Package org.intermine.dwr

Class AjaxServices

  • public class AjaxServices
extends java.lang.Object
    This class contains the methods called through DWR Ajax
    Author:
    Xavier Watkins, Daniela Butano

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected static org.apache.log4j.Logger LOG  

    • Constructor Summary

      Constructors 
      Constructor Description
      AjaxServices()  

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      static java.lang.String addTag​(java.lang.String tag, java.lang.String taggedObject, java.lang.String type)
      Adds tag and assures that there is only one tag for this combination of tag name, tagged Object and type.
      void addToSortOrder​(java.lang.String path, java.lang.String direction)
      Add a Node from the sort order
      java.lang.String addUserToShareBag​(java.lang.String userName, java.lang.String bagName)
      Share the bag given in input with the user which userName is input and send email
      java.lang.String changeViewPathDescription​(java.lang.String pathString, java.lang.String description)
      Set the description of a view path.
      java.lang.String deleteApiKey​(java.lang.String username)
      Delete a user's API key, thus disabling webservice access.
      static java.lang.String deleteTag​(java.lang.String tagName, java.lang.String tagged, java.lang.String type)
      Deletes tag.
      java.lang.String deleteUserToShareBag​(java.lang.String userName, java.lang.String bagName)
      Un-share the bag given in input with the user which userName is input
      static java.util.List<java.lang.String> deSelectId​(java.lang.String deSelectId, java.lang.String tableId)
      remove an Id from the PagedTable
      static java.util.List<? extends java.lang.Object> filterWebSearchables​(java.lang.String scope, java.lang.String type, java.util.List<java.lang.String> tags, java.lang.String filterText, java.lang.String filterAction, java.lang.String callId)
      Given a scope, type, tags and some filter text, produce a list of matching WebSearchable, in a format useful in JavaScript.
      java.lang.String generateApiKey​(java.lang.String username)
      Generate a new API key for a given user.
      static java.util.List<? extends java.lang.Object> getColumnSummary​(java.lang.String tableName, java.lang.String summaryPath)
      Get the summary for the given column
      static java.lang.String getConstraintLogic()
      Get the grouped constraint logic
      java.lang.String[] getContent​(java.lang.String suffix, boolean wholeList, java.lang.String field, java.lang.String className)  
      static int getConvertCountForBag​(java.lang.String bagName, java.lang.String type)
      For a given bag name and a type different from the bag type, give the number of converted objects
      static java.lang.String getCustomConverterCounts​(java.lang.String bagName, java.lang.String converterName)
      For a list and a converter, return types and related counts
      static java.util.Collection<PartnerLink> getFriendlyMineLinks​(java.lang.String mineName, java.lang.String domains, java.lang.String idents)
      used on REPORT page For a gene, generate links to other intermines.
      static java.lang.String getNewsPreview​(java.lang.String rssURL)
      Work as a proxy for fetching remote file (RSS)
      static java.util.Set<java.lang.String> getObjectTags​(java.lang.String type, java.lang.String tagged)
      Returns all tags by which is specified object tagged.
      static java.util.Map<java.lang.String,​java.lang.Object> getRatDiseases​(java.lang.String orthologues)
      Return list of disease ontology terms associated with list of provided rat genes.
      static java.lang.Integer getResultsSize​(java.lang.String qid)
      Return the number of rows of results from the query with the given query id.
      java.lang.String getSavedBagStatus()
      This method gets the latest bags from the session (SessionMethods) and returns them in JSON
      static java.lang.String getSingleUseKey()
      Return the single use API key for the current profile
      static java.util.Set<java.lang.String> getTags​(java.lang.String type)
      Returns all tags of specified tag type together with prefixes of these tags.
      static java.lang.String getToggledElements()
      This method gets a map of ids of elements that were in the past (during session) toggled and returns them in JSON
      java.util.Collection<java.lang.String> getUsersSharingBag​(java.lang.String bagName)
      Return the list of users who have access to this bag because it has been shared with them.
      java.lang.String preCompute​(java.lang.String templateName)
      Precomputes the given template query
      java.lang.String rename​(java.lang.String name, java.lang.String type, java.lang.String reName)
      Rename a element such as history, name, bag
      void reorder​(java.lang.String newOrder, java.lang.String oldOrder)
      AJAX request - reorder view.
      void reorderConstraints​(java.lang.String newOrder, java.lang.String oldOrder)
      AJAX request - reorder the constraints.
      java.lang.String saveBagDescription​(java.lang.String bagName, java.lang.String description)
      For a given bag, set its description
      static void saveToggleState​(java.lang.String elementId, boolean opened)
      Saves information, that some element was toggled - displayed or hidden.
      static void selectAll​(int index, java.lang.String tableId)
      Select all the elements in a PagedTable
      static java.util.List<java.lang.String> selectId​(java.lang.String selectedId, java.lang.String tableId, java.lang.String columnIndex)
      Add an ID to the PagedTable selection
      static java.lang.String setConstraintLogic​(java.lang.String expression)
      Set the constraint logic on a query to be the given expression.
      void setFavourite​(java.lang.String name, java.lang.String type, boolean isFavourite)
      Creates a favourite Tag for the given templateName
      static void setState​(java.lang.String name, java.lang.String value)
      Set state that should be saved during the session.
      java.lang.String summarise​(java.lang.String templateName)
      Summarises the given template query.
      void updateTemplate​(java.lang.String field, java.lang.String value)
      Update with the value given in input the field of the previous template saved into the session
      static java.lang.String validateBagName​(java.lang.String bagName)
      validate bag upload
      static java.lang.String validateBagOperations​(java.lang.String bagName, java.lang.String[] selectedBags, java.lang.String operation)
      validation that happens before new bag is saved

