Bug #347: Remove spaces from all db fields in Appion - Appion - Electron Microscopy Group

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Bug #347

closed

Remove spaces from all db fields in Appion

Added by Neil Voss over 14 years ago. Updated over 14 years ago.

Status:

Closed

Priority:

Normal

Assignee:

Anchi Cheng

Category:

Target version:

Appion/Leginon 2.0.0

Start date:

04/13/2010

Due date:

% Done:

100%

Estimated time:

Affected Version:

Show in known bugs:

Workaround:

Description

Remove spaces from all db fields. This is a requirement that will be part of the schema change.

Related issues 1 (0 open — 1 closed)

Related to Appion - Bug #328: Major Appion database schema change

Closed

Amber Herold

04/07/2010

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Updated by Neil Voss over 14 years ago

Appion columns:

class ApMaskMakerParamsData(Data):
'mask type'
'region diameter'
'edge blur'
'edge low'
'edge high'
'region std'
'convex hull'

class ApInitialModelData(Data):
'original density'
'original model'

class ApProtomoParamsData(Data):
'series name'

class ApProtomoAlignerParamsData(Data):
'refine cycle'
'good cycle'
'good start'
'good end'

class ApTomoAlignerParamsData(Data):
'refine cycle'
'good cycle'
'good start'
'good end'

class ApTomoAvgParticleData(Data):
'aligned particle'
'z shift'

Looks like Anchi has the most entries

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Updated by Neil Voss over 14 years ago

Leginon has 427 columns with spaces in them!!!

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Updated by Eric Hou over 14 years ago

Target version set to Appion/Leginon 2.0.0

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Updated by Anchi Cheng over 14 years ago

I was following Leginon schema :). Question: are the spaces simply removed or replaced with "_"? I hope it is the latter. Some of the terms will be hard to read without a break.

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Updated by Neil Voss over 14 years ago

Status changed from New to Assigned
Assignee set to Neil Voss

Just for appion will be completed soon

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Updated by Neil Voss over 14 years ago

Subject changed from Remove spaces from all db fields to Remove spaces from all db fields in Appion
% Done changed from 0 to 90

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Updated by Neil Voss over 14 years ago

Status changed from Assigned to In Test
% Done changed from 90 to 100

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Updated by Neil Voss over 14 years ago

Assignee changed from Neil Voss to Anchi Cheng

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Updated by Anchi Cheng over 14 years ago

Status changed from In Test to Assigned
Assignee changed from Anchi Cheng to Neil Voss

ApTomoAlignerParamsData rename column did not work right. I found REF|ApProtomoRefinementParamsData|refine cycle
and REF|ApProtomoRefinementParamsData|good cycle still in ap218. Should the column name include the reference?

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#10

Updated by Neil Voss over 14 years ago

Status changed from Assigned to In Test
Assignee changed from Neil Voss to Anchi Cheng

I would be nice to change any things with spaces, but we are approaching the deadline. How are things working?

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#11

Updated by Anchi Cheng over 14 years ago

Status changed from In Test to Assigned

Neil,
It does not work without it changed. Do you mean that although the upgrade scripts take care of this now, the ones missed by the original upgrade should
be changed by hand? Or do you mean that the upgrade script does not handle such cases and it is too late to make it do that? Looking at the current python code, it should have been taken care of during the upgrade, hence my returning the assignment back. Apart from that, it seems o.k.

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#12