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Merged
merged 2 commits into from
Sep 7, 2022
Merged

Codespell #16

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cc1d22a
Fix typos found by codespell
DimitriPapadopoulos Sep 7, 2022
efe2623
Fix typo not found by codespell
DimitriPapadopoulos Sep 7, 2022
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12 changes: 6 additions & 6 deletions README.md
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Expand Up @@ -12,11 +12,11 @@ The backend of Amnesia is implemented in Java using the Spring framework. Its co

To successfully build the Amnesia engine follow these steps:
1. Clone the project
2. Download pixelmed.jar from http://www.dclunie.com/pixelmed/software/webstart/pixelmed.jar and install manaully to amnesia's Dependencies.
2. Download pixelmed.jar from http://www.dclunie.com/pixelmed/software/webstart/pixelmed.jar and install manually to amnesia's Dependencies.
3. Go to controller/AppCon.java and set the variable "os" with desired operation system ("windows" or "linux")
4. Build the project
5. Take the .jar from the "scr/target" directory.
6. Downoload https://amnesia.openaire.eu/countryDistributionZip.ser and put it in the same folder where Amnesia's jar file will be executed.
6. Download https://amnesia.openaire.eu/countryDistributionZip.set and put it in the same folder where Amnesia's jar file will be executed.
7. Run via terminal java -Xms1024m -Xmx4096m -Dorg.eclipse.jetty.server.Request.maxFormKeys=1000000 -Dorg.eclipse.jetty.server.Request.maxFormContentSize=1000000 -jar "path_to_jar_file" --server.port=8181
⋅⋅⋅Then you can use the Amnesia’s API as in the following steps.

Expand Down Expand Up @@ -281,7 +281,7 @@ The anonymized data are stored in “anonymized_mixedData.csv” file

**getAnonRules [POST]**
- sol: json string array which contain the anonymize level of each quasi-identifier e.g. [1,2] only for simple table data
- suppresed: boolean for only for simple table data
- suppressed: boolean for only for simple table data
- session: Set session id as header parameter

The current endpoint is not supported for disk-based data (Disk based simple table) because the algorithm is executed using clustering and similarities that do not generate anonymization rules.
Expand Down Expand Up @@ -586,7 +586,7 @@ $ curl -X POST -H "Cookie: JSESSIONID=D6DF59C4A03432B79BC61961F1671EDB" http:

- New clustering disk based algorithm.

- Setted limits on dataset's records and on hierarchy's nodes for on-line version.
- Set limits on dataset's records and on hierarchy's nodes for on-line version.

- Faster loading of date values in dataset.

Expand All @@ -604,7 +604,7 @@ $ curl -X POST -H "Cookie: JSESSIONID=D6DF59C4A03432B79BC61961F1671EDB" http:

- The on-line version of Amnesia is restricted to 3 minutes of processing time per anonymization task.

- Fixed bug with characher encoding on several Linux distributions.
- Fixed bug with character encoding on several Linux distributions.

**version: 1.1.0**

Expand Down Expand Up @@ -656,7 +656,7 @@ $ curl -X POST -H "Cookie: JSESSIONID=D6DF59C4A03432B79BC61961F1671EDB" http:

**version: 1.0.1**

- Better inteface in pie graph.
- Better interface in pie graph.

- Changes in suppressing.

Expand Down
10 changes: 5 additions & 5 deletions src/main/java/algorithms/clusterbased/Clusters.java
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Expand Up @@ -294,7 +294,7 @@ public void executeDeleteBatch(int clusterId){
this.counterDeletions -= counterDelete;
}
}catch(Exception e){
System.err.println("Error : cluster excute batch "+e.getMessage());
System.err.println("Error : cluster execute batch "+e.getMessage());
e.printStackTrace();
try {
this.conn.rollback();
Expand Down Expand Up @@ -343,7 +343,7 @@ public void executeDeleteBatch(){
this.counterDeletions = 0;
}
}catch(Exception e){
System.err.println("Error : cluster excute batch "+e.getMessage());
System.err.println("Error : cluster execute batch "+e.getMessage());
e.printStackTrace();
try {
this.conn.rollback();
Expand Down Expand Up @@ -399,7 +399,7 @@ public void executeBatch(int clusterId){
counterInserts -= counterUpdate;
}
}catch(Exception e){
System.err.println("Error : cluster excute batch "+e.getMessage());
System.err.println("Error : cluster execute batch "+e.getMessage());
System.err.println(errMessage);
e.printStackTrace();
try {
Expand Down Expand Up @@ -503,7 +503,7 @@ public void executeBatch(){
counterInserts = 0;
}
}catch(Exception e){
System.err.println("Error : cluster excute batch "+e.getMessage());
System.err.println("Error : cluster execute batch "+e.getMessage());
System.err.println(errMessage);
e.printStackTrace();
try {
Expand Down Expand Up @@ -692,7 +692,7 @@ public Map<Integer,Double[][]> getClusterDatasetRecs(List<Integer> clusters, boo

