Remove API scripts for axed APIs.

scripts/api/form_create_from_xml.py

@@ -1,17 +0,0 @@
-#!/usr/bin/env python
-from __future__ import print_function
-
-import os
-import sys
-
-from common import submit
-
-try:
-    data = {}
-    data['xml_text'] = open(sys.argv[3]).read()
-except IndexError:
-    print('usage: %s key url form_xml_description_file' % os.path.basename(sys.argv[0]))
-    sys.exit(1)
-
-
-submit(sys.argv[1], sys.argv[2], data)

scripts/api/request_type_create_from_xml.py

@@ -1,23 +0,0 @@
-#!/usr/bin/env python
-from __future__ import print_function
-
-import os
-import sys
-
-from common import submit
-
-try:
-    data = {}
-    data['request_form_id'] = sys.argv[3]
-    data['sample_form_id'] = sys.argv[4]
-    data['sequencer_id'] = sys.argv[5]
-    data['xml_text'] = open(sys.argv[6]).read()
-except IndexError:
-    print('usage: %s key url request_form_id sample_form_id request_type_xml_description_file [access_role_ids,]' % os.path.basename(sys.argv[0]))
-    sys.exit(1)
-try:
-    data['role_ids'] = [i for i in sys.argv[7].split(',') if i]
-except IndexError:
-    data['role_ids'] = []
-
-submit(sys.argv[1], sys.argv[2], data)

scripts/api/requests_update_state.py

@@ -1,16 +0,0 @@
-#!/usr/bin/env python
-from __future__ import print_function
-
-import os
-import sys
-
-from common import update
-
-try:
-    data = {}
-    data['update_type'] = 'request_state'
-except IndexError:
-    print('usage: %s key url' % os.path.basename(sys.argv[0]))
-    sys.exit(1)
-
-update(sys.argv[1], sys.argv[2], data, return_formatted=True)

scripts/api/sample_configurations/sample_tracking/request_form.xml

@@ -1,15 +0,0 @@
-<form type="request" name="Sample Request Form" description="Sample Request Form description">
-    <fields>
-        <field name="field1" type="text" label="Request form field1" description="Description of request form field1" value="" required="True"/>
-        <field name="field2" type="text" area="True" label="Request form field2" description="Description of request form field2" value=""/>
-        <field name="field3" type="select" label="Request form field3" description="Description of request form field3" value="">
-            <option value="option1" />
-            <option value="option2" />
-        </field>
-        <field name="field4" type="select" label="Request form field4" description="Description of request form field4" value="" checkboxes="True">
-            <option value="option1" />
-            <option value="option2" />
-        </field>
-        <field name="field5" type="address" label="Request form field5" description="Description of request form field5"/>
-    </fields>
-</form>

scripts/api/sample_configurations/sample_tracking/request_type.xml

@@ -1,9 +0,0 @@
-<sequencer name="Sample Sequencer configuration" description="Sample Sequencer configuration description">
-    <sample_states>
-        <state name="New" description="Sample entered into the system"/>
-        <state name="Received" description="Sample tube received"/>
-        <state name="Library Started" description="Sample library preparation"/>
-        <state name="Run Started" description="Sequence run in progress"/>
-        <state name="Done" description="Sequence run complete"/>
-    </sample_states>
-</sequencer>

scripts/api/sample_configurations/sample_tracking/sample_form.xml

@@ -1,18 +0,0 @@
-<form type="sample" name="Sample Sample Form" description="Sample Sample Form description">
-    <layout>
-        <grid name="Run details" />
-    </layout>
-    <fields>
-        <field name="field1" type="text" label="Sample form field1" description="Description of sample form field1" value="" required="True" layout="Run details"/>
-        <field name="field2" type="text" area="True" label="Sample form field2" description="Description of sample form field2" value="" layout="Run details"/>
-        <field name="field3" type="select" label="Sample form field3" description="Description of sample form field3" value="" layout="Run details">
-            <option value="option1" />
-            <option value="option2" />
-        </field>
-        <field name="field4" type="select" label="Sample form field4" description="Description of sample form field4" value="" checkboxes="True" layout="Run details">
-            <option value="option1" />
-            <option value="option2" />
-        </field>
-        <field name="field5" type="address" label="Sample form field5" description="Description of sample form field5" layout="Run details"/>
-    </fields>
-</form>

