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Task #10807 (closed)

Opened 7 years ago

Closed 5 years ago

Final DB modifications

Reported by: jamoore Owned by:
Priority: critical Milestone: Unscheduled
Component: Model Version: 5.0.0
Keywords: fs Cc: fs@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description (last modified by jamoore)

If we have time to perform further DB changes, the following would simplify much of the OriginalFile? and binary logic put in place for FS:

Mimetype

  • register() should check for mimetypes
  • originalfile super class so there's no mimetype??
  • OriginalFile? extends BaseFile? to remove sha1, mimetype, etc.: Dropping several of the OriginalFile? fields would significantly simplify synchronization between the FS and the DB.
  • Move DIRECTORY_MIMETYPE to constants.
  • Mimetypes (including "Directory") should be compared to standards: There are various mimetypes relating to directories. Perhaps we could either use of those, or use an "application/vnn.openmicroscopy.dir" style

filesets

  • add javaVersion to FilesetVersionInfo?. (And Python?) (see 888)
  • Review all the version info set by python/Java/C++
  • where to put tags during upload
  • check for other definitions of "Reader" (with formatString.replaceAll)
  • include FileInfo (e.g. companion=true, series=2 in filesetEntry (See #10979)

Misc

Change History (31)

comment:1 Changed 7 years ago by mtbcarroll

Things like repositories and directories and whatnot should perhaps each have separate classes in the hierarchy.

comment:2 Changed 7 years ago by jamoore

  • Description modified (diff)

comment:3 Changed 7 years ago by jamoore

  • Keywords fs added

comment:4 Changed 7 years ago by jamoore

  • Description modified (diff)
  • Priority changed from major to critical
  • Sprint changed from FS demo 4.x to FS demo 4.2
  • Summary changed from Final OriginalFile modifications to Final DB modifications

comment:5 Changed 7 years ago by jburel

  • Sprint changed from FS demo 4.2 to FS Demo 4.3

Moved from sprint FS demo 4.2

comment:6 Changed 7 years ago by jamoore

  • Description modified (diff)

comment:7 Changed 7 years ago by mtbcarroll

The java version information could be stored in a hstore column; will that need extra code in Property.java and a new ParameterizedType implementation used by PostgresSqlAction?

comment:8 Changed 7 years ago by jamoore

  • Sprint changed from FS Demo 4.3 to FS demo 4.x

Pushing.

comment:10 Changed 7 years ago by mtbcarroll

also note #7069

comment:11 Changed 7 years ago by mtbcarroll

Is there any further work for beta2 here that must be accounted for by #11516?

comment:12 Changed 7 years ago by jamoore

Some of these it would certainly be good to address for 5.0.0, but whether or not we get that done for beta2 is unclear.

comment:13 Changed 7 years ago by jamoore

  • Milestone changed from OMERO-5 to 5.0.0-beta2
  • Sprint FS demo 4.x deleted
  • Version set to 4.4.9

Moving to beta2 for evaluation.

comment:14 Changed 7 years ago by jamoore

  • Description modified (diff)

comment:15 Changed 7 years ago by jburel

Last edited 7 years ago by jburel (previous) (diff)

comment:16 Changed 7 years ago by jburel

Model changes will happen in Beta3.
Pushing for code freeze for Beta2. Moving to Beta3

Last edited 7 years ago by jburel (previous) (diff)

comment:17 Changed 7 years ago by jamoore

  • Milestone changed from 5.0.0-beta2 to 5.0.0-beta3

comment:18 Changed 6 years ago by mtbcarroll

So, should we get rid of filesetversioninfo and turn it instead into a map property of fileset?

comment:19 Changed 6 years ago by jamoore

  • Milestone changed from 5.1.0 to 5.1.0-m1
  • Version changed from 4.4.9 to 5.0.0

Quite likely. Moving this. Let's discuss ASAP.

comment:20 Changed 6 years ago by jamoore

In conversation with J-m and Mark, brain-storming other uses of maps / map-annotations:

  • experimenter.config (e.g. "userPreferences")
  • script provenance
  • perhaps something for open-with (per-user-per-host)
  • mounted drives for in-place
  • location of files/data/images (url/cloud/etc)
  • external links (connection to other DB) (Josh: NS and map annotation?)

Need a discussion with the wider team on any of other similar uses. Mark to open an initial PR that others can discuss and possibly open secondary PRs against his.

comment:21 Changed 6 years ago by mtbcarroll

Once MapAnnotation is merged I'll rebase and force-push https://github.com/openmicroscopy/openmicroscopy/pull/2301 and will then be happy to change its title / description as other PRs come in against it.

comment:22 Changed 6 years ago by mtbcarroll

This whole story and worthwhile comments could be migrated to Trello.

comment:23 Changed 6 years ago by mtbcarroll

Maps with model enumerations as keys might be useful. Clients can reference their string values and they can be stored efficiently in the database with foreign keys into the enumeration table.

comment:24 Changed 6 years ago by jamoore

and filesets should like have a link to their repository objects.

comment:25 Changed 6 years ago by jburel

  • Milestone changed from 5.1.0-m1 to 5.1.0-m2

few more changes to come. so pushing to m2.

comment:26 Changed 6 years ago by jamoore

Whatever bits of this are going to be done for 5.1.0 should definitely be done for m2 and the rest pushed to post 5.1.0.

comment:27 Changed 6 years ago by jamoore

  • Milestone changed from 5.1.0-m2 to 5.x

Per https://trello.com/c/cur5hd3e/44-5-2-db-changes (and in discussion with Mark), moving all of these changes to 5.x. Intended for 5.2.0-m1 (or similar)

comment:28 Changed 6 years ago by mtbcarroll

Regarding FileInfo, it seems that at present files like test_images_good/bruker/wis/RA_060110.051/, with many images in the fileset, are annotating every image with every companion file: in that case, causing 6,006 file annotations, so there might be a significant win there for certain kinds of MIF.

comment:29 Changed 5 years ago by mtbcarroll

"Intended for 5.2.0-m1" and "Priority: critical": should we start chatting? The OriginalFile reworking also bears on https://trello.com/c/dPfFR1H4/15-duplicate-request-in-cmd.

comment:30 Changed 5 years ago by jamoore

  • Milestone changed from 5.x to Unscheduled

comment:31 Changed 5 years ago by jburel

  • Resolution set to fixed
  • Status changed from new to closed
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