}catch(Exception e){
e.printStackTrace();
System.err.println("Error getClusterDatasetRecs : "+e.getMessage()+" clusterId "+cluster+" lenght "+this.currentSizeCl.get(cluster));
System.err.println("Error getClusterDatasetRecs : "+e.getMessage()+" clusterId "+cluster+" length "+this.currentSizeCl.get(cluster));
}finally{
if(stm!=null){
try {
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/algorithms/kmanonymity/Apriori.java
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Expand Up @@ -107,7 +107,7 @@ public void populateTree(int size){
for (Map.Entry<Integer,String> entry : dict.idToString.entrySet()) {
System.out.println(entry.getKey()+" : "+entry.getValue());
}*/
System.out.println("trie construct start for m="+size);
System.out.println("try construct start for m="+size);

while((transaction = getNextTransaction()) != null){
// System.out.println("transaction = ");
Expand Down Expand Up @@ -157,7 +157,7 @@ public void populateTree(int size){
//System.out.println("i am hereeeeeee");
}

System.out.println("trie constrcted for m="+size);
System.out.println("tried construct for m="+size);

//System.out.println("Trieeeeeeeeeeeee " );
//trie.printTree(trie.getRoot());
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/algorithms/mixedkmanonymity/MixedApriori.java
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Expand Up @@ -671,7 +671,7 @@ else if(this.anonymize_property.equals("relational") || this.anonymize_property.
while((transaction =(this.anonymize_property.equals("relational") ? getNextTransactionRelational() : getNextTransactionMixed())) != null){
// System.out.println("TRansaction "+Arrays.toString(transaction.toArray()));
Set<Pair<Integer,Object>> expandedTransaction = expandTransaction(transaction);
// System.out.println("Expaned TRansaction "+Arrays.toString(expandedTransaction.toArray()));
// System.out.println("Expanded TRansaction "+Arrays.toString(expandedTransaction.toArray()));
combinations = MixedCombinations.getCombinations(expandedTransaction, size, hierarchies);

if (combinations != null && !combinations.isEmpty()){
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/algorithms/mixedkmanonymity/MixedSolutionCombinations.java
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Expand Up @@ -197,7 +197,7 @@ else if(o1.getValue() instanceof Double && o2.getValue() instanceof RangeDate){
}
}
}catch(Exception e){
System.out.println("PRoble with parsing "+e.getMessage());
System.out.println("PRoblem with parsing "+e.getMessage());
return 0;
}
}
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/anonymizeddataset/AnonymizedDataset.java
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Expand Up @@ -2249,7 +2249,7 @@ else if(colNamesType.get(column).contains("double")){
*/
private Object anonymizeValue(Object value, Hierarchy h, int level) throws ParseException{
Object anonymizedValue = value;
// System.out.println("level "+level+" heirarchy "+h.getName()+"value "+value);
// System.out.println("level "+level+" hierarchy "+h.getName()+"value "+value);
for(int i=0; i<level; i++){
h.setLevel(i);
if(h.getHierarchyType().equals("range")){
Expand Down
26 changes: 13 additions & 13 deletions src/main/java/controller/AppCon.java
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Expand Up @@ -681,7 +681,7 @@ else if(data instanceof DICOMData || data instanceof TXTData || data instanceof
DataInputStream in = null;
BufferedReader br = null;
String strLine = null;
String delimeter = null;
String delimiter = null;
String result = null;
Map<String,Hierarchy> hierarchies = null;
DictionaryString dict = null;
Expand Down Expand Up @@ -726,10 +726,10 @@ else if(data instanceof DICOMData || data instanceof TXTData || data instanceof
else if (datatype.equals("tabular")){

if ( del == null ){
delimeter = ",";
delimiter = ",";
}
else{
delimeter = del;
delimiter = del;
}

