diff --git a/README.md b/README.md
index 080854d0..175bead8 100644
--- a/README.md
+++ b/README.md
@@ -72,7 +72,8 @@ This project is set up to build docker images for the server and for the Google
docker push username/repo_name:tag_name_and_version
```
4. To build and push a docker image for GAS,
- - Update `current_release`(a variable) in [ip_addon_script.py](https://github.com/SD2E/experimental-intent-parser/blob/master/intent_parser/addons/ip_addon_script.py) to reflect the tool's version for release.
+ - Update `current_release`(a variable) in [ip_addon_script.py](https://github.com/SD2E/experimental-intent-parser/blob/master/intent_parser/addons/ip_addon_script.py) to reflect the tool's version for release.
+ - Update version in [setup.py](https://github.com/SD2E/experimental-intent-parser/blob/a0e3108888dfaa12e139dbb516a262dd63ddf271/intent_parser/setup.py#L5) to reflect the tool's version for release.
- Run the following dockerhub commands:
```
diff --git a/intent_parser/accessor/google_doc_accessor.py b/intent_parser/accessor/google_doc_accessor.py
index c72af05c..d9f2944b 100644
--- a/intent_parser/accessor/google_doc_accessor.py
+++ b/intent_parser/accessor/google_doc_accessor.py
@@ -1,5 +1,4 @@
from googleapiclient.discovery import build
-from intent_parser.constants.google_doc_api_constants import TextStyleFields
import intent_parser.constants.google_doc_api_constants as doc_constants
import logging
import statistics
@@ -111,12 +110,6 @@ def merge_table_cells(self,
return {doc_constants.REQUEST_MERGE_TABLE_CELLS: merge_properties}
- def update_text_style(self, text_start_index, text_end_index):
- text_style_properties = {doc_constants.TEXT_STYLE: '',
- doc_constants.FIELDS: TextStyleFields.BOLD,
- doc_constants.RANGE: self.create_range(text_start_index, text_end_index)}
- return {doc_constants.REQUEST_UPDATE_TEXT_STYLE: text_style_properties}
-
def execute_batch_request(self, requests, document_id):
return self._docs_service.documents().batchUpdate(documentId=document_id,
body={'requests': requests}).execute()
diff --git a/intent_parser/accessor/google_drive_accessor.py b/intent_parser/accessor/google_drive_accessor.py
index 24cd6284..7c7f65d6 100644
--- a/intent_parser/accessor/google_drive_accessor.py
+++ b/intent_parser/accessor/google_drive_accessor.py
@@ -14,6 +14,14 @@ def __init__(self, credentials):
self._service = build('drive', 'v3', credentials=credentials)
self._authed_session = AuthorizedSession(credentials)
+ def insert_comment_with_anchor(self, file_id, comment_text, quoted_tex, anchor_data):
+ body = {'content': comment_text,
+ 'quotedFileContent': {'value': quoted_tex},
+ 'anchor': json.dumps(anchor_data)}
+ results = self._service.comments.create(fileId=file_id,
+ fields='*',
+ body=body).execute()
+
def get_documents_from_folder(self, folder_id):
"""
Get all Google Docs from a Google Drive folder.
@@ -130,6 +138,52 @@ def get_file_with_revision(self, file_id, revision_id, mime_type):
response = self._authed_session.request('GET', url)
return response
+ def insert_comment_box(self, file_id, comment_message, quoted_text=None):
+ """Insert a comment box to the desired document.
+
+ Args:
+ file_id: ID of a document.
+ comment_message: message to display in comment box
+ quoted_text: text in document that comment box refers to.
+ """
+ new_comment = {'content': comment_message}
+ if quoted_text:
+ new_comment['context'] = {'value': quoted_text}
+ try:
+ response = self._service.comments().insert(fileId=file_id,
+ body=new_comment).execute()
+ except errors.HttpError as error:
+ self.logger.warning('Unable to insert comment box to file: %s due to %s' % (file_id, error))
+
+ def retrieve_comments(self, file_id):
+ """Retrieve a list of comments.
+
+ Args:
+ service: Drive API service instance.
+ file_id: ID of the file to retrieve comments for.
+ Returns:
+ List of comments.
+ """
+ try:
+ comments = self._service.comments().list(fileId=file_id).execute()
+ return comments.get('items', [])
+ except errors.HttpError as error:
+ self.logger.warning('Unable to retrieve comments from file: %s due to %s' % (file_id, error))
+
+ def remove_comment(self, file_id, comment_id):
+ """Remove a comment.
+
+ Args:
+ service: Drive API service instance.
+ file_id: ID of the file to remove the comment for.
+ comment_id: ID of the comment to remove.
+ """
+ try:
+ self._service.comments().delete(
+ fileId=file_id, commentId=comment_id).execute()
+ except errors.HttpError as error:
+ self.logger.warning('Unable to remove comment box from file: %s due to %s' % (file_id, error))
+
def upload_revision(self, document_name, document, folder_id, original_format, title='Untitled',
target_format='*/*'):
"""Upload file to a Google Drive folder.
diff --git a/intent_parser/accessor/item-map.json b/intent_parser/accessor/item-map.json
index 524d7981..cd0f08b9 100644
--- a/intent_parser/accessor/item-map.json
+++ b/intent_parser/accessor/item-map.json
@@ -1 +1 @@
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pSNR52::sgpCUP1-1 2xMS2|pGPD::dCAs9| pGPD::NLS-MCP-VP64 LEU|URA|HIS|TRP": "https://hub.sd2e.org/user/sd2e/design/pCENK20x20Diploid0x20pCUP10x3A0x3AeYFP0x7C0x20pSNR520x3A0x3AsgpCUP10x2D10x202xMS20x7CpGPD0x3A0x3AdCAs90x7C0x20pGPD0x3A0x3ANLS0x2DMCP0x2DVP640x20LEU0x7CURA0x7CHIS0x7CTRP/1", "24781": "https://hub.sd2e.org/user/sd2e/design/pCENK20x20Diploid0x20pCUP10x3A0x3AeYFP0x7C0x20pSNR520x3A0x3AsgpCUP10x2D10x202xMS20x7CpGPD0x3A0x3AdCAs90x7C0x20pGPD0x3A0x3ANLS0x2DMCP0x2DVP640x20LEU0x7CURA0x7CHIS0x7CTRP/1", "pCENK2 Diploid pCUP1::eYFP| pSNR52::sgpCUP1-1 2xMS2|pGPD::dCAs9| pGPD::NLS-PCP-VP64 LEU|URA|HIS|TRP": "https://hub.sd2e.org/user/sd2e/design/pCENK20x20Diploid0x20pCUP10x3A0x3AeYFP0x7C0x20pSNR520x3A0x3AsgpCUP10x2D10x202xMS20x7CpGPD0x3A0x3AdCAs90x7C0x20pGPD0x3A0x3ANLS0x2DPCP0x2DVP640x20LEU0x7CURA0x7CHIS0x7CTRP/1", "24789": 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pSNR52::sgpCUP1-6 1xMS2|pGPD::dCAs9| pGPD::NLS-MCP-VP64 