Skip to content
Snippets Groups Projects
search.md 7.55 KiB
Newer Older
  • Learn to ignore specific revisions
  • Marco Del Tufo's avatar
    .  
    Marco Del Tufo committed
    # Search
    
    Marco Del Tufo's avatar
    Marco Del Tufo committed
    
    
    Marco Del Tufo's avatar
    .  
    Marco Del Tufo committed
    ## Advanced search
    
    Marco Del Tufo's avatar
    Marco Del Tufo committed
    
    
    Marco Del Tufo's avatar
    .  
    Marco Del Tufo committed
    The **Advanced Search** can be accessed from the main menu, under
    **Utilities**. Alternatively, the advanced search can also be used after
    performing a global search (see
    
    Marco Del Tufo's avatar
    Marco Del Tufo committed
    [Search](https://openbis.readthedocs.io/en/latest/user-documentation/general-users/search.html)),
    
    Marco Del Tufo's avatar
    .  
    Marco Del Tufo committed
    to refine the obtained results.
    
    ![image info](img/advanced-search-navigation-menu-1024x448.png)
    
    In the advanced search users can combine several search criteria using
    either the **AND** or **OR** operators. Users can choose to search for:
    
    1.  **All (prefix match, faster)**: search for the first 3 letters of a
        word. The search is performed across all fields of all entities
        (Experiments/Collections, Objects, Datasets).
    2.  **All (full word match, faster)**: search for a complete word. The
        search is performed across all fields of all entities
        (Experiments/Collections, Objects, Datasets).
    3.  **All (partial match, slower)**: search for a partial word. The
        search is performed across all fields of all entities
        (Experiments/Collections, Objects, Datasets).
    4.  **Experiment/Collection**: search is performed across all fields of
        all Experiments/Collections.
    5.  **Object**: search is performed across all fields of all Objects.
    6.  **Dataset**: search is performed across all fields of all Datasets.
    7.  **A specific Object type** (e.g. Antibody, Bacteria, Cell Line, in
        the picture below): search is performed across all fields of the
        selected Object type only.
    
    ![image info](img/advanced-search-criteria.png)
    
    After selecting what to search for, the search can be further restricted
    to specific fields, in the **Field Type** drop down menu. The available
    fields for a search vary depending on what the search is performed.
    
    ### Search for: All
    
    This includes all 3 “All” options described above.
    
    Available **Field Types**:
    
    1.  **All**: search across all fields of all entities.
    
    ![image info](img/advanced-search-all-field-type.png)
    
    In this case, this is the only available option and it is not possible
    to restrict the search.
    
    ### Search for: Experiment/Collection
    
    Available **Field Types**:
    
    1.  **All**: search across all fields of all Experiments/Collections
    2.  **Property**: Can select a specific property to search on. This can
        be selected in the **Field Name**.
    
    ![image info](img/adv-search-experiment-1024x307.png)
    
    It is possible to exclude terms from the search by selecting the NOT in
    the first column of the table.
    
    If **Property** is selected in the **Field Type**, a list of all
    available properties becomes available in the **Field Name** drop down.
    According to the type of property selected, the comparator operator will
    be different (e.g for a date field it is possible to select an exact
    date, or everything before a given date or everything after). It is
    possible to search on more than one field by clicking on the **+**
    button in the table and build complex queries in this way. By selecting
    the NOT checkbox in the table certain fields can be excluded from the
    search.
    
    ![image info](img/adv-search-experiments-property-1024x373.png)
    
    ### Search for: Object
    
    Available **Field Types**:
    
    1.  **All**: search across all fields of all Objects
    2.  **Property**: can select one or more specific properties to search
        on. These can be selected in the **Field Name** (see above)
    3.  **Experiment/Collection**: search for Objects in a given
        Experiment/Collection 
    4.  **Parent**: search for Objects that have the specified parents
    5.  **Children**: search for Objects that have the specified children
    
    ![image info](img/adv-search-objects-1024x382.png)
    
    Also in this case, fields can be excluded from the search by selecting
    the NOT checkbox in the table.
    
