Reception

Reception.html

The reception.html page is a separate entry point for the Lims. It allows a user who is aware of this URL to perform actions which are not directly accessible in the lab (normally). It acts as an admin panel, even if there is no real security/checking etc.

The reception page, as a URL, is then an admin panel. It allows (until now) to perform two specific actions, used for the physical reception of the samples (hence the name).

Reception

The sample reception is the first step of the whole work process. It encapsulates two specific tasks:

• The creation of the manifests describing the samples
• The registration of the samples

Creation

Here is the explanation behind this step: Someone wants to send 6 samples to Reception, in order to perform some DNA/RNA magic. Reception will then issue one manifest for 6 samples, and send it to this person. With each sample, one unique ID has been attached (the sanger_sample_id), as well as one barcode. On the way back, the manifest contains more details about each sample (Gender, etc.). This manifest comes back as a CSV file. This CSV file is then loaded in S2, updating the samples details. Finally, when the samples arrive physically in Reception, they are scanned by a lab user. This finalises them, registering them in S2, and creating an order for them.

Samples

The samples are created in S2 even before that the manifest has been created. They are empty, with no information, with a 'draft' status.

For each one of them, a barcoded tube (=== a tube + a barcode + their association) is created, and the sample placed inside. These actions are bulk actions, because one could ask to create 100 samples, creating a lot of traffic.

Manifest

The manifest is an excel spreadsheet describing the samples, with a sanger_sample_id, a barcode, and other information hidden. All this information is different for every sample, or batch of sample. An external service is used, which, providing a valid CSV file, generates a valid excel spreadsheet.

Reading

The CSV version of the manifest contains hidden information, regarding the study etc. This allows the Lims to load specific template data to generate the correct request during the sample reception.

Indeed, once the file loaded, it should be possible to update certain parameters regarding the sample, in particular the type of work to be done (eg: DNA/RNA manual, DNA/RNA QiaCube). For this, the json_templater library is used.