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Improve the KAM store API; see OpenBEL#40
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Summary:
* KamStore -> KAMStore
* KamStoreImpl -> KAMStoreImpl
* KamStoreException -> KAMStoreException
* KAMStore API changes (aims to be as backwards compatible as possible)
    - added exists methods to check for KAM availability
    - readCatalog -> getCatalog
    - getCatalog never throws exceptions
    - KAMStoreException is an unchecked exception to indicate a severe
      problem vice the old use of these exceptions which was admittedly
      poor
    - Improved documentation; which arguments are optional, which
      required, specific behavior, etc.
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Nick Bargnesi committed Aug 10, 2012
1 parent a61af2e commit 83b85d0
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Showing 31 changed files with 1,553 additions and 1,530 deletions.
12 changes: 6 additions & 6 deletions org.openbel.framework.api/src/main/java/org/openbel/framework/api/DefaultDialect.java
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@
import org.openbel.framework.api.Kam.KamNode;
import org.openbel.framework.api.internal.KAMCatalogDao.KamInfo;
import org.openbel.framework.api.internal.KAMStoreDaoImpl.BelTerm;
import org.openbel.framework.api.KamStore;
import org.openbel.framework.api.KAMStore;
import org.openbel.framework.common.bel.parser.BELParser;
import org.openbel.framework.common.model.Term;

Expand All @@ -62,7 +62,7 @@
public class DefaultDialect implements Dialect {

private final KamInfo kamInfo;
private final KamStore kamStore;
private final KAMStore kAMStore;
private final boolean displayLongForm;

private Map<String, String> labelCache =
Expand All @@ -71,11 +71,11 @@ public class DefaultDialect implements Dialect {
/**
* Package constructor
* @param kamInfo
* @param kamStore
* @param kAMStore
*/
public DefaultDialect(KamInfo kamInfo, KamStore kamStore, boolean displayLongForm) {
public DefaultDialect(KamInfo kamInfo, KAMStore kAMStore, boolean displayLongForm) {
this.kamInfo = kamInfo;
this.kamStore = kamStore;
this.kAMStore = kAMStore;
this.displayLongForm = displayLongForm;
}

Expand All @@ -88,7 +88,7 @@ public String getLabel(KamNode kamNode) {
if (label == null) {
label = kamNode.getLabel();
try {
List<BelTerm> terms = kamStore.getSupportingTerms(kamNode);
List<BelTerm> terms = kAMStore.getSupportingTerms(kamNode);
if (!terms.isEmpty()) {
BelTerm bt = terms.get(0);
Term t = BELParser.parseTerm(bt.getLabel());
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22 changes: 11 additions & 11 deletions ...openbel.framework.api/src/main/java/org/openbel/framework/api/DefaultKamCacheService.java
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Expand Up @@ -103,24 +103,24 @@ public class DefaultKamCacheService implements KamCacheService {
// Maps filtered KAMs to handles
private final Map<FilteredKAMKey, String> fltrdMap;

/** {@link KamStore} */
protected final KamStore kamStore;
/** {@link KAMStore} */
protected final KAMStore kAMStore;

private final ReadLock read;
private final WriteLock write;
private final ExecutorService execSvc;

/**
* Creates a default KAM cache service with a supplied {@link KamStore}.
* Creates a default KAM cache service with a supplied {@link KAMStore}.
*
* @param kamStore {@link KamStore}
* @param kAMStore {@link KAMStore}
* @throws InvalidArgument Thrown if {@code kamStore} is null
*/
public DefaultKamCacheService(KamStore kamStore) {
if (kamStore == null) {
throw new InvalidArgument("kamStore", kamStore);
public DefaultKamCacheService(KAMStore kAMStore) {
if (kAMStore == null) {
throw new InvalidArgument("kamStore", kAMStore);
}
this.kamStore = kamStore;
this.kAMStore = kAMStore;

kamMap = new HashMap<String, Kam>();
unfltrdMap = new HashMap<KamInfo, String>();
Expand Down Expand Up @@ -386,7 +386,7 @@ private class CacheCallable implements Callable<String> {
* {@inheritDoc}
*/
@Override
public String call() throws KamStoreException {
public String call() throws KAMStoreException {
String ret = null;

if (kf != null) {
Expand All @@ -402,7 +402,7 @@ public String call() throws KamStoreException {
return ret;
}

Kam k = kamStore.getKam(ki, kf);
Kam k = kAMStore.getKam(ki, kf);

write.lock();
try {
Expand Down Expand Up @@ -432,7 +432,7 @@ public String call() throws KamStoreException {
}

// get an unfiltered KAM
Kam k = kamStore.getKam(ki);
Kam k = kAMStore.getKam(ki);

write.lock();
try {
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12 changes: 6 additions & 6 deletions org.openbel.framework.api/src/main/java/org/openbel/framework/api/DefaultSpeciesDialect.java
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Original file line number Diff line number Diff line change
Expand Up @@ -60,20 +60,20 @@
*/
public class DefaultSpeciesDialect implements SpeciesDialect {

private final KamStore kamStore;
private final KAMStore kAMStore;
private final Map<String, Namespace> nsmap;
private final List<Namespace> speciesNs;
private final Map<String, String> labelCache;
private final boolean displayLongForm;

public DefaultSpeciesDialect(final KamInfo info, final KamStore kamStore,
public DefaultSpeciesDialect(final KamInfo info, final KAMStore kAMStore,
final int taxId, final boolean displayLongForm) {
this.kamStore = kamStore;
this.kAMStore = kAMStore;
this.labelCache = new HashMap<String, String>();
try {
Namespaces ns = Namespaces.loadNamespaces();

List<KAMStoreDaoImpl.Namespace> nsl = kamStore.getNamespaces(info);
List<KAMStoreDaoImpl.Namespace> nsl = kAMStore.getNamespaces(info);
nsmap = constrainedHashMap(nsl.size());
for (final KAMStoreDaoImpl.Namespace n : nsl) {
nsmap.put(n.getPrefix(),
Expand Down Expand Up @@ -105,7 +105,7 @@ public String getLabel(KamNode kamNode, TermParameter speciesParam) {

try {
// find first term and convert to species namespaces
final List<BelTerm> terms = kamStore
final List<BelTerm> terms = kAMStore
.getSupportingTerms(kamNode);
if (hasItems(terms)) {
final BelTerm term = terms.get(0);
Expand All @@ -121,7 +121,7 @@ public String getLabel(KamNode kamNode, TermParameter speciesParam) {
// if there are no supporting terms, return node label,
// should never be true
return nodeLabel;
} catch (KamStoreException e) {
} catch (KAMStoreException e) {
// error returns original label
return nodeLabel;
}
Expand Down
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