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timyardley wants to merge 9 commits into from
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Some code cleanup #2

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dc13227
random things
Dec 18, 2019
00d1fa7
random cleanup
Dec 19, 2019
e99d472
whitespace cleanup
Dec 19, 2019
a6b3cca
update for consistency and style
Dec 19, 2019
1eb4cb0
fix spelling errors on success and occurred
Dec 19, 2019
92fdd3d
decouple bagit from clowder.ncsa.illinois.edu to just clowder as an app
Dec 19, 2019
615a25e
remove some hardcoded clowder.ncsa links, and add fixme for others
Dec 19, 2019
01447f5
revert Global.scala change... not sure where that came from
Dec 19, 2019
52b68d2
cleanup spurious beta character
timyardley Jan 9, 2020
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58 changes: 29 additions & 29 deletions app/Iterators/BagItIterator.scala
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Expand Up @@ -19,72 +19,72 @@ class BagItIterator(pathToFolder : String, collection : Option[models.Collection
var bytes : Long = 0L

private def addBagItTextToZip(pathToFolder : String, totalbytes: Long, totalFiles: Long, zip: ZipOutputStream, collection: models.Collection, user: Option[models.User]) = {
zip.putNextEntry(new ZipEntry(pathToFolder+"/bagit.txt"))
val softwareLine = "Bag-Software-Agent: clowder.ncsa.illinois.edu\n"
val baggingDate = "Bagging-Date: "+(new SimpleDateFormat("yyyy-MM-dd hh:mm:ss")).format(Calendar.getInstance.getTime)+"\n"
zip.putNextEntry(new ZipEntry(pathToFolder + "/bagit.txt"))
val softwareLine = "Bag-Software-Agent: clowder\n"
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@lmarini lmarini Jan 24, 2020

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I couldn't find any specific information about what should go in this field. Did you find something regarding this? I saw something along the lines emails: clowder <https://clowderframework.org/>.

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@timyardley timyardley Jan 30, 2020

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the agent definition is typically the name of the software, along with versioning. For example, this is how a similar field is used in the HTTP standard:

https://en.wikipedia.org/wiki/User_agent

My reasoning here would be that at a minimum it should be clowder rather than a specific domain as a clowder instance can (and will) be installed in other locations than at NCSA

val baggingDate = "Bagging-Date: " + (new SimpleDateFormat("yyyy-MM-dd hh:mm:ss")).format(Calendar.getInstance.getTime) + "\n"
val baggingSize = "Bag-Size: " + totalbytes + "\n"
val payLoadOxum = "Payload-Oxum: "+ totalbytes + "." + totalFiles +"\n"
val senderIdentifier="Internal-Sender-Identifier: "+collection.id+"\n"
val senderDescription = "Internal-Sender-Description: "+collection.description+"\n"
val payLoadOxum = "Payload-Oxum: " + totalbytes + "." + totalFiles + "\n"
val senderIdentifier = "Internal-Sender-Identifier: " + collection.id + "\n"
val senderDescription = "Internal-Sender-Description: " + collection.description + "\n"
var s:String = ""
if (user.isDefined) {
val contactName = "Contact-Name: " + user.get.fullName + "\n"
val contactEmail = "Contact-Email: " + user.get.email.getOrElse("") + "\n"
s = softwareLine+baggingDate+baggingSize+payLoadOxum+contactName+contactEmail+senderIdentifier+senderDescription
s = softwareLine + baggingDate + baggingSize + payLoadOxum + contactName + contactEmail + senderIdentifier + senderDescription
} else {
s = softwareLine+baggingDate+baggingSize+payLoadOxum+senderIdentifier+senderDescription
s = softwareLine + baggingDate + baggingSize + payLoadOxum + senderIdentifier + senderDescription
}

Some(new ByteArrayInputStream(s.getBytes("UTF-8")))
}

// If no collection provided, assume this is for Selected download
private def addBagItTextToZip(pathToFolder : String, totalbytes: Long, totalFiles: Long, zip: ZipOutputStream, user: Option[models.User]) = {
zip.putNextEntry(new ZipEntry(pathToFolder+"/bagit.txt"))
val softwareLine = "Bag-Software-Agent: clowder.ncsa.illinois.edu\n"
val baggingDate = "Bagging-Date: "+(new SimpleDateFormat("yyyy-MM-dd hh:mm:ss")).format(Calendar.getInstance.getTime)+"\n"
zip.putNextEntry(new ZipEntry(pathToFolder + "/bagit.txt"))
val softwareLine = "Bag-Software-Agent: clowder\n"
val baggingDate = "Bagging-Date: " + (new SimpleDateFormat("yyyy-MM-dd hh:mm:ss")).format(Calendar.getInstance.getTime) + "\n"
val baggingSize = "Bag-Size: " + totalbytes + "\n"
val payLoadOxum = "Payload-Oxum: "+ totalbytes + "." + totalFiles +"\n"
val payLoadOxum = "Payload-Oxum: " + totalbytes + "." + totalFiles + "\n"

