public class SraDownload extends SequenceReadArchive implements ApiModule, InputDataModule, OutsidePipelineWriter
Modifier and Type | Field and Description |
---|---|
static String |
DEST_DIR |
static String |
EXE_FASTERQ |
static String |
METADATA_SRA_ID_COL_NAME |
DB_DIR, DB_DIR_DESC, DB_NAME, SRA_ACC_LIST, SRA_ACC_LIST_DESC, SRP, SRP_DESC
GZIP_EXT, LOG_EXT, PDF_EXT, RETURN, SH_EXT, TAB_DELIM, TSV_EXT, TXT_EXT
LOG_DIR, MAIN_SCRIPT_PREFIX, NO_VERSION, OUTPUT_DIR, RES_DIR, TEMP_DIR
Constructor and Description |
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SraDownload() |
Modifier and Type | Method and Description |
---|---|
List<List<String>> |
buildScript(List<File> files)
Return an inner list of lines to execute for each sample.
|
void |
checkDependencies()
Validate module dependencies:
Require
Config . exists
Require Config . is positive integer
Require Config . is positive integer
Verify Config . is positive integer if set
Start the AWS DB sync to S3 if a novel DB has been configure and
"aws.copyDbToS3" is enabled
|
void |
cleanUp()
If metadata exists in module output directory, refresh MetaUtil.
|
String |
getCitationString()
At a minimum, this should return the name and/or url for the wrapped tool.
|
String |
getDataSource() |
String |
getDescription()
Briefly describe what this module does.
|
String |
getDetails()
A extension of
getDescription . |
String |
getDockerImageName()
Get the docker image to use for this module.
|
String |
getDockerImageOwner()
Get the name of the docker hub user that owns the image to use for this module.
|
String |
getDockerImageTag()
Get the version / tag to use for the docker image.
|
Set<String> |
getInputDataTypes() |
List<File> |
getInputFiles()
BioModule
BioModuleImpl.getInputFiles() is called to initialize upon first call and cached. |
List<String> |
getPreRequisiteModules()
By default, no prerequisites are required.
|
String |
getSummary()
Returns summary message to be displayed by Email module so must not contain confidential info.
|
Set<String> |
getWriteDirs() |
Boolean |
isValidProp(String property)
Tests to see if the value val is valid for property prop; primarily tests format.
|
String |
version()
Changes to a module class should be accompanied by a increment in version.
|
buildScriptForPairedReads, executeTask, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getTimeout, getWorkerScriptFunctions, hasScripts
addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getFileCache, getID, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getTempDir, getTitle, hashCode, init, isValidInputModule, listProps, setAlias, toString
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
getDescription, getMenuPlacement, getPropType, getTitle, listProps
executeTask, getAlias, getID, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPropDefault, getResourceDir, getTempDir, init, isValidInputModule, setAlias
public static final String METADATA_SRA_ID_COL_NAME
public static final String DEST_DIR
public static final String EXE_FASTERQ
public List<File> getInputFiles()
BioModuleImpl
BioModuleImpl.getInputFiles()
is called to initialize upon first call and cached.getInputFiles
in interface BioModule
getInputFiles
in class BioModuleImpl
public List<List<String>> buildScript(List<File> files) throws Exception
ScriptModuleImpl
buildScript
in interface ScriptModule
buildScript
in class ScriptModuleImpl
files
- Files in the input directory that contain only forward readsException
- if unable to generate script linespublic List<String> getPreRequisiteModules() throws Exception
BioModuleImpl
getPreRequisiteModules
in interface BioModule
getPreRequisiteModules
in class BioModuleImpl
Exception
- if invalid Class names are returned as prerequisitespublic Boolean isValidProp(String property) throws Exception
ApiModule
BioModule.checkDependencies()
. Using switch/case or a stack of if/else is recommended.
Within each case, call any/all method that is used by this module to access the value from the config file,
leveraging the checks in the Config.get* methods.
This method should never actually return false. If the value is not valid, it should throw an exception that
includes a helpful message about whats not valid. As part of a throwable, that message is passed along to
wherever the call started. Any time that "false" is actually the desired form, this method should be wrapped in
a try/catch.isValidProp
in interface ApiModule
isValidProp
in class SequenceReadArchive
Exception
public void checkDependencies() throws Exception
ScriptModuleImpl
Config
. exists
Config
. is positive integer
Config
. is positive integer
Config
. is positive integer if set
checkDependencies
in interface BioModule
checkDependencies
in class ScriptModuleImpl
Exception
- thrown if missing or invalid dependencies are foundpublic String getDescription()
ApiModule
getDetails
.getDescription
in interface ApiModule
public String getDetails()
ApiModule
getDescription
. Beyond the brief description, give details such as
the interaction between properties.getDetails
in interface ApiModule
getDetails
in class BioModuleImpl
public String getCitationString()
ApiModule
getCitationString
in interface ApiModule
public String version()
BioModule
public String getDockerImageOwner()
BioModule
getDockerImageOwner
in interface BioModule
getDockerImageOwner
in class BioModuleImpl
public String getDockerImageName()
BioModule
getDockerImageName
in interface BioModule
public String getDockerImageTag()
BioModule
getDockerImageTag
in interface BioModule
getDockerImageTag
in class BioModuleImpl
public String getSummary() throws Exception
ScriptModuleImpl
getSummary
in interface BioModule
getSummary
in class ScriptModuleImpl
Exception
- if any error occurspublic String getDataSource()
public Set<String> getInputDataTypes()
getInputDataTypes
in interface InputDataModule
public void cleanUp() throws Exception
BioModuleImpl
cleanUp
in interface BioModule
cleanUp
in class BioModuleImpl
Exception
- thrown if any runtime error occurspublic Set<String> getWriteDirs() throws DockerVolCreationException, ConfigPathException
getWriteDirs
in interface OutsidePipelineWriter
DockerVolCreationException
ConfigPathException