What is Simple View Mode

The Simple View Mode is a version of openBis Web GUI, that:

• always shows exactly one view (e.g. Experiment Details or Sample Browser)
• has no top menu
• has no tab bar
• does not allow any data management (report only view; add,edit,delete... buttons are disabled).
• links in the Simple View Mode are regular hyperlinks, so they can be bookmarked and opened in new browser window (or browser tab)
• supports browser history buttons (back/forward) allowing to navigate between already visited views
• is entered by following a URL, e.g. a perm link

What operations are supported by Simple View Mode

• browse meta data
• search for meta data
• show data sets
• run reports on data sets
• run custom queries (like e.g. versus a bespoke data schema)

How to access Simple View Mode

openBIS switches to Simple View Mode, if a special parameter (viewMode=simple) is found in the URL.

For the OpenBIS available at https://openbis.mydomain.ch/openbis/ , the Simple View Mode will be: https://openbis.mydomain.ch/openbis/?viewMode=simple .

How to embed openBIS on external pages

Embedded mode is a small extension of the Simple View Mode.
It is suitable for embedding openBIS inside external web pages:

• toolbar at the top and footer are not displayed
• each table has only one button which allows to export it. There are no buttons for filtering, refreshing and changing the settings.

Special parameter (viewMode=embedded) should be attached to the URL to switch embedded mode on, the whole URL will look like this: https://openbis.mydomain.ch/openbis/?viewMode=embedded .
It can be also configured on the server side that embedded mode is the default one.

How to create bookmarks for Simple View Mode

Browsers

• Experiment browser:
  • without any preselection:
    https://openbis.mydomain.ch/openbis/?viewMode=simple#action=BROWSE&entity=EXPERIMENT
  • with preselected space SPACE1:
    https://openbis.mydomain.ch/openbis/?viewMode=simple#action=BROWSE&entity=EXPERIMENT&space=SPACE1
  • with preselected space SPACE1 and experiment type TYPE1:
    https://openbis.mydomain.ch/openbis/?viewMode=simple#action=BROWSE&entity=EXPERIMENT&space=SPACE1&type=TYPE1
  • with preselected project /SPACE1/PROJECT1:
    https://openbis.mydomain.ch/openbis/?viewMode=simple#action=BROWSE&entity=EXPERIMENT&project=/SPACE1/PROJECT1
  • with preselected project /SPACE1/PROJECT1 and experiment type TYPE1:
    https://openbis.mydomain.ch/openbis/?viewMode=simple#action=BROWSE&entity=EXPERIMENT&project=/SPACE1/PROJECT1&type=TYPE1

• Sample browser:
  • without any preselection:
    https://openbis.mydomain.ch/openbis/?viewMode=simple#action=BROWSE&entity=SAMPLE
  • with preselected space SPACE1:
    https://openbis.mydomain.ch/openbis/?viewMode=simple#action=BROWSE&entity=SAMPLE&space=SPACE1
  • with preselected space SPACE1 and sample type TYPE1:
    https://openbis.mydomain.ch/openbis/?viewMode=simple#action=BROWSE&entity=SAMPLE&space=SPACE1&type=TYPE1

• Material browser:
  
  • without any preselection:
    https://openbis.mydomain.ch/openbis/?viewMode=simple#action=BROWSE&entity=MATERIAL
  • with preselected material type TYPE1:
    https://openbis.mydomain.ch/openbis/?viewMode=simple#action=BROWSE&entity=MATERIAL&type=TYPE1
• Metaproject browser:
  
  • https://openbis.mydomain.ch/openbis/?viewMode=simple# action=BROWSE&entity=METAPROJECT

Detail views, search, queries

• Detail view of project with code PROJECT1 in space SPACE1:
  
  • https://openbis.mydomain.ch/openbis/?viewMode=simple#action=VIEW&entity=PROJECT&code=PROJECT1&space=SPACE1
• Detail view of material with code MATERIAL1 of type TYPE1:
  
  • https://openbis.mydomain.ch/openbis/?viewMode=simple#action=VIEW&entity=MATERIAL&code=MATERIAL1&type=TYPE1
• Detail view of sample with code SAMPLE1:
  
  • https://openbis.mydomain.ch/openbis/?viewMode=simple#action=SEARCH&entity=SAMPLE&code=SAMPLE1
• Search for data sets of type TYPE1:
  
  • https://openbis.mydomain.ch/openbis/?viewMode=simple#action=SEARCH&entity=DATA_SET&data_set_type=TYPE1
• Results of a query named QUERY1:
  
  • https://openbis.mydomain.ch/openbis/?viewMode=simple#action=QUERY&name=QUERY1
• Results of a query named QUERY1 that has two parameters PARAM1 and PARAM2:
  
  • https://openbis.mydomain.ch/openbis/?viewMode=simple#action=QUERY&name=QUERY1&_PARAM1=value1&_PARAM2=value2
  • there is '_' before every parameter name in the bookmark
• Global search with a query text searchTerm and an optional type of the searched entities Sample
  • https://openbis.mydomain.ch/openbis/?viewMode=simple#action=GLOBAL_SEARCH&query=searchTerm
  • https://openbis.mydomain.ch/openbis/?viewMode=simple#action=GLOBAL_SEARCH&type=Sample&query=searchTerm

High Content Screening specific links

• Detail view of material with code MATERIAL1 of type TYPE1 with preselected experiment with identifier /SPACE1/PROJECT1/EXP1:
  
