Lucene wildcard matching fails on chemical notations(?) - java

Using Hibernate Search Annotations (mostly just #Field(index = Index.TOKENIZED)) I've indexed a number of fields related to a persisted class of mine called Compound. I've setup text search over all the indexed fields, using the MultiFieldQueryParser, which has so far worked fine.
Among the fields indexed and searchable is a field called compoundName, with sample values:
3-Hydroxyflavone
6,4'-Dihydroxyflavone
When I search for either of these values in full the related Compound instances are returned. However problems occur when I use the partial name and introduce wildcards:
searching for 3-Hydroxyflav* still gives the correct hit, but
searching for 6,4'-Dihydroxyflav* fails to find anything.
Now as I'm quite new to Lucene / Hibernate-search, I'm not quite sure where to look at this point.. I think it might have something to do with the ' present in the second query, but I don't know how to proceed.. Should I look into Tokenizers / Analyzers / QueryParsers or something else entirely?
Or can anyone tell me how I can get the second wildcard search to match, preferably without breaking the MultiField-search behavior?
I'm using Hibernate-Search 3.1.0.GA & Lucene-core 2.9.3.
Some relevant code bits to illustrate my current approach:
Relevant parts of the indexed Compound class:
#Entity
#Indexed
#Data
#EqualsAndHashCode(callSuper = false, of = { "inchikey" })
public class Compound extends DomainObject {
#NaturalId
#NotEmpty
#Length(max = 30)
#Field(index = Index.TOKENIZED)
private String inchikey;
#ManyToOne
#IndexedEmbedded
private ChemicalClass chemicalClass;
#Field(index = Index.TOKENIZED)
private String commonName;
...
}
How I currently search over the indexed fields:
String[] searchfields = Compound.getSearchfields();
MultiFieldQueryParser parser =
new MultiFieldQueryParser(Version.LUCENE_29, searchfields, new StandardAnalyzer(Version.LUCENE_29));
FullTextSession fullTextSession = Search.getFullTextSession(getSession());
FullTextQuery fullTextQuery =
fullTextSession.createFullTextQuery(parser.parse("searchterms"), Compound.class);
List<Compound> hits = fullTextQuery.list();

Use WhitespaceAnalyzer instead of StandardAnalyzer. It will just split at whitespace, and not at commas, hyphens etc. (It will not lowercase them though, so you will need to build your own chain of whitespace + lowercase, assuming you want your search to be case-insensitive). If you need to do things differently for different fields, you can use a PerFieldAnalyzer.
You can't just set it to un-tokenized, because that will interpret your entire body of text as one token.

I think your problem is a combination of analyzer and query language problems. It is hard to say what exactly causes the problem. To find this out I recommend you inspect you index using the Lucene index tool Luke.
Since in your Hibernate Search configuration you are not using a custom analyzer the default - StandardAnalyzer - is used. This would be consistent with the fact that you use StandardAnalyzer in the constructor of MultiFieldQueryParser (always use the same analyzer for indexing and searching!). What I am not so sure of is how "6,4'-Dihydroxyflavone" gets tokenized by StandardAnalyzer. That the first thing you have to find out. For example the javadoc says:
Splits words at hyphens, unless
there's a number in the token, in
which case the whole token is
interpreted as a product number and is
not split.
It might be that you need to write your own analyzer which tokenizes your chemical names the way you need it for your use cases.
Next the query parser. Make sure you understand the query syntax - Lucene query syntax. Some characters have special meaning, for example a '-'. It could be that your query is parsed the wrong way.
Either way, first step os to find out how your chemical names get tokenized. Hope that helps.

I wrote my own analyzer:
import java.util.Set;
import java.util.regex.Pattern;
import org.apache.lucene.index.memory.PatternAnalyzer;
import org.apache.lucene.util.Version;
public class ChemicalNameAnalyzer extends PatternAnalyzer {
private static Version version = Version.LUCENE_29;
private static Pattern pattern = compilePattern();
private static boolean toLowerCase = true;
private static Set stopWords = null;
public ChemicalNameAnalyzer(){
super(version, pattern, toLowerCase, stopWords);
}
public static Pattern compilePattern() {
StringBuilder sb = new StringBuilder();
sb.append("(-{0,1}\\(-{0,1})");//Matches an optional dash followed by an opening round bracket followed by an optional dash
sb.append("|");//"OR" (regex alternation)
sb.append("(-{0,1}\\)-{0,1})");
sb.append("|");//"OR" (regex alternation)
sb.append("((?<=([a-zA-Z]{2,}))-(?=([^a-zA-Z])))");//Matches a dash ("-") preceded by two or more letters and succeeded by a non-letter
return Pattern.compile(sb.toString());
}
}

