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Merge pull request #5 from qbicsoftware/feature/statistics
Add space-based statistics
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135 changes: 135 additions & 0 deletions
135
src/main/java/life/qbic/io/commandline/SpaceStatisticsCommand.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,135 @@ | ||
| package life.qbic.io.commandline; | ||
|
|
||
| import ch.ethz.sis.openbis.generic.OpenBIS; | ||
| import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSet; | ||
| import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.Experiment; | ||
| import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.Sample; | ||
| import java.io.IOException; | ||
| import java.nio.file.Path; | ||
| import java.nio.file.Paths; | ||
| import java.time.Instant; | ||
| import java.time.LocalDateTime; | ||
| import java.time.ZoneOffset; | ||
| import java.time.format.DateTimeFormatter; | ||
| import java.util.ArrayList; | ||
| import java.util.Arrays; | ||
| import java.util.List; | ||
| import java.util.Map; | ||
| import life.qbic.App; | ||
| import life.qbic.model.Configuration; | ||
| import life.qbic.model.download.FileSystemWriter; | ||
| import life.qbic.model.download.SummaryWriter; | ||
| import life.qbic.model.download.OpenbisConnector; | ||
| import picocli.CommandLine.Command; | ||
| import picocli.CommandLine.Mixin; | ||
| import picocli.CommandLine.Option; | ||
|
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| @Command(name = "statistics", | ||
| description = "lists the number of collections, sample objects and attached datasets (by type)" | ||
| + "for one or all spaces accessible by the user") | ||
| public class SpaceStatisticsCommand implements Runnable { | ||
|
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| @Option(arity = "1", paramLabel = "<space>", description = "optional openBIS spaces to filter samples", names = {"-s", "--space"}) | ||
| private String space; | ||
| @Option(arity = "1", paramLabel = "<output file path>", description = "optional output path", names = {"-o", "--out"}) | ||
| private String outpath; | ||
| @Option(arity = "0", description = "shows results for openBIS settings and material spaces. Ignored if a specific space is selected.", | ||
| names = {"--show-settings"}) | ||
| private boolean allSpaces; | ||
| @Mixin | ||
| AuthenticationOptions auth = new AuthenticationOptions(); | ||
|
|
||
| @Override | ||
| public void run() { | ||
| List<String> summary = new ArrayList<>(); | ||
| List<String> blackList = new ArrayList<>(Arrays.asList("ELN_SETTINGS", "MATERIAL.GLOBAL")); | ||
| List<String> spaces = new ArrayList<>(); | ||
| if (space != null) { | ||
| summary.add("Querying samples in space: " + space); | ||
| spaces.add(space); | ||
| } else { | ||
| summary.add("Querying samples in all available spaces..."); | ||
| } | ||
| OpenBIS authentication = App.loginToOpenBIS(auth.getPassword(), auth.getUser(), auth.getAS()); | ||
| OpenbisConnector openbis = new OpenbisConnector(authentication); | ||
|
|
||
| if (spaces.isEmpty()) { | ||
| spaces = openbis.getSpaces(); | ||
| if(!allSpaces) { | ||
| spaces.removeAll(blackList); | ||
| } | ||
| } | ||
|
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| Map<String, Map<String, List<Experiment>>> experiments = openbis.getExperimentsByTypeAndSpace(spaces); | ||
| Map<String, Map<String, List<Sample>>> samples = openbis.getSamplesByTypeAndSpace(spaces); | ||
| Map<String, Map<String, List<DataSet>>> datasets = openbis.getDatasetsByTypeAndSpace(spaces); | ||
|
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| for(String space : spaces) { | ||
| summary.add("-----"); | ||
| summary.add("Summary for "+space); | ||
| summary.add("-----"); | ||
| int numExps = 0; | ||
| if (experiments.containsKey(space)) { | ||
| numExps = experiments.get(space).values().stream().mapToInt(List::size).sum(); | ||
| } | ||
| summary.add("Experiments ("+numExps+"):"); | ||
| summary.add(""); | ||
| if(!experiments.isEmpty()) { | ||
| Map<String, List<Experiment>> exps = experiments.get(space); | ||
| for (String type : exps.keySet()) { | ||
| summary.add(type + ": " + exps.get(type).size()); | ||
| } | ||
| } | ||
| summary.add(""); | ||
| int numSamples = 0; | ||
| if (samples.containsKey(space)) { | ||
| numSamples = samples.get(space).values().stream().mapToInt(List::size).sum(); | ||
