Fill shipment from CSV
EXI allows to fill in a shipment uploading a CSV file. Such file should contain information about the sample, container, parcel and diffraction plan. Some parameters are mandatory and others will be optional.
A CSV file is a plain text format mainly used to store tabular data. CSV means Comma-Separated Values then each value is separated with a comma. Example:
myParcelName,myContainer,Unipuck,1,5HT3,sample1,barcode,Default,P1,90,90,90,0,0,0,beam,1,111,11,1,P121,smiles,comments
This line describes a sample located in a parcel called 'myParcelName' that contains one container called 'myContainer' which type is Unipuck.
If a column has no value then it is left empty. Example:
myParcelName,myContainer,Unipuck,1,5HT3,sample1,,,,,,,,,,,,,,,,,
CSV is a stardard format capable to be read for all different operating systems and it does not depend on any program.
| Value | Description | Example | |
|---|---|---|---|
| parcel name | mandatory | identifier of the parcel | |
| container name | mandatory | identifier of the container | |
| Container type | mandatory | Controlled list: Unipuck, SPINEpuck | |
| Container position | mandatory | sample position within the container | |
| protein acronym | mandatory | Acronym of the protein. It should exist in ISPyB (coming from the sample sheet declared in the user portal). It is case sensitive. | |
| sample acronym | mandatory | Name of the sample that should be unique within the shipment | |
| Pin barcode | optional | Barcode identifier | |
| SPG & cell | optional | If present, used for strategy calculation and autoprocessing. If a SPG is suspected but no unit cell associated is known, the Forced SPG parameter is more adequate to use | |
| Experiment Type | optional | Controlled list: Default (no workflow), MXPressE, MXPressO, MXpressE_SAD, MXpressI, MXpressP.. | |
| Aimed resolution | optional | Resolution that will be used for the experiment - A default value of 2Å is taken if this parameter is not filled | |
| Required resolution | optional | If observed resolution is worse than this value some automatic workflows will not launch the data collection following the crystal analysis (e.g. MxpressE) | |
| Beam diameter | optional | Several workflows adapt the beam size to the volume of the sample found during the Xtal characterisation but it is possible to force it in some cases (e.g. MxpressO) | |
| Number of positions | optional | if you expect several samples (N) on the same support you can ask to collect automatically a full dataset on each of the N positions requested and found in the initial 2D mesh scan of some workflows | |
| Aimed multiplicity | optional | ||
| Aimed completeness | optional | ||
| Radiation sensitivity | optional | ||
| Forced SPG | optional | If present, used for strategy calculation and autoprocessing and will overwrite the SPG described in the SPG & cell columns of the sample | |
| SMILES | optional | ||
| Already observed resolution | optional | For user purpose only (not used in the pipelines) | |
| Comments | optional | For user purpose |
- Parcel name can not be empty and has to be unique for this shipment
- Container name can not be empty and has to be unique for this shipment
- Container type is a controlled list of values (case sensitive): Unipuck or Spinepuck
- Sample position has to be an integer and depends on container type. If container type is Unipuck then accepted values are between 1 and 16. In case of Spinepuck values should be in the range of 1 and 10.
- Protein has to be in the list of proteins of your proposal (case sensitive)
- Sample name and the protein attached has to be unique for the whole proposal. That means that it will not be possible to have the same sample described twice in the same proposal (even from various shipments).