scripts/api/sample_dataset_update_status.py

@@ -1,22 +0,0 @@
-#!/usr/bin/env python
-from __future__ import print_function
-
-import os
-import sys
-
-from common import update
-
-try:
-    data = {}
-    data['update_type'] = 'sample_dataset_transfer_status'
-    data['sample_dataset_ids'] = sys.argv[3].split(',')
-    data['new_status'] = sys.argv[4]
-except IndexError:
-    print('usage: %s key url sample_dataset_ids new_state [error msg]' % os.path.basename(sys.argv[0]))
-    sys.exit(1)
-try:
-    data['error_msg'] = sys.argv[5]
-except IndexError:
-    data['error_msg'] = ''
-print(data)
-update(sys.argv[1], sys.argv[2], data, return_formatted=True)

scripts/api/sample_update_state.py

@@ -1,21 +0,0 @@
-#!/usr/bin/env python
-from __future__ import print_function
-
-import os
-import sys
-
-from common import update
-
-try:
-    data = {}
-    data['update_type'] = 'sample_state'
-    data['new_state'] = sys.argv[3]
-except IndexError:
-    print('usage: %s key url new_state [comment]' % os.path.basename(sys.argv[0]))
-    sys.exit(1)
-try:
-    data['comment'] = sys.argv[4]
-except IndexError:
-    data['comment'] = ''
-
-update(sys.argv[1], sys.argv[2], data, return_formatted=True)

scripts/api/sequencer_configuration_create.py

@@ -1,51 +0,0 @@
-#!/usr/bin/env python
-from __future__ import print_function
-
-import os
-import sys
-
-from common import get, submit
-
-
-def create_sequencer_configuration(key, base_url, request_form_filename, sample_form_filename, request_type_filename, email_addresses, return_formatted=True):
-    # create request_form
-    data = {}
-    data['xml_text'] = open(request_form_filename).read()
-    request_form = submit(key, "%sforms" % base_url, data, return_formatted=False)[0]
-    # create sample_form
-    data = {}
-    data['xml_text'] = open(sample_form_filename).read()
-    sample_form = submit(key, "%sforms" % base_url, data, return_formatted=False)[0]
-    # get user ids
-    user_ids = [user['id'] for user in get(key, "%susers" % base_url) if user['email'] in email_addresses]
-    # create role, assign to user
-    data = {}
-    data['name'] = "request_type_role_%s_%s_%s name" % (request_form['id'], sample_form['id'], '_'.join(email_addresses))
-    data['description'] = "request_type_role_%s_%s_%s description" % (request_form['id'], sample_form['id'], '_'.join(email_addresses))
-    data['user_ids'] = user_ids
-    role_ids = [role['id'] for role in submit(key, "%sroles" % base_url, data, return_formatted=False)]
-    # create request_type
-    data = {}
-    data['request_form_id'] = request_form['id']
-    data['sample_form_id'] = sample_form['id']
-    data['role_ids'] = role_ids
-    data['xml_text'] = open(request_type_filename).read()
-    return submit(key, "%srequest_types" % base_url, data, return_formatted=return_formatted)  # create and print out results for request type
-
-
-def main():
-    try:
-        key = sys.argv[1]
-        base_url = sys.argv[2]
-        request_form_filename = sys.argv[3]
-        sample_form_filename = sys.argv[4]
-        request_type_filename = sys.argv[5]
-        email_addresses = sys.argv[6].split(',')
-    except IndexError:
-        print('usage: %s key base_url request_form_xml_description_file sample_form_xml_description_file request_type_xml_description_file email_address1[,email_address2]' % os.path.basename(sys.argv[0]))
-        sys.exit(1)
-    return create_sequencer_configuration(key, base_url, request_form_filename, sample_form_filename, request_type_filename, email_addresses, return_formatted=True)
-
-
-if __name__ == "__main__":
-    main()