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • LOG

        protected static final org.apache.log4j.Logger LOG

    • Constructor Detail

      • AjaxServices

        public AjaxServices()

    • Method Detail

      • setFavourite

        public void setFavourite​(java.lang.String name,
                         java.lang.String type,
                         boolean isFavourite)
        Creates a favourite Tag for the given templateName
        Parameters:
        name - the name of the template we want to set as a favourite
        type - type of tag (bag or template)
        isFavourite - whether or not this item is currently a favourite

      • preCompute

        public java.lang.String preCompute​(java.lang.String templateName)
        Precomputes the given template query
        Parameters:
        templateName - the template query name
        Returns:
        a String to guarantee the service ran properly

      • summarise

        public java.lang.String summarise​(java.lang.String templateName)
        Summarises the given template query.
        Parameters:
        templateName - the template query name
        Returns:
        a String to guarantee the service ran properly

      • rename

        public java.lang.String rename​(java.lang.String name,
                               java.lang.String type,
                               java.lang.String reName)
                        throws java.lang.Exception
        Rename a element such as history, name, bag
        Parameters:
        name - the name of the element
        type - history, saved, bag
        reName - the new name for the element
        Returns:
        the new name of the element as a String
        Throws:
        java.lang.Exception - if the application business logic throws an exception

      • generateApiKey

        public java.lang.String generateApiKey​(java.lang.String username)
                                throws java.lang.Exception
        Generate a new API key for a given user.
        Parameters:
        username - the user to generate the key for.
        Returns:
        A new API key, or null if something untoward happens.
        Throws:
        java.lang.Exception - an exception.

      • deleteApiKey

        public java.lang.String deleteApiKey​(java.lang.String username)
                              throws java.lang.Exception
        Delete a user's API key, thus disabling webservice access. A message "deleted" is returned to confirm success.
        Parameters:
        username - The user whose key we should delete.
        Returns:
        A confirmation string.
        Throws:
        java.lang.Exception - if somethign bad happens

      • saveBagDescription

        public java.lang.String saveBagDescription​(java.lang.String bagName,
                                           java.lang.String description)
                                    throws java.lang.Exception
        For a given bag, set its description
        Parameters:
        bagName - the bag
        description - the description as entered by the user
        Returns:
        the description for display on the jsp page
        Throws:
        java.lang.Exception - an exception

      • changeViewPathDescription

        public java.lang.String changeViewPathDescription​(java.lang.String pathString,
                                                  java.lang.String description)
        Set the description of a view path.
        Parameters:
        pathString - the string representation of the path
        description - the new description
        Returns:
        the description, or null if the description was empty

      • getToggledElements

        public static java.lang.String getToggledElements()
        This method gets a map of ids of elements that were in the past (during session) toggled and returns them in JSON
        Returns:
        JSON serialized to a String
        Throws:
        org.json.JSONException

      • getColumnSummary

        public static java.util.List<? extends java.lang.Object> getColumnSummary​(java.lang.String tableName,
                                                                          java.lang.String summaryPath)
                                                                   throws java.lang.Exception
        Get the summary for the given column
        Parameters:
        summaryPath - the path for the column as a String
        tableName - name of column-owning table
        Returns:
        a collection of rows
        Throws:
        java.lang.Exception - an exception

      • getResultsSize

        public static java.lang.Integer getResultsSize​(java.lang.String qid)
        Return the number of rows of results from the query with the given query id. If the size isn't yet available, return null. The query must be started with SessionMethods.startPagedTableCount().
        Parameters:
        qid - the id
        Returns:
        the row count or null if not yet available

      • filterWebSearchables

        public static java.util.List<? extends java.lang.Object> filterWebSearchables​(java.lang.String scope,
                                                                              java.lang.String type,
                                                                              java.util.List<java.lang.String> tags,
                                                                              java.lang.String filterText,
                                                                              java.lang.String filterAction,
                                                                              java.lang.String callId)
        Given a scope, type, tags and some filter text, produce a list of matching WebSearchable, in a format useful in JavaScript.

