interminer_layout.md

interminer package layout

• /R

  • service-regions.r

  | | synopsis | service | uri | |:----------:|:----------------------------------------------:|:--------------------------:|:--------------:| | im_regions(as = "gff3") | Get Genomic Features overlapping given Regions | Genomic Intervals as GFF3 | /regions/gff3 | | im_regions(as = "fasta") | Get Genomic Features overlapping given Regions | Genomic Intervals as FASTA | /regions/fasta | | im_regions(as = "bed") | Get Genomic Features overlapping given Regions | Genomic Intervals as BED | /regions/bed |

  • service-lists.r

  	synopsis	service	uri
  im_lists(ls_name=NULL)	Find lists on the server.	Lists	/lists

  • service-list.r

  | | synopsis | service | uri | |:----------:|:------------------------------------:|:-------------:|:-------------------:| | im_lists(as = "gff3") | Get the Contents of a List as GFF3. | List as GFF3 | /list/results/gff3 | | im_lists(as = "fasta") | Get the Contents of a List as FASTA. | List as FASTA | /list/results/fasta |

  • service-query.r

  | interminer | synopsis | service | uri | |:--------------------:|:---------------------------------------------:|:-------------------:|:--------------------:| | im_query(as = "gff3") | Query the Database for Sequence Annotations. | GFF3 Query Results | /query/results/gff3 | | im_query(as = "fasta") | Query the Database for Sequence. | FASTA Query Results | /query/results/fasta | | im_query(as = "bed") | Query the Database for Locations. | BED Query Results | /query/results/bed | | im_query(as = "tab") | Get results for a query against the database. | Query Results | /query/results |

what works:

• query/service/list/result/gff3
• query/service/list/result/fasta
• query/service/lists
• query/service/query/results/gff3
• query/service/query/results/fasta
• query/service/query/results/bed
• query/service/query/results
• query/service/regions/gff3 (GET will fail if you accept application/json first...)
• query/service/regions/fasta (and here...)
• query/service/regions/bed (and here...)

template stuff that works?

• query/service/template/results (www.flymine.org/query/service/template/results?name=Gene_GO&start=1&columnheaders=friendly&constraint1=Gene&op1=LOOKUP&value1=Notch&code1=A&extra1=D.%20melanogaster)
• query/service/templates (www.flymine.org/query/service/templates)

service things that also work:

• query/service/version/release
• query/service/version
• query/service

data model things taht work:

• query/service/model
• query/service/summaryfields

widget things

• query/service/widgets

auth things that work:

• query/service/users (POST new user account)
• query/service/user/token (GET 24hr token) which one then sends as a query element
• query/service/user/whoami
• query/service/listswithobject (www.flymine.org/query/service/listswithobject?publicId=CG10142&type=Gene&extraValue=D.%20melanogaster)

auth things:

with a username i created on the webs:
- [email protected] - flymine1740