val s:String = if (user.isDefined) {
val senderIdentifier="Internal-Sender-Identifier: user "+user.get.id+"\n"
val senderIdentifier = "Internal-Sender-Identifier: user " + user.get.id + "\n"
val senderDescription = "Internal-Sender-Description: User Dataset Selections\n"
val contactName = "Contact-Name: " + user.get.fullName + "\n"
val contactEmail = "Contact-Email: " + user.get.email.getOrElse("") + "\n"
softwareLine+baggingDate+baggingSize+payLoadOxum+contactName+contactEmail+senderIdentifier+senderDescription
softwareLine + baggingDate + baggingSize + payLoadOxum + contactName + contactEmail + senderIdentifier + senderDescription
} else {
val senderIdentifier="Internal-Sender-Identifier: unknown user\n"
val senderIdentifier = "Internal-Sender-Identifier: unknown user\n"
val senderDescription = "Internal-Sender-Description: User Dataset Selections\n"
softwareLine+baggingDate+baggingSize+payLoadOxum+senderIdentifier+senderDescription
softwareLine + baggingDate + baggingSize + payLoadOxum + senderIdentifier + senderDescription
}

Some(new ByteArrayInputStream(s.getBytes("UTF-8")))
}

private def addBagInfoToZip(pathToFolder : String ,zip : ZipOutputStream) : Option[InputStream] = {
zip.putNextEntry(new ZipEntry(pathToFolder+"/bag-info.txt"))
val s : String = "BagIt-Version: 0.97\n"+"Tag-File-Character-Encoding: UTF-8\n"
zip.putNextEntry(new ZipEntry(pathToFolder + "/bag-info.txt"))
val s : String = "BagIt-Version: 0.97\n" + "Tag-File-Character-Encoding: UTF-8\n"
Some(new ByteArrayInputStream(s.getBytes("UTF-8")))
}

private def addManifestMD5ToZip(pathToFolder : String, md5map : Map[String,MessageDigest] ,zip : ZipOutputStream) : Option[InputStream] = {
zip.putNextEntry(new ZipEntry(pathToFolder+"/manifest-md5.txt"))
zip.putNextEntry(new ZipEntry(pathToFolder + "/manifest-md5.txt"))
var s : String = ""
md5map.foreach{
case (filePath,md) => {
val current = Hex.encodeHexString(md.digest())+" "+filePath+"\n"
val current = Hex.encodeHexString(md.digest()) + " " + filePath + "\n"
s = s + current
}
}
Some(new ByteArrayInputStream(s.getBytes("UTF-8")))
}

private def addTagManifestMD5ToZip(pathToFolder : String, md5map : Map[String,MessageDigest],zip : ZipOutputStream) : Option[InputStream] = {
zip.putNextEntry(new ZipEntry(pathToFolder+"/tagmanifest-md5.txt"))
zip.putNextEntry(new ZipEntry(pathToFolder + "/tagmanifest-md5.txt"))
var s : String = ""
md5map.foreach{
case (filePath,md) => {
val current = Hex.encodeHexString(md.digest())+" "+filePath+"\n"
val current = Hex.encodeHexString(md.digest()) + " " + filePath + "\n"
s = s + current
}
}
Expand All @@ -109,38 +109,38 @@ class BagItIterator(pathToFolder : String, collection : Option[models.Collection
case 1 => {
is = collection match {
case Some(coll) => {
addBagItTextToZip(pathToFolder,bytes,0,zip,coll,user)
addBagItTextToZip(pathToFolder, bytes, 0, zip, coll, user)
}
case None => {
addBagItTextToZip(pathToFolder,bytes,0,zip,user)
addBagItTextToZip(pathToFolder, bytes, 0, zip, user)
}
}

val md5 = MessageDigest.getInstance("MD5")
md5Bag.put("bagit.txt",md5)
md5Bag.put("bagit.txt", md5)
file_type = 2
Some(new DigestInputStream(is.get, md5))

}
case 0 => {
is = addBagInfoToZip(pathToFolder,zip)
val md5 = MessageDigest.getInstance("MD5")
md5Bag.put("bag-info.txt",md5)
md5Bag.put("bag-info.txt", md5)
file_type = 1
Some(new DigestInputStream(is.get, md5))

