Plug-in for batch upload/modification of items

[Jari Häkkinen]

References to the latest versions of files (please keep this list up to date):

• Developer view​ (batchimport.txt)
• User perspective​ (batchimport_userperspective.txt)

Sample files:

• ​Sample spreadsheet with comments (batchimport_sample.ods). The spreadsheet contains multiple sample sheets for use with the importer. Each item type to be supported has a separate sheet, the sheet content may have comments below the legend on this page. Currently the BASE internal 'id' is not used. Types to be done are Hybridization, Scan, RawBioassay, and Experiment.

[Nicklas Nordborg]

First draft of a developers view

[Jari Häkkinen]

I have added a version 2 of the specification doc. There are a couple of comments, look for JH. I'll create sample docs matching the specs, and I am looking into the list of importable objects.

[Jari Häkkinen]

First draft of a users view

[Jari Häkkinen]

In the batchimport.txt document there is a discussion on multi-item references:

Data for a single item may be split onto multiple lines. The first
line contains simple properties and single-item references, and the
first multi-item reference. If there are more multi-item references
they should be on the following lines with empty values in all other
columns, except for the column holding the item identifier, which
must have the same value on all lines. If the following lines
contains other data, this should be ignored, or it may be considered
an error condition. It may be caused by giving two items the same
name by accident.

In the above text there is a reference to the item reference column. Maybe it is implied, but I think we should specifically state that this column is the same as used by single item references. In the openoffice sample document I have used the same column for simple and pooled samples (see Sample sheet in attached spreadsheet).

[Jari Häkkinen]

I added a spreadsheet with sample sheets for use with the batch item importer.

[Jari Häkkinen]

batchimport_userperspective.txt updated.

[Jari Häkkinen]

Updated spreadsheet, sample information to the labeled extracts step with pooling is available in the doc.

[Jari Häkkinen]

Major revision of the user perspective, and the sample openoffice is now complete. All items that should be supported by the importer is discussed and described in the docs.

[Nicklas Nordborg]

(In [4366]) References #1028: Plug-in for batch upload/modification of items

Prototype for biosurce and sample import added.

[Nicklas Nordborg]

(In [4372]) References #1028: Plug-in for batch upload/modification of items

Added importers for extract and labeled extract.

[Nicklas Nordborg]

3rd version of developers view

[Nicklas Nordborg]

(In [4408]) References #1028: Plug-in for batch upload/modification of items

Fixes a NPE when creating a configuration.

[Nicklas Nordborg]

(In [4413]) References #1028: Plug-in for batch upload/modification of items

Made some parameter descriptions clearer.

[Nicklas Nordborg]

(In [4414]) References #1028: Plug-in for batch upload/modification of items

No duplicate column mapping for item identification.

[Jari Häkkinen]

Updated sample spreadsheet. Biosources, Samples, Extracts, Labeled extracs are tested with the batch importers.

[Nicklas Nordborg]

(In [4423]) References #1028: Plug-in for batch upload/modification of items

Added "mode" parameter for selecting "create" and/or "update" mode. Reordered parameters on first wizard page.

[Nicklas Nordborg]

(In [4426]) References #1028: Plug-in for batch upload/modification of items

Added:

• HybridizationImporter
• ScanImporter
• RawBioAssayImporter (not complete)

[Jari Häkkinen]

Updated the sample spreadsheet, now decimal point is used instead of decimal comma.

[Nicklas Nordborg]

(In [4434]) References #1028 :Plug-in for batch upload/modification of items

Completed raw bioassay importer and added array design, batch and slide importers.

[Nicklas Nordborg]

(In [4449]) References #1028: Plug-in for batch upload/modification of items

Do not offer "create" mode to users which lacks CREATE permission.

[Nicklas Nordborg]

4th version of developers view

[Nicklas Nordborg]

(In [4451]) References #1028: Plug-in for batch upload/modification of items

Fixes a NPE when "File" column is empty.