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