LEU|URA|HIS|TRP": "https://hub.sd2e.org/user/sd2e/design/pCENK20x20Diploid0x20pCUP10x3A0x3AeYFP0x7C0x20pSNR520x3A0x3AsgpCUP10x2D60x201xMS20x7CpGPD0x3A0x3AdCAs90x7C0x20pGPD0x3A0x3ANLS0x2DMCP0x2DVP640x20LEU0x7CURA0x7CHIS0x7CTRP/1", "24762": "https://hub.sd2e.org/user/sd2e/design/pCENK20x20Diploid0x20pCUP10x3A0x3AeYFP0x7C0x20pSNR520x3A0x3AsgpCUP10x2D60x201xMS20x7CpGPD0x3A0x3AdCAs90x7C0x20pGPD0x3A0x3ANLS0x2DMCP0x2DVP640x20LEU0x7CURA0x7CHIS0x7CTRP/1", "pCENK2 Diploid pCUP1::eYFP| pSNR52::sgpCUP1-6 1xMS2|pGPD::dCAs9| pGPD::NLS-PCP-VP64 LEU|URA|HIS|TRP": "https://hub.sd2e.org/user/sd2e/design/pCENK20x20Diploid0x20pCUP10x3A0x3AeYFP0x7C0x20pSNR520x3A0x3AsgpCUP10x2D60x201xMS20x7CpGPD0x3A0x3AdCAs90x7C0x20pGPD0x3A0x3ANLS0x2DPCP0x2DVP640x20LEU0x7CURA0x7CHIS0x7CTRP/1", "24770": 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"https://hub.sd2e.org/user/sd2e/design/pCENK20x20Diploid0x20pCUP10x3A0x3AeYFP0x7C0x20pSNR520x3A0x3AsgpCUP10x2D30x201xPP70x7CpGPD0x3A0x3AdCAs90x7C0x20pGPD0x3A0x3ANLS0x2DMCP0x2DVP640x20LEU0x7CURA0x7CHIS0x7CTRP/1", "24807": "https://hub.sd2e.org/user/sd2e/design/pCENK20x20Diploid0x20pCUP10x3A0x3AeYFP0x7C0x20pSNR520x3A0x3AsgpCUP10x2D30x201xPP70x7CpGPD0x3A0x3AdCAs90x7C0x20pGPD0x3A0x3ANLS0x2DMCP0x2DVP640x20LEU0x7CURA0x7CHIS0x7CTRP/1", "pCENK2 Diploid pCUP1::eYFP| pSNR52::sgpCUP1-4 1xPP7|pGPD::dCAs9| pGPD::NLS-MCP-VP64 LEU|URA|HIS|TRP": "https://hub.sd2e.org/user/sd2e/design/pCENK20x20Diploid0x20pCUP10x3A0x3AeYFP0x7C0x20pSNR520x3A0x3AsgpCUP10x2D40x201xPP70x7CpGPD0x3A0x3AdCAs90x7C0x20pGPD0x3A0x3ANLS0x2DMCP0x2DVP640x20LEU0x7CURA0x7CHIS0x7CTRP/1", "24808": "https://hub.sd2e.org/user/sd2e/design/pCENK20x20Diploid0x20pCUP10x3A0x3AeYFP0x7C0x20pSNR520x3A0x3AsgpCUP10x2D40x201xPP70x7CpGPD0x3A0x3AdCAs90x7C0x20pGPD0x3A0x3ANLS0x2DMCP0x2DVP640x20LEU0x7CURA0x7CHIS0x7CTRP/1", "pCENK2 Diploid pCUP1::eYFP| 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pSNR52::sgpCUP1-4 2xCOM|pGPD::dCAs9| pGPD::NLS-COM-VP64 LEU|URA|HIS|TRP": "https://hub.sd2e.org/user/sd2e/design/pCENK20x20Diploid0x20pCUP10x3A0x3AeYFP0x7C0x20pSNR520x3A0x3AsgpCUP10x2D40x202xCOM0x7CpGPD0x3A0x3AdCAs90x7C0x20pGPD0x3A0x3ANLS0x2DCOM0x2DVP640x20LEU0x7CURA0x7CHIS0x7CTRP/1", "24848": "https://hub.sd2e.org/user/sd2e/design/pCENK20x20Diploid0x20pCUP10x3A0x3AeYFP0x7C0x20pSNR520x3A0x3AsgpCUP10x2D40x202xCOM0x7CpGPD0x3A0x3AdCAs90x7C0x20pGPD0x3A0x3ANLS0x2DCOM0x2DVP640x20LEU0x7CURA0x7CHIS0x7CTRP/1", "pCENK2 Diploid pCUP1::eYFP| pSNR52::sgpCUP1-4 2xCOM|pGPD::dCAs9| pGPD::NLS-MCP-VP64 LEU|URA|HIS|TRP": "https://hub.sd2e.org/user/sd2e/design/pCENK20x20Diploid0x20pCUP10x3A0x3AeYFP0x7C0x20pSNR520x3A0x3AsgpCUP10x2D40x202xCOM0x7CpGPD0x3A0x3AdCAs90x7C0x20pGPD0x3A0x3ANLS0x2DMCP0x2DVP640x20LEU0x7CURA0x7CHIS0x7CTRP/1", "24832": 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"https://hub.sd2e.org/user/sd2e/design/pCENK20x20Diploid0x20pCUP10x3A0x3AeYFP0x7C0x20pSNR520x3A0x3AsgpCUP10x2D50x201xPP70x7CpGPD0x3A0x3AdCAs90x7C0x20pGPD0x3A0x3ANLS0x2DPCP0x2DVP640x20LEU0x7CURA0x7CHIS0x7CTRP/1", "24817": "https://hub.sd2e.org/user/sd2e/design/pCENK20x20Diploid0x20pCUP10x3A0x3AeYFP0x7C0x20pSNR520x3A0x3AsgpCUP10x2D50x201xPP70x7CpGPD0x3A0x3AdCAs90x7C0x20pGPD0x3A0x3ANLS0x2DPCP0x2DVP640x20LEU0x7CURA0x7CHIS0x7CTRP/1", "pCENK2 Diploid pCUP1::eYFP| pSNR52::sgpCUP1-6 1xMS2|pGPD::dCAs9| pGPD::NLS-COM-VP64 LEU|URA|HIS|TRP": "https://hub.sd2e.org/user/sd2e/design/pCENK20x20Diploid0x20pCUP10x3A0x3AeYFP0x7C0x20pSNR520x3A0x3AsgpCUP10x2D60x201xMS20x7CpGPD0x3A0x3AdCAs90x7C0x20pGPD0x3A0x3ANLS0x2DCOM0x2DVP640x20LEU0x7CURA0x7CHIS0x7CTRP/1", "24778": "https://hub.sd2e.org/user/sd2e/design/pCENK20x20Diploid0x20pCUP10x3A0x3AeYFP0x7C0x20pSNR520x3A0x3AsgpCUP10x2D60x201xMS20x7CpGPD0x3A0x3AdCAs90x7C0x20pGPD0x3A0x3ANLS0x2DCOM0x2DVP640x20LEU0x7CURA0x7CHIS0x7CTRP/1", "pCENK2 Diploid pCUP1::eYFP| pSNR52::sgpCUP1-6 1xMS2|pGPD::dCAs9| pGPD::NLS-MCP-VP64 LEU|URA|HIS|TRP": "https://hub.sd2e.org/user/sd2e/design/pCENK20x20Diploid0x20pCUP10x3A0x3AeYFP0x7C0x20pSNR520x3A0x3AsgpCUP10x2D60x201xMS20x7CpGPD0x3A0x3AdCAs90x7C0x20pGPD0x3A0x3ANLS0x2DMCP0x2DVP640x20LEU0x7CURA0x7CHIS0x7CTRP/1", "24762": "https://hub.sd2e.org/user/sd2e/design/pCENK20x20Diploid0x20pCUP10x3A0x3AeYFP0x7C0x20pSNR520x3A0x3AsgpCUP10x2D60x201xMS20x7CpGPD0x3A0x3AdCAs90x7C0x20pGPD0x3A0x3ANLS0x2DMCP0x2DVP640x20LEU0x7CURA0x7CHIS0x7CTRP/1", "pCENK2 Diploid pCUP1::eYFP| pSNR52::sgpCUP1-6 1xMS2|pGPD::dCAs9| pGPD::NLS-PCP-VP64 LEU|URA|HIS|TRP": "https://hub.sd2e.org/user/sd2e/design/pCENK20x20Diploid0x20pCUP10x3A0x3AeYFP0x7C0x20pSNR520x3A0x3AsgpCUP10x2D60x201xMS20x7CpGPD0x3A0x3AdCAs90x7C0x20pGPD0x3A0x3ANLS0x2DPCP0x2DVP640x20LEU0x7CURA0x7CHIS0x7CTRP/1", "24770": 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"https://hub.sd2e.org/user/sd2e/design/pCENK20x20Diploid0x20pCUP10x3A0x3AeYFP0x7C0x20pSNR520x3A0x3AsgpCUP10x2D70x201xMS20x7CpGPD0x3A0x3AdCAs90x7C0x20pGPD0x3A0x3ANLS0x2DCOM0x2DVP640x20LEU0x7CURA0x7CHIS0x7CTRP/1", "24779": "https://hub.sd2e.org/user/sd2e/design/pCENK20x20Diploid0x20pCUP10x3A0x3AeYFP0x7C0x20pSNR520x3A0x3AsgpCUP10x2D70x201xMS20x7CpGPD0x3A0x3AdCAs90x7C0x20pGPD0x3A0x3ANLS0x2DCOM0x2DVP640x20LEU0x7CURA0x7CHIS0x7CTRP/1", "pCENK2 Diploid pCUP1::eYFP| pSNR52::sgpCUP1-7 1xMS2|pGPD::dCAs9| pGPD::NLS-MCP-VP64 LEU|URA|HIS|TRP": "https://hub.sd2e.org/user/sd2e/design/pCENK20x20Diploid0x20pCUP10x3A0x3AeYFP0x7C0x20pSNR520x3A0x3AsgpCUP10x2D70x201xMS20x7CpGPD0x3A0x3AdCAs90x7C0x20pGPD0x3A0x3ANLS0x2DMCP0x2DVP640x20LEU0x7CURA0x7CHIS0x7CTRP/1", "24763": "https://hub.sd2e.org/user/sd2e/design/pCENK20x20Diploid0x20pCUP10x3A0x3AeYFP0x7C0x20pSNR520x3A0x3AsgpCUP10x2D70x201xMS20x7CpGPD0x3A0x3AdCAs90x7C0x20pGPD0x3A0x3ANLS0x2DMCP0x2DVP640x20LEU0x7CURA0x7CHIS0x7CTRP/1", "pCENK2 Diploid pCUP1::eYFP| pSNR52::sgpCUP1-7 1xMS2|pGPD::dCAs9| pGPD::NLS-PCP-VP64 LEU|URA|HIS|TRP": "https://hub.sd2e.org/user/sd2e/design/pCENK20x20Diploid0x20pCUP10x3A0x3AeYFP0x7C0x20pSNR520x3A0x3AsgpCUP10x2D70x201xMS20x7CpGPD0x3A0x3AdCAs90x7C0x20pGPD0x3A0x3ANLS0x2DPCP0x2DVP640x20LEU0x7CURA0x7CHIS0x7CTRP/1", "24771": "https://hub.sd2e.org/user/sd2e/design/pCENK20x20Diploid0x20pCUP10x3A0x3AeYFP0x7C0x20pSNR520x3A0x3AsgpCUP10x2D70x201xMS20x7CpGPD0x3A0x3AdCAs90x7C0x20pGPD0x3A0x3ANLS0x2DPCP0x2DVP640x20LEU0x7CURA0x7CHIS0x7CTRP/1", "pCENK2 Diploid pCUP1::eYFP| pSNR52::sgpCUP1-7 1xPP7|pGPD::dCAs9| pGPD::NLS-PCP-VP64 LEU|URA|HIS|TRP": "https://hub.sd2e.org/user/sd2e/design/pCENK20x20Diploid0x20pCUP10x3A0x3AeYFP0x7C0x20pSNR520x3A0x3AsgpCUP10x2D70x201xPP70x7CpGPD0x3A0x3AdCAs90x7C0x20pGPD0x3A0x3ANLS0x2DPCP0x2DVP640x20LEU0x7CURA0x7CHIS0x7CTRP/1", "24819": 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\ No newline at end of file