}
case 2 => {
is = addManifestMD5ToZip(pathToFolder,md5Files.toMap[String,MessageDigest],zip)
val md5 = MessageDigest.getInstance("MD5")
md5Bag.put("manifest-md5.txt",md5)
md5Bag.put("manifest-md5.txt", md5)
file_type = 3
Some(new DigestInputStream(is.get, md5))
}
case 3 => {
is = addTagManifestMD5ToZip(pathToFolder,md5Bag.toMap[String,MessageDigest],zip)
val md5 = MessageDigest.getInstance("MD5")
md5Bag.put("tagmanifest-md5.txt",md5)
md5Bag.put("tagmanifest-md5.txt", md5)
file_type = 4
Some(new DigestInputStream(is.get, md5))
}
Expand All @@ -149,4 +149,4 @@ class BagItIterator(pathToFolder : String, collection : Option[models.Collection
}
}
}
}
}
40 changes: 20 additions & 20 deletions app/Iterators/CollectionIterator.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -56,15 +56,15 @@ class CollectionIterator(pathToFolder : String, parent_collection : models.Colle
}

private def addCollectionInfoToZip(folderName: String, collection: models.Collection, zip: ZipOutputStream): Option[InputStream] = {
val path = folderName + "/"+collection.name+"_info.json"
zip.putNextEntry(new ZipEntry(folderName + "/"+collection.name+"_info.json"))
val path = folderName + "/" + collection.name + "_info.json"
zip.putNextEntry(new ZipEntry(folderName + "/" + collection.name + "_info.json"))
val infoListMap = Json.prettyPrint(jsonCollection(collection))
Some(new ByteArrayInputStream(infoListMap.getBytes("UTF-8")))
}

private def addCollectionMetadataToZip(folderName : String , collection : models.Collection, zip : ZipOutputStream) : Option[InputStream] = {
val path = folderName+"/"+collection.name+"_metadata.json"
zip.putNextEntry(new ZipEntry(folderName+"/"+collection.name+"_metadata.json"))
val path = folderName + "/" + collection.name + "_metadata.json"
zip.putNextEntry(new ZipEntry(folderName + "/" + collection.name + "_metadata.json"))
val collectionMetadata = getCollectionInfoAsJson(collection)
val metadataMap = Json.prettyPrint(collectionMetadata)
Some(new ByteArrayInputStream(metadataMap.getBytes("UTF-8")))
Expand All @@ -74,14 +74,14 @@ class CollectionIterator(pathToFolder : String, parent_collection : models.Colle
if (file_type < 2){
true
}
else if (file_type ==2){
else if (file_type == 2){
if (datasetIterator.hasNext()){
true
} else if (numChildCollections > 0){

currentCollectionIterator = Some(new CollectionIterator(pathToFolder+"/"+child_collections(childCollectionCount).name, child_collections(childCollectionCount),zip,md5Files,user,collections,datasets,files,
folders,metadataService,spaces))
file_type +=1
currentCollectionIterator = Some(new CollectionIterator(pathToFolder + "/" + child_collections(childCollectionCount).name, child_collections(childCollectionCount), zip, md5Files, user, collections, datasets, files,
folders, metadataService, spaces))
file_type += 1
true
} else {
false
Expand All @@ -91,14 +91,14 @@ class CollectionIterator(pathToFolder : String, parent_collection : models.Colle
case Some(collectionIterator) => {
if (collectionIterator.hasNext()){
true
} else if (childCollectionCount < numChildCollections -2){
childCollectionCount+=1
currentCollectionIterator = Some(new CollectionIterator(pathToFolder+"/"+child_collections(childCollectionCount).name, child_collections(childCollectionCount),zip,md5Files,user,
collections,datasets,files,
folders,metadataService,spaces))
} else if (childCollectionCount < numChildCollections - 2){
childCollectionCount += 1
currentCollectionIterator = Some(new CollectionIterator(pathToFolder + "/" + child_collections(childCollectionCount).name, child_collections(childCollectionCount), zip, md5Files, user,
collections, datasets, files,
folders, metadataService, spaces))
true
} else {
file_type+=1
file_type += 1
false
}
}
Expand All @@ -114,17 +114,17 @@ class CollectionIterator(pathToFolder : String, parent_collection : models.Colle
//collection info
case 0 => {
val md5 = MessageDigest.getInstance("MD5")
md5Files.put(pathToFolder+"_info.json",md5)
val is = addCollectionInfoToZip(pathToFolder, parent_collection,zip)
file_type+=1
md5Files.put(pathToFolder + "_info.json", md5)
val is = addCollectionInfoToZip(pathToFolder, parent_collection, zip)
file_type += 1
Some(new DigestInputStream(is.get, md5))
}
//collection metadata
case 1 => {
val md5 = MessageDigest.getInstance("MD5")
md5Files.put(pathToFolder+"_metadata.json",md5)
val is = addCollectionMetadataToZip(pathToFolder, parent_collection,zip)
file_type+=1
md5Files.put(pathToFolder + "_metadata.json", md5)
val is = addCollectionMetadataToZip(pathToFolder, parent_collection, zip)
file_type += 1
Some(new DigestInputStream(is.get, md5))
}
//datasets in this collection
Expand Down
20 changes: 10 additions & 10 deletions app/Iterators/DatasetIterator.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -44,15 +44,15 @@ class DatasetIterator(pathToFolder : String, dataset : models.Dataset, zip: ZipO
}

