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## es.upm.gib.aewrapper.queryprocessing
Class QueryProcessor

    java.lang.Object
      es.upm.gib.aewrapper.queryprocessing.QueryProcessor

    public class QueryProcessor

extends java.lang.Object

Project entry class. Contains the methods that allow performing SPARQL queries against the AE database.

[E-GEOD-9295, E-GEOD-24996, E-GEOD-11810, E-GEOD-10037, E-GEOD-13660, E-GEOD-4511, E-GEOD-8404, E-GEOD-5797, E-GEOD-5798, E-GEOD-24072, E-MEXP-2742, E-GEOD-19338, E-GEOD-16757, E-GEOD-15049, E-GEOD-18207, E-GEOD-23527, E-MEXP-265, E-MEXP-2338, E-GEOD-18745, E-GEOD-23521, E-GEOD-2346, E-GEOD-6233, E-GEOD-4607, E-GEOD-11054, E-GEOD-12527, E-GEOD-469, E-GEOD-5739, E-GEOD-17294, E-GEOD-19256, E-GEOD-13129, E-GEOD-10360, E-GEOD-27092, E-GEOD-5187, E-MTAB-546, E-GEOD-4879, E-GEOD-10358, E-GEOD-19937, E-GEOD-4064, E-GEOD-14464, E-GEOD-27225, E-TABM-815, E-GEOD-20203, E-GEOD-5646, E-GEOD-26773, E-GEOD-27221, E-MEXP-1812, E-GEOD-18292, E-GEOD-7364, E-GEOD-11934, E-GEOD-8019, E-GEOD-1110, E-GEOD-11089, E-GEOD-1111, E-GEOD-21201, E-GEOD-26897, E-GEOD-5725, E-GEOD-7853, E-GEOD-782, E-GEOD-16970, E-GEOD-25245, E-GEOD-13837, E-GEOD-7909, E-GEOD-9006, E-MEXP-2764, E-GEOD-5157, E-GEOD-26740, E-GEOD-5206, E-GEOD-5657, E-GEOD-7441, E-MTAB-308, E-GEOD-22757, E-GEOD-15199, E-GEOD-11315, E-GEOD-22472, E-GEOD-13047, E-GEOD-2627, E-GEOD-5166, E-MEXP-693, E-GEOD-6677, E-GEOD-13043, E-GEOD-12593, E-GEOD-4729, E-GEOD-5339, E-GEOD-10377, E-GEOD-10070, E-GEOD-27004, E-GEOD-1262, E-MTAB-434, E-GEOD-7635, E-GEOD-16063, E-GEOD-22467, E-GEOD-24228, E-MTAB-460, E-GEOD-14201, E-GEOD-26813, E-BASE-4, E-GEOD-6936, E-BASE-5, E-GEOD-8649, E-GEOD-11919, E-GEOD-19774, E-GEOD-21372, E-GEOD-14342, E-GEOD-10511, E-GEOD-27051, E-MEXP-44, E-GEOD-21467, E-GEOD-28386, E-GEOD-10860, E-GEOD-18588, E-GEOD-13700, E-GEOD-1509, E-GEOD-20528, E-GEOD-7454, E-GEOD-18303, E-GEOD-10008, E-GEOD-26077, E-GEOD-28836, E-GEOD-15879, E-GEOD-831, E-GEOD-9648, E-GEOD-29580, E-GEOD-14751, E-GEOD-2399, E-GEOD-2710, E-GEOD-3843, E-GEOD-19016, E-GEOD-8453, E-GEOD-19013, E-MEXP-197, E-GEOD-13892, E-GEOD-7268, E-GEOD-20714, E-GEOD-20717, E-GEOD-17917, E-GEOD-18450, E-MEXP-940, E-MEXP-3109, E-TABM-148, E-GEOD-26083, E-GEOD-5018, E-GEOD-22905, E-GEOD-6151, E-GEOD-11202, E-MEXP-2141, E-GEOD-15446, E-TABM-995, E-GEOD-5615, E-GEOD-23855, E-GEOD-5616, E-GEOD-29273, E-GEOD-24875, E-GEOD-17135, E-GEOD-15500, E-GEOD-18567, E-GEOD-13866, E-GEOD-26653, E-GEOD-24795, E-GEOD-21502, E-GEOD-14721, E-GEOD-22089, E-GEOD-8245, E-GEOD-5814, E-GEOD-19035, E-GEOD-2376, E-GEOD-26390, E-GEOD-16916, E-GEOD-26644, E-GEOD-16996, E-GEOD-18935, E-MEXP-452, E-BASE-2, E-GEOD-18578, E-BASE-1, E-BUGS-115]