diff --git a/intent_parser/accessor/sbol_dictionary_accessor.py b/intent_parser/accessor/sbol_dictionary_accessor.py
index a9b6e002..b8b8cd99 100644
--- a/intent_parser/accessor/sbol_dictionary_accessor.py
+++ b/intent_parser/accessor/sbol_dictionary_accessor.py
@@ -1,4 +1,5 @@
from datetime import timedelta
+from intent_parser.experiment_variables.experiment_variables import ExperimentVariable
from intent_parser.accessor.google_accessor import GoogleAccessor
from intent_parser.intent_parser_exceptions import DictionaryMaintainerException
import intent_parser.table.cell_parser as cell_parser
@@ -370,7 +371,7 @@ def gen_row_data(self, entry, tab):
def map_common_names_and_tacc_id(self):
result = {}
- attribute_tab = self.get_tab_sheet(dictionary_constants.ATTRIBUTE_TAB)
+ attribute_tab = self.get_tab_sheet(dictionary_constants.TAB_ATTRIBUTE)
for row in attribute_tab:
if dictionary_constants.COLUMN_COMMON_NAME in row and dictionary_constants.COLUMN_TACC_UID in row:
common_name = row[dictionary_constants.COLUMN_COMMON_NAME]
@@ -394,20 +395,34 @@ def get_mapped_strain(self, lab_name):
raise DictionaryMaintainerException(message)
lab_uid = dictionary_constants.MAPPED_LAB_UID[lab_name]
- strain_tab = self.get_tab_sheet(dictionary_constants.STRAIN_TAB)
+ strain_tab = self.get_tab_sheet(dictionary_constants.TAB_STRAIN)
for row in strain_tab:
- if dictionary_constants.COLUMN_COMMON_NAME in row \
- and dictionary_constants.COLUMN_SYNBIOHUB_URI in row\
- and lab_uid in row:
+ if (dictionary_constants.COLUMN_COMMON_NAME in row
+ and dictionary_constants.COLUMN_SYNBIOHUB_URI in row
+ and lab_uid in row):
sbh_uri = row[dictionary_constants.COLUMN_SYNBIOHUB_URI]
common_name = row[dictionary_constants.COLUMN_COMMON_NAME]
lab_strain_names = {}
if row[lab_uid]:
lab_strain_names = [name for name in cell_parser.PARSER.extract_name_value(row[lab_uid])]
- mapped_strains[sbh_uri] = StrainMapping(sbh_uri, lab_name, common_name, lab_names=lab_strain_names)
-
+ mapped_strains[sbh_uri] = ExperimentVariable(sbh_uri, lab_name, common_name, lab_names=lab_strain_names)
return mapped_strains
+ def create_experiment_variables_from_spreadsheet_tab(self, tab):
+ experiment_variables ={}
+ for row in tab:
+ if (dictionary_constants.COLUMN_COMMON_NAME in row and dictionary_constants.COLUMN_SYNBIOHUB_URI in row):
+ sbh_uri = row[dictionary_constants.COLUMN_SYNBIOHUB_URI]
+ common_name = row[dictionary_constants.COLUMN_COMMON_NAME]
+ for lab_name, lab_uid in dictionary_constants.MAPPED_LAB_UID.items():
+ if lab_uid and lab_uid in row:
+ if row[lab_uid]:
+ lab_strain_names = [name for name in cell_parser.PARSER.extract_name_value(row[lab_uid])]
+ experiment_variables[common_name] = ExperimentVariable(sbh_uri, lab_name, common_name, lab_names=lab_strain_names)
+ else:
+ experiment_variables[common_name] = ExperimentVariable(sbh_uri, lab_name, common_name)
+ return experiment_variables
+
def get_common_name_from_transcriptic_id(self, transcriptic_id):
mappings = self.map_common_names_and_transcriptic_id()
for key, value in mappings.items():
@@ -417,7 +432,7 @@ def get_common_name_from_transcriptic_id(self, transcriptic_id):
def map_common_names_and_transcriptic_id(self):
result = {}
- attribute_tab = self.get_tab_sheet(dictionary_constants.ATTRIBUTE_TAB)
+ attribute_tab = self.get_tab_sheet(dictionary_constants.TAB_ATTRIBUTE)
for row in attribute_tab:
if dictionary_constants.COLUMN_COMMON_NAME in row and dictionary_constants.COLUMN_TRANSCRIPT_UID in row:
common_name = row[dictionary_constants.COLUMN_COMMON_NAME]
@@ -492,19 +507,3 @@ def get_common_names_to_uri(self, use_cache=False):
self.logger.info('Num items in item_map: %d' % len(item_map))
return item_map
-class StrainMapping(object):
-
- def __init__(self, sbh_uri, lab_id, common_name, lab_names={}):
- self._sbh_uri = sbh_uri
- self._lab_id = lab_id
- self._common_name = common_name
- self._lab_names = lab_names
-
- def get_common_name(self):
- return self._common_name
-
- def get_lab_id(self):
- return self._lab_id
-
- def has_lab_name(self, lab_name):
- return lab_name in self._lab_names
diff --git a/intent_parser/addons/Code.js b/intent_parser/addons/Code.js
index 68bcda28..7b0fa2cc 100644
--- a/intent_parser/addons/Code.js
+++ b/intent_parser/addons/Code.js
@@ -1,5 +1,5 @@
var serverURL = 'http://intentparser.sd2e.org';
-var versionString = '2.8';
+var versionString = '2.9';
function onOpen() {
const ui = DocumentApp.getUi();
@@ -8,6 +8,15 @@ function onOpen() {
tablesMenu.addItem('Parameters', 'createParameterTable');
tablesMenu.addItem('Measurements', 'createTableMeasurements');
+ const tableHelpMenu = ui.createMenu('Tables');
+ tableHelpMenu.addItem('Controls', 'reportControlsInfo');
+ tableHelpMenu.addItem('Lab', 'reportLabInfo');
+ tableHelpMenu.addItem('Measurements', 'reportMeasurementsInfo');
+
+ const helpMenu = ui.createMenu('Help');
+ helpMenu.addSubMenu(tableHelpMenu);
+ helpMenu.addItem('About', 'showHelp');
+
const menu = ui.createMenu('Parse Intent');
menu.addItem('Analyze from top', 'sendAnalyzeFromTop');
menu.addItem('Analyze from cursor', 'sendAnalyzeFromCursor');
@@ -23,10 +32,62 @@ function onOpen() {
menu.addItem('Report Experiment Status', 'reportExperimentStatus');
menu.addSubMenu(tablesMenu);
menu.addItem('File Issues', 'reportIssues');
- menu.addItem('Help', 'showHelp');
+ menu.addSubMenu(helpMenu);
menu.addToUi();
}
+function reportControlsInfo(){
+ html_content = ' Controls Table \n' +
+ 'Description : control definition based on time, strain, contents, etc.
