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Commit 947c64ca authored by juanf's avatar juanf
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SSDM-3092 : Export functionality, ongoing work 

SVN: 36601
parent c13a4b54
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openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exports-api.py
+ 20
− 13
View file @ 947c64ca
...@@ -16,6 +16,7 @@ ...@@ -16,6 +16,7 @@
from collections import deque from collections import deque
import time import time
import jarray
#Java Core #Java Core
from java.io import ByteArrayInputStream from java.io import ByteArrayInputStream
...@@ -129,8 +130,8 @@ def exportAll(tr, params): ...@@ -129,8 +130,8 @@ def exportAll(tr, params):
params.put("entities", entitiesToExport); params.put("entities", entitiesToExport);
return export(tr, params); return export(tr, params);
def getFileName(rootDir, spaceCode, projCode, expCode, sampCode, dataCode): def getFileName(spaceCode, projCode, expCode, sampCode, dataCode):
fileName = rootDir; fileName = "";
if spaceCode is not None: if spaceCode is not None:
fileName += "/" + spaceCode; fileName += "/" + spaceCode;
if projCode is not None: if projCode is not None:
...@@ -143,13 +144,12 @@ def getFileName(rootDir, spaceCode, projCode, expCode, sampCode, dataCode): ...@@ -143,13 +144,12 @@ def getFileName(rootDir, spaceCode, projCode, expCode, sampCode, dataCode):
fileName += "/" + dataCode; fileName += "/" + dataCode;
return fileName; return fileName;
def addToZipFile(fileName, zos): def addToZipFile(path, file, zos):
file = File(fileName);
fis = FileInputStream(file); fis = FileInputStream(file);
zipEntry = ZipEntry(fileName); zipEntry = ZipEntry(path);
zos.putNextEntry(zipEntry); zos.putNextEntry(zipEntry);
bytes = byte[1024]; bytes = jarray.zeros(1024, "b");
length = fis.read(bytes); length = fis.read(bytes);
while length >= 0: while length >= 0:
zos.write(bytes, 0, length); zos.write(bytes, 0, length);
...@@ -170,6 +170,10 @@ def export(tr, params): ...@@ -170,6 +170,10 @@ def export(tr, params):
rootDirFile.mkdir(); rootDirFile.mkdir();
rootDir = rootDirFile.getCanonicalPath(); rootDir = rootDirFile.getCanonicalPath();
#Create Zip File
fos = FileOutputStream(rootDir + ".zip");
zos = ZipOutputStream(fos);
for entity in params.get("entities"): for entity in params.get("entities"):
type = entity["type"]; type = entity["type"];
permId = entity["permId"]; permId = entity["permId"];
...@@ -187,7 +191,7 @@ def export(tr, params): ...@@ -187,7 +191,7 @@ def export(tr, params):
fetchOps.withRegistrator(); fetchOps.withRegistrator();
fetchOps.withModifier(); fetchOps.withModifier();
entityObj = v3.searchProjects(sessionToken, criteria, fetchOps).getObjects().get(0); entityObj = v3.searchProjects(sessionToken, criteria, fetchOps).getObjects().get(0);
entityFilePath = getFileName(rootDir, entityObj.getSpace().getCode(), entityObj.getCode(), None, None, None); entityFilePath = getFileName(entityObj.getSpace().getCode(), entityObj.getCode(), None, None, None);
if type == "EXPERIMENT": if type == "EXPERIMENT":
criteria = ExperimentSearchCriteria(); criteria = ExperimentSearchCriteria();
criteria.withPermId().thatEquals(permId); criteria.withPermId().thatEquals(permId);
...@@ -199,7 +203,7 @@ def export(tr, params): ...@@ -199,7 +203,7 @@ def export(tr, params):
fetchOps.withProperties(); fetchOps.withProperties();
fetchOps.withTags(); fetchOps.withTags();
entityObj = v3.searchExperiments(sessionToken, criteria, fetchOps).getObjects().get(0); entityObj = v3.searchExperiments(sessionToken, criteria, fetchOps).getObjects().get(0);
entityFilePath = getFileName(rootDir, entityObj.getProject().getSpace().getCode(), entityObj.getProject().getCode(), entityObj.getCode(), None, None); entityFilePath = getFileName(entityObj.getProject().getSpace().getCode(), entityObj.getProject().getCode(), entityObj.getCode(), None, None);
if type == "SAMPLE": if type == "SAMPLE":
criteria = SampleSearchCriteria(); criteria = SampleSearchCriteria();
criteria.withPermId().thatEquals(permId); criteria.withPermId().thatEquals(permId);
...@@ -213,7 +217,7 @@ def export(tr, params): ...@@ -213,7 +217,7 @@ def export(tr, params):
fetchOps.withParents(); fetchOps.withParents();
fetchOps.withChildren(); fetchOps.withChildren();
entityObj = v3.searchSamples(sessionToken, criteria, fetchOps).getObjects().get(0); entityObj = v3.searchSamples(sessionToken, criteria, fetchOps).getObjects().get(0);
entityFilePath = getFileName(rootDir, entityObj.getExperiment().getProject().getSpace().getCode(), entityObj.getExperiment().getProject().getCode(), entityObj.getExperiment().getCode(), entityObj.getCode(), None); entityFilePath = getFileName(entityObj.getExperiment().getProject().getSpace().getCode(), entityObj.getExperiment().getProject().getCode(), entityObj.getExperiment().getCode(), entityObj.getCode(), None);
if type == "DATASET": if type == "DATASET":
criteria = DataSetSearchCriteria(); criteria = DataSetSearchCriteria();
criteria.withPermId().thatEquals(permId); criteria.withPermId().thatEquals(permId);
...@@ -227,13 +231,16 @@ def export(tr, params): ...@@ -227,13 +231,16 @@ def export(tr, params):
fetchOps.withParents(); fetchOps.withParents();
fetchOps.withChildren(); fetchOps.withChildren();
entityObj = v3.searchDataSets(sessionToken, criteria, fetchOps).getObjects().get(0); entityObj = v3.searchDataSets(sessionToken, criteria, fetchOps).getObjects().get(0);
entityFilePath = getFileName(rootDir, entityObj.getSample().getExperiment().getProject().getSpace().getCode(), entityObj.getSample().getExperiment().getProject().getCode(), entityObj.getSample().getExperiment().getCode(), entityObj.getSample().getCode(), entityObj.getCode()); entityFilePath = getFileName(entityObj.getSample().getExperiment().getProject().getSpace().getCode(), entityObj.getSample().getExperiment().getProject().getCode(), entityObj.getSample().getExperiment().getCode(), entityObj.getSample().getCode(), entityObj.getCode());
if entityObj is not None and entityFilePath is not None: if entityObj is not None and entityFilePath is not None:
entityJson = String(objectMapper.writeValueAsString(entityObj)); entityJson = String(objectMapper.writeValueAsString(entityObj));
jsonEntityFile = File(entityFilePath + ".json"); jsonEntityFile = File(rootDir + entityFilePath + ".json");
jsonEntityFile.getParentFile().mkdirs(); jsonEntityFile.getParentFile().mkdirs();
IOUtils.write(entityJson.getBytes(), FileOutputStream(jsonEntityFile)); IOUtils.write(entityJson.getBytes(), FileOutputStream(jsonEntityFile));
addToZipFile(entityFilePath + ".json", jsonEntityFile, zos);
print "Folder found at: " + rootDir
zos.close();
fos.close();
print "Zip file found at: " + rootDir + ".zip"
return True return True
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