| } | ||
| summary.add("Samples ("+numSamples+"):"); | ||
| summary.add(""); | ||
| if(!samples.isEmpty()) { | ||
| Map<String, List<Sample>> samps = samples.get(space); | ||
| for (String type : samps.keySet()) { | ||
| summary.add(type + ": " + samps.get(type).size()); | ||
| } | ||
| } | ||
| summary.add(""); | ||
| int numData = 0; | ||
| if (datasets.containsKey(space)) { | ||
| numData = datasets.get(space).values().stream().mapToInt(List::size).sum(); | ||
| } | ||
| summary.add("Attached datasets (" + numData + "):"); | ||
| summary.add(""); | ||
| if (datasets.get(space) != null) { | ||
| Map<String, List<DataSet>> dsets = datasets.get(space); | ||
| for (String dataType : dsets.keySet()) { | ||
| summary.add(dataType + ": " + dsets.get(dataType).size()); | ||
| } | ||
| } | ||
|
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| summary.add(""); | ||
| } | ||
|
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| for(String line : summary) { | ||
| System.out.println(line); | ||
| } | ||
|
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| Path outputPath = Paths.get(Configuration.LOG_PATH.toString(), | ||
| "spaces_summary_"+getTimeStamp()+".txt"); | ||
| if(outpath!=null) { | ||
| outputPath = Paths.get(outpath); | ||
| } | ||
| SummaryWriter summaryWriter = new FileSystemWriter(outputPath); | ||
| try { | ||
| summaryWriter.reportSummary(summary); | ||
| } catch (IOException e) { | ||
| throw new RuntimeException("Could not write summary file."); | ||
| } | ||
| } | ||
|
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| private String getTimeStamp() { | ||
| final String PATTERN_FORMAT = "YYYY-MM-dd_HHmmss"; | ||
| DateTimeFormatter formatter = DateTimeFormatter.ofPattern(PATTERN_FORMAT); | ||
| return LocalDateTime.ofInstant(Instant.now(), ZoneOffset.UTC).format(formatter).toString(); | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,60 @@ | ||
| package life.qbic.model; | ||
|
|
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| import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSet; | ||
| import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSetType; | ||
| import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.Experiment; | ||
| import ch.ethz.sis.openbis.generic.asapi.v3.dto.person.Person; | ||
| import java.util.Date; | ||
| import java.util.HashMap; | ||
| import java.util.Map; | ||
|
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| /** | ||
| * Wrapper class for openBIS DataSets that collects additional information, e.g. from samples, | ||
| * experiments etc. further up in the hierarchy. | ||
| */ | ||
| public class DatasetWithProperties { | ||
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| private final DataSet dataset; | ||
| private final Map<String, String> properties; | ||
|
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| public DatasetWithProperties(DataSet dataset) { | ||
| this.dataset = dataset; | ||
| this.properties = new HashMap<>(); | ||
| } | ||
|
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| public void addProperty(String key, String value) { | ||
| this.properties.put(key, value); | ||
| } | ||
|
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| public String getProperty(String key) { | ||
| return properties.get(key); | ||
| } | ||
|
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| public Map<String, String> getProperties() { | ||
| return properties; | ||
| } | ||
|
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| public DataSet getDataset() { | ||
| return dataset; | ||
| } | ||
|
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| public String getCode() { | ||
| return dataset.getCode(); | ||
| } | ||
|
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| public Experiment getExperiment() { | ||
| return dataset.getExperiment(); | ||
| } | ||
|
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| public DataSetType getType() { | ||
| return dataset.getType(); | ||
| } | ||
|
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| public Person getRegistrator() { | ||
| return dataset.getRegistrator(); | ||
| } | ||
|
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| public Date getRegistrationDate() { | ||
| return dataset.getRegistrationDate(); | ||
| } | ||
| } |
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