def addDatasetInfoToZip(folderName: String, dataset: models.Dataset, zip: ZipOutputStream): Option[InputStream] = {
val path = folderName + "/"+dataset.name+"_info.json"
zip.putNextEntry(new ZipEntry(folderName + "/"+dataset.name+"_info.json"))
val path = folderName + "/" + dataset.name + "_info.json"
zip.putNextEntry(new ZipEntry(folderName + "/" + dataset.name + "_info.json"))
val infoListMap = Json.prettyPrint(getDatasetInfoAsJson(dataset))
Some(new ByteArrayInputStream(infoListMap.getBytes("UTF-8")))
}

def addDatasetMetadataToZip(folderName: String, dataset : models.Dataset, zip: ZipOutputStream): Option[InputStream] = {
val path = folderName + "/"+dataset.name+"_dataset_metadata.json"
zip.putNextEntry(new ZipEntry(folderName + "/"+dataset.name+"_metadata.json"))
val path = folderName + "/" + dataset.name + "_dataset_metadata.json"
zip.putNextEntry(new ZipEntry(folderName + "/" + dataset.name + "_metadata.json"))
val datasetMetadata = metadataService.getMetadataByAttachTo(ResourceRef(ResourceRef.dataset, dataset.id))
.map(JSONLD.jsonMetadataWithContext(_))
val s : String = Json.prettyPrint(Json.toJson(datasetMetadata))
Expand Down Expand Up @@ -85,7 +85,7 @@ class DatasetIterator(pathToFolder : String, dataset : models.Dataset, zip: ZipO
while(f1.parentType == "folder") {
folders.get(f1.parentId) match {
case Some(fparent) => {
name = fparent.displayName + "/"+ name
name = fparent.displayName + "/" + name
f1 = fparent
}
case None =>
Expand Down Expand Up @@ -125,7 +125,7 @@ class DatasetIterator(pathToFolder : String, dataset : models.Dataset, zip: ZipO
if (fileIterator.hasNext()){
true
} else if (fileCounter < numFiles -1){
fileCounter +=1
fileCounter += 1
currentFileIterator = Some(new FileIterator(folderNameMap(inputFiles(fileCounter).id),inputFiles(fileCounter),zip,md5Files,files,folders,metadataService))
true
} else {
Expand All @@ -146,18 +146,18 @@ class DatasetIterator(pathToFolder : String, dataset : models.Dataset, zip: ZipO
is = addDatasetInfoToZip(pathToFolder,dataset,zip)
val md5 = MessageDigest.getInstance("MD5")
md5Files.put("_info.json",md5)
file_type+=1
file_type += 1
Some(new DigestInputStream(is.get, md5))
}
case 1 => {
is = addDatasetMetadataToZip(pathToFolder,dataset,zip)
val md5 = MessageDigest.getInstance("MD5")
md5Files.put("_metadata.json",md5)
if (numFiles > 0){
file_type+=1
file_type += 1
currentFileIterator = Some(new FileIterator(folderNameMap(inputFiles(fileCounter).id),inputFiles(fileCounter),zip,md5Files,files,folders,metadataService))
} else {
file_type+=2
file_type += 2
}

