diff --git a/pom.xml b/pom.xml index fe749fc73..e56318255 100755 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ org.jbei ice war - 5.9.2 + 5.9.3 ice Inventory of Composable Elements (ICE) for Synthetic Biology @@ -39,7 +39,7 @@ org.postgresql postgresql - 42.2.16 + 42.2.18 com.h2database @@ -66,7 +66,7 @@ org.hibernate hibernate-search-orm - 5.11.8.Final + 5.11.9.Final javax.validation @@ -76,7 +76,7 @@ org.hibernate.validator hibernate-validator - 6.1.3.Final + 6.2.0.Final javax.el @@ -86,7 +86,7 @@ org.hibernate hibernate-c3p0 - 5.4.22.Final + 5.5.3.Final commons-io @@ -101,7 +101,7 @@ com.opencsv opencsv - 5.2 + 5.4 ch.qos.logback diff --git a/src/main/java/DevelopmentServer.java b/src/main/java/DevelopmentServer.java index ab0807796..069a44f62 100644 --- a/src/main/java/DevelopmentServer.java +++ b/src/main/java/DevelopmentServer.java @@ -46,6 +46,7 @@ public static void main(String[] args) throws Exception { PredicatesHandler handler = Handlers.predicates(PredicatedHandlersParser.parse( "path-prefix('search') or " + "path-prefix('folders') or " + + "path-prefix('upload') or " + "path-prefix('download') or " + "path-prefix('entry') or path-prefix('admin') and regex('/.+') -> rewrite('/')", ClassLoader.getSystemClassLoader()), servletHandler); diff --git a/src/main/java/org/jbei/ice/lib/bulkupload/BulkCSVUpload.java b/src/main/java/org/jbei/ice/lib/bulkupload/BulkCSVUpload.java index e44d39f55..8f50b4d05 100644 --- a/src/main/java/org/jbei/ice/lib/bulkupload/BulkCSVUpload.java +++ b/src/main/java/org/jbei/ice/lib/bulkupload/BulkCSVUpload.java @@ -1,9 +1,6 @@ package org.jbei.ice.lib.bulkupload; -import com.opencsv.CSVParser; -import com.opencsv.CSVParserBuilder; -import org.apache.commons.io.IOUtils; -import org.apache.commons.io.LineIterator; +import com.opencsv.CSVReader; import org.apache.commons.lang3.StringUtils; import org.jbei.ice.lib.common.logging.Logger; import org.jbei.ice.lib.dto.StorageLocation; @@ -20,7 +17,7 @@ import java.io.IOException; import java.io.InputStream; -import java.nio.charset.StandardCharsets; +import java.io.InputStreamReader; import java.util.*; /** @@ -131,7 +128,7 @@ private HashMap processColumnHeaders(String[] headerArray) HashMap headers = new HashMap<>(); for (int i = 0; i < headerArray.length; i += 1) { - String fieldStr = headerArray[i].trim(); + String fieldStr = headerArray[i].replaceAll("[^\\x20-\\x7e]", " ").trim(); // account for asterisk that indicates a header is required fieldStr = fieldStr.replace(FileBulkUpload.ASTERISK_SYMBOL, ""); @@ -176,89 +173,63 @@ private HashMap processColumnHeaders(String[] headerArray) List getBulkUploadDataFromFile(InputStream inputStream) throws IOException { List partDataList = new LinkedList<>(); - // parse CSV file - try (LineIterator it = IOUtils.lineIterator(inputStream, StandardCharsets.UTF_8)) { - HashMap headers; - CSVParser parser; - - // - // process headers - // - if (it.hasNext()) { - String headerString = it.nextLine(); - // check the separator char (header will use the same separator) - // to indicate the type of parser to use (tab or comma separated) - if (headerString.contains("\t") && !headerString.contains(",")) { - parser = new CSVParserBuilder().withSeparator('\t').build(); - } else { - parser = new CSVParser(); - } + HashMap headers = null; + CSVReader reader = new CSVReader(new InputStreamReader(inputStream)); + int row = -1; + for (String[] nextLine : reader) { + row += 1; - // get column headers - String[] fieldStrArray = parser.parseLine(headerString); - headers = processColumnHeaders(fieldStrArray); - } else { - throw new IllegalStateException("No headers found in csv file"); + if (row == 0) { + // parse headers + headers = processColumnHeaders(nextLine); + continue; } - // - // process data - // - int index = 0; - while (it.hasNext()) { - String line = it.nextLine().trim(); + // parse data + PartData partData = new PartData(addType); + PartSample