\n' +
+ 'Required fields: \n' +
+ '\n' +
+ '\t Type : an expected type for this control. Example: HIGH_FITCStrains : a list of one or more string values representing a strain listed in the SBOL Dictionary lab name. Example: B_subtilis_comKS_mCherry_1x \n' +
+ 'Optional fields: \n' +
+ '\n' +
+ '\tChannel : a string value representing FCS channel. Example: BL1-AContents : a list of one or more string values representing the content of a control. A content can come in the form of a name or a name followed by a value, followed by a timepoint unit. Example: beta_estradiol or beta_estradiol 0.05 micromoleTimepoints Example: 2, 4 hours ';
+ showSidebar(html_content);
+}
+
+function reportLabInfo(){
+ html_content = ' Lab Table \n' +
+ 'Description : information linked to a lab.
\n' +
+ 'Required fields: \n' +
+ '\n' +
+ '\t Lab : a string value representing the lab that performed this experiment. Example: TACC \n' +
+ 'Optionalfields: \n' +
+ '\n' +
+ '\tExperiment_id : a string identifier, namespaced performer, for the experiment. Example: 123 ';
+ showSidebar(html_content);
+}
+
+function reportMeasurementsInfo(){
+ html_content = ' Measurements Table \n' +
+ 'Description : measurements expected to be produced for a run, broken down by measurement type and sample conditions.
\n' +
+ 'Required fields: \n' +
+ '\n' +
+ '\t Measurement Type : an expected file type for this measurement. Example: RNA_SEQ File Type : a list of one or more expected file type for this measurement. Example: MSWORD, SPREADSHEET \n' +
+ 'Optional fields: \n' +
+ '\n' +
+ '\tBatch : a list of one or more numerical values representing the batches a measurement belongs to. Example: 1, 2, 3Controls : a list of Control Table captions for representing expected control elements for this run. Example: Table 1, Table 2Ods : a list of one or more numerical values representing expected optical densities for this measurement. Example: 5Replicates : a list of one or more numerical values representing expected number of replicates. Example: 6Strains : a list of one or more string values representing expected strains for this measurement. Strains listed in this field must have a hyperlink that references to a SBH URI. Example: UWBF_6390Temperatures Example : 30 celsiusTimepoints Example: 0, 4, 8, 12, 16 hour ';
+ showSidebar(html_content);
+}
+
function showHelp() {
var helpHTML = '\
\
diff --git a/intent_parser/addons/addon_file.json b/intent_parser/addons/addon_file.json
index 20145056..6edff8ed 100644
--- a/intent_parser/addons/addon_file.json
+++ b/intent_parser/addons/addon_file.json
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/intent_parser/constants/google_doc_api_constants.py b/intent_parser/constants/google_doc_api_constants.py
index 5ad3de86..858df483 100644
--- a/intent_parser/constants/google_doc_api_constants.py
+++ b/intent_parser/constants/google_doc_api_constants.py
@@ -1,5 +1,3 @@
-from enum import Enum
-
REQUEST_DELETE_CONTENT_RANGE = 'deleteContentRange'
REQUEST_DELETE_TABLE_ROW = 'deleteTableRow'
REQUEST_INSERT_TABLE = 'insertTable'
@@ -8,13 +6,9 @@
REQUEST_MERGE_TABLE_CELLS = 'mergeTableCells'
REQUEST_UPDATE_TEXT_STYLE = 'updateTextStyle'
-BOLD = 'bold'
-ITALIC = 'italic'
-UNDERLINE = 'underline'
-STRIKETHROUGH = 'strikethrough'
-SMALL_CAPS = 'smallCaps'
-HEADING_ID = 'headingId'
+
BODY = 'body'
+BOLD = 'bold'
BOOKMARK_ID = 'bookmarkId'
CONTENT = 'content'
COLUMN_INDEX = 'columnIndex'
@@ -24,8 +18,10 @@
END_INDEX = 'endIndex'
END_OF_SEGMENT_LOCATION = 'endOfSegmentLocation'
FIELDS = 'fields'
+HEADING_ID = 'headingId'
INDEX = 'index'
INSERT_BELOW = 'insertBelow'
+ITALIC = 'italic'
LINK = 'link'
LOCATION = 'location'
NUMBER_OF_COLUMNS = 'columns'
@@ -35,7 +31,9 @@
ROW_INDEX = 'rowIndex'
ROW_SPAN = 'rowSpan'
SEGMENT_ID = 'segmentId'
+SMALL_CAPS = 'smallCaps'
START_INDEX = 'startIndex'
+STRIKETHROUGH = 'strikethrough'
TABLE = 'table'
TABLE_CELLS = 'tableCells'
TABLE_CELL_LOCATION = 'tableCellLocation'
@@ -45,8 +43,6 @@
TEXT = 'text'
TEXT_RUN = 'textRun'
TEXT_STYLE = 'textStyle'
+UNDERLINE = 'underline'
URL = 'url'
-class TextStyleFields(Enum):
- BOLD = 'bold'
- UNKNOWN = '*'
diff --git a/intent_parser/constants/intent_parser_constants.py b/intent_parser/constants/intent_parser_constants.py
index 37e5a17a..546dd17f 100644
--- a/intent_parser/constants/intent_parser_constants.py
+++ b/intent_parser/constants/intent_parser_constants.py
@@ -45,10 +45,12 @@
GOOGLE_DOC_MIMETYPE = 'application/vnd.google-apps.document'
WORD_DOC_MIMETYPE = 'application/vnd.openxmlformats-officedocument.wordprocessingml.document'
+# Stateos Protocols Supported in IP
GROWTH_CURVE_PROTOCOL = 'GrowthCurve'
OBSTACLE_COURSE_PROTOCOL = 'ObstacleCourse'
TIME_SERIES_HTP_PROTOCOL = 'TimeSeriesHTP'
+# Mapping protocols to human readible names
PARAMETER_PROTOCOL = 'protocol'
PROTOCOL_NAMES = {GROWTH_CURVE_PROTOCOL: 'Growth Curves',
TIME_SERIES_HTP_PROTOCOL: 'Time Series',
@@ -57,6 +59,7 @@
PARAMETER_EXPERIMENT_REFERENCE_URL_FOR_XPLAN = 'experiment_reference_url_for_xplan'
PARAMETER_TEST_MODE = 'test_mode'
PARAMETER_SUBMIT = 'submit'
+PARAMETER_BASE_DIR = 'xplan_base_dir'
PARAMETER_XPLAN_REACTOR = 'xplan_reactor'
PARAMETER_PLATE_SIZE = 'plate_size'
PARAMETER_PLATE_NUMBER = 'plate_number'
@@ -66,7 +69,9 @@
PARAMETER_PROTOCOL_ID = 'protocol_id'
PARAMETER_EXP_INFO_MEDIA_WELL_STRINGS = 'exp_info.media_well_strings'
+PARAMETER_INDUCTION_INFO_REAGENTS = 'induction_info.induction_reagents'
PARAMETER_INDUCTION_INFO_REAGENTS_INDUCER = 'induction_info.induction_reagents.inducer'
+PARAMETER_INDUCTION_INFO_SAMPLING_INFO = 'induction_info.sampling_info'
PARAMETER_MEASUREMENT_INFO_36_HR_READ = 'measurement_info.36_hr_read'
PARAMETER_MEASUREMENT_INFO_FLOW_INFO = 'measurement_info.flow_info'
PARAMETER_MEASUREMENT_INFO_PLATE_READER_INFO = 'measurement_info.plate_reader_info'
@@ -85,7 +90,7 @@
TEST_SPREADSHEET_ID = '1wHX8etUZFMrvmsjvdhAGEVU1lYgjbuRX5mmYlKv7kdk' # Intent parser test dict
UNIT_TEST_SPREADSHEET_ID = '1r3CIyv75vV7A7ghkB0od-TM_16qSYd-byAbQ1DhRgB0' #sd2 unit test dictionary
-# Header types
+# Table headers
HEADER_BATCH_VALUE = 'batch'
HEADER_CHANNEL_VALUE = 'Channel'
HEADER_CONTENTS_VALUE = 'Contents'
@@ -110,6 +115,7 @@
HEADER_TEMPERATURE_VALUE = 'temperature'
HEADER_TIMEPOINT_VALUE = 'Timepoint'
+# Table header types
HEADER_BATCH_TYPE = 'BATCH'
HEADER_CHANNEL_TYPE = 'CHANNEL'
HEADER_CONTENTS_TYPE = 'CONTENTS'
diff --git a/intent_parser/constants/ip_app_script_constants.py b/intent_parser/constants/ip_app_script_constants.py
index 1ab0e13e..68103f59 100644
--- a/intent_parser/constants/ip_app_script_constants.py
+++ b/intent_parser/constants/ip_app_script_constants.py
@@ -1,8 +1,29 @@
"""
List of constants used in intent parser's Google App Script Add-on
"""
+ACTION_UPDATE_PROGRESS = 'updateProgress'
+
+ANALYZE_CONTENT_TERM = 'content_term'
+ANALYZE_END_OFFSET = 'end_offset'
+ANALYZE_LINK = 'link'
+ANALYZE_NEVER_LINK = 'process_never_link'
+ANALYZE_NO = 'process_analyze_no'
+ANALYZE_NO_TO_ALL = 'process_no_to_all'
+ANALYZE_PARAGRAPH_INDEX = 'paragraph_index'
+ANALYZE_PROGRESS = 'progress'
+ANALYZE_OFFSET = 'offset'
+ANALYZE_SEARCH_RESULTS = 'search_results'
+ANALYZE_SEARCH_RESULT_INDEX = 'search_result_index'
+ANALYZE_TERM = 'term'
+ANALYZE_YES = 'process_analyze_yes'
+ANALYZE_YES_TO_ALL = 'process_link_all'
+
+BUTTON_ID = 'buttonId'
CHILD_INDEX = 'childIndex'
CURSOR_CHILD_INDEX = 'cursorChildIndex'
+DATA = 'data'
+DOCUMENT_ID = 'documentId'
+USER_ID = 'user_id'
HTML_BATCH = 'batch'
HTML_CAPTION = 'caption'
@@ -31,3 +52,4 @@
TABLE_TYPE_LAB = 'tableLab'
TABLE_TYPE_MEASUREMENTS = 'measurements'
TABLE_TYPE_PARAMETERS = 'parameters'
+
diff --git a/intent_parser/constants/sbol_dictionary_constants.py b/intent_parser/constants/sbol_dictionary_constants.py
index fdf913a4..94593592 100644
--- a/intent_parser/constants/sbol_dictionary_constants.py
+++ b/intent_parser/constants/sbol_dictionary_constants.py
@@ -1,10 +1,14 @@
+from enum import Enum
import intent_parser.constants.sd2_datacatalog_constants as dc_constants
"""
List of constants used for referring to terms in SBOL Dictionary spreadsheet.
