page is still being edited and reviewed.

Generic segments and elements#

Generic elements and segments are structured according to the different levels layer and field. Each generic element or segment can contain different, multiple layers and each layer can consist of multiple and differnt fields.

generic feature outline

Generic segments#

Generic segment can be embedded in different elements, such as sample, reaction...etc., it can also be embedded in generic element.

After clicking on menu item Generic Segment, a button is shown as default and the segment list is displayed if any data exists.

generic_segment_admin

The segment list includes all the segments, and it shows the attribute data and provides further functions, such as “copy”, “edit template” and so on. The segments are sorted alphabetically by the status (active first), segment label and description.

generic_segment_list_tip

symbolexplanation
to duplicate the segment
to edit segment attributes
to edit segment template
to edit segment template in json format

Create#

You can create as many segments as possible for an element, e.g., sample, reaction, or any generic element. Please note, once the segment is created, it can not be re-assigned to another element.

To create a segment, press the button , fill in the data of segment attributes, and then press to save the data into database or to cancel the operation.

generic_segment_new

the definition of each attributes:

attributerequiredexplanation
Segment LabelYesthe name used to display on the UI tab
DescriptionNoused to describe the segment and shown as a tooltip when the mouse hovers over the UI tab
Assign to ElementYesdefine which element this segment belongs to

Generic elements#

Chemotion ELN contains five original elements which are the samples, reactions, wellplates, screens, and research plans. However, other generic elements can be added as needed by the administration.

Create generic element

For an admin to create a new generic element, go to the page Generic Elements and press . This opens the window New Element to enter the attributes of your new generic element. Those attributes are shown in the next table:

Attributes#

attributerequiredexplanation
KlassYesThe name used to identify the element in the system
PrefixYesA prefix for naming the generated objects that belong to the generic element, e.g., if the user name abbreviation is "user" and the Prefix is "t", then generating new "Mixture" objects will lead to the following names: "user-t1 New Mixture", "user-t2 New Mixture", etc
LabelYesthe name displayed in the UI, e.g., the labels Sample, Reaction, Wellplate
IconYesThe icon to be displayed in the elements list and in the toolbar for creating new objects. Icons can be obtained from Font Awesome 4
DescriptionNoExplanation of the intended functionality of the element

When all the required attributes are provided, press to create the element, or cancel the process with .

Create generic element

After an element is created, it can either be added to the Chemotion ELN interfaces of all the users , or only to specific users. This option is also controlled by the administration. For the users that can access the element, they have to add it manually to their accounts. To do so, they have to go to their Account & Profile, and go to the Element Counter, and update the counter of the specific element with with . Still, the element will be hidden by default, and it will not appear in the element bar unless the user manually adds them.

In the administration account, in the Generic Elements page, after an element is created, it appears in the elements list (not to be confused with the elements list in the Chemotion ELN). The elements list includes all the elements generated by the admin’s account, and it shows the attribute data and provides further functions. The elements are sorted alphabetically by the status (active first), element label and description.

Elements list
symbolexplanation
to copy the attributes of an element
to edit element attributes, delete the element or deactivate it
to edit element template
to edit element template in json format

Choosing to edit the element's template enables adding new layers and lists to the Properties tab of the element. More on that in the next chapter.

Create#

Layers#

Layers are the fundamental building block that contains the content of generic elements/segments/datasets. They enable organization of the fields related to a certain topic into groups, along with their layout and appearance. Layers can be added to elements and segments by clicking on edit element/segment template in the elements/segments list, and then clicking .Add Layer

Attributes#

attributerequiredexplanation
NameyesThe name used to identify the layer in the system, must be unique in the template
Display nameNoThe name displayed in the details modal
Columns per rowYesThe maximum number of fields to be aligned in one row (default is 1)
Sequential positionNoA number added to sort the layers, if left empty, they are ordered by the order of creation
RestrictionNoA number that can set a maximum for certain fields
Header colorNoA color for the Display name and its surrounding
Style OptionYesStyling the Display name, "bold" is the default
Add Layer

After a new layer is created, it appears in the layers list, where its Name, Display name, the number of columns per row, and the number of fields can be found. A number of buttons allow the following functions:

symbolexplanation
to edit the layer's attributes
to delete the layer
to add new fields
to add dummy fields

Whenever a new layer is added, or an existing one is edited, changes need to be saved with , at this point, if the user that already has access to the element or segment reload the page in their user account, and then press the button , they will be able to see the new layer. By having layers, the admins can add fields there. More details on the Fields in the next chapter.

