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PipeWork and Selector
Raymond Ripp
A simple PipeWork : Calculette
Add
Output
Enter the values and press
Add
Output
4 5
Output
= 9
Predefined inputs
Add
Output
5
Edit the PipeWork
Add
Output
Multiply
Processing Elements
ProcessingElement
Output
Any php function With 0, 1, 2, … n arguments One output
Defined in class PW:: Security Centralisation Adaptation
Reflection
Processing Elements 1/6
HtmlTable Html PWSessionVariables PWMultipleSelectFrom_listOfPW PWselectFrom_listOfPW PWlistOfPW PWcompareArray PWsearchInAllPipeWorks PWsearchReplaceInAllPipeWork PWdate PWappend PWmemo PWnop
PWswitchBetween PWisLess PWisLessOrEqual PWisEqual PWisDifferent PWisGreaterOrEqual PWisGreater PWdecrement PWadd PWdivide PWmultiply PWsubstract PWemptyString PWcount PWarrayDiff PWemptyArray PWtoArray
Processing Elements 2/6
PWappendToArray PWcombine PWfromArray PWsubArrayTabulated PWsubArray PWsubArray0 PWsubArray1 PWsubArray2 PWsetInArray PWset2InArray PWsplitInWordsWithSemiColon PWsplitInWordsWithComma PWsplitInWords PWsplitInLines PWfirstWordOfLines PWfirstWordsInArray PWbrowse PWenter PWselect PWtext
PWselectFrom_ListOfYesNo PWListOfYesNo PWselectFrom_ListOfUnionInterAn
otBnotA PWListOfUnionInterAnotBnotA PWarrayOfSubElement PWlowercase PWUnionInterAnotBnotA PWintersection PWunion4 PWunion PWinAnotB PWinBnotA PWsort PWreindex PWunique PWuniqueReindex PWinArray
Processing Elements 3/6
PWtoStore PWdeleteStore PWfromStore PWfileOfStore PWnameOfStore PWdirOfStore PWMultipleSelectFrom_listOfStoreX PWselectFrom_listOfStoreX PWlistOfStoreX PWMultipleSelectFrom_listOfStore PWselectFrom_listOfStore PWlistOfStore
Processing Elements 4/6 GXClusterList GXClusterComposition GXMultipleSelectFrom_listOfTissue GXselectFrom_listOfTissue GXlistOfTissue GXTissue GXselectFrom_listOfProbesetsOfGeneList GXlistOfProbesetsOfGeneList GXselectFrom_listOfProbesetsOfGeneName GXlistOfProbesetsOfGeneName GXMultipleSelectFrom_listOfRealExp GXselectFrom_listOfRealExp GXlistOfRealExp GXProbesetFromRealexp GXProbesetFromRealexpSoftware GXProbesetFromArraytype GXProbesetsConcerning GXProbeset GXManageRealExp GXRealExp
GXselectFrom_listOfArraytype GXlistOfArraytype GXArraytype GXDbInput GXselectFrom_listOfGxDbInput GXlistOfGxDbInput GXselectFrom_listOfAffyAnnotFiles GXlistOfAffyAnnotFiles GXselectFrom_listOfIndividual GXlistOfIndividual GXIndividual GXselectFrom_listOfGenotype GXlistOfGenotype GXGenotype GXselectFrom_listOfOrganism GXlistOfOrganism GXOrganism etc.