        Each element of the returned List is a List containing a WebSearchable name, a score (from Lucene) and a string with the matching parts of the description highlighted.

        ie - search for "me": 

           [
     [ "Some name", 0.123, "So<i>me</i> name" ],
     ...
   ]
        Parameters:
        scope - the scope (either Scope.GLOBAL or Scope.USER).
        type - the type (from TagTypes).
        tags - the tags to filter on.
        filterText - the text to pass to Lucene.
        filterAction - toggles favourites filter off and on; will be blank or 'favourites'
        callId - unique id
        Returns:
        a List of Lists

      • getConvertCountForBag

        public static int getConvertCountForBag​(java.lang.String bagName,
                                        java.lang.String type)
        For a given bag name and a type different from the bag type, give the number of converted objects
        Parameters:
        bagName - the name of the bag
        type - the type to convert to
        Returns:
        the number of converted objects

      • getCustomConverterCounts

        public static java.lang.String getCustomConverterCounts​(java.lang.String bagName,
                                                        java.lang.String converterName)
        For a list and a converter, return types and related counts
        Parameters:
        bagName - the name of the bag
        converterName - Java class that processes the data
        Returns:
        the number of converted objects

      • getFriendlyMineLinks

        public static java.util.Collection<PartnerLink> getFriendlyMineLinks​(java.lang.String mineName,
                                                                     java.lang.String domains,
                                                                     java.lang.String idents)
        used on REPORT page For a gene, generate links to other intermines. Include gene and orthologues. Returns NULL if no values found. It's possible that the identifier in the local mine will match more than one entry in the remote mine but this will be handled by the portal of the remote mine.
        Parameters:
        mineName - name of mine to query
        domains - The domains the domains these identifiers are valid for (eg. organisms).
        idents - The external object identifiers.
        Returns:
        the links to friendly intermines

      • getRatDiseases

        public static java.util.Map<java.lang.String,​java.lang.Object> getRatDiseases​(java.lang.String orthologues)
        Return list of disease ontology terms associated with list of provided rat genes. Returns JSONObject as string with ID (intermine ID) and name (ontologyTerm.name)
        Parameters:
        orthologues - list of rat genes
        Returns:
        JSONObject of the shape {status :: string, mineUrl :: string, results :: [[string]]}

      • saveToggleState

        public static void saveToggleState​(java.lang.String elementId,
                                   boolean opened)
        Saves information, that some element was toggled - displayed or hidden.
        Parameters:
        elementId - element id
        opened - new aspect state

      • setState

        public static void setState​(java.lang.String name,
                            java.lang.String value)
        Set state that should be saved during the session.
        Parameters:
        name - name of state
        value - value of state

      • validateBagName

        public static java.lang.String validateBagName​(java.lang.String bagName)
        validate bag upload
        Parameters:
        bagName - name of new bag to be validated
        Returns:
        error msg to display, if any

      • validateBagOperations

        public static java.lang.String validateBagOperations​(java.lang.String bagName,
                                                     java.lang.String[] selectedBags,
                                                     java.lang.String operation)
        validation that happens before new bag is saved
        Parameters:
        bagName - name of new list
        selectedBags - bags involved in operation
        operation - which operation is taking place - delete, union, intersect or subtract
        Returns:
        error msg, if any

      • selectId

        public static java.util.List<java.lang.String> selectId​(java.lang.String selectedId,
                                                        java.lang.String tableId,
                                                        java.lang.String columnIndex)
        Add an ID to the PagedTable selection
        Parameters:
        selectedId - the id
        tableId - the identifier for the PagedTable
        columnIndex - the column of the selected id
        Returns:
        the field values of the first selected objects

      • deSelectId

        public static java.util.List<java.lang.String> deSelectId​(java.lang.String deSelectId,
                                                          java.lang.String tableId)
        remove an Id from the PagedTable
        Parameters:
        deSelectId - the ID to remove from the selection
        tableId - the PagedTable identifier
        Returns:
        the field values of the first selected objects

      • selectAll

        public static void selectAll​(int index,
                             java.lang.String tableId)
        Select all the elements in a PagedTable
        Parameters:
        index - the index of the selected column
        tableId - the PagedTable identifier

