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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,7 @@ | ||
| Added chains column in export (-chains and -topChains) | ||
| Report file appends made atomic. Now you can safely specify the same report file in several invocations of MiXCR even if you run several instances of MiXCR in parallel. Should also work for NFS etc if file locking is supported. | ||
| (beta) Added JSON-formatted reports. Use `--json-report` option in `align`, `extendAlignments`, `assemblePartial` or `assemble` actions to append json report to the end of the file ([jsonl](http://jsonlines.org/)). This feature intended ot simplify batch analysis, and analysis automation. E.g. [jq](https://stedolan.github.io/jq/) util can be used to aggregate information from multi-json-report file. | ||
| Added chains column in export (`-chains` and `-topChains`) | ||
| minor: Several new counters added to `align` report | ||
| minor: Added proper filtering for alleles with wildcard symbols in `featureToAlign` region | ||
| minor: Fixed bug in align report (wrong total count in rare cases) #265 | ||
| minor: Documentation added for `filterAlignments` |
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src/main/java/com/milaboratory/mixcr/cli/AbstractActionReport.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,120 @@ | ||
| /* | ||
| * Copyright (c) 2014-2017, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail | ||
| * (here and after addressed as Inventors) | ||
| * All Rights Reserved | ||
| * | ||
| * Permission to use, copy, modify and distribute any part of this program for | ||
| * educational, research and non-profit purposes, by non-profit institutions | ||
| * only, without fee, and without a written agreement is hereby granted, | ||
| * provided that the above copyright notice, this paragraph and the following | ||
| * three paragraphs appear in all copies. | ||
| * | ||
| * Those desiring to incorporate this work into commercial products or use for | ||
| * commercial purposes should contact the Inventors using one of the following | ||
| * email addresses: chudakovdm@mail.ru, chudakovdm@gmail.com | ||
| * | ||
| * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, | ||
| * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, | ||
| * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN | ||
| * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | ||
| * | ||
| * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS | ||
| * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR | ||
| * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO | ||
| * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT | ||
| * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A | ||
| * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY | ||
| * PATENT, TRADEMARK OR OTHER RIGHTS. | ||
| */ | ||
| package com.milaboratory.mixcr.cli; | ||
|
|
||
| import com.fasterxml.jackson.annotation.JsonFormat; | ||
| import com.fasterxml.jackson.annotation.JsonProperty; | ||
| import com.milaboratory.mixcr.util.MiXCRVersionInfo; | ||
| import com.milaboratory.util.TimeUtils; | ||
|
|
||
| import java.util.Date; | ||
|
|
||
| public abstract class AbstractActionReport implements ActionReport { | ||
| private Date date = new Date(); | ||
| private String commandLine; | ||
| private String[] inputFiles, outputFiles; | ||
| private long startMillis, finishMillis; | ||
|
|
||
| @JsonProperty("timestamp") | ||
| @JsonFormat(shape = JsonFormat.Shape.STRING, pattern = "yyyy-MM-dd HH:mm:ss.SSSZ") | ||
| public Date getDate() { | ||
| return date; | ||
| } | ||
|
|
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| @JsonProperty("commandLine") | ||
| public String getCommandLine() { | ||
| return commandLine; | ||
| } | ||
|
|
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| @JsonProperty("inputFiles") | ||
| public String[] getInputFiles() { | ||
| return inputFiles; | ||
| } | ||
|
|
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| @JsonProperty("outputFiles") | ||
| public String[] getOutputFiles() { | ||
| return outputFiles; | ||
| } | ||
|
|
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| @JsonProperty("executionTimeMillis") | ||
| public long getExecutionTimeMillis() { | ||
| return finishMillis - startMillis; | ||
| } | ||
|
|
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| @JsonProperty("version") | ||
| public String getVersion() { | ||
| return MiXCRVersionInfo.get().getShortestVersionString(); | ||
| } | ||
|
|
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| public void setCommandLine(String commandLine) { | ||
| this.commandLine = commandLine; | ||
| } | ||
|
|
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| public void setInputFiles(String... inputFiles) { | ||
| this.inputFiles = inputFiles; | ||
| } | ||
|
|
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| public void setOutputFiles(String... outputFiles) { | ||
| this.outputFiles = outputFiles; | ||
| } | ||
|
|
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| public void setStartMillis(long startMillis) { | ||
| this.startMillis = startMillis; | ||
| } | ||
|
|
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| public void setFinishMillis(long finishMillis) { | ||
| this.finishMillis = finishMillis; | ||
| } | ||
|
|
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| private static String join(String[] strs) { | ||
| StringBuilder builder = new StringBuilder(); | ||
| for (int i = 0; ; ++i) { | ||
| builder.append(strs[i]); | ||
| if (i == strs.length - 1) | ||
| break; | ||
| builder.append(','); | ||
| } | ||
| return builder.toString(); | ||
| } | ||
|
|
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| public void writeSuperReport(ReportHelper helper) { | ||
| if (!helper.isStdout()) | ||
| helper.writeField("Analysis Date", getDate()) | ||
| .writeField("Input file(s)", join(getInputFiles())) | ||
| .writeField("Output file(s)", join(getOutputFiles())) | ||
| .writeField("Version", getVersion()); | ||
|
|
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| if (!helper.isStdout()) | ||
| if (getCommandLine() != null) | ||
| helper.writeField("Command line arguments", getCommandLine()); | ||
|
|
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| if (getExecutionTimeMillis() >= 0) | ||
| helper.writeField("Analysis time", TimeUtils.nanoTimeToString(getExecutionTimeMillis() * 1000_000)); | ||
| } | ||
| } |
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