"""
-ATTRIBUTE_TAB = 'Attribute'
-STRAIN_TAB = 'Strain'
+TAB_ATTRIBUTE = 'Attribute'
+TAB_GENETIC_CONSTRUCTS = 'Genetic Construct'
+TAB_PROTEIN = 'Protein'
+TAB_REAGENT = 'Reagent'
+TAB_STRAIN = 'Strain'
COLUMN_BIOFAB_UID = 'BioFAB UID'
COLUMN_CALTECH_UID = 'CalTech UID'
@@ -32,3 +36,28 @@
dc_constants.LAB_UCSB_YEUNG: None,
dc_constants.LAB_UW_BIOFAB: COLUMN_BIOFAB_UID
}
+
+TYPE_ATTRIBUTE = 'Attribute'
+TYPE_BEAD = 'Bead'
+TYPE_BUFFER = 'Buffer'
+TYPE_CHEBI = 'CHEBI'
+TYPE_DNA = 'DNA'
+TYPE_MEDIA = 'Media'
+TYPE_PROTEIN = 'Protein'
+TYPE_RNA = 'RNA'
+TYPE_SOLUTION = 'Solution'
+TYPE_STAIN = 'Stain'
+TYPE_STRAIN = 'Strain'
+
+class VariableType(Enum):
+ ATTRIBUTE = 1
+ BEAD = 2
+ BUFFER = 3
+ CHEBI = 4
+ DNA = 5
+ MEDIA = 6
+ PROTEIN = 7
+ RNA = 8
+ SOLUTION = 9
+ STAIN = 10
+ STRAIN = 11
diff --git a/intent_parser/constants/sd2_datacatalog_constants.py b/intent_parser/constants/sd2_datacatalog_constants.py
index e662e2be..70f67f26 100644
--- a/intent_parser/constants/sd2_datacatalog_constants.py
+++ b/intent_parser/constants/sd2_datacatalog_constants.py
@@ -14,7 +14,7 @@
EXPERIMENT_REFERENCE_URL = 'experiment_reference_url'
EXPERIMENT_VERSION = 'experiment_version'
FILE_TYPE ='file_type'
-
+GENERATE = 'generate'
LAB = 'lab'
LAB_CALTECH = 'Caltech'
LAB_DUKE_HAASE = 'Duke_Haase'
diff --git a/intent_parser/document/__init__.py b/intent_parser/document/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/intent_parser/document/intent_parser_document.py b/intent_parser/document/intent_parser_document.py
new file mode 100644
index 00000000..23ed7890
--- /dev/null
+++ b/intent_parser/document/intent_parser_document.py
@@ -0,0 +1,13 @@
+class IntentParserDocument(object):
+ """
+ An internal data structure for representing the contents of a table cell.
+ """
+
+ def __init__(self):
+ self.paragraphs = []
+
+ def add_paragraph(self, paragraph):
+ self.paragraphs.append(paragraph)
+
+ def get_paragraphs(self):
+ return self.paragraphs
diff --git a/intent_parser/document/intent_parser_document_factory.py b/intent_parser/document/intent_parser_document_factory.py
new file mode 100644
index 00000000..34ee9c47
--- /dev/null
+++ b/intent_parser/document/intent_parser_document_factory.py
@@ -0,0 +1,120 @@
+from intent_parser.document.intent_parser_document import IntentParserDocument
+import intent_parser.constants.google_doc_api_constants as doc_constants
+
+class IntentParserDocumentFactory(object):
+
+ def __init__(self):
+ self._google_document_parser = GoogleDocumentParser()
+
+ def from_google_doc(self, document):
+ ip_document = self._google_document_parser.parse_document(document)
+ return ip_document
+
+class DocumentParser(object):
+
+ def parse_document(self, document):
+ pass
+
+
+class GoogleDocumentParser(DocumentParser):
+
+ def __init__(self):
+ pass
+
+ def parse_document(self, document):
+ intent_parser_doc = IntentParserDocument()
+ doc_properties = document[doc_constants.BODY][doc_constants.CONTENT]
+ paragraph_index = 0
+ while len(doc_properties) > 0:
+ property = doc_properties.pop(0)
+ if doc_constants.PARAGRAPH in property:
+ paragraph = self._parse_paragraphs(property[doc_constants.PARAGRAPH])
+ paragraph.set_start_index(property[doc_constants.START_INDEX])
+ paragraph.set_end_index(property[doc_constants.END_INDEX])
+ paragraph.set_paragraph_index(paragraph_index)
+ intent_parser_doc.add_paragraph(paragraph)
+ paragraph_index += 1
+ elif doc_constants.TABLE in property:
+ doc_properties = self._get_properties_from_table(property[doc_constants.TABLE]) + doc_properties
+
+ return intent_parser_doc
+
+ def _get_properties_from_table(self, table_property):
+ properties = []
+
+ if doc_constants.TABLE_ROWS in table_property:
+ for row_property in table_property[doc_constants.TABLE_ROWS]:
+ properties.extend(self._get_properties_from_table_row(row_property))
+ return properties
+
+ def _get_properties_from_table_row(self, row_property):
+ properties = []
+
+ if doc_constants.TABLE_CELLS in row_property:
+ for cell_property in row_property[doc_constants.TABLE_CELLS]:
+ if doc_constants.CONTENT in cell_property:
+ for content_property in cell_property[doc_constants.CONTENT]:
+ properties.append(content_property)
+ return properties
+
+ def _parse_paragraphs(self, paragraph):
+ ip_paragraph = self.Paragraph()
+ for element in paragraph[doc_constants.ELEMENTS]:
+ text_run = element[doc_constants.TEXT_RUN]
+ text = text_run[doc_constants.CONTENT]
+ if doc_constants.TEXT_STYLE in text_run and doc_constants.LINK in text_run[doc_constants.TEXT_STYLE]:
+ link = text_run[doc_constants.TEXT_STYLE][doc_constants.LINK]
+ if doc_constants.URL in link:
+ url = link[doc_constants.URL]
+ ip_element = self.Element(text, element[doc_constants.START_INDEX], element[doc_constants.END_INDEX], hyperlink=url)
+ ip_paragraph.add_element(ip_element)
+ else:
+ ip_element = self.Element(text, element[doc_constants.START_INDEX], element[doc_constants.END_INDEX])
+ ip_paragraph.add_element(ip_element)
+ return ip_paragraph
+
+ class Paragraph(object):
+ def __init__(self):
+ self.element = []
+ self._start_index = None
+ self._end_index = None
+ self._paragraph_index = None
+
+ def add_element(self, element):
+ self.element.append(element)
+
+ def get_paragraph_index(self):
+ return self._paragraph_index
+
+ def get_text(self):
+ flatten = [e.text for e in self.element]
+ return ''.join(flatten)
+
+ def get_elements_with_hyperlink(self):
+ hyperlinked_elements = []
+ for element in self.element:
+ if element.hyperlink:
+ hyperlinked_elements.append(element)
+ return hyperlinked_elements
+
+ def get_start_index(self):
+ return self._start_index
+
+ def get_end_index(self):
+ return self._end_index
+
+ def set_start_index(self, value):
+ self._start_index = value
+
+ def set_end_index(self, value):
+ self._end_index = value
+
+ def set_paragraph_index(self, value):
+ self._paragraph_index = value
+
+ class Element(object):
+ def __init__(self, text, start_index, end_index, hyperlink=None):
+ self.text = text
+ self.start_index = start_index
+ self.end_index = end_index
+ self.hyperlink = hyperlink
\ No newline at end of file
diff --git a/intent_parser/experiment_variables/__init__.py b/intent_parser/experiment_variables/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/intent_parser/experiment_variables/experiment_variables.py b/intent_parser/experiment_variables/experiment_variables.py
new file mode 100644
index 00000000..8a7a2689
--- /dev/null
+++ b/intent_parser/experiment_variables/experiment_variables.py
@@ -0,0 +1,24 @@
+class ExperimentVariable(object):
+
+ def __init__(self, sbh_uri, lab_id, common_name, lab_names=[]):
+ self._sbh_uri = sbh_uri
+ self._lab_id = lab_id
+ self._common_name = common_name
+ self._lab_names = lab_names
+
+ def get_common_name(self):
+ return self._common_name
+
+ def get_lab_id(self):
+ return self._lab_id
+
+ def get_lab_names(self):
+ return self._lab_names
+
+ def get_sbh_uri(self):
+ return self._sbh_uri
+
+ def has_lab_name(self, lab_name):
+ return lab_name in self._lab_names
+
+
diff --git a/intent_parser/intent/measurement_intent.py b/intent_parser/intent/measurement_intent.py
index ecf17b2d..a47a0caf 100644
--- a/intent_parser/intent/measurement_intent.py
+++ b/intent_parser/intent/measurement_intent.py
@@ -1,16 +1,3 @@
-
-class MeasurementIntent(object):
-
- def __init__(self):
- self.intent = []
-
- def add_measurement(self, measurement):
- self.intent.append(measurement)
-
- def to_structured_request(self):
-
- return [measurement.to_structured_request() for measurement in self.intent if self.intent]
-
class Measurement(object):
def __init__(self):
diff --git a/intent_parser/intent_parser.py b/intent_parser/intent_parser.py
index db486203..95e6ad73 100644
--- a/intent_parser/intent_parser.py
+++ b/intent_parser/intent_parser.py
@@ -127,6 +127,9 @@ def process_structure_request(self):
def process_experiment_run_request(self):
self.process_tables()
filtered_tables = self._filter_tables_by_type()
+ if not filtered_tables[TableType.PARAMETER]:
+ self.validation_errors.append('Cannot execute experiment without a parameter table.')
