Inconsistent CSV format required for populate metadata on Plate vv Project

[will-moore]

Looking at examples added to the README in #28
it seems that the CSV format has different rules for Screen compared with Project:

Screen example has columns of Well,Plate and the column types are well,plate.
Omitting the # header has no effect on column types of well and plate.

# header well,plate,s,d,l,d
Well,Plate,Drug,Concentration,Cell_Count,Percent_Mitotic
A1,plate01,DMSO,10.1,10,25.4
A2,plate01,DMSO,0.1,1000,2.54
A3,plate01,DMSO,5.5,550,4
B1,plate01,DrugX,12.3,50,44.43

This creates an OMERO.table with additional Well Name and Plate Name columns and the previous Well and Plate columns now have IDs instead of Names.

Well	Plate	Drug	Concentration	Cell Count	Percent Mitotic	Well Name	Plate Name
9154	3855	DMSO	10.1	10	25.4	a1	plate01
9155	3855	DMSO	0.1	1000	2.54	a2	plate01

If I use column named Plate Name instead of Plate in the csv, the script fails:

  File "/Users/willadmin/Virtual/omero/lib/python2.7/site-packages/omero_metadata/populate.py", line 1241, in post_process
    plate = columns_by_name['plate'].values[i]   # FIXME

and it also fails if I use Well Name instead of Well.

When the target is a Project, we need columns named Dataset Name and Image Name in the CSV and these columns are of type String.

# header s,s,d,l,s
Image Name,Dataset Name,Bounding_Box,Channel_Index,Channel_Name
img-01.png,dataset01,0.0469,1,DAPI
img-02.png,dataset01,0.142,2,GFP
img-03.png,dataset01,0.093,3,TRITC
img-04.png,dataset01,0.429,4,Cy5

This creates an OMERO.table with an additional Image ID column:

Image Name	Dataset Name	Bounding_Box	Channel_Index	Channel_Name	Image
img-01.png	dataset01	0.0469	1	DAPI	36638
img-02.png	dataset01	0.142	2	GFP	36639

If I name the first column to Image I get a failure with

ValueError: invalid literal for long() with base 10: 'img-01.png'

I'm just documenting this to clarify the results of my investigations and document the current behaviour. It seems inconsistent for Plate that we use Well and Plate columns that are really Well Name and Plate Name. The Project behaviour is more expected.

[will-moore]

Also, if the project.csv has any existing column named Image, even if it is the correct Image ID or some other number or string then the script fails.