      • reorder

        public void reorder​(java.lang.String newOrder,
                    java.lang.String oldOrder)
        AJAX request - reorder view.
        Parameters:
        newOrder - the new order as a String
        oldOrder - the previous order as a String

      • reorderConstraints

        public void reorderConstraints​(java.lang.String newOrder,
                               java.lang.String oldOrder)
        AJAX request - reorder the constraints.
        Parameters:
        newOrder - the new order as a String
        oldOrder - the previous order as a String

      • addToSortOrder

        public void addToSortOrder​(java.lang.String path,
                           java.lang.String direction)
                    throws java.lang.Exception
        Add a Node from the sort order
        Parameters:
        path - the Path as a String
        direction - the direction to sort by
        Throws:
        java.lang.Exception - if the application business logic throws

      • getNewsPreview

        public static java.lang.String getNewsPreview​(java.lang.String rssURL)
        Work as a proxy for fetching remote file (RSS)
        Parameters:
        rssURL - the url
        Returns:
        String representation of a file

      • addTag

        public static java.lang.String addTag​(java.lang.String tag,
                                      java.lang.String taggedObject,
                                      java.lang.String type)
        Adds tag and assures that there is only one tag for this combination of tag name, tagged Object and type.
        Parameters:
        tag - tag name
        taggedObject - object id that is tagged by this tag
        type - tag type
        Returns:
        'ok' string if succeeded else error string

      • deleteTag

        public static java.lang.String deleteTag​(java.lang.String tagName,
                                         java.lang.String tagged,
                                         java.lang.String type)
        Deletes tag.
        Parameters:
        tagName - tag name
        tagged - id of tagged object
        type - tag type
        Returns:
        'ok' string if succeeded else error string

      • getTags

        public static java.util.Set<java.lang.String> getTags​(java.lang.String type)
        Returns all tags of specified tag type together with prefixes of these tags. For instance: for tag 'bio:experiment' it automatically adds 'bio' tag.
        Parameters:
        type - tag type
        Returns:
        tags

      • getObjectTags

        public static java.util.Set<java.lang.String> getObjectTags​(java.lang.String type,
                                                            java.lang.String tagged)
        Returns all tags by which is specified object tagged.
        Parameters:
        type - tag type
        tagged - id of tagged object
        Returns:
        tags

      • getSingleUseKey

        public static java.lang.String getSingleUseKey()
        Return the single use API key for the current profile
        Returns:
        the single use APi key

      • setConstraintLogic

        public static java.lang.String setConstraintLogic​(java.lang.String expression)
                                           throws PathException
        Set the constraint logic on a query to be the given expression.
        Parameters:
        expression - the constraint logic for the query
        Returns:
        messages to display in the jsp page
        Throws:
        PathException - if the query is invalid

      • getConstraintLogic

        public static java.lang.String getConstraintLogic()
        Get the grouped constraint logic
        Returns:
        a list representing the grouped constraint logic

      • getContent

        public java.lang.String[] getContent​(java.lang.String suffix,
                                     boolean wholeList,
                                     java.lang.String field,
                                     java.lang.String className)
        Parameters:
        suffix - string of input before request for more results
        wholeList - whether or not to show the entire list or a truncated version
        field - field name from the table for the lucene search
        className - class name (table in the database) for lucene search
        Returns:
        an array of values for this classname.field

      • getSavedBagStatus

        public java.lang.String getSavedBagStatus()
                                   throws org.json.JSONException
        This method gets the latest bags from the session (SessionMethods) and returns them in JSON
        Returns:
        JSON serialized to a String
        Throws:
        org.json.JSONException - json exception

      • updateTemplate

        public void updateTemplate​(java.lang.String field,
                           java.lang.String value)
        Update with the value given in input the field of the previous template saved into the session
        Parameters:
        field - the field to update
        value - the value

      • addUserToShareBag

        public java.lang.String addUserToShareBag​(java.lang.String userName,
                                          java.lang.String bagName)
        Share the bag given in input with the user which userName is input and send email
        Parameters:
        userName - the user which the bag has to be shared with
        bagName - the bag name to share
        Returns:
        'ok' string if succeeded else error string

      • deleteUserToShareBag

        public java.lang.String deleteUserToShareBag​(java.lang.String userName,
                                             java.lang.String bagName)
        Un-share the bag given in input with the user which userName is input
        Parameters:
        userName - the user which the bag has to be un-shared with
        bagName - the bag name to un-share
        Returns:
        'ok' string if succeeded else error string

      • getUsersSharingBag

        public java.util.Collection<java.lang.String> getUsersSharingBag​(java.lang.String bagName)
        Return the list of users who have access to this bag because it has been shared with them.
        Parameters:
        bagName - the bag name that the users share
        Returns:
        the list of users