partSample = null; - // skip any empty lines (holes) in the csv file - if (StringUtils.isBlank(line) || line.replaceAll(",", "").trim().isEmpty()) - continue; - - // parser != null; process line contents with available headers - String[] valuesArray = parser.parseLine(line); - PartData partData = new PartData(addType); - PartSample partSample = null; + if (subType != null) { + partData.getLinkedParts().add(new PartData(subType)); + } - if (subType != null) { - partData.getLinkedParts().add(new PartData(subType)); - } + // for each column + for (int i = 0; i < nextLine.length; i += 1) { + HeaderValue headerForColumn = headers.get(i); + String value = nextLine[i].replaceAll("[^\\x20-\\x7e]", " "); - // for each column - for (int i = 0; i < valuesArray.length; i += 1) { - HeaderValue headerForColumn = headers.get(i); - String value = valuesArray[i]; - - // process sample information - if (headerForColumn.isSampleField()) { - if (partSample == null) - partSample = new PartSample(); - - setPartSampleData(((SampleHeaderValue) headerForColumn).getSampleField(), partSample, value); - } else if (headerForColumn.isCustomField()) { - // process custom field - setCustomField(value, partData, (EntryHeaderValue) headerForColumn); - } else { - // process existing field - setExistingField(value, partData, (EntryHeaderValue) headerForColumn); - } - } + // process sample information + if (headerForColumn.isSampleField()) { + if (partSample == null) + partSample = new PartSample(); - // validate - List fields = EntryUtil.validates(partData); - if (!fields.isEmpty()) { - invalidFields.clear(); - invalidFields.addAll(fields); - return null; + setPartSampleData(((SampleHeaderValue) headerForColumn).getSampleField(), partSample, value); + } else if (headerForColumn.isCustomField()) { + // process custom field + setCustomField(value, partData, (EntryHeaderValue) headerForColumn); + } else { + // process existing field + setExistingField(value, partData, (EntryHeaderValue) headerForColumn); } + } - partData.setIndex(index); - PartWithSample partWithSample = new PartWithSample(partSample, partData); - partDataList.add(partWithSample); - index += 1; + // validate + List fields = EntryUtil.validates(partData); + if (!fields.isEmpty()) { + invalidFields.clear(); + invalidFields.addAll(fields); + return null; } + + partData.setIndex(row); + PartWithSample partWithSample = new PartWithSample(partSample, partData); + partDataList.add(partWithSample); } + return partDataList; } - private boolean setCustomField(String value, PartData partData, EntryHeaderValue headerValue) throws IOException { + private void setCustomField(String value, PartData partData, EntryHeaderValue headerValue) throws IOException { // todo : e.g. {entryField: host} can be existing field or custom field CustomEntryFieldDAO fieldDAO = DAOFactory.getCustomEntryFieldDAO(); EntryType type; @@ -270,9 +241,9 @@ private boolean setCustomField(String value, PartData partData, EntryHeaderValue } Optional optional = fieldDAO.getLabelForType(type, headerValue.getLabel()); - if (!optional.isPresent()) { + if (optional.isEmpty()) { Logger.error("Could not retrieve custom field for \"" + headerValue.getLabel() + "\""); - return false; + return; } CustomEntryFieldModel customEntryFieldModel = optional.get(); @@ -280,10 +251,10 @@ private boolean setCustomField(String value, PartData partData, EntryHeaderValue // validate if (customEntryFieldModel.getRequired() && StringUtils.isEmpty(value)) { // todo : return error - return false; + return; } setExistingField(value, partData, headerValue); - return true; + return; } CustomEntryField customEntryField = new CustomEntryField(); @@ -291,7 +262,6 @@ private boolean setCustomField(String value, PartData partData, EntryHeaderValue customEntryField.setValue(value); // todo : check if the value is from a pre-selected list of options partData.getCustomEntryFields().add(customEntryField); - return