+ return
self._generate_experiment_request(filtered_tables[TableType.PARAMETER])
def process_experiment_status_request(self):
@@ -393,17 +396,15 @@ def _generate_request(self, control_tables, lab_tables, measurement_tables, para
def _generate_experiment_request(self, parameter_tables):
experiment_request = self._process_parameter_table(parameter_tables, generate_experiment_request=True)
- if experiment_request is None:
- message = 'Cannot execute experiment without a parameter table.'
- self.validation_warnings.extend(message)
- return
- experiment_request[ip_constants.PARAMETER_TEST_MODE] = False
- experiment_request[ip_constants.PARAMETER_SUBMIT] = True
- self.experiment_request = experiment_request
+ if experiment_request:
+ experiment_request[ip_constants.PARAMETER_TEST_MODE] = False
+ experiment_request[ip_constants.PARAMETER_SUBMIT] = True
+ self.experiment_request = experiment_request
def _process_control_tables(self, control_tables):
ref_controls = {}
if not control_tables:
+ self.validation_warnings.append('No controls table to parse from document.')
return ref_controls
for table in control_tables:
@@ -499,7 +500,12 @@ def _process_measurement_table(self, measurement_tables, ref_controls, lab_name)
def _process_parameter_table(self, parameter_tables, generate_experiment_request=False):
if not parameter_tables:
- return None
+ if generate_experiment_request:
+ self.validation_errors.append('Unable to generate an experiment request without a parameter table.')
+ else:
+ self.validation_warnings.append('No parameter table to parse from document.')
+ return []
+
if len(parameter_tables) > 1:
message = ('There are more than one parameter table specified in this experiment.'
'Only the last parameter table identified in the document will be used for generating a request.')
@@ -516,6 +522,7 @@ def _process_parameter_table(self, parameter_tables, generate_experiment_request
return [parameter_table.get_structured_request()]
except (DictionaryMaintainerException, TableException) as err:
self.validation_errors.extend([err.get_message()])
+ return {}
def _filter_tables_by_type(self):
measurement_tables = []
diff --git a/intent_parser/requirements.txt b/intent_parser/requirements.txt
index 91c1e3c9..1913b579 100644
--- a/intent_parser/requirements.txt
+++ b/intent_parser/requirements.txt
@@ -11,4 +11,5 @@ requests_oauthlib
sbol2
tenacity
transcriptic
+flashtext
diff --git a/intent_parser/server/intent_parser_server.py b/intent_parser/server/intent_parser_server.py
index 4731f668..082225f1 100644
--- a/intent_parser/server/intent_parser_server.py
+++ b/intent_parser/server/intent_parser_server.py
@@ -210,6 +210,8 @@ def handle_GET(self, http_message, socket_manager):
response = self.process_experiment_status(http_message)
elif resource == '/update_experiment_status':
response = self.process_update_experiment_status(http_message)
+ elif resource == '/insert_table_hints':
+ response = self.process_table_hints(http_message)
else:
response = self._create_http_response(HTTPStatus.NOT_FOUND, 'Resource Not Found')
logger.warning('Did not find ' + resource)
@@ -243,6 +245,12 @@ def process_document_request(self, http_message):
return self._create_http_response(HTTPStatus.OK, json.dumps(intent_parser.get_structured_request()), 'application/json')
+ def process_table_hints(self, http_message):
+ resource = http_message.get_resource()
+ document_id = resource.split('?')[1]
+ drive_accessor = GoogleAccessor().get_google_drive_accessor()
+ intent_parser = self.intent_parser_factory.create_intent_parser(document_id)
+
def process_experiment_request_documents(self, http_message):
"""
Retrieve experiment request documents.
@@ -280,8 +288,10 @@ def process_run_experiment(self, http_message):
intent_parser = self.intent_parser_factory.create_intent_parser(document_id)
intent_parser.process_experiment_run_request()
if len(intent_parser.get_validation_errors()) > 0:
+ errors = [intent_parser.get_validation_errors()]
+ warnings = [intent_parser.get_validation_warnings()]
return self._create_http_response(HTTPStatus.BAD_REQUEST,
- json.dumps({'errors': intent_parser.get_validation_errors()}),
+ json.dumps({'errors': errors, 'warnings': warnings}),
'application/json')
request_data = intent_parser.get_experiment_request()
@@ -365,22 +375,23 @@ def process_analyze_document(self, http_message):
docBeingProcessed = document_id in self.analyze_processing_map
self.analyze_processing_map_lock.release()
- if docBeingProcessed: # Doc being processed, check progress
+ if docBeingProcessed: # Doc being processed, check progress
time.sleep(self.ANALYZE_PROGRESS_PERIOD)
self.analyze_processing_map_lock.acquire()
progress_percent = self.analyze_processing_map[document_id]
self.analyze_processing_map_lock.release()
- if progress_percent < 100: # Not done yet, update client
+ if progress_percent < 100: # Not done yet, update client
action = {}
action['action'] = 'updateProgress'
action['progress'] = str(int(progress_percent * 100))
actions = {'actions': [action]}
return self._create_http_response(HTTPStatus.OK, json.dumps(actions), 'application/json')
- else: # Document is analyzed, start navigating results
+ else: # Document is analyzed, start navigating results
try:
- self.analyze_processing_lock[document_id].acquire() # This ensures we've waited for the processing thread to release the client connection
+ self.analyze_processing_lock[
+ document_id].acquire() # This ensures we've waited for the processing thread to release the client connection
(__, client_state) = self.get_client_state(http_message)
actionList = self.report_search_results(client_state)
actions = {'actions': actionList}
@@ -389,7 +400,7 @@ def process_analyze_document(self, http_message):
self.analyze_processing_map.pop(document_id)
self.analyze_processing_lock[document_id].release()
self.release_connection(client_state)
- else: # Doc not being processed, spawn new processing thread
+ else: # Doc not being processed, spawn new processing thread
self.analyze_processing_map[document_id] = 0
analyze_thread = threading.Thread(
target=self._initiate_document_analysis,
@@ -399,7 +410,7 @@ def process_analyze_document(self, http_message):
dialogAction = intent_parser_view.progress_sidebar_dialog()
actions = {'actions': [dialogAction]}
return self._create_http_response(HTTPStatus.OK, json.dumps(actions), 'application/json')
-
+
def report_search_results(self, client_state):
search_results = client_state['search_results']
item_map = self.sbol_dictionary.get_common_names_to_uri()
@@ -505,7 +516,7 @@ def process_submit_form(self, http_message):
for action in reportActions:
result['actions'].append(action)
elif action == 'createControlsTable':
- actions = self.process_controls_table(data)
+ actions = self.process_controls_table(data, json_body['documentId'])
result = {'actions': actions,
'results': {'operationSucceeded': True}
}
@@ -652,7 +663,7 @@ def internal_add_to_syn_bio_hub(self, document_id, start_paragraph, end_paragrap
def get_paragraph_text(self, paragraph):
elements = paragraph['elements']
- paragraph_text = '';
+ paragraph_text = ''
for element_index in range(len(elements)):
element = elements[element_index]
@@ -821,29 +832,31 @@ def process_form_link_all(self, data):
return actions
-
+ def _get_button_id(self, data):
