Package omeroweb :: Package webemdb :: Module views
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Module views

source code

Functions [hide private]
 
eman(request, imageId, **kwargs) source code
 
script_run(request, scriptId)
Runs a script using values in a POST
source code
 
script_results(request, jobId) source code
 
script_form(request, scriptId)
Generates an html form for the parameters of a defined script.
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dataset_stack(request, datasetId)
Downloads a dataset of single-plane images as a .mrc file
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projection(request, imageId, projkey)
Simply add the projkey (intmean, intsum or intmax) to the request and delegate to webgateway render_image()
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projection_axis(request, imageId, axis, get_slice=False) source code
 
mapmodelemdb(request, entryId)
We need to work out the OMERO imageId for the emd_map for this entryId, then call mapmodel().
source code
 
get_entry_map(project)
For a project, named by entryId (E.g.
source code
 
mapmodel(request, imageId, entryId=None)
Shows an image projections, slices etc.
source code
 
image(request, imageId)
Shows an image preview (single plane), Name, Description etc.
source code
 
dataset(request, datasetId)
Shows the thumbnails in a dataset, provides a link back to EMDB entry (project)
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data(request, entryId) source code
 
entry(request, entryId) source code
 
oa_viewer(request, fileId)
Returns simply the <applet> element of Open Astex Viewer, for loading into another page.
source code
 
viewport(request, imageId) source code
 
gif(request, entryId)
Looks up the preview gif E.g.
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getFile(request, fileId)
Gets the file by Id and returns it according to mime type for display.
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logout(request)
Shouldn't ever be used (public db)
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loggedout(request) source code
 
about(request) source code
 
index(request)
Show a selection of the latest EMDB entries
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autocompleteQuery(request)
Returns json data for autocomplete.
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search(request) source code
 
getSpfFiles(queryService, rawFileService)
list original files ending with .spf and get text for each, but provide the annotation ID (same as Insight) returns a list of (id, name, text)
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entries(request) source code
 
publications(request)
List all the publications, which are stored as CommentAnnotations with namespace
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getEntriesByPub(request, publicationId) source code
 
getConnection(request) source code
 
image_viewer(request, iid, **kwargs)
This view is responsible for showing pixel data as images
source code
Variables [hide private]
  logger = logging.getLogger('webemdb')
  PUBLICATION_NAMESPACE = "openmicroscopy.org/omero/emdb/publica...
  RESOLUTION_NAMESPACE = "openmicroscopy.org/omero/emdb/resoluti...
  FITTED_PDB_NAMESPACE = "openmicroscopy.org/omero/emdb/fittedPD...
  EMAN2_IMPORTED = True

Imports: HttpResponseRedirect, HttpResponse, Http404, reverse, render_to_response, simplejson, cache, getBlitzConnection, _session_logout, webgateway_views, settings, logging, traceback, omero, rstring, rint, rlong, robject, unwrap, rdouble, Parameters, Filter, scriptUtil, os, FileWrapper, random, math, zeros


Function Details [hide private]

mapmodelemdb(request, entryId)

source code 

We need to work out the OMERO imageId for the emd_map for this entryId, then call mapmodel(). Do this via project, named entryId etc...

get_entry_map(project)

source code 

For a project, named by entryId (E.g. "1003") this returns the image named "emd_1003.map" in a dataset named "1003"

image(request, imageId)

source code 

Shows an image preview (single plane), Name, Description etc. links to datasets.

oa_viewer(request, fileId)

source code 

Returns simply the <applet> element of Open Astex Viewer, for loading into another page. The <applet> contains a script that will load a bit mask, identified by fileId

gif(request, entryId)

source code 

Looks up the preview gif E.g. "80_1001.gif" for the specified entry, based on name of originalfile.

TODO: This method gets the file via it's project, because it's wrapped nicely. Same as def file() below...

autocompleteQuery(request)

source code 

Returns json data for autocomplete. Search terms must be provided in the request "GET". E.g. returns a list of ("1003": "Title") results for entries that start with numbers specified.


Variables Details [hide private]

PUBLICATION_NAMESPACE

Value:
"openmicroscopy.org/omero/emdb/publication"

RESOLUTION_NAMESPACE

Value:
"openmicroscopy.org/omero/emdb/resolutionByAuthor"

FITTED_PDB_NAMESPACE

Value:
"openmicroscopy.org/omero/emdb/fittedPDBEntry"