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genotoul-bioinfo
jflow
Commits
aed8d257
Commit
aed8d257
authored
Feb 21, 2017
by
Floreal Cabanettes
Browse files
Add doc for input/output objects (list)
parent
6a8e0244
Changes
1
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docs/jflow_core_component.html
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aed8d257
...
...
@@ -551,6 +551,90 @@ class MyComponent (Component):
</table>
</div>
<h3>
add_input_object()
</h3>
<p>
Add a python object as input. The object is defined as a class inherited from object.
</p>
<h4>
Example
</h4>
<p>
Considering the following object:
</p>
<pre
class=
"pre-hl "
><code
class=
"python"
>
class MyObject(object):
def __init__(self, value):
self.value = value
def add_five(self):
self.value = self.value + 5
def multiply_by_ten(self):
self.value = self.value * 10
</code></pre>
<p>
We define this object and give it as a component argument. Into the component, the input is defined
like that:
</p>
<pre
class=
"pre-hl "
><code
class=
"python"
>
self.add_input_object("i_object", "The input object to add 5", default=i_object)
</code></pre>
<p>
Note: the object is accessible only into a python function loaded from an "add_python_execution".
</p>
<h4>
Options
</h4>
<p>
There are two positional argument :
<code>
name
</code>
and
<code>
help
</code>
. All other options are keyword options.
</p>
<div
class=
"table-responsive"
>
<table
class=
"table table-bordered table-striped"
>
<thead>
<tr
style=
"white-space:nowrap"
>
<th>
Name
</th>
<th>
Type
</th>
<th>
Required
</th>
<th>
Default value
</th>
<th>
Description
</th>
</tr>
</thead>
<tbody>
<tr>
<td>
name
</td>
<td>
string
</td>
<td>
true
</td>
<td>
None
</td>
<td>
The name of the parameter. The parameter value is accessible
within the workflow object through the attribute named
<code>
self.parameter_name
</code>
.
</td>
</tr>
<tr>
<td>
help
</td>
<td>
string
</td>
<td>
true
</td>
<td>
None
</td>
<td>
The parameter help message.
</td>
</tr>
<tr>
<td>
default
</td>
<td>
string
</td>
<td>
false
</td>
<td>
None
</td>
<td>
The default object.
</td>
</tr>
<tr>
<td>
required
</td>
<td>
boolean
</td>
<td>
false
</td>
<td>
false
</td>
<td>
Wether or not the parameter can be ommitted.
</td>
</tr>
</tbody>
</table>
</div>
<h3>
add_input_object_list()
</h3>
<p>
This method takes the same arguments as
<code>
add_input_object()
</code>
. However, adding this parameter,
the component can take a list of objects and the object attribut
<code>
self.parameter_name
</code>
will be
settled as a Python list.
</p>
</div>
...
...
@@ -950,6 +1034,111 @@ class MyComponent (Component):
</tbody>
</table>
</div>
<h3>
add_output_object()
</h3>
<h4>
Example
</h4>
<p>
In the following example, an output named
<code>
o_object
</code>
is defined. The python function
defined for execution has to return a python object, which will be stored into this object.
</p>
<pre
class=
"pre-hl "
><code
class=
"python"
>
self.add_output_object("o_object", "The output object")
</code></pre>
<h4>
Options
</h4>
<div
class=
"table-responsive"
>
<table
class=
"table table-bordered table-striped"
>
<thead>
<tr
style=
"white-space:nowrap"
>
<th>
Name
</th>
<th>
Type
</th>
<th>
Required
</th>
<th>
Default value
</th>
<th>
Description
</th>
</tr>
</thead>
<tbody>
<tr>
<td>
name
</td>
<td>
string
</td>
<td>
true
</td>
<td>
None
</td>
<td>
The name of the output object.
</td>
</tr>
</tbody>
<tbody>
<tr>
<td>
help
</td>
<td>
string
</td>
<td>
true
</td>
<td>
None
</td>
<td>
The description of the object.
</td>
</tr>
</tbody>
<tbody>
<tr>
<td>
required
</td>
<td>
bool
</td>
<td>
false
</td>
<td>
false
</td>
<td>
Is required.
</td>
</tr>
</tbody>
</table>
</div>
<h3>
add_output_object_list()
</h3>
<h4>
Example
</h4>
<p>
In the following example, an output named
<code>
o_object
</code>
is defined. The python function defined
for execution has to return a list of python objects, with the exact numbers of items mentioned in the
argument
<code>
nb_items
</code>
(2 in this example).
</p>
<pre
class=
"pre-hl "
><code
class=
"python"
>
self.add_output_object_list("o_object", "The output object", nb_items=2)
</code></pre>
<h4>
Options
</h4>
<div
class=
"table-responsive"
>
<table
class=
"table table-bordered table-striped"
>
<thead>
<tr
style=
"white-space:nowrap"
>
<th>
Name
</th>
<th>
Type
</th>
<th>
Required
</th>
<th>
Default value
</th>
<th>
Description
</th>
</tr>
</thead>
<tbody>
<tr>
<td>
name
</td>
<td>
string
</td>
<td>
true
</td>
<td>
None
</td>
<td>
The name of the output object.
</td>
</tr>
</tbody>
<tbody>
<tr>
<td>
help
</td>
<td>
string
</td>
<td>
true
</td>
<td>
None
</td>
<td>
The description of the object.
</td>
</tr>
</tbody>
<tbody>
<tr>
<td>
nb_items
</td>
<td>
int
</td>
<td>
true
</td>
<td>
0
</td>
<td>
Number of objects into the list.
</td>
</tr>
</tbody>
<tbody>
<tr>
<td>
required
</td>
<td>
bool
</td>
<td>
false
</td>
<td>
false
</td>
<td>
Is required.
</td>
</tr>
</tbody>
</table>
</div>
</div>
</section>
...
...
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