Processing Elements 5/6 ImAnnoListOfAnnotatedGPaintGene ImAnnoGPaintGene ImAnnoGPaintGenes ImAnnoSelectFrom_ListOfGPaintGene ImAnnoListOfGPaintGene ImAnnoSelectFrom_TissueType ImAnnoTissueType ImAnnoSelectFrom_ListOfTissueType ImAnnoListOfTissueType ImAnnoSelectFrom_ListOfSieve ImAnnoListOfSieve ImAnnoSelectFrom_ListOfSieveEye ImAnnoListOfSieveEye
ImAnnoListOfSieveEar ImAnnoFromSieves ImAnnoFromSieve ImAnnoCorrelateTissues ImAnnoCadre ImAnnoOrgan ImAnnoSelectFrom_ListOfCadre ImAnnoListOfCadre ImAnnoSelectFrom_ListOfOrgan ImAnnoListOfOrgan ImAnnoCreateSieve ImAnnoSelectFrom_ListOfEGEKeys ImAnnoListOfEGEKeys ImAnnoListOfEGEHeader ImAnnoEGE
Processing Elements 6/6
Go GoSelectFrom_ListOfAction GoListOfAction GoSelectFrom_ListOfFields GoListOfFields AmdCommon FedMultipleSelectFrom_ListOfGrog FedSelectFrom_ListOfGrog FedListOfGrog FedGrogTable FedPeople FedSelectFrom_ListOfPeopleFields FedListOfPeopleFields FedDatafile FedSelectFrom_ListOfDatafileFields FedListOfDatafileFields Wscope …
Enter - Select - MultipleSelect
Select and fill in the enter values
… the MultipleSelect … and Press the orange button.
… in graphical mode.
Output
type
name
AlsaChipmanufacturer probesetcount
keywordsBadGoodCheep
descriptionBlaBlabla
url
chips Chicken
action update
ArrayType
Create Edit Manage PipeWorks
Store and Restore
Every data can be stored as a php serialized data
… and restored
What is in the pipes ?
Numbers Texts Arrays Objects
All what the Working Elements can manage
Managing arrays
PWemptyArray PWtoArray PWappendToArray PWcombine PWfromArray PWsubArray PWsplitInWords PWsplitInLines PWfirstWordOfLines PWfirstWordsInArray
PWintersection PWunion PWinAnotB PWinBnotA PWsort PWreindex PWunique PWuniqueReindex PWinArray etc.
GX Radar Generator
ImAnno Gene List
How to combine list of genes from ImAnno search tool through sieves
(using ImAnno SQL query) Transcriptomic Expression
(GscopeWebService) Diseases related genes (serialized
stores) With Union, Intersection, AnotB, etc.
sievesCochleaSacculusUtriculus
Select Storecochleasacculusutriculus
other
Select DiseaseJaxIhr
SangerAll
ISHAnnotation
Intersection
GenePaintGenesInformation
Intersection
Transcriptomic
Diseases
ImAnno Gene List
Output
cadre
sievesCochleaSacculusUtriculus
action
UnionInter
AnotBBnotA
organ
key
action
UnionInter
AnotBBnotA
Select StoreEGEcochEGEsacEGEutri
EGEother
action
UnionInter
AnotBBnotA
Select DiseaseJaxIhr
SangerAll
What to display
name,descript,entrez,ege,go
FromSieves
UnionInterAnotBnotA
GenePaintgenes
UnionInterAnotBnotA
HtmlTable
FromStore
FromStore
ImAnno Gene List
GxDb Uploading interface
How to offer to the user an uploading tool allowing to combine experiments, arraytypes, samples, organisms, genotype, individuals, etc.
using and connecting existing data, creating new one or updating it.
GxDb
GxDb Input Upload interface
Tricks and useful tools
Store and Restore Works well as HTML form Allows to combine several pipeworks The user can create or extend
Can be integrated in any .php page Can be called as a PHP function
as function call as WebService
PipeWork ToDo list …
Collapse parts Graphical interface Ajax requests
Apply to other applications
Selector !
How to find the Experiments which were done with a given Organism and a set of Treatmentypes ?
And for a Genotype and a Sample How to combine Experiments,
RealExps, Sample, Arraytypes etc.
GxDb
… use Selector ! An application of the pipework’s MultipleSelectFromListOf
Selector … select from left to right
Select one or more lines in a column Press the orange button to update the
connected columns right from here Go to the next column When all is updated press the big
orange button
5 => 60, 61, 62 => 27, 28 and 11
11 => 5, 34, 37 (hourrah 5 is present ! )
GxDb
Find the way …
Selector and PipeWork
A Selector can contain PipeWorks (it is a PipeWork with special properties) Select, Press Select, Press Select, Press And press the output button to process
A Selector can not yet be embedded in a PipeWork ??
Selector ToDo list …
Graphical interface … any idea ? Customisable in size and display Ajax Ajax Ajax
Apply to other applications Test it outside Genoret or Gx
require_once, etc.
Merci à
Laëtitia Nicolas Guillaume