System.out.println("del "+del);
Expand All @@ -740,16 +740,16 @@ else if (datatype.equals("tabular")){

if(!fullPath.toLowerCase().endsWith(".xml")){
while ((strLine = br.readLine()) != null){
if ( strLine.contains(delimeter)){
data = new TXTData(fullPath,delimeter,dict);
if ( strLine.contains(delimiter)){
data = new TXTData(fullPath,delimiter,dict);
}
else{
if ((strLine = br.readLine()) != null){
if ( strLine.contains(delimeter)){
//data = new SETData(fullPath,delimeter);
if ( strLine.contains(delimiter)){
//data = new SETData(fullPath,delimiter);
}
else{
data = new TXTData(fullPath,delimeter,dict);
data = new TXTData(fullPath,delimiter,dict);
}
}
}
Expand Down Expand Up @@ -2187,7 +2187,7 @@ else if(data.getClass().toString().contains("Disk")){


byte[] outputByte = new byte[50000];
//copy binary contect to output stream
//copy binary context to output stream
while(fileIn.read(outputByte, 0, 50000) != -1)
{
out.write(outputByte, 0, 50000);
Expand Down Expand Up @@ -2884,7 +2884,7 @@ else if(tempNew.length == 2)
}
}
else{
//// TODO add check intdouble existance
//// TODO add check intdouble existence
if(newNode.equals("(null)")){
if(h.getParent(Double.NaN)!=null || h.getParent(2147483646.0)!=null){
return "The node exists in hierarchy";
Expand Down Expand Up @@ -3027,7 +3027,7 @@ else if(h.getDictionaryData().isEmpty()){
}
}
else{ // distinct
//// TODO edit check intdouble existance
//// TODO edit check intdouble existence
h.edit(Double.parseDouble(oldNode), Double.parseDouble(newNode));
}
}
Expand Down Expand Up @@ -4957,7 +4957,7 @@ public void getSuppressPercentage (@RequestParam("sol") String sol, HttpSession
jsonAnswer.put("Message","To produce a k="+k+" anonymity solution, it must be suppressed by "+suppress+"%");
}
else{
jsonAnswer.put("Message","The solution: ["+sol+"] statisfies k="+k+" anonymity");
jsonAnswer.put("Message","The solution: ["+sol+"] satisfies k="+k+" anonymity");
}
response.getOutputStream().print(jsonAnswer.toString());
}catch(Exception e){
Expand Down Expand Up @@ -5224,7 +5224,7 @@ else if(sol == null){
response.setStatus(HttpServletResponse.SC_INTERNAL_SERVER_ERROR);
JSONObject jsonAnswer = new JSONObject();
jsonAnswer.put("Status","Fail");
jsonAnswer.put("Message","The \"sol\" field needs only fot simple table data!");
jsonAnswer.put("Message","The \"sol\" field needs only for simple table data!");
response.getOutputStream().print(jsonAnswer.toString());
}
else if(sol!=null){
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/data/CheckVariables.java
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Expand Up @@ -86,7 +86,7 @@ public boolean isDate (String s){
Date date = sdf.parse(s);
if (s.equals(sdf.format(date))){
this.lastFormat = parse;
System.out.println("Printing the value of requst parse " + parse);
System.out.println("Printing the value of request parse " + parse);
return true;
}
System.out.println("Printing the value of " + parse);
Expand Down
6 changes: 3 additions & 3 deletions src/main/java/data/DICOMData.java
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Expand Up @@ -224,7 +224,7 @@ public String save(boolean[] checkColumns) throws LimitException, DateParseExcep