Related

Hibernate search and elastic search analysers for exact search

I have StandardAnalyser above the field in entity
#Field(name = "myField", index = Index.YES, analyze = Analyze.YES, analyzer = #Analyzer(impl = StandardAnalyzer.class)),
But I wonder how to then make it possible to:
1) Search by words like: I like bananas -> ["I", "like", "bananas"] (which my analyser currently allows me to do)
2) Search by exact input: "I like bananas" -> "I like bananas" (which StandardAnalyser does not allow and the fitting change would be to impl = KeywordAnalyser)
Should I change my analyser or maybe in java code, based on input (if it starts and ends with double quotes) change the way of searching?
Regards
Maybe you want a phrase query? A phrase query looks for a sequence of tokens, instead of just one token.
Query luceneQuery = queryBuilder.phrase()
.onField("myField")
.sentence("I like bananas")
.createQuery();
See https://docs.jboss.org/hibernate/search/5.11/reference/en-US/html_single/#_phrase_queries
Phrase queries are still sort of "fuzzy", however, since the analyzer is still involved: case will be ignored, etc. It's just about looking for a sequence of (analyzed) tokens.
If you really need exact search, including case sensitivity, you can simply declare two fields:
#Field(name = "myField", index = Index.YES, analyze = Analyze.YES, analyzer = #Analyzer(impl = StandardAnalyzer.class))
#Field(name = "myField_exact", index = Index.YES, analyze = Analyze.NO)
Then you can target either myField or myField_exact at query time, depending on your needs.
Of course, you will need to reindex your data before myField_exact becomes available.

How to use CriteriaBuilder to call db function

I have a string that might eventually contain spaces. I would like to replace those spaces with a regex that matches against \t,\r,\n. After replacing I would like to call regexp_like (an oracle function) to match a field against this string.
I know it is possible to call db functions using criteria builder as described for example in this link
I am not very familiar with the difference between regex in java versus oracle or how to cobble this together (I have never called functions from criteriabuilder). Here are my tentative steps with places where I am stuck in the comments
// first replace all spaces with regex for \s,\r,\t, value is the original string
value.replaceAll(" +", "[\\t\\n\\r]+")
// build the db function call expression, seems I cant do table.<String>get(field) and cant pass value as a string
Expression<String> regExp = cb.function("regexp_like", String.class, table.<String>get(field), value);
// now create a predicate not sure how
Predicate fieldMatch = cb.equal(...)
Is this possible?
Its possible. You only need to do few small changes.
Extends your Oracle dialog
public class Oracle10gCustomDialect extends Oracle10gDialect {
public Oracle10gCustomDialect() {
super();
registerFunction("regexp_like", new SQLFunctionTemplate(StandardBasicTypes.BOOLEAN,
"(case when (regexp_like(?1, ?2)) then 1 else 0 end)"));
}
}
Then use this path at your application.properties or hibernate properties config.
Then in your specification, need to do something like this.
Expression<Boolean> regExprLike = criteriaBuilder.function("regexp_like", Boolean.class, root.get("yourColumn"), criteriaBuilder.literal("<your regexp value>"));
predicates.add(criteriaBuilder.isTrue(regExprLike));
...
And thats all!