Method Summary
`static java.lang.String` | `processQuery(java.lang.String queryString, java.util.Collection<java.lang.String> keywords)` Executes a SPARQL query against the arrayexpress database, using a set of keywords for extracting the relevant experiment list.
`static java.lang.String` | `processQuery(java.lang.String queryString, java.util.Collection<java.lang.String> keywords, ProgressNotification progressNotification)` Executes a SPARQL query against the arrayexpress database, using a set of keywords for extracting the relevant experiment list.
`static java.lang.String` | `processQuery(java.lang.String queryString, java.lang.String experiment)` Executes a SPARQL query against the arrayexpress database, using a specific experiment.
`static java.lang.String` | `processQuery(java.lang.String queryString, java.lang.String experiment, ProgressNotification progressNotification)` Executes a SPARQL query against the arrayexpress database, using a specific experiment.

Methods inherited from class java.lang.Object
`clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Method Detail

### processQuery

    public static java.lang.String processQuery(java.lang.String queryString,
                                                java.util.Collection<java.lang.String> keywords)
                                         throws java.lang.Exception

  Executes a SPARQL query against the arrayexpress database, using a set of keywords for extracting the relevant experiment list. A file containing the results in SPARQL Result format is generated.

  The keyword list should be a non-empty list of strings containing the desired keywords. For example, the following keyword list could be submitted: <'organism', 'rattus', 'mammary', 'glands'>.

  The keyword list will be resolved against the arrayexpress database itself, producing a list of experiment identifiers. The provided SPARQL query will be executed against all those experiments, and the individual results will be integrated into a single result.

  Parameters:
    `queryString` - the SPARQL query
    `keywords` - the keywords for extracting the relevant experiments
  Returns:
    the path to the generated results file, or null if there was some error. This result file contains the results to the original SPARQL query, and its format is SPARQL Result format (http://www.w3.org/TR/rdf-sparql-XMLres/).
  Throws:
    `ExperimentAccessException` - could not access the page of the given experiment
    `OWLModelNotLoadedException` - could not load the owl model
    `MageParsingException` - could not parse the mage document of an experiment
    `java.io.IOException` - errors accessing the local cache
    `LocalConfigException` - error accessing the xml config file
    `org.jdom.JDOMException` - xml parsing error when reading the config file
    `com.hp.hpl.jena.query.QueryParseException` - syntax errors in the SPARQL query
    `com.hp.hpl.jena.shared.JenaException` - error reading the generated rdf model
    `java.lang.Exception` - undefined error

### processQuery

    public static java.lang.String processQuery(java.lang.String queryString,
                                                java.util.Collection<java.lang.String> keywords,
                                                ProgressNotification progressNotification)
                                         throws java.lang.Exception

  Executes a SPARQL query against the arrayexpress database, using a set of keywords for extracting the relevant experiment list. A file containing the results in SPARQL Result format is generated.

  The keyword list should be a non-empty list of strings containing the desired keywords. For example, the following keyword list could be submitted: <'organism', 'rattus', 'mammary', 'glands'>.

