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shareFAIR
BioFlow-Insight
Commits
d6c9bfc8
Commit
d6c9bfc8
authored
1 month ago
by
George Marchment
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Started adding DB file
parent
636505d7
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src/DBfile.py
+73
-0
73 additions, 0 deletions
src/DBfile.py
src/workflow.py
+5
-0
5 additions, 0 deletions
src/workflow.py
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78 additions
and
0 deletions
src/DBfile.py
0 → 100644
+
73
−
0
View file @
d6c9bfc8
import
json
import
glob
import
os
import
re
from
.ro_crate
import
RO_Crate
from
.
import
constant
class
DBfile
(
RO_Crate
):
def
__init__
(
self
,
workflow
,
personnal_acces_token
=
None
,
display_info
=
False
):
RO_Crate
.
__init__
(
self
,
workflow
,
personnal_acces_token
=
personnal_acces_token
,
display_info
=
display_info
)
self
.
file_contents
=
"""
@prefix sf: <http://sharefair.org/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix schema: <https://schema.org/> .
@prefix edam: <http://edamontology.org/> .
@prefix p-plan: <http://purl.org/net/p-plan#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix efo: <https://www.ebi.ac.uk/gwas/efotraits/> .
"""
print
(
self
.
info_dico_workflow
)
#print(self.log)
def
initialise
(
self
):
workflow_name
=
self
.
workflow
.
get_name
()
workflow_long_name
=
self
.
info_dico_workflow
[
"
full_name
"
]
description
=
self
.
get_description
()
creator
=
self
.
info_dico_workflow
[
"
owner
"
][
"
html_url
"
]
authors_tab
,
authors_temp
=
[],
self
.
get_authors
()
for
author
in
authors_temp
:
#These are filters to keep in "real" authors
if
(
"
@users.noreply.github.com
"
not
in
author
[
'
email
'
]
and
"
@machine
"
not
in
author
[
'
email
'
]):
if
(
"
"
not
in
author
[
"
@id
"
]):
authors_tab
.
append
(
author
)
maintainer
=
f
"
https://github.com/
{
authors_tab
[
0
][
'
@id
'
]
}
"
date_created
=
self
.
get_datePublished
()
keywords
=
self
.
get_keywords
()
steps_string
=
[]
for
p
in
self
.
workflow
.
get_processes_called
():
steps_string
.
append
(
f
"
step
{
p
.
get_alias
()
}
"
)
steps_string
=
"
,
"
.
join
(
steps_string
)
#TODO update the input and output of the workflow
header
=
f
"""
### Main workflow
sf:
{
workflow_name
}
Workflow rdf:type sf:Workflow ;
schema:name
"
{
workflow_long_name
}
"
;
schema:description
"
{
description
}
"
;
schema:creator <
{
creator
}
> ;
schema:maintainer <
{
maintainer
}
> ;
schema:dateCreated
"
f
{
date_created
}
"
^^xsd:date ;
schema:programmingLanguage <https://w3id.org/workflowhub/workflow-ro-crate#nextflow> ;
schema:step
{
steps_string
}
;
sf:inputVariable sf:samplesheet, sf:ch_versions, sf:ch_fasta,
sf:ch_fasta_index, sf:ch_bismark_index, sf:ch_bwameth_index ;
sf:outputVariable sf:output_bam, sf:output_bai, sf:output_qualimap, sf:output_preseq, sf:output_versions ;
schema:keywords
"
{
keywords
}
"
.
"""
self
.
file_contents
+=
f
"
\n\n
{
header
}
"
for
author
in
authors_tab
:
self
.
file_contents
+=
f
"
\n\n
<https://github.com/
{
author
[
'
@id
'
]
}
> rdf:type schema:Person .
"
self
.
file_contents
+=
"""
\n\n
<https://w3id.org/workflowhub/workflow-ro-crate#nextflow> rdf:type schema:ComputerLanguage ;
rdfs:label
"
Nextflow
"
.
"""
print
(
self
.
file_contents
)
#TODO ADD Inputs values
#TODO ADD Outputs value
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src/workflow.py
+
5
−
0
View file @
d6c9bfc8
...
@@ -2,6 +2,7 @@
...
@@ -2,6 +2,7 @@
#Local
#Local
from
.nextflow_file
import
Nextflow_File
from
.nextflow_file
import
Nextflow_File
from
.ro_crate
import
RO_Crate
from
.ro_crate
import
RO_Crate
from
.DBfile
import
DBfile
from
.
import
constant
from
.
import
constant
from
.outils
import
is_git_directory
,
format_with_tabs
,
replace_thing_by_call
,
replace_group1
,
group_together_ifs
,
extract_curly
,
remove_extra_jumps
,
get_channels_to_add_in_false_conditions
,
extract_conditions
,
remove_empty_conditions_place_anker
from
.outils
import
is_git_directory
,
format_with_tabs
,
replace_thing_by_call
,
replace_group1
,
group_together_ifs
,
extract_curly
,
remove_extra_jumps
,
get_channels_to_add_in_false_conditions
,
extract_conditions
,
remove_empty_conditions_place_anker
from
.outils_graph
import
get_flatten_dico
,
initia_link_dico_rec
,
get_number_cycles
,
generate_graph
,
enrich_json_with_positions
from
.outils_graph
import
get_flatten_dico
,
initia_link_dico_rec
,
get_number_cycles
,
generate_graph
,
enrich_json_with_positions
...
@@ -316,6 +317,10 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
...
@@ -316,6 +317,10 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
producer
=
producer
)
producer
=
producer
)
self
.
rocrate
.
initialise
()
self
.
rocrate
.
initialise
()
def
get_DBfile
(
self
):
file
=
DBfile
(
self
)
file
.
initialise
()
#Returns a dico of number of processes called per each condition
#Returns a dico of number of processes called per each condition
#For example : {condition1: 14, condition2: 10, condition:3}
#For example : {condition1: 14, condition2: 10, condition:3}
...
...
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