  • https://openbis.mydomain.ch/openbis/?viewMode=simple#action=VIEW&entity=MATERIAL&code=MATERIAL1&type=TYPE1&experiment=/SPACE1/PROJECT1/EXP1
  • optionally analysis procedure can be specified by adding &analysisProcedure=ANALYSIS_PROCEDURE_CODE
  • only in embedded mode (in other modes all the links open the same material detail view)
    • Open material summary for all experiments. Material is specified by material code MATERIAL1, material type TYPE1. Experiments can be restricted to a single project (in the example /SPACE1/PROJECT1). The spaceCode and projectCodeparameters are optional. When not specified an aggregated view of all known experiments will be returned.
      • https://openbis.mydomain.ch/openbis/?viewMode=embedded#action=VIEW&entity=MATERIAL&code=MATERIAL1&type=TYPE1&spaceCode=SPACE1&projectCode=PROJECT1
    • Open material replicas summary for given experiment with identifier /SPACE1/PROJECT1/EXP1, material code MATERIAL1 and material type TYPE1
      • https://openbis.mydomain.ch/openbis/?viewMode=embedded#action=VIEW&entity=MATERIAL&code=MATERIAL1&type=TYPE1&experiment=/SPACE1/PROJECT1/EXP1
      • whenever experiment is specified, one can add restrictGlobalSearchToProject=true parameter. It causes that if someone opens the "material summary for all experiments" view, only the experiments from the same project as the current experiment will be taken into account.

• To show images of the well with code WELL_CODE (e.g. E1) from a platewith perm id PLATE_PERM_ID (e.g. 20100823133908215-912), even if the well sample does not exist, one can use a following syntax:
  • https://openbis.mydomain.ch/openbis/?viewMode=SIMPLE#entity=SAMPLE&permId=PLATE_PERM_ID:WELL_CODE
• To show images of the well with code WELL_CODE (e.g. E1) from a image datasetwith perm id DATASET_PERM_ID (e.g. 201008132132132-123), even if the well sample does not exist, one can use a following syntax:
  • https://openbis.mydomain.ch/openbis/?viewMode=SIMPLE#entity=DATA_SET&permId=PLATE_PERM_ID:WELL_CODE

• Find all wells which are connected to materials of the specified type TYPE_CODE with a given material code or property MATERIAL_CODE_OR_PROPERTY in the experiment with a given permId EXP_PERM_ID. If showCombinedResultsis set to false the link displays materials without the accompanying plates/wells/datasets.
  • https://openbis.mydomain.ch/openbis/?viewMode=simple#action=WELL_SEARCH&experimentPermId=EXP_PERM_ID&isExactSearch=true&types=TYPE_CODE&items=MATERIAL_CODE_OR_PROPERTY&showCombinedResults=true
  • if experimentPermId parameter is specified, one can add restrictGlobalSearchToProject=true parameter. It causes that if someone reaches the "material summary for all experiments" view, only the experiments from the same project as the specified experiment will be taken into account.
  • one can restrict the search to one project instead of one experiment using optional spaceCode and projectCode parameters. For project /SPACE1/PROJECT1 the URL should contain spaceCode=SPACE1&projectCode=PROJECT1, experimentPermId parameter should not be specified in this case.
  • in case of finding no matching materials openBIS can perform a redirection to a specified page. The url can be specified with an optional noResultsRedirectionUrl parameter, e.g. noResultsRedirectionUrl=http://my-portat.org?no-results-found

• Open a global well search panel
  • without search parameters
    • https://openbis.mydomain.ch/openbis/?viewMode=simple#action=GLOBAL_WELL_SEARCH
  • with search parameters. The meaning of the parameters isExactSearch and items is exactly the same as for the action WELL_SEARCH
    • https://openbis.mydomain.ch/openbis/?viewMode=simple#action=GLOBAL_WELL_SEARCH&isExactSearch=true&items=MATERIAL_CODE_OR_PROPERTY
• Open feature vector summary for the materials within an experiment with given permId EXP_PERM_ID and optional analysis procedure ANALYSIS_PROCEDURE
  • https://openbis.mydomain.ch/openbis/?viewMode=simple#action=FEATURE_VECTOR_SUMMARY&experimentPermId=EXP_PERM_ID&analysisProcedure=ANALYSIS_PROCEDURE

• Plate metadata report for a plate with permId ID1:
  • https://openbis.mydomain.ch/openbis/?viewMode=simple#action=PLATE_METADATA_REPORT&permId=ID1

Permlinks

Permlinks are already in use in the standard View Mode and instead of creating them by hand one
can copy them from openbis.

• Permlink for showing detail viewof a sample/experimen/dataset can be copied from:
  • Show Detail Link column of tables where the entities are listed
  • PermId property value in detail view of the entity
• Permlink for downloading file attachment can be copied from Permlink column of Attachments table in detail view of the entity to which the attachment was assigned.

Example permlinks:

• Permlink to detail view of sample set with permId ID1 (for experiment/data set set entity=EXPERIMENT/DATA_SET):
  https://openbis.mydomain.ch/openbis/?viewMode=simple#action=VIEW&entity=SAMPLE&permId=ID1
• Permlink for dowloading file attachment with name FILE1.PDF in version 1
  
  • for project with code PROJECT1 in space SPACE1:
    https://openbis.mydomain.ch/openbis/?viewMode=simple#action=DOWNLOAD_ATTACHMENT&file=FILE.PDF&version=1&entity=PROJECT&code=PROJECT1&space=SPACE1
  • for sample with permId ID1 (for experiment set entity=EXPERIMENT):
    https://openbis.mydomain.ch/openbis/?viewMode=simple#action=DOWNLOAD_ATTACHMENT&file=FILE.PDF&version=1&entity=SAMPLE&permId=ID1

Custom import

• https://openbis.mydomain.ch/openbis/?viewMode=simple#action=CUSTOM_IMPORT