Package ubic.gemma.core.loader.entrez

Class EntrezUtils

java.lang.Object

ubic.gemma.core.loader.entrez.EntrezUtils

public class EntrezUtils
extends Object

Low-level utilities for generating Entrez URLs.

Read more about this in The E-utilities In-Depth: Parameters, Syntax and More.

Author:

poirigui

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static interface	EntrezUtils.EntrezCall<T>

Field Summary

Fields

Modifier and Type	Field	Description
static String	EFETCH
static String	ELINK
static String	ESEARCH
static String	ESUMMARY

Constructor Summary

Constructors

Constructor	Description
EntrezUtils()

Method Summary

Modifier and Type	Method	Description
static <T> T	doNicely(EntrezUtils.EntrezCall<T> task, String apiKey)	Coordinate calls to the Entrez API so that we always respect the recommended usage.
static URL	fetch(String db, EntrezQuery query, EntrezRetmode retmode, String rettype, int retstart, int retmax, String apiKey)	Retrieve the results of a previous search(String, String, EntrezRetmode, String) query.
static URL	fetchById(String db, String id, EntrezRetmode retmode, String rettype, String apiKey)	Retrieve a record from an Entrez database by ID.
static URL	link(String db, String dbfrom, EntrezQuery query, String cmd, EntrezRetmode retmode, String apiKey)	Retrieve related records from an Entrez database from a previous search(String, String, EntrezRetmode, String) query.
static URL	linkById(String db, String dbfrom, String id, String cmd, EntrezRetmode retmode, String apiKey)	Retrieve related records from an Entrez database by ID.
static <T> SimpleRetryCallable<T,IOException>	retryNicely(SimpleRetryCallable<T,IOException> callable, String apiKey)	Wrap a SimpleRetryCallable such that it will respect the recommended usage of the Entrez API.
static URL	search(String db, String term, EntrezRetmode retmode, String apiKey)	Perform a search on an Entrez database.
static URL	search(String db, EntrezQuery query, EntrezRetmode retmode, int retstart, int retmax, String apiKey)	Replay a previous search(String, String, EntrezRetmode, String) query.
static URL	summary(String db, EntrezQuery query, EntrezRetmode retmode, int retstart, int retmax, String apiKey)	Summarize a previous search(String, String, EntrezRetmode, String) query.

Methods inherited from class java.lang.Object

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

Field Detail

ESEARCH

public static final String ESEARCH

See Also:

Constant Field Values

ESUMMARY

public static final String ESUMMARY

See Also:

Constant Field Values

EFETCH

public static final String EFETCH

See Also:

Constant Field Values

ELINK

public static final String ELINK

See Also:

Constant Field Values

Constructor Detail

EntrezUtils

public EntrezUtils()

Method Detail

doNicely

public static <T> T doNicely(EntrezUtils.EntrezCall<T> task,
                             @Nullable
                             String apiKey)
                      throws IOException

Coordinate calls to the Entrez API so that we always respect the recommended usage.

Refer to A General Introduction to the E-utilities for more information about usage policies.

Throws:

IOException

retryNicely

public static <T> SimpleRetryCallable<T,IOException> retryNicely(SimpleRetryCallable<T,IOException> callable,
                                                                       @Nullable
                                                                       String apiKey)

Wrap a SimpleRetryCallable such that it will respect the recommended usage of the Entrez API.

See Also:

doNicely(EntrezCall, String)

search

public static URL search(String db,
                         String term,
                         EntrezRetmode retmode,
                         @Nullable
                         String apiKey)

Perform a search on an Entrez database.

Results must be subsequently retrieved with fetch(String, EntrezQuery, EntrezRetmode, String, int, int, String) or summary(String, EntrezQuery, EntrezRetmode, int, int, String). The query key and WebEnv values must be extracted from the payload.

search

public static URL search(String db,
                         EntrezQuery query,
                         EntrezRetmode retmode,
                         int retstart,
                         int retmax,
                         @Nullable
                         String apiKey)

Replay a previous search(String, String, EntrezRetmode, String) query.

summary

public static URL summary(String db,
                          EntrezQuery query,
                          EntrezRetmode retmode,
                          int retstart,
                          int retmax,
                          @Nullable
                          String apiKey)

Summarize a previous search(String, String, EntrezRetmode, String) query.

fetchById

public static URL fetchById(String db,
                            String id,
                            EntrezRetmode retmode,
                            String rettype,
                            @Nullable
                            String apiKey)

Retrieve a record from an Entrez database by ID.

fetch

public static URL fetch(String db,
                        EntrezQuery query,
                        EntrezRetmode retmode,
                        String rettype,
                        int retstart,
                        int retmax,
                        @Nullable
                        String apiKey)

Retrieve the results of a previous search(String, String, EntrezRetmode, String) query.

linkById

public static URL linkById(String db,
                           String dbfrom,
                           String id,
                           String cmd,
                           EntrezRetmode retmode,
                           @Nullable
                           String apiKey)

Retrieve related records from an Entrez database by ID.

Parameters:

db - target database

dbfrom - source database, the ID must come from this database

id - the ID to link from

cmd - the command to use, e.g. "neighbor"

link

public static URL link(String db,
                       String dbfrom,
                       EntrezQuery query,
                       String cmd,
                       EntrezRetmode retmode,
                       @Nullable
                       String apiKey)

Retrieve related records from an Entrez database from a previous search(String, String, EntrezRetmode, String) query.