Some(new DigestInputStream(is.get, md5))
Expand All @@ -172,4 +172,4 @@ class DatasetIterator(pathToFolder : String, dataset : models.Dataset, zip: ZipO
}
}
}
}
}
12 changes: 6 additions & 6 deletions app/Iterators/DatasetsInCollectionIterator.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -37,8 +37,8 @@ class DatasetsInCollectionIterator(pathToFolder : String, collection : models.Co

var currentDatasetIterator : Option[DatasetIterator] = if (numDatasets > 0){

Some(new DatasetIterator(pathToFolder+"/"+currentDataset.get.name,currentDataset.get, zip, md5Files,
folders, files,metadataService,datasets,spaces))
Some(new DatasetIterator(pathToFolder + "/" + currentDataset.get.name, currentDataset.get, zip, md5Files,
folders, files, metadataService, datasets, spaces))
} else {
None
}
Expand All @@ -51,13 +51,13 @@ class DatasetsInCollectionIterator(pathToFolder : String, collection : models.Co
if (datasetIterator.hasNext()){
true
} else {
if (datasetCount < numDatasets -1){
datasetCount +=1
if (datasetCount < numDatasets - 1){
datasetCount += 1
currentDataset = Some(datasetsInCollection(datasetCount))
currentDataset match {
case Some(cd) => {
currentDatasetIterator = Some(new DatasetIterator(pathToFolder+"/"+cd.name,cd, zip, md5Files,
folders, files,metadataService,datasets,spaces))
currentDatasetIterator = Some(new DatasetIterator(pathToFolder + "/" + cd.name, cd, zip, md5Files,
folders, files, metadataService, datasets, spaces))
true
}
case None => false
Expand Down
22 changes: 11 additions & 11 deletions app/Iterators/FileIterator.scala
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Expand Up @@ -10,7 +10,7 @@ import services.{FolderService, MetadataService, FileService}
import util.JSONLD

//this is used for file downloads
//called by the dataset interator
//called by the dataset iterator
class FileIterator (pathToFile : String, file : models.File,zip : ZipOutputStream, md5Files :scala.collection.mutable.HashMap[String, MessageDigest], files : FileService, folders : FolderService , metadataService : MetadataService) extends Iterator[Option[InputStream]] {

def getFileInfoAsJson(file : models.File) : JsValue = {
Expand All @@ -31,7 +31,7 @@ class FileIterator (pathToFile : String, file : models.File,zip : ZipOutputStrea
Json.obj("id" -> file.id, "filename" -> file.filename, "author" -> file.author.email, "uploadDate" -> file.uploadDate.toString,"contentType"->file.contentType,"description"->file.description,"license"->licenseInfo)
}
def addFileInfoToZip(folderName: String, file: models.File, zip: ZipOutputStream): Option[InputStream] = {
zip.putNextEntry(new ZipEntry(folderName + "/"+file.filename+"_info.json"))
zip.putNextEntry(new ZipEntry(folderName + "/" + file.filename + "_info.json"))
val fileInfo = getFileInfoAsJson(file)
val s : String = Json.prettyPrint(fileInfo)
Some(new ByteArrayInputStream(s.getBytes("UTF-8")))
Expand All @@ -48,7 +48,7 @@ class FileIterator (pathToFile : String, file : models.File,zip : ZipOutputStrea
}

def addFileMetadataToZip(folderName: String, file: models.File, zip: ZipOutputStream): Option[InputStream] = {
zip.putNextEntry(new ZipEntry(folderName + "/"+file.filename+"_metadata.json"))
zip.putNextEntry(new ZipEntry(folderName + "/" + file.filename + "_metadata.json"))
val fileMetadata = metadataService.getMetadataByAttachTo(ResourceRef(ResourceRef.file, file.id)).map(JSONLD.jsonMetadataWithContext(_))
val s : String = Json.prettyPrint(Json.toJson(fileMetadata))
Some(new ByteArrayInputStream(s.getBytes("UTF-8")))
Expand All @@ -66,24 +66,24 @@ class FileIterator (pathToFile : String, file : models.File,zip : ZipOutputStrea
def next() = {
file_type match {
case 0 => {
file_type +=1
file_type += 1
is = addFileInfoToZip(pathToFile, file, zip)
val md5 = MessageDigest.getInstance("MD5")
md5Files.put(file.filename+"_info.json",md5)
md5Files.put(file.filename + "_info.json", md5)
Some(new DigestInputStream(is.get,md5))
}
case 1 => {
file_type+=1
is = addFileMetadataToZip(pathToFile,file,zip)
file_type += 1
is = addFileMetadataToZip(pathToFile, file, zip)
val md5 = MessageDigest.getInstance("MD5")
md5Files.put(file.filename+"_metadata.json",md5)
md5Files.put(file.filename + "_metadata.json", md5)
Some(new DigestInputStream(is.get,md5))
}
case 2 => {
file_type+=1
is = addFileToZip(pathToFile,file,zip)
file_type += 1
is = addFileToZip(pathToFile, file, zip)
val md5 = MessageDigest.getInstance("MD5")
md5Files.put(file.filename,md5)
md5Files.put(file.filename, md5)
Some(new DigestInputStream(is.get,md5))
}
case _ => None
Expand Down
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