    
    ### Search for: Dataset
    
    Available **Field Types**:
    
    1.  **All**: search across all fields of all Datasets
    2.  **Property**: can select one or more specific properties to search
        on. These can be selected in the **Field Name** (see above)
    3.  **Object**: search for Datasets in a given Object 
    4.  **Experiment/Collection**: search for Datasets in a given
        Experiment/Collection
    
    ![image info](img/adv-search-datasets-1024x349.png)
    
    Also in this case, fields can be excluded from the search by selecting
    the NOT checkbox in the table.
    
    ### Search for: specific Object Type (e.g Experimental Step)
    
    In this case, the available Field Types are the same as when searching
    for an Object.
    
    Available **Field Types**:
    
    1.  **All**: search across all fields of the specific Object type (e.g.
        Experimental Step)
    2.  **Property**: can select one or more specific properties to search
        on. These can be selected in the **Field Name** (see above)
    3.  **Experiment/Collection**: search for Objects of the selected type
        in a given Experiment/Collection 
    4.  **Parent**: search for Objects of the selected type that have the
        specified parents
    5.  **Children**: search for Objects of the selected type that have the
        specified children
    
    ![image info](img/adv-search-exp-step-1024x366.png)
    
    ### Search Collection
    
    It is possible to launch an advanced search limited to Objects of one
    Collection from a Collection page, by selecting **Search in Collection**
    from the **More** drop down. This redirects to the Advanced Search page
    where the Collection is already pre-defined.
    
    ![image info](img/search-in-collection-1024x378.png)
    
    Updated on July 5, 2023
    
    ## Search
      
    Different types of searches are available from the main menu in openBIS:
    
    1.  Global search
    2.  BLAST search
    3.  Data Set Files Search
    4.  Advanced Search
    
    ![image info](img/search-types-in-ELN-UI.png)
    
    ### Global search
    
    This functionality, available from the main menu, performs a search
    across all database fields. Results are presented in a table in the
    **Advanced Search** page. The search can be also be further refined (see
    [Advanced
    
    Marco Del Tufo's avatar
    Marco Del Tufo committed
    search](https://openbis.readthedocs.io/en/latest/user-documentation/general-users/search.html#advanced-search)).
    
    Marco Del Tufo's avatar
    .  
    Marco Del Tufo committed
    
    ![image info](img/general-search-1024x486.png)
    
    ### BLAST search
    
    This performs a BLAST search over nucleotide sequences contained either
    in the **Sequence** property of an Object type (e.g Plasmid or Oligo) or
    in Datasets of type **SEQ\_FILES**. Results are shown in a table, sorted
    by E-value.
    
    ### Data Set File search
    
    This search allows users to search across names of files stored in
    openBIS Datasets.
    
    Please note that it is not possible to search the content of the files.
    
    In the example below, we search for files that contain “mass-loss” in
    the name, and we find 1 dataset that contains a file called
    mass-loss-data.csv.
    
    By clicking on the table row that shows the Dataset containing the
    searched file, you will be redirected to the Dataset page.
    
    ![image info](img/dataset-file-search-2-1024x292.png)
    
    Updated on April 25, 2023
    
    ## Save and reuse searches
    
    Marco Del Tufo's avatar
    Marco Del Tufo committed
    
    It is possible to save and re-use searches created in the [Advanced
    
    Marco Del Tufo's avatar
    Marco Del Tufo committed
    search](https://openbis.readthedocs.io/en/latest/user-documentation/general-users/search.html#advanced-search).
    
    Marco Del Tufo's avatar
    Marco Del Tufo committed
    *Space* *admin* rights are required to save searches in a given Space.
    Searches can be used by anyone with *User* or *Observer* rights to a
    given Space.
    
    In the Advanced Search page, build your search criteria (see example
    below). To save the search, click the **Save** button and enter:
    
    1.  The **Name** of the search
    2.  The **Experiment/Collection** where the search should be stored
    
    Searches are stored in *Experiments/Collections*.
    
    ![image info](img/advanced-search-create-and-save-query.png)
    
    Saved searches are available from the **load a saved search** drop down
    menu, at the top of the **Advanced Search** page.  
    
    ![image info](img/advanced-search-load-saved-query.png)
    
    
    Marco Del Tufo's avatar
    Marco Del Tufo committed
    Updated on July 28, 2022