  The keyword list will be resolved against the arrayexpress database itself, producing a list of experiment identifiers. The provided SPARQL query will be executed against all those experiments, and the individual results will be integrated into a single result.

  A progress notification implementation is used to keep track of the task progress (null if not used).

  Parameters:
    `queryString` - the SPARQL query
    `keywords` - the keywords for extracting the relevant experiments
    `progressNotification` - a progress notification implementation. Its method percentageCompleted(Integer) will be invoked with values from 0 to 100. The completeTask() method will be invoked when the task has been completed successfully
  Returns:
    the path to the generated results file, or null if there was some error. This result file contains the results to the original SPARQL query, and its format is SPARQL Result format (http://www.w3.org/TR/rdf-sparql-XMLres/).
  Throws:
    `ExperimentAccessException` - could not access the page of the given experiment
    `OWLModelNotLoadedException` - could not load the owl model
    `MageParsingException` - could not parse the mage document of an experiment
    `java.io.IOException` - errors accessing the local cache
    `LocalConfigException` - error accessing the xml config file
    `org.jdom.JDOMException` - xml parsing error when reading the config file
    `com.hp.hpl.jena.query.QueryParseException` - syntax errors in the SPARQL query
    `com.hp.hpl.jena.shared.JenaException` - error reading the generated rdf model
    `java.lang.Exception` - undefined error

### processQuery

    public static java.lang.String processQuery(java.lang.String queryString,
                                                java.lang.String experiment)
                                         throws java.lang.Exception

  Executes a SPARQL query against the arrayexpress database, using a specific experiment. A file containing the results in SPARQL Result format is generated.

  Parameters:
    `queryString` - the SPARQL query
    `experiment` - the only experiment to be queried
  Returns:
    the path to the generated results file, or null if there was some error. This result file contains the results to the original SPARQL query, and its format is SPARQL Result format (http://www.w3.org/TR/rdf-sparql-XMLres/).
  Throws:
    `ExperimentAccessException` - could not access the page of the given experiment
    `OWLModelNotLoadedException` - could not load the owl model
    `MageParsingException` - could not parse the mage document of an experiment
    `java.io.IOException` - errors accessing the local cache
    `LocalConfigException` - error accessing the xml config file
    `org.jdom.JDOMException` - xml parsing error when reading the config file
    `com.hp.hpl.jena.query.QueryParseException` - syntax errors in the SPARQL query
    `com.hp.hpl.jena.shared.JenaException` - error reading the generated rdf model
    `java.lang.Exception` - undefined error

### processQuery

    public static java.lang.String processQuery(java.lang.String queryString,
                                                java.lang.String experiment,
                                                ProgressNotification progressNotification)
                                         throws java.lang.Exception

  Executes a SPARQL query against the arrayexpress database, using a specific experiment. A file containing the results in SPARQL Result format is generated.

  A progress notification implementation is used to keep track of the task progress (null if not used).

  Parameters:
    `queryString` - the SPARQL query
    `experiment` - the only experiment to be queried
    `progressNotification` - a progress notification implementation. Its method percentageCompleted(Integer) will be invoked with values from 0 to 100. The completeTask() method will be invoked when the task has been completed successfully
  Returns:
    the path to the generated results file, or null if there was some error. This result file contains the results to the original SPARQL query, and its format is SPARQL Result format (http://www.w3.org/TR/rdf-sparql-XMLres/).
  Throws:
    `ExperimentAccessException` - could not access the page of the given experiment
    `OWLModelNotLoadedException` - could not load the owl model
    `MageParsingException` - could not parse the mage document of an experiment
    `java.io.IOException` - errors accessing the local cache
    `LocalConfigException` - error accessing the xml config file
    `org.jdom.JDOMException` - xml parsing error when reading the config file
    `com.hp.hpl.jena.query.QueryParseException` - syntax errors in the SPARQL query
    `com.hp.hpl.jena.shared.JenaException` - error reading the generated rdf model
    `java.lang.Exception` - undefined error

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