Generate lab protocol for clustering

[Nicklas Nordborg]

After flow cells have been designed (Create flow cell wizard, #502) it should be possible to generate a lab protocol for the clustering. It should show which pools that go on each lane. A preliminary "ReadString" (for the sequencing) should be printed since this steps ends with loading the flow cells into the HiSeq.

The protocol should include fields for noting various dates (cluster date, sequencing start date, etc). Flow cell ID is also needed.

When the flow cells have been loaded into the HiSeq the information from this protocol is registered in BASE (#481).

[olle]

Non-link camel-cased entities are now escaped, for increased readability.

[olle]

Typo fixed.

[olle]

Design discussion.

• The clustering protocol wizard will consist of two JSP scripts, flowcell_protocol.jsp and flowcell_protocol2.jsp, both in reggie/resources/libprep/, as well as modifications of Java servlet FlowCellServlet.java in reggie/src/net/sf/basedb/reggie/servlet/.
• JSP script flowcell_protocol.jsp will be based on existing JSP scripts flowcell_registration.jsp (which also includes selection of flowcells) and libprep_protocol.jsp, while flowcell_protocol2.jsp will be loosely based the list part of libprep_protocol2.jsp and mrna_protocol2.jsp.
• JSP script flowcell_protocol.jsp will display a selection box of flow cells, that have not yet been processed. It will contain "Create protocol" and "Cancel" buttons. Function init() will call function getFlowCells() to get a list of unprocessed flow cells from Java servlet FlowCellServlet.java. The "Create protocol" button will be coupled to function goCreate(), which will call function getSelectBoxResults(elementId) to get a comma-separated list of selected flow cell database id values, that is inserted into hidden input field "flowcellidlist", which makes it possible for java scriptlet code to retrieve the list string after the document has been submitted to JSP script flowcell_protocol2.jsp. In the same manner, function getFlowCellNumLanesList(idList) is called to get a comma-separated list of the number of lanes for the selected flow cells, that is inserted into hidden input field numlaneslist.
• JSP script flowcell_protocol2.jsp uses java scriptlet code to retrieve the selected flow cell database id values, and number of lanes per flow cell. The scriptlet code uses this data to produce the right number and size of tables for the flow cell data in the protocol. The comma-separated flow cell database id values are inserted into hidden input field fcIdList, to make it avaiable to javascript code in the JSP script. Javascript function init() retrieves the id list string, and calls function getFlowCellInfo(idList) (identical to the function with the same name in JSP file flowcell_protocol.jsp) to get a JSONArray of data for the flow cells, which is used as argument, when calling function viewAsList(flowCellInfoArray). Function viewAsList(flowCellInfoArray) inserts data from the flow cells into the tables prepared by the Java scriptlet code.
• Java servlet FlowCellServlet.java in reggie/src/net/sf/basedb/reggie/servlet/ is updated with new Ajax command "GetFlowCellInfo". It will retrieve data from the database for requested flow cell database id values, and return a JSONArray with data for the flow cells. The flow cell data that are reported are name, description, ReadString, number of lanes, and pool names for the lanes.

[olle]

Note on the table data in first version of the lab protocol for clustering:

1. The protocol contains one section for each flow cell selected in the wizard.
2. Each flow cell section contains two tables, one with general data and fields to be filled in, and one table with pool names for each lane.
3. The layout of the general data table is based on the general table section of mrna_protocol2.jsp.
   
   The reported data is:
   a. Flow cell name.
   b. Flow cell description.
   c. ReadString.
   
   Fields to be filled in are available for:
   a. Clustering date.
   b. Clustering operator.
   c. Sequencing date.
   d. Sequencing operator.
   e. Flow cell ID.
   f. Comments.
   

[olle]

(In [2033]) Refs #501. First version of wizard for clustering lab protocol.

[olle]

(In [2034]) Refs #501. Directory that was erroneously copied in changeset 2033 is deleted.

[olle]

(In [2035]) Refs #501. Lab protocol for clustering updated in JSP script flowcell_protocol2.jsp in reggie/resources/libprep/ by adding column for remarks in table showing pool data in flow cell lanes.

[olle]

(In [2046]) Refs #501. Lab protocol for clustering updated in JSP script flowcell_protocol2.jsp in reggie/resources/libprep/ by setting height of general comments column in "em" units, instead of adding four empty rows. Row span of flow cell description column changed from 9 to 5.

[olle]

(In [2047]) Refs #501. Lab protocol for clustering updated in JSP script flowcell_protocol2.jsp in reggie/resources/libprep/ by removing resizing recommendation from the print instruction, since it is currently not needed.

[olle]

(In [2055]) Refs #501. Lab protocol for clustering updated in JSP script flowcell_protocol.jsp in reggie/resources/libprep/ by removing the "Cancel" button, since it is not essential for a protocol wizard.

[olle]

Note: The subversion message text for change set ​[2055] erroneously referred to JSP script flowcell_protocol2.jsp, instead of the correct flowcell_protocol.jsp.

[olle]

Design update:

• The general data table in each flow cell section should be extended with a row to fill in what machine position was used for the flow cell ('A' or 'B'). This entry will be inserted below the entry for flow cell ID.
• A new entry will be added for the sequencing machine id, located after the flow cell tables.

[olle]

(In [2056]) Refs #501. Lab protocol for clustering updated in JSP script flowcell_protocol2.jsp in reggie/resources/libprep/ by adding rows for entry of flow cell machine position, and sequencing machine id:

1. The general data table in each flow cell section has been extended with a row to fill in what machine position was used for the flow cell ('A' or 'B'). This entry is inserted below the entry for flow cell ID.
2. A new entry has been added for the sequencing machine id, located after the flow cell tables.

[Nicklas Nordborg]

(In [2061]) References #501: Generate lab protocol for clustering

Changed the HiSeq position field to checkboxes.

[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 [2063]) References #501: Generate lab protocol for clustering

Re-organized the lab protocol to make it more similar to the registration wizard. It is now divided into two parts. One for the clustering and one for the sequencing startup.

[Nicklas Nordborg]

(In [2069]) References #501: Generate lab protocol for clustering

Larger column for HiSeq position to avoid line break.

[Nicklas Nordborg]

(In [2086]) References #501: Generate lab protocol for clustering

Replaced ReadString with SequenceString.

[Nicklas Nordborg]

(In [2087]) References #502 and #501. Renamed SequenceString to SequencingCycles since it should better describe what is stored in that annotation. Changes to the text in the registration interface and lab protocol as well.

[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 [2112]) References #501: Generate lab protocol for clustering

Added a section with used pools at the top of the protocol. Color coded the pools to make it easier to find the corresponding pools on the flow cells.