JPA Select query not returning results with one letter word

I have a query that when given a word that starts with a one-letter word followed by space character and then another word (ex: "T Distribution"), does not return results. While given "Distribution" alone returns results including the results for "T Distribution". It is the same behavior with all search terms beginning with a one-letter word followed by space character and then another word.
The problem appears when the search term is of this pattern:
"[one-letter][space][letter/word]". example: "o ring".
What would be the problem that the LIKE operator not working correctly in this case?
Here is my query:
#Cacheable(value = "filteredConcept")
#Query("SELECT NEW sina.backend.data.model.ConceptSummaryVer04(s.id, s.arabicGloss, s.englishGloss, s.example, s.dataSourceId,
s.synsetFrequnecy, s.arabicWordsCache, s.englishWordsCache, s.superId, s.categoryId, s.dataSourceCacheAr, s.dataSourceCacheEn,
s.superTypeCasheAr, s.superTypeCasheEn, s.area, s.era, s.rank, s.undiacritizedArabicWordsCache, s.normalizedEnglishWordsCache,
s.isTranslation, s.isGloss, s.arabicSynonymsCount, s.englishSynonymsCount) FROM Concept s
where s.undiacritizedArabicWordsCache LIKE %:searchTerm% AND data_source_id != 200 AND data_source_id != 31")
List<ConceptSummaryVer04> findByArabicWordsCacheAndNotConcept(#Param("searchTerm") String searchTerm, Sort sort);
the result of the query on the database itself:
link to screenshot
results on the database are returned no matter the letters case:
link to screenshot
I solved this problem.
It was due to the default configuration of the Full-text index on mysql database which is by default set to 2 (ft_min_word_len = 2).
I changed that and rebuilt the index. Then, one-letter words were returned by the query.
12.9.6 Fine-Tuning MySQL Full-Text Search
Use some quotes:
LIKE '%:searchTerm%';
Set searchTerm="%your_word%" and use it on query like this :
... s.undiacritizedArabicWordsCache LIKE :searchTerm ...

ElasticSearch - define custom letter order for sorting

I'm using ElasticSearch 2.4.2 (via HibernateSearch 5.7.1.Final from Java).
I have a problem with string sorting.
The language of my application has diacritics, which have a specific alphabetic
ordering. For example Ł goes directly after L, Ó goes after O, etc.
So you are supposed to sort the strings like this:
Dla
Dła
Doa
Dóa
Dza
Eza
ElasticSearch sorts by typical letters first, and moves all strange
letters to at the end:
Dla
Doa
Dza
Dła
Dóa
Eza
Can I add a custom letter ordering for ElasticSearch?
Maybe there are some plugins for this?
Do I need to write my own plugin? How do I start?
I found a plugin for Polish language for ElasticSearch,
but as I understand it is for analysing, and analysing is not a solution
in my case, because it will ignore diacritics and leave words with L and Ł mixed:
Dla
Dłb
Dlc
This would sometimes be acceptable, but is not acceptable in my specific usecase.
I will be grateful for any remarks on this.
I've never used it, but there is a plugin that could fit your needs: the ICU collation plugin.
You will have to use the icu_collation token filter, which will turns the tokens into collation keys. For that reason you will need to use a separate #Field (e.g. myField_sort) in Hibernate Search.
You can assign a specific analyzer to your field with #Field(name = "myField_sort", analyzer = #Analyzer(definition = "myCollationAnalyzer")), and define this analyzer (type, parameters) with something like that on one of your entities:
#Entity
#Indexed
#AnalyzerDef(
name = "myCollationAnalyzer",
filters = {
#TokenFilterDef(
name = "polish_collation",
factory = ElasticsearchTokenFilterFactory.class,
params = {
#Parameter(name = "type", value = "'icu_collation'"),
#Parameter(name = "language", value = "'pl'")
}
)
}
)
public class MyEntity {
See the documentation for more information: https://docs.jboss.org/hibernate/stable/search/reference/en-US/html_single/#_custom_analyzers
It's admittedly a bit clumsy right now, but analyzer configuration will get a bit cleaner in the next Hibernate Search version with normalizers and analyzer definition providers.
Note: as usual, your field will need to be declared as sortable (#SortableField(forField = "myField_sort")).