try{
if(dictionary.isEmpty() && dictHier.isEmpty()){
System.out.println("Both empy load data");
System.out.println("Both empty load data");
stringCount = 1;
}
else if(!dictionary.isEmpty() && !dictHier.isEmpty()){
Expand Down Expand Up @@ -977,7 +977,7 @@ public SimpleDateFormat getDateFormat(int column) {
public void setMask(int column, int[] positions, char character, String option) {
int stringCount;
if(dictionary.isEmpty() && dictHier.isEmpty()){
System.out.println("Both empy load data");
System.out.println("Both empty load data");
stringCount = 1;
}
else if(!dictionary.isEmpty() && !dictHier.isEmpty()){
Expand Down Expand Up @@ -1079,7 +1079,7 @@ public Map<String, Double> getInformationLoss() {
public void setRegex(int column, char character, String regex) {
int stringCount;
if(dictionary.isEmpty() && dictHier.isEmpty()){
System.out.println("Both empy load data");
System.out.println("Both empty load data");
stringCount = 1;
}
else if(!dictionary.isEmpty() && !dictHier.isEmpty()){
Expand Down
20 changes: 10 additions & 10 deletions src/main/java/data/DiskData.java
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Expand Up @@ -78,7 +78,7 @@ public class DiskData implements Data,Serializable{
private String inputFile = null;
@JsonView(View.GetColumnNames.class)
private String dataType = "disk";
private String delimeter = null;
private String delimiter = null;
private int sizeOfRows = 0;
private String urlDatabase = null;
private Connection conn = null;
Expand Down Expand Up @@ -134,7 +134,7 @@ public class DiskData implements Data,Serializable{
public DiskData(String inputfile,String del,DictionaryString dict){
this.recordsTotal = 0;
this.inputFile = inputfile;
this.delimeter = del;
this.delimiter = del;
colNamesType = new TreeMap<Integer,String>();
colNamesPosition = new HashMap<Integer,String>();
chVar = new CheckVariables();
Expand Down Expand Up @@ -530,7 +530,7 @@ else if(dataType.equals("date") || dataType.equals("string")){
if(strLine.trim().isEmpty()){
continue;
}
temp = strLine.split(delimeter,-1);
temp = strLine.split(delimiter,-1);
counter1 = 0;
for (int i = 0; i < temp.length ; i ++ ){
if (checkColumns[i] == true){
Expand Down Expand Up @@ -1112,7 +1112,7 @@ public void SaveClmnsAndTypeOfVar(String[] columnTypes, boolean[] checkColumns)

//save column names
if (FLAG == true){
colNames = strLine.split(delimeter,-1);
colNames = strLine.split(delimiter,-1);
for ( int i = 0 ; i < colNames.length ; i ++){
if ( checkColumns[i] == true){
colNamesType.put(counter,null);
Expand Down Expand Up @@ -1187,7 +1187,7 @@ public String findColumnTypes() {
while ((strLine = br.readLine()) != null) {
//escape first row
if (FLAG == true){
temp = strLine.split(delimeter,-1);
temp = strLine.split(delimiter,-1);
columnNames = new String[temp.length];
smallDataSet = new String[6][temp.length];
this.formatsDate = new String[temp.length];
Expand All @@ -1209,7 +1209,7 @@ else if(strLine.trim().isEmpty()){
}
//save column types
else{
temp = strLine.split(delimeter,-1);
temp = strLine.split(delimiter,-1);

if( temp.length != columnNames.length){
System.out.println("columnNames = " + columnNames.length +"\t temp = " + temp.length );
Expand Down Expand Up @@ -1454,7 +1454,7 @@ public Double[][] getSpecificDataset(int start,int max,boolean withIdenticals){
System.out.println("Records "+counterRow);

}catch (OutOfMemoryError e) {
System.err.println("Error outofMemory free"+Runtime.getRuntime().freeMemory()+" Curent "+Runtime.getRuntime().totalMemory()+" max "+Runtime.getRuntime().maxMemory());
System.err.println("Error outofMemory free"+Runtime.getRuntime().freeMemory()+" Current "+Runtime.getRuntime().totalMemory()+" max "+Runtime.getRuntime().maxMemory());
e.printStackTrace();
}

Expand Down Expand Up @@ -2607,7 +2607,7 @@ public boolean tableExists(String name){
return result;
}catch(SQLException ex){
ex.printStackTrace();
System.err.println("Error: "+ex.getMessage()+" check table existance disk");
System.err.println("Error: "+ex.getMessage()+" check table existence disk");
Logger.getLogger(Clusters.class.getName()).log(Level.SEVERE, null, ex);

if(rs!=null){
Expand Down Expand Up @@ -2678,7 +2678,7 @@ public void setMask(int column, int[] positions, char character, String option)

int stringCount;
if(dictionary.isEmpty() && dictHier.isEmpty()){
System.out.println("Both empy load data");
System.out.println("Both empty load data");
stringCount = 1;
}
else if(!dictionary.isEmpty() && !dictHier.isEmpty()){
Expand Down Expand Up @@ -2860,7 +2860,7 @@ public void setRegex(int column, char character, String regex) {

int stringCount;
if(dictionary.isEmpty() && dictHier.isEmpty()){
System.out.println("Both empy load data");
System.out.println("Both empty load data");
stringCount = 1;
}
else if(!dictionary.isEmpty() && !dictHier.isEmpty()){
Expand Down
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