+ if ip_addon_constants.BUTTON_ID not in data:
+ error_message = 'Expected to get %s assigned to this HTTP data: %s but none was found.' % (ip_addon_constants.BUTTON_ID, data)
+ raise ConnectionException(HTTPStatus.BAD_REQUEST, error_message)
+
+ if type(data[ip_addon_constants.BUTTON_ID]) is dict:
+ buttonDat = data[ip_addon_constants.BUTTON_ID]
+ button_id = buttonDat[ip_addon_constants.BUTTON_ID]
+ return button_id
+ return data[ip_addon_constants.BUTTON_ID]
+
def process_button_click(self, http_message):
(json_body, client_state) = self.get_client_state(http_message)
if 'data' not in json_body:
- errorMessage = 'Missing data'
- raise ConnectionException(HTTPStatus.BAD_REQUEST, errorMessage)
+ error_message = 'Missing data'
+ raise ConnectionException(HTTPStatus.BAD_REQUEST, error_message)
data = json_body['data']
- if 'buttonId' not in data:
- errorMessage = 'data missing buttonId'
- raise ConnectionException(HTTPStatus.BAD_REQUEST, errorMessage)
- if type(data['buttonId']) is dict:
- buttonDat = data['buttonId']
- buttonId = buttonDat['buttonId']
- else:
- buttonId = data['buttonId']
-
- method = getattr( self, buttonId )
+ button_id = self._get_button_id(data)
+ method = getattr(self, button_id)
try:
- actionList = method(json_body, client_state)
- actions = {'actions': actionList}
+ action_list = method(json_body, client_state)
+ actions = {'actions': action_list}
return self._create_http_response(HTTPStatus.OK, json.dumps(actions), 'application/json')
except Exception as e:
raise e
@@ -919,22 +932,31 @@ def process_generate_structured_request(self, http_message):
dialog_action = intent_parser_view.invalid_request_model_dialog('Structured request validation: Failed!', all_messages)
actionList = [dialog_action]
actions = {'actions': actionList}
- return self._create_http_response(HTTPStatus.OK, json.dumps(actions), 'application/json')
+ return self._create_http_response(HTTPStatus.OK, json.dumps(actions), 'application/json')
def process_analyze_yes(self, json_body, client_state):
"""
Handle "Yes" button as part of analyze document.
"""
- search_results = client_state['search_results']
- search_result_index = client_state['search_result_index'] - 1
+ search_results = client_state[ip_addon_constants.ANALYZE_SEARCH_RESULTS]
+ search_result_index = client_state[ip_addon_constants.ANALYZE_SEARCH_RESULT_INDEX]
search_result = search_results[search_result_index]
- if type(json_body['data']['buttonId']) is dict:
- new_link = json_body['data']['buttonId']['link']
+ if type(json_body[ip_addon_constants.DATA][ip_addon_constants.BUTTON_ID]) is dict:
+ new_link = json_body[ip_addon_constants.DATA][ip_addon_constants.BUTTON_ID][ip_addon_constants.ANALYZE_LINK]
else:
new_link = None
- actions = self.add_link(search_result, new_link);
+ actions = self.add_link(search_result, new_link)
+ curr_idx = client_state[ip_addon_constants.ANALYZE_SEARCH_RESULT_INDEX]
+ next_idx = curr_idx + 1
+ new_search_results = search_results[1:]
+ if len(new_search_results) < 1:
+ return [intent_parser_view.simple_sidebar_dialog('Finished Analyzing Document.', [])]
+ new_idx = new_search_results.index(search_results[next_idx])
+ # Update client state
+ client_state[ip_addon_constants.ANALYZE_SEARCH_RESULTS] = new_search_results
+ client_state[ip_addon_constants.ANALYZE_SEARCH_RESULT_INDEX] = new_idx
actions += self.report_search_results(client_state)
return actions
@@ -942,7 +964,18 @@ def process_analyze_no(self, json_body, client_state):
"""
Handle "No" button as part of analyze document.
"""
- json_body # Remove unused warning
+ # Find out what term to point to
+ curr_idx = client_state[ip_addon_constants.ANALYZE_SEARCH_RESULT_INDEX]
+ next_idx = curr_idx + 1
+ search_results = client_state[ip_addon_constants.ANALYZE_SEARCH_RESULTS]
+
+ new_search_results = search_results[1:]
+ if len(new_search_results) < 1:
+ return [intent_parser_view.simple_sidebar_dialog('Finished Analyzing Document.', [])]
+ new_idx = new_search_results.index(search_results[next_idx])
+ # Update client state
+ client_state[ip_addon_constants.ANALYZE_SEARCH_RESULTS] = new_search_results
+ client_state[ip_addon_constants.ANALYZE_SEARCH_RESULT_INDEX] = new_idx
return self.report_search_results(client_state)
def process_link_all(self, json_body, client_state):
@@ -950,7 +983,7 @@ def process_link_all(self, json_body, client_state):
Handle "Link all" button as part of analyze document.
"""
search_results = client_state['search_results']
- search_result_index = client_state['search_result_index'] - 1
+ search_result_index = client_state['search_result_index']
search_result = search_results[search_result_index]
term = search_result['term']
term_search_results = list(filter(lambda x : x['term'] == term,
@@ -962,27 +995,24 @@ def process_link_all(self, json_body, client_state):
new_link = None
actions = []
-
for term_result in term_search_results:
actions += self.add_link(term_result, new_link);
actions += self.report_search_results(client_state)
-
return actions
def process_no_to_all(self, json_body, client_state):
"""
Handle "No to all" button as part of analyze document.
"""
- json_body # Remove unused warning
- curr_idx = client_state['search_result_index'] - 1
+ curr_idx = client_state['search_result_index']
next_idx = curr_idx + 1
search_results = client_state['search_results']
while next_idx < len(search_results) and search_results[curr_idx]['term'] == search_results[next_idx]['term']:
next_idx = next_idx + 1
# Are we at the end? Then just exit
if next_idx >= len(search_results):
- return []
+ return [intent_parser_view.simple_sidebar_dialog('Finished Analyzing Document.', [])]
term_to_ignore = search_results[curr_idx]['term']
# Generate results without term to ignore
@@ -1001,25 +1031,23 @@ def process_never_link(self, json_body, client_state):
Handle "Never Link" button as part of analyze document.
This works like "No to all" but also stores the association to ignore it in subsequent runs.
"""
- json_body # Remove unused warning
-
- curr_idx = client_state['search_result_index'] - 1
- search_results = client_state['search_results']
+ curr_idx = client_state[ip_addon_constants.ANALYZE_SEARCH_RESULT_INDEX]
+ search_results = client_state[ip_addon_constants.ANALYZE_SEARCH_RESULTS]
- dict_term = search_results[curr_idx]['term']
+ dict_term = search_results[curr_idx][ip_addon_constants.ANALYZE_TERM]
content_text = search_results[curr_idx]['text']
- userId = client_state['user_id']
+ userId = client_state[ip_addon_constants.USER_ID]
# Make sure we have a list of link preferences for this userId
- if not userId in self.analyze_never_link:
+ if userId not in self.analyze_never_link:
link_pref_file = os.path.join(self.link_pref_path, userId + '.json')
if os.path.exists(link_pref_file):
try:
with open(link_pref_file, 'r') as fin:
self.analyze_never_link[userId] = json.load(fin)
logger.info('Loaded link preferences for userId, path: %s' % link_pref_file)
- except:
+ except Exception as e:
logger.error('ERROR: Failed to load link preferences file!')
else:
self.analyze_never_link[userId] = {}
@@ -1036,7 +1064,7 @@ def process_never_link(self, json_body, client_state):
try:
with open(link_pref_file, 'w') as fout:
json.dump(self.analyze_never_link[userId], fout)
- except:
+ except Exception as e:
logger.error('ERROR: Failed to write link preferences file!')
