Updated datasource version parsing #5149
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Added in a unit test to check the version regex.
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@jonn-smith Minor stuff... feel free to merge when addressed.
| @@ -461,12 +462,14 @@ private static Properties readConfigFileProperties(final Path configFilePath) { | |||
| * user can create their own data sources directory, which may not contain the metadata we seek. | |||
| * | |||
| * NOTE: The README file in a Data Sources directory is assumed to have the following properties: | |||
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Should this now read: The MANIFEST file in a Data ....?
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| //================================================================================================================== | ||
| // Public Static Members: | ||
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| /** The minimum version of the data sources required for funcotator to run. */ | ||
| public static final String CURRENT_MINIMUM_DATA_SOURCE_VERSION = String.format("v%d.%d.%d%02d%02d", MIN_MAJOR_VERSION_NUMBER, MIN_MINOR_VERSION_NUMBER, MIN_YEAR_RELEASED, MIN_MONTH_RELEASED, MIN_DAY_RELEASED); | ||
| public static final String README_FILE_NAME = "README.txt"; | ||
| public static final String MANIFEST_FILE_NAME = "MANIFEST.txt"; |
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Did you just rename README.txt to MANIFEST.txt, or is this a more substantial change? Ie., is MANIFEST.txt now a file with a well-defined structured format, or is it still basically a textual README with another name?
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@droazen I added a MANIFEST.txt file to the packages. MANIFEST.txt contains the version and provenance information for each data source package, as well as a new decorator/information field to distinguish somatic and germline files. This version information is duplicated in the readme, but the readme is not parsed.
MANIFEST.txt a plain-text formatted file with 1 field per line. The formatting is loosely enforced with the regex in DataSourceUtils and is of the syntax:
<FIELD>: <VALUE>
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Ok, sounds good @jonn-smith, thanks for the clarification.
Codecov Report
@@ Coverage Diff @@
## master #5149 +/- ##
==============================================
+ Coverage 86.733% 86.763% +0.03%
- Complexity 29305 29450 +145
==============================================
Files 1810 1813 +3
Lines 135527 136056 +529
Branches 15031 15140 +109
==============================================
+ Hits 117547 118046 +499
- Misses 12566 12575 +9
- Partials 5414 5435 +21
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Now looks at manifest file, not readme.
Now supports version decorators (e.g.
somatic) after version numbers in manifest file.Added in a unit test to check the version regex.
Fixes #4582
Fixes #4692