Register prepared flow cells

[Nicklas Nordborg]

This wizard is used to register that a set of flow cells have been clustered and sequencing has started (unless the clustering failed).

See also #501 and #502.

[Nicklas Nordborg]

(In [2020]) References #481: Register prepared flow cells

Preliminary wizards for flow cell creation and registration.

NOTE! Part of this work belong to #502 but that ticket wasn't created until later.

[Nicklas Nordborg]

(In [2031]) References #481: Register prepared flow cells

Added fields for "FlowCellID", "ReadString" and sequence start date/operator when registering flow cells. But so far, only some of the information is saved in the database.

Not sure if we should introduce a DERIVEDBIOASSAY to represent the sequencing already at this point. If so, it would make sense to register the start date and operator on this item instead of on the flow cells.

Failure to cluster a flow cell is also not handled vere well at the moment.

[Nicklas Nordborg]

(In [2049]) References #481: Register prepared flow cells

The wizard now creates a SequencingRunNNNN (derived bioassay) item and link the flow cells to it. The SequencingStartDate and SequencingOperator are added as annotation to the derived bioassay.

[Nicklas Nordborg]

(In [2057]) References #481: Register prepared flow cells

Added support for registering the HiSeq used for sequencing. Actual hardware items must be created by the server administrator with the subtype 'Sequencer'. Automatic selection follow the same pattern as for protocols, eg. the last added item which is set as 'project default' is the default choice.

[Nicklas Nordborg]

(In [2059]) References #481: Register prepared flow cells

Re-organized the registration wizard. There are now three steps instead of two. The first step is the same for selecting flow cells. The second step is for clustering information. The third step is for sequence startup information and is skipped if the 'Failed' option is selected.

Comments in the clustering step can now be made per flow cell.

A protocol can now be specified for the sequencing step.

[Nicklas Nordborg]

(In [2060]) References #481: Register prepared flow cells

Added HiSeqPosition annotation to the reggie installation and to the registration wizard.

[Nicklas Nordborg]

(In [2062]) References #481 and #501. If 'Flow cell ID' is already known for a flow cell, print it on the lab protocol and pre-fill the registration form.

[Nicklas Nordborg]

(In [2064]) References #481: Register prepared flow cells

Changed orientation of the HiSeq position/ReadString table.

[Nicklas Nordborg]

(In [2068]) References #481: Register prepared flow cells

Disabled the 'failed' option before beta release since it is not yet fully implemented.

[Nicklas Nordborg]

(In [2070]) References #481: Register prepared flow cells

Duplicate the entered 'Flow cell ID' values on the third step to avoid registration mistakes. Check that the same 'Flow cell ID' is not entered into both fields.

[Nicklas Nordborg]

(In [2077]) References #481: Register prepared flow cells

Implemented support for registering a failed clustering. The pools on the flow cells are flagged with ClusteringFailed annotation and put into the Flagged PooledLibrary biomaterial list. The "Create flow cells" wizard has been modified to ignore flagged pools unless they also have been annotated with AutoProcess=ReProcess.

[Nicklas Nordborg]

(In [2079]) References #481: Register prepared flow cells

Allow registration of different cluster dates/operator on two flow cells. Added ClusterStart and ClusterOperator annotations to flow cells.

[Nicklas Nordborg]

(In [2089]) References #481: Register prepared flow cells

Replaces ReadString with SequencingCycles.

[Nicklas Nordborg]

(In [2094]) References #481 and #501. Make selection of flow cells easier by including the names of the pools in the selection list.

[Nicklas Nordborg]

(In [2107]) References #481 and #501. Adding support for registering which cBot that was used when clustering.

[Nicklas Nordborg]

(In [2109]) References #502 and #481.

Added PooledLibraryAliquot subtype which must be used by the intermediary aliquots connecting flow cells with pooled libraries. This is required so that we can maintain an unbroken link of related subtypes. The previous version linked FlowCell directly to PooledLibrary which was incorrect.

The registration wizard now also sets the creation date for the aliquots to the ClusterDate.

Existing aliquot items should be updated manually or by a batch importer to set subtype=PooledLibraryAliquot and creation date=ClusterDate (taken from the flow cell the aliquot is used on).