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Funcotator: added a maximum version number for data sources. (#6807)
Added max version check for data sources in Funcotator. This will automatically be used when validating a data sources version for running. Fixes #6712
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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|
@@ -23,6 +23,8 @@ | |
| import java.io.IOException; | ||
| import java.io.InputStream; | ||
| import java.nio.file.*; | ||
| import java.time.LocalDate; | ||
| import java.time.Month; | ||
| import java.util.*; | ||
| import java.util.regex.Matcher; | ||
| import java.util.regex.Pattern; | ||
|
|
@@ -57,24 +59,37 @@ private DataSourceUtils() {} | |
|
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| // Track our minimum version number here: | ||
| @VisibleForTesting | ||
| static final int MIN_MAJOR_VERSION_NUMBER = 1; | ||
| static final int MIN_MAJOR_VERSION_NUMBER = 1; | ||
| @VisibleForTesting | ||
| static final int MIN_MINOR_VERSION_NUMBER = 6; | ||
| static final int MIN_MINOR_VERSION_NUMBER = 6; | ||
| @VisibleForTesting | ||
| static final int MIN_YEAR_RELEASED = 2019; | ||
| static final LocalDate MIN_DATE = LocalDate.of(2019, Month.JANUARY, 24); | ||
|
|
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| // Track out maximum version number here: | ||
| @VisibleForTesting | ||
| static final int MAX_MAJOR_VERSION_NUMBER = 1; | ||
| @VisibleForTesting | ||
| static final int MIN_MONTH_RELEASED = 1; | ||
| static final int MAX_MINOR_VERSION_NUMBER = 7; | ||
| @VisibleForTesting | ||
| static final int MIN_DAY_RELEASED = 24; | ||
| static final LocalDate MAX_DATE = LocalDate.of(2020, Month.MAY, 21); | ||
|
|
||
| //================================================================================================================== | ||
| // 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 CURRENT_MINIMUM_DATA_SOURCE_VERSION = getDataSourceMinVersionString(); | ||
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| /** The maximum supported version of the data sources for funcotator to run. */ | ||
| public static final String CURRENT_MAXIMUM_DATA_SOURCE_VERSION = getDataSourceMaxVersionString(); | ||
|
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||
| public static final String MANIFEST_FILE_NAME = "MANIFEST.txt"; | ||
| public static final String DATA_SOURCES_FTP_PATH = "ftp://[email protected]/bundle/funcotator/"; | ||
| public static final String DATA_SOURCES_BUCKET_PATH = "gs://broad-public-datasets/funcotator/"; | ||
| public static final String DATA_SOURCES_NAME_PREFIX = "funcotator_dataSources"; | ||
| public static final String DS_SOMATIC_NAME_MODIFIER = "s"; | ||
| public static final String DS_GERMLINE_NAME_MODIFIER = "g"; | ||
| public static final String DS_EXTENSION = ".tar.gz"; | ||
| public static final String DS_CHECKSUM_EXTENSION = ".sha256"; | ||
|
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||
| // TODO: Turn these into an enum (Issue #5465 - https://github.com/broadinstitute/gatk/issues/5465): | ||
| public static final String CONFIG_FILE_FIELD_NAME_NAME = "name"; | ||
|
|
@@ -100,6 +115,51 @@ private DataSourceUtils() {} | |
| //================================================================================================================== | ||
| // Public Static Methods: | ||
|
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||
| /** | ||
| * Get the string representing the Min version information for funcotator as it would be written in the data sources | ||
| * release files. | ||
| * Max version info is specified in the following variables: | ||
| * {@link #MIN_MAJOR_VERSION_NUMBER} | ||
| * {@link #MIN_MINOR_VERSION_NUMBER} | ||
| * {@link #MIN_DATE} | ||
| * @return A {@link String} representing the Min version information as it would appear in the data sources file name. | ||
| */ | ||
| public static String getDataSourceMinVersionString() { | ||
| return getDataSourceVersionString(MIN_MAJOR_VERSION_NUMBER, MIN_MINOR_VERSION_NUMBER, MIN_DATE); | ||
| } | ||
|
|
||
| /** | ||
| * Get the string representing the Max version information for funcotator as it would be written in the data sources | ||
| * release files. | ||
| * Max version info is specified in the following variables: | ||
| * {@link #MAX_MAJOR_VERSION_NUMBER} | ||
| * {@link #MAX_MINOR_VERSION_NUMBER} | ||
| * {@link #MAX_DATE} | ||
| * @return A {@link String} representing the Max version information as it would appear in the data sources file name. | ||
| */ | ||
| public static String getDataSourceMaxVersionString() { | ||
| return getDataSourceVersionString(MAX_MAJOR_VERSION_NUMBER, MAX_MINOR_VERSION_NUMBER, MAX_DATE); | ||
| } | ||
|
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||
|
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| /** | ||
| * Get the string representing the given version information for funcotator as it would be written in the data sources | ||
| * release files. | ||
| * @param major {@code int} representing the major version of the data sources to use. | ||
| * @param minor {@code int} representing the minor version of the data sources to use. | ||
| * @param date {@link LocalDate} representing the date of the data sources to use. | ||
| * @return A {@link String} representing the given version information as it would appear in the data sources file name. | ||
| */ | ||
| public static String getDataSourceVersionString(final int major, final int minor, final LocalDate date) { | ||
| return String.format("v%d.%d.%d%02d%02d", | ||
| major, | ||
| minor, | ||
| date.getYear(), | ||
| date.getMonthValue(), | ||
| date.getDayOfMonth() | ||
| ); | ||
| } | ||
|
|
||
| /** | ||