Extract attributes of an string

I got to deal here with a problem, caused by a dirty design. I get a list of string and want to parse attributes out of it. Unfortunately, I can't change the source, where these String were created.
Example:
String s = "type=INFO, languageCode=EN-GB, url=http://www.stackoverflow.com, ref=1, info=Text, that may contain all kind of chars., deactivated=false"
Now I want to extract the attributes type, languageCode, url, ref, info and deactivated.
The problem here is the field info, whose text is not limited by quote mark. Also commas may occur in this field, so I can't use the comma at the end of the string, to find out where is ends.
Additional, those strings not always contain all attributes. type, info and deactivated are always present, the rest is optional.
Any suggestions how I can solve this problem?
One possible solution is to search for = characters in the input and then take the single word immediately before it as the field name - it seems that all your field names are single words (no whitespace). If that's the case, you can then take everything after the = until the next field name (accounting for separating ,) as the value.
This assumes that the value cannot contain =.
Edit:
As a possible way to handle embedded =, you can see if the word in front of it is one your known field names - if not, you can possibly treat the = as an embedded character rather than an operator. This, however, assumes that you have a fixed set of known fields (some of which may not always appear). This assumption may be eased if you know that the field names are case-sensitive.
Assuming that order of elements is fixed you could write solution using regex like this one
String s = "type=INFO, languageCode=EN-GB, url=http://www.stackoverflow.com, ref=1, info=Text, that may contain all kind of chars., deactivated=false";
String regex = //type, info and deactivated are always present
"type=(?<type>.*?)"
+ "(?:, languageCode=(?<languageCode>.*?))?"//optional group
+ "(?:, url=(?<url>.*?))?"//optional group
+ "(?:, ref=(?<rel>.*?))?"//optional group
+ ", info=(?<info>.*?)"
+ ", deactivated=(?<deactivated>.*?)";
Pattern p = Pattern.compile(regex);
Matcher m = p.matcher(s);
if(m.matches()){
System.out.println("type -> "+m.group("type"));
System.out.println("languageCode -> "+m.group("languageCode"));
System.out.println("url -> "+m.group("url"));
System.out.println("rel -> "+m.group("rel"));
System.out.println("info -> "+m.group("info"));
System.out.println("deactivated -> "+m.group("deactivated"));
}
Output:
type -> INFO
languageCode -> EN-GB
url -> http://www.stackoverflow.com
rel -> 1
info -> Text, that may contain all kind of chars.
deactivated -> false
EDIT: Version2 regex searching for oneOfPossibleKeys=value where value ends with:
, oneOfPossibleKeys=
or has end of string after it (represented by $).
Code:
String s = "type=INFO, languageCode=EN-GB, url=http://www.stackoverflow.com, ref=1, info=Text, that may contain all kind of chars., deactivated=false";
String[] possibleKeys = {"type","languageCode","url","ref","info","deactivated"};
String keysStrRegex = String.join("|", possibleKeys);
//above will contain type|languageCode|url|ref|info|deactivated
String regex = "(?<key>\\b(?:"+keysStrRegex+")\\b)=(?<value>.*?(?=, (?:"+keysStrRegex+")=|$))";
// (?<key>\b(?:type|languageCode|url|ref|info|deactivated)\b)
// =
// (?<value>.*?(?=, (?:type|languageCode|url|ref|info|deactivated)=|$))System.out.println(regex);
Pattern p = Pattern.compile(regex);
Matcher m = p.matcher(s);
while(m.find()){
System.out.println(m.group("key")+" -> "+m.group("value"));
}
Output:
type -> INFO
languageCode -> EN-GB
url -> http://www.stackoverflow.com
ref -> 1
info -> Text, that may contain all kind of chars.
deactivated -> false
You could use a regular expression, capturing all the "fixed" groups and using whatever remains for info. This should even work if the info part contains , or = characters. Here's some quick example (using Python, but that should not be a problem...).
>>> p = r"(type=[A-Z]+), (languageCode=[-A-Z]+), (url=[^,]+), (ref=\d), (info=.+?), (deactivated=(?:true|false))"
>>> s = "type=INFO, languageCode=EN-GB, url=http://www.stackoverflow.com, ref=1, info=Text, that may contain all kind of chars, even deactivated=true., deactivated=false"
>>> re.search(p, s).groups()
('type=INFO',
'languageCode=EN-GB',
'url=http://www.stackoverflow.com',
'ref=1',
'info=Text, that may contain all kind of chars, even deactivated=true.',
'deactivated=false')
If any of those elements are optional, you can put a ? after those groups, and make the comma optional. If the order can be different, then it's more complicated. In this case, instead of using one RegEx to capture everything at once, use several RegExes to capture the individual attributes and then remove (replace with '') those in the string before matching the next attribute. Finally, match info.
On further consideration, given that those attributes could have any order, it may be more promising to capture just everything spanning from one keyword to the next, regardless of its actual content, very similar to Pshemo's solution:
keys = "type|languageCode|url|ref|info|deactivated"
p = r"({0})=(.+?)(?=\, (?:{0})=|$)".format(keys)
matches = re.findall(p, s)
But this, too, might fail in some very obscure cases, e.g. if the info attribute contains something like ', ref=foo', including the comma. However, there seems to be no way around those ambiguities. If you had a string like info=in this string, ref=1, and in another, ref=2, ref=1, does it contain one ref attribute, or three, or none at all?

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