true; } private void setExistingField(String value, PartData partData, EntryHeaderValue headerValue) throws IOException { @@ -340,33 +310,26 @@ private void setExistingField(String value, PartData partData, EntryHeaderValue private void setPartSampleData(SampleField sampleField, PartSample partSample, String data) { switch (sampleField) { - case LABEL: - partSample.setLabel(data); - break; - - case SHELF: + case LABEL -> partSample.setLabel(data); + case SHELF -> { StorageLocation storageLocation = new StorageLocation(); storageLocation.setType(SampleType.SHELF); storageLocation.setDisplay(data); partSample.setLocation(storageLocation); - break; - - case BOX: + } + case BOX -> { StorageLocation childLocation = new StorageLocation(); childLocation.setDisplay(data); childLocation.setType(SampleType.BOX_INDEXED); partSample.getLocation().setChild(childLocation); - break; - - case WELL: + } + case WELL -> { StorageLocation grandChildLocation = new StorageLocation(); grandChildLocation.setType(SampleType.WELL); grandChildLocation.setDisplay(data); partSample.getLocation().getChild().setChild(grandChildLocation); - break; - - default: - throw new IllegalArgumentException("No handler for sample field " + sampleField); + } + default -> throw new IllegalArgumentException("No handler for sample field " + sampleField); } } } diff --git a/src/main/java/org/jbei/ice/lib/config/SiteSettings.java b/src/main/java/org/jbei/ice/lib/config/SiteSettings.java index ec163f99f..b390239ef 100644 --- a/src/main/java/org/jbei/ice/lib/config/SiteSettings.java +++ b/src/main/java/org/jbei/ice/lib/config/SiteSettings.java @@ -9,7 +9,7 @@ */ public class SiteSettings implements IDataTransferModel { - private String version = "5.9.2"; + private String version = "5.9.3"; private String assetName; private boolean hasLogo; private boolean hasLoginMessage; diff --git a/src/main/webapp/scripts/lib/open-vector-editor/main.css b/src/main/webapp/scripts/lib/open-vector-editor/main.css index 86b865aa1..f8561d4e7 100644 --- a/src/main/webapp/scripts/lib/open-vector-editor/main.css +++ b/src/main/webapp/scripts/lib/open-vector-editor/main.css @@ -1,6 +1,6 @@ @charset "UTF-8"; /*! - * open-vector-editor v16.1.31 + * open-vector-editor v16.1.34 * MIT Licensed - */html{box-sizing:border-box}*,:after,:before{box-sizing:inherit}body{font-size:14px;font-weight:400;letter-spacing:0;line-height:1.28581;text-transform:none;color:#182026;font-family:-apple-system,BlinkMacSystemFont,Segoe UI,Roboto,Oxygen,Ubuntu,Cantarell,Open Sans,Helvetica Neue,Icons16,sans-serif}p{margin-bottom:10px;margin-top:0}small{font-size:12px}strong{font-weight:600}::selection{background:rgba(125,188,255,.6)}.bp3-heading{color:#182026;font-weight:600;margin:0 0 10px;padding:0}.bp3-dark .bp3-heading{color:#f5f8fa}.bp3-running-text h1,h1.bp3-heading{font-size:36px;line-height:40px}.bp3-running-text h2,h2.bp3-heading{font-size:28px;line-height:32px}.bp3-running-text h3,h3.bp3-heading{font-size:22px;line-height:25px}.bp3-running-text 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p=this.diff_text1(o.diffs).substring(0,this.Patch_Margin);""!==p&&(c.length1+=p.length,c.length2+=p.length,0!==c.diffs.length&&0===c.diffs[c.diffs.length-1][0]?c.diffs[c.diffs.length-1][1]+=p:c.diffs.push([0,p])),l||e.splice(++r,0,c)}}},t.prototype.patch_toText=function(e){for(var t=[],n=0;n'+t+"")}},{key:"formatValue",value:function(e,t){e.out("
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")}},{key:"formatTextDiffString",value:function(e,t){var n=this.parseTextDiff(t);e.out('
    ');for(var r=0,o=n.length;r
    '+a.location.line+''+a.location.chr+'
    ');for(var i=a.pieces,s=0,c=i.length;s'+re(decodeURI(l.text))+"")}e.out("
    ")}e.out("
")}},{key:"rootBegin",value:function(e,t,n){var r="jsondiffpatch-"+t+(n?" jsondiffpatch-child-node-type-"+n:"");e.out('
')}},{key:"rootEnd",value:function(e){e.out("
"+(e.hasArrows?'