| * Initializes the data sources for {@link Funcotator}. | ||
| * @param refVersion The version of the reference we're using to create annotations. Must not be {@code null}. | ||
|
|
@@ -196,7 +256,7 @@ else if ( !hasGencodeDataSource ) { | |
| * @param directory The {@link Path} of the directory in which to search for a config file. Must not be {@code null}. | ||
| * @return The {@link Path} to the config file found in the given {@code directory}. | ||
| */ | ||
| public static Path getConfigfile(final Path directory) { | ||
| private static Path getConfigfile(final Path directory) { | ||
|
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| Utils.nonNull(directory); | ||
|
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|
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@@ -225,7 +285,7 @@ else if ( configFileSet.size() == 0 ) { | |
| } | ||
|
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| /** @return {@code true} if the given {@link Path} exists, is readable, and is a directory; {@code false} otherwise. */ | ||
| public static boolean isValidDirectory(final Path p) { | ||
| private static boolean isValidDirectory(final Path p) { | ||
| Utils.nonNull(p); | ||
| return Files.exists(p) && Files.isReadable(p) && Files.isDirectory(p); | ||
| } | ||
|
|
@@ -628,7 +688,7 @@ private static boolean logDataSourcesInfo(final Path dataSourcesPath) { | |
| Integer versionYear = null; | ||
| Integer versionMonth = null; | ||
| Integer versionDay = null; | ||
| String versionDecorator = null; | ||
| String versionDecorator; | ||
| String source = null; | ||
| String alternateSource = null; | ||
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@@ -711,46 +771,51 @@ private static boolean logDataSourcesInfo(final Path dataSourcesPath) { | |
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| // Warn the user if they need newer stuff. | ||
| if ( !dataSourcesPathIsAcceptable ) { | ||
|
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| String message = ""; | ||
| message = message + "ERROR: Given data source path is too old! Minimum required version is: " + CURRENT_MINIMUM_DATA_SOURCE_VERSION + " (yours: " + version + ")\n"; | ||
| message = message + " You must download a newer version of the data sources from the Broad Institute FTP site: " + DATA_SOURCES_FTP_PATH + "\n"; | ||
| message = message + "ERROR: Given data source path is too old or too new! \n"; | ||
| message = message + " Minimum required version is: " + CURRENT_MINIMUM_DATA_SOURCE_VERSION + "\n"; | ||
| message = message + " Maximum allowed version is: " + CURRENT_MAXIMUM_DATA_SOURCE_VERSION + "\n"; | ||
| message = message + " Yours: " + version + "\n"; | ||
| message = message + " You must download a compatible version of the data sources from the Broad Institute FTP site: " + DATA_SOURCES_FTP_PATH + "\n"; | ||
| message = message + " or the Broad Institute Google Bucket: " + DATA_SOURCES_BUCKET_PATH + "\n"; | ||
| throw new UserException( message ); | ||
| } | ||
|
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| return dataSourcesPathIsAcceptable; | ||
| } | ||
|
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| /** | ||
| * Checks that the version information given is within the valid range for data source versions. | ||
| * | ||
| * @param major int containing the major version number to be checked. | ||
| * @param minor int containing the minor version number to be checked. | ||
| * @param year int containing the year version number to be checked.RecQ DNA helicase WRN | ||
| * @param month int containing the month version number to be checked. | ||
| * @param day int containing the day version number to be checked. | ||
| * | ||
| * @return {@code true} iff the given version information is valid for the current data source ranges. {@code false} otherwise. | ||
| */ | ||
| @VisibleForTesting | ||
| static boolean validateVersionInformation(final int major, final int minor, final int year, final int month, final int day) { | ||
|
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| // Compare from largest to smallest differences: | ||
|
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| if ( major < MIN_MAJOR_VERSION_NUMBER ) { | ||
| // Compare Major Version: | ||
| if ((major < MIN_MAJOR_VERSION_NUMBER) || (major > MAX_MAJOR_VERSION_NUMBER)) { | ||
| return false; | ||
| } | ||
|
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| if ( minor < MIN_MINOR_VERSION_NUMBER ) { | ||
| // Compare minor version if we're on the edge of versions: | ||
| if ( major == MIN_MAJOR_VERSION_NUMBER && minor < MIN_MINOR_VERSION_NUMBER ) { | ||
| return false; | ||
| } | ||
|
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| if ( year < MIN_YEAR_RELEASED ) { | ||
| if ( major == MAX_MAJOR_VERSION_NUMBER && minor > MAX_MINOR_VERSION_NUMBER ) { | ||
| return false; | ||
| } | ||
|
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| else if ( year == MIN_YEAR_RELEASED ) { | ||
| if ( month < MIN_MONTH_RELEASED ) { | ||
| return false; | ||
| } | ||
| else if ( month == MIN_MONTH_RELEASED ) { | ||
| if ( day < MIN_DAY_RELEASED ) { | ||
| return false; | ||
| } | ||
| } | ||
| } | ||
| // Now make sure the date is between or equal to the min and max date: | ||
| final LocalDate versionDate = LocalDate.of(year, month, day); | ||
|
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| return true; | ||
| // A valid date is between min and max date inclusive. | ||
| return (!versionDate.isBefore(MIN_DATE)) && (!versionDate.isAfter(MAX_DATE)); | ||
| } | ||
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| // ======================================================================================================== | ||
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