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User Story #2603 (closed)

Opened 9 years ago

Closed 5 years ago

EMDB web client

Reported by:	wmoore	Owned by:	wmoore
Priority:	major	Milestone:	Unscheduled
Component:	Web	Keywords:	n.a.
Cc:		Story Points:	n.a.
Sprint:	n.a.	Importance:	n.a.
Total Remaining Time:	0.0d	Estimated Remaining Time:	n.a.

Description (last modified by wmoore)

Implement the current functionality and EMDB entries of the EM Data Bank in an OMERO-based web application. Store all metadata for each entry as an emd.xml attached to Project. Also include OpenAstex? Viewer for viewing maps.

For each EMDB entry, store

Project, named by EMDB-id. E.g. 1006. Attach to Project:
- emd.xml metadata
- pdb structures, if maps have been fitted.
- gif image of structure, for preview
- bit masks (file.bit) in Ingvar's format
Dataset.
Image (mrc map)

Use curl script (below) to download data from EMDB.

Use a Python script to populate OMERO with the data.

set -v

baseurl="ftp://emdb-beta.emdatabank.org/structures"

for ((i=1001; i<1007; i++)) 
do 
    
    echo "downloading $i"
    
    curl -O "$baseurl/EMD-$i/header/emd-$i.xml"
    curl -O "$baseurl/EMD-$i/images/$i.gif"
    curl -O "$baseurl/EMD-$i/map/emd_$i.map.gz"
done

References

Referenced by:

← Requirement (#1924): Collaborations
References:
→ Task (#2641): pdb display ( Owner: wmoore Remaining Time: 0 ) → Task (#2723): mage: EMAN2 + IMOD ( Owner: wmoore ) → Task (#2646): Vis buttons ( Owner: wmoore ) → Task (#2664): View EMAN2 processing ( Owner: wmoore Remaining Time: 0 ) → Task (#2739): Upload scripts in bin/omero plugin ( Owner: wmoore ) → Task (#2983): Small fixes from Ingvar ( Owner: wmoore ) → Task (#2690): Scripting service ( Owner: wmoore Remaining Time: 0 ) → Task (#2720): Script validation ( Owner: wmoore ) → Task (#2722): Script 'Cancel' ( Owner: wmoore ) → Task (#2790): Run scripts from Image or Dataset ( Owner: wmoore ) → Task (#2736): OA-viewer level slider ( Owner: wmoore Remaining Time: 0 ) → Task (#2605): OA-Viewer bit masks ( Owner: wmoore ) → Task (#3047): More fixes from Ingvar ( Owner: wmoore ) → Task (#2649): Link to full viewer ( Owner: wmoore Remaining Time: 0 ) → Task (#2704): Image-Image link ( Keywords: dbmodelcompare, schema ) → Task (#2751): Home page ( Owner: wmoore Remaining Time: 0 ) → Task (#2644): Handle big map viewing ( Owner: wmoore Remaining Time: 0 ) → Task (#2643): Get big files ( Owner: wmoore Remaining Time: 0 ) → Task (#2738): Full viewer link for maps ( Owner: wmoore ) → Task (#2756): Full Text Search ( Owner: wmoore Remaining Time: 0 ) → Task (#2604): Finish XML metadata display ( Owner: wmoore Remaining Time: 0 ) → Task (#2606): Entire EMDB repo into OMERO ( Owner: wmoore ) → Task (#2655): Downsample bit masks ( Owner: wmoore ) → Task (#2737): Display Segger results ( Owner: wmoore ) → Task (#2607): Deploy EMDB web to mage ( Owner: wmoore ) → Task (#2838): Demo movie(s) ( Owner: wmoore ) → Task (#2755): Date annotations ( Owner: wmoore ) → Task (#2721): Database for processors ( Owner: wmoore Remaining Time: 0 ) → Task (#2771): Custom settings for EMDB ( Owner: wmoore ) → Task (#2642): Check all parts of every entry ( Owner: wmoore ) → Task (#2752): Browse entries page ( Owner: wmoore Remaining Time: 0 ) → Task (#2608): Browse entries by publication ( Owner: wmoore ) → Task (#2645): BUG: Viewport ( Owner: atarkowska ) → Task (#2735): 'MapModel' page ( Owner: wmoore Remaining Time: 0 )

Change History (22)

comment:1 Changed 9 years ago by wmoore

Description modified (diff)

comment:2 Changed 9 years ago by wmoore

(In [7716]) Fixed preview gif to use same code as getFile() for EMDB. See #2603

comment:3 Changed 9 years ago by wmoore

(In [7720]) Use 'map replace' to help memory issues of Open Astex viewer. See #2603

comment:4 Changed 9 years ago by wmoore

(In [7721]) Reverting the 'replace' command for Open Astex Viewer and fixing bit mask download. See #2603

comment:5 Changed 9 years ago by jmoore

Milestone set to Work in Progress

comment:6 Changed 9 years ago by jmoore

Milestone changed from Work in Progress to OMERO-Beta4.2.1

comment:7 Changed 9 years ago by wmoore

(In [7963]) Fixed bug in Map-model page. See #2603

comment:8 Changed 9 years ago by wmoore

(In [8005]) Turning off web emdb for release. See #2603

comment:9 Changed 9 years ago by wmoore

(In [8125]) Fixes for display and download of maps and xml from webemdb. See #2603

comment:10 Changed 9 years ago by jmoore

Milestone changed from OMERO-Beta4.2.1 to Unscheduled

comment:11 Changed 9 years ago by wmoore

(In [8197]) webemdb edits related to Jason's e-mail yesterday. See #2603.

comment:12 Changed 9 years ago by wmoore

(In [8207]) Fixed bug in previous commit. See #2603

comment:13 Changed 9 years ago by wmoore

(In [8263]) Removing mean and sum projections from webemdb. See #2603

comment:14 Changed 9 years ago by wmoore

(In [8276]) Added logos and 'About' page to webemdb. See #2603

comment:15 Changed 9 years ago by wmoore

(In [8277]) Adding link to webemdb demo movie in 'about' page. See #2603.

comment:16 Changed 9 years ago by wmoore

(In [8278]) Updating OAV jar to fix bit mask centering bug. See #2603

comment:17 Changed 9 years ago by wmoore

(In [8572]) Fixing EMAN2 import statement in omeroweb/settings.py see #2603

comment:18 Changed 9 years ago by wmoore

(In [8588]) Adding webemdb config instructions to webemdb/README.txt. See #2603

comment:19 Changed 9 years ago by wmoore

(In [8660]) Updating OAV jar for webemdb. Also remove display of docked pdbs. See #2603

comment:20 Changed 9 years ago by wmoore

(In [8934/omero]) Adding multiple datasets handling to Ctf_Correction.py script. See #2603

comment:21 Changed 9 years ago by wmoore

(In [8935/omero]) Small fix to Eman_Filters.py See #2603

comment:22 Changed 5 years ago by wmoore

Resolution set to fixed
Status changed from new to closed

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