Fields#

Fields are a wide variety of components with input, display, drag-and-drop functions, depends on the type. Use an appropriate type attribute to take advantage of these UI controls like formula field, system-defined, and more.

Attributes#

attributerequiredexplanation
Field NameYesthe name given by the admin when first creating the field. It is the name used to identify the field in the system. It must be unique in the template
Display NameNothe name displayed in the details modal. It has the same value as the "Field Name" by default, but the admin can still modify it or delete it to create a field without a displayed name.
Hover InfoNoan explanatory text to be shown when the mouse hovers over the "display name"
TypeYesto specify the type of the field (more details about it in the next paragraph). Its value is "text" by default, but can be modified by the admin

Field types#

typeavailabilitydependenciesexplanation
checkboxv0.9.0+---a checkbox is shown as a small square box to let the user make a binary choice
drag moleculev0.9.0+---an icon with drag-and-drop function to let user to add a molecule into a generic element/segment by drag-and-drop operation; it will display the molecule image after being added successfully
drag samplev0.9.0+ (generic element only)---an icon with drag-and-drop function to let the user add a sample into a generic element by drag-and-drop operation; it will display the sample image after adding successfully. It also enables using the exact dragge-and-dropped sample, a split of it, or a copy
formula fieldv0.9.0+---a calculation field; as an admin, define a formula using other fields, and the system does the calculation automatically
input groupv0.9.0+---a group of fields; the fields can be 'label', 'text', or 'number'. 'label' is used for display only, and the user can't modify its default value, while 'text' and 'integer' are used as an input field, but still the admins can give them a default value ar first
integerv0.9.0+---an input field for number entries
selectv0.9.0+---a dropdown list to let user to select
system-definedv0.9.0+---an interconvertible unit field; with a numerical input field and a button for unit conversion (details)
textv0.9.0+---an input field to let user to enter a single editable line of text
text areav0.9.0+---an input field with adaptable size to let user to enter multi-line text
text formulav0.9.0+---a combine(display only) field to let user to combine other fields or necessary descriptions together

Field-type: System-defined#

The field type System-defined allows to add values with a unit. Units are assigned to certain standards in the community of the research field but should meet common conventions and definitions. Depending on the unit that is used, different conversions are available.

unit nameunit defaultinterconversion 1interconversion 2interconversion 3interconversion 4
Accelerationmm/s²------------
Agitationrpm------------
Amount enzyme as nmol/minUmU---------
Chem. concentration (Molarity)mol/L (M)mmol/L (mM)nmol/L (nM)pmol/L (pM)---
Chem. distancesÅ------------
Concentrationng/Lmg/Lg/L------
ConductivityS/m------------
Degree°------------
Durationday(s)hour(s)min(s)sec(s)---
Elastic modulusMPakPaPa------
Enzyme activityU/LU/mL---------
FrequencyHzkHz---------
Heating rateK/min------------
Lengthpmnmmmcmm
Massgmgµg------
Mass of moleculeDkD---------
Molecular weightg/mol------------
Percentage%------------
PressureatmPaTorr------
Reaction ratemol/Lminmol/Ls---------
Speedcm/smm/scm/hmm/h---
Surfacemm²cm²------
Temperature°C°FK------
Turnover number1/s------------
ViscositymL/g------------
VoltagemVV---------
Volumeslmlµlnl---
Last updated on by maipy