# Remove all of these associations from the results
@@ -1048,7 +1076,7 @@ def process_never_link(self, json_body, client_state):
# Are we at the end? Then just exit
if next_idx >= len(search_results):
- return []
+ return [intent_parser_view.simple_sidebar_dialog('Finished Analyzing Document.', [])]
term_to_ignore = search_results[curr_idx]['term']
text_to_ignore = search_results[curr_idx]['text']
@@ -1398,8 +1426,14 @@ def process_lab_table(self, data):
table_template.append([lab_name])
table_template.append([experiment_id])
return table_template
+
+ def _process_new_table_index(self, document_id):
+ intent_parser = self.intent_parser_factory.create_intent_parser(document_id)
+ intent_parser.process_table_indices()
+ return intent_parser.get_largest_table_index()+1
- def process_controls_table(self, data):
+ def process_controls_table(self, data, document_id):
+ table_index = self._process_new_table_index(document_id)
table_template = []
header_row = [intent_parser_constants.HEADER_CONTROL_TYPE_VALUE,
intent_parser_constants.HEADER_STRAINS_VALUE]
@@ -1413,7 +1447,7 @@ def process_controls_table(self, data):
# column_offset = column size - # of columns with generated default value
column_offset = len(header_row) - 1
if data[ip_addon_constants.HTML_CAPTION]:
- table_caption = ['Table 1: Control']
+ table_caption = ['Table %d: Control' % table_index]
table_caption.extend(['' for _ in range(column_offset)])
table_template.append(table_caption)
table_template.append(header_row)
@@ -1556,10 +1590,10 @@ def process_create_parameter_table(self, data):
def get_client_state(self, http_message):
json_body = intent_parser_utils.get_json_body(http_message)
- if 'documentId' not in json_body:
+ if ip_addon_constants.DOCUMENT_ID not in json_body:
raise ConnectionException(HTTPStatus.BAD_REQUEST,
- 'Missing documentId')
- document_id = json_body['documentId']
+ 'Expecting to get a %s from this http_message: %s but none was given' % (ip_addon_constants.DOCUMENT_ID, http_message))
+ document_id = json_body[ip_addon_constants.DOCUMENT_ID]
try:
client_state = self.get_connection(document_id)
except:
@@ -1568,16 +1602,16 @@ def get_client_state(self, http_message):
return (json_body, client_state)
def add_link(self, search_result, new_link=None):
+ """ Add a hyperlink to the desired search_result
"""
- """
- paragraph_index = search_result['paragraph_index']
- offset = search_result['offset']
- end_offset = search_result['end_offset']
+ paragraph_index = search_result[ip_addon_constants.ANALYZE_PARAGRAPH_INDEX]
+ offset = search_result[ip_addon_constants.ANALYZE_OFFSET]
+ end_offset = search_result[ip_addon_constants.ANALYZE_END_OFFSET]
if new_link is None:
link = search_result['uri']
else:
link = new_link
- search_result['link'] = link
+ search_result[ip_addon_constants.ANALYZE_LINK] = link
action = intent_parser_view.link_text(paragraph_index, offset,
end_offset, link)
diff --git a/intent_parser/setup.py b/intent_parser/setup.py
index e3337417..a023b68c 100644
--- a/intent_parser/setup.py
+++ b/intent_parser/setup.py
@@ -2,7 +2,7 @@
setuptools.setup(
name='intent-parser',
- version='2.8',
+ version='2.9',
packages=setuptools.find_packages(),
python_requires='>=3.6',
include_package_data=True, # include everything in source control
diff --git a/intent_parser/table/cell_parser.py b/intent_parser/table/cell_parser.py
index c96acbe7..2f7b4ae1 100644
--- a/intent_parser/table/cell_parser.py
+++ b/intent_parser/table/cell_parser.py
@@ -165,7 +165,7 @@ def parse_content_item(self, text, text_with_uri, fluid_units={}, timepoint_unit
list_of_contents = []
tokens = self._cell_tokenizer.tokenize(text, keep_skip=False)
if len(tokens) < 1:
- raise TableException('Invalid value: %s does not contain a name' % text.get_text())
+ raise TableException('Invalid value: %s does not contain a name' % text.get_matched_term())
cell_type = self._get_token_type(self._cell_parser.parse(tokens))
if cell_type == 'NAME_VALUE_UNIT_TIMEPOINT':
label, value, unit, timepoint_value, timepoint_unit = self._get_name_values_unit_timepoint(tokens)
diff --git a/intent_parser/table/intent_parser_cell.py b/intent_parser/table/intent_parser_cell.py
index cd533eec..ee508ad1 100644
--- a/intent_parser/table/intent_parser_cell.py
+++ b/intent_parser/table/intent_parser_cell.py
@@ -30,7 +30,7 @@ def get_end_index(self):
def get_text(self):
flatten = [p.paragraph for p in self.paragraphs]
- return ' '.join(flatten)
+ return ''.join(flatten)
def get_text_with_url(self):
return {p.paragraph: p.link for p in self.paragraphs}
diff --git a/intent_parser/table/measurement_table.py b/intent_parser/table/measurement_table.py
index 11a54485..8bc87026 100644
--- a/intent_parser/table/measurement_table.py
+++ b/intent_parser/table/measurement_table.py
@@ -1,4 +1,4 @@
-from intent_parser.intent.measurement_intent import Measurement, MeasurementIntent
+from intent_parser.intent.measurement_intent import Measurement
from intent_parser.intent_parser_exceptions import TableException
import intent_parser.table.cell_parser as cell_parser
import intent_parser.constants.intent_parser_constants as intent_parser_constants
@@ -32,10 +32,10 @@ def __init__(self,
self._validation_warnings = []
self._intent_parser_table = intent_parser_table
self._table_caption = None
- self.measurement_intent = MeasurementIntent()
+ self.measurements = []
def get_structured_request(self):
- return self.measurement_intent.to_structured_request()
+ return [measurement.to_structured_request() for measurement in self.measurements]
def process_table(self, control_tables={}, bookmarks={}):
self._table_caption = self._intent_parser_table.caption()
@@ -43,25 +43,36 @@ def process_table(self, control_tables={}, bookmarks={}):
for row_index in range(self._intent_parser_table.data_row_start_index(), self._intent_parser_table.number_of_rows()):
measurement = self._process_row(row_index, control_mappings)
if measurement.to_structured_request():
- self.measurement_intent.add_measurement(measurement)
+ self.measurements.append(measurement)
def _process_control_mapping(self, control_tables, bookmarks):
+ table_caption_index = {}
if bookmarks:
- return self._map_bookmarks_to_captions(control_tables, bookmarks)
- return self._map_captions_to_control(control_tables)
+ table_caption_index = self._map_bookmarks_to_captions(control_tables, bookmarks)
+ # if bookmarks produce empty result, process control table's caption
+ if not table_caption_index:
+ try:
+ if control_tables:
+ table_caption_index = self._map_captions_to_control(control_tables)
+ except TableException as err:
+ self._validation_errors.append('Measurement table has invalid %s value: %s' % (intent_parser_constants.HEADER_CONTROL_VALUE, err))
+ return table_caption_index
def _map_captions_to_control(self, control_tables):
control_map = {}
for table_caption, control_data in control_tables.items():
if table_caption:
control_map[table_caption] = control_data
+ if not control_map:
+ raise TableException('No reference to a Control table.')
return control_map
def _map_bookmarks_to_captions(self, control_tables, bookmarks):
control_map = {}
for bookmark in bookmarks:
- if bookmark['text'] in control_tables:
- control_map[bookmark['id']] = control_tables[bookmark['text']]
+ table_index = cell_parser.PARSER.process_table_caption_index(bookmark['text'])
+ if table_index in control_tables:
+ control_map[table_index] = control_tables[table_index]
return control_map
def _process_row(self, row_index, control_data):
@@ -154,7 +165,11 @@ def _process_batch(self, cell, measurement):
self._validation_errors.append(message)
def _process_control(self, cell, control_tables, measurement):
- result = []
+ result = []
+ if not control_tables:
+ self._validation_errors.append('Unable to process controls from a Measurement table without Control Tables.')
+ return result
+
if cell.get_bookmark_ids():
result = self._process_control_with_bookmarks(cell, control_tables)
diff --git a/intent_parser/table/parameter_table.py b/intent_parser/table/parameter_table.py
index e5d4f377..dfc26552 100644
--- a/intent_parser/table/parameter_table.py
+++ b/intent_parser/table/parameter_table.py
@@ -1,30 +1,35 @@
-from intent_parser.intent_parser_exceptions import TableException, DictionaryMaintainerException
+from intent_parser.intent_parser_exceptions import TableException
+from json import JSONDecodeError
import intent_parser.constants.intent_parser_constants as intent_parser_constants
+import intent_parser.constants.sd2_datacatalog_constants as dc_constants
import intent_parser.table.cell_parser as cell_parser
import json
import logging
+
class ParameterTable(object):
"""
Process information from Intent Parser's Parameter Table
"""
_logger = logging.getLogger('intent_parser')
-
- FIELD_WITH_BOOLEAN_VALUE = [intent_parser_constants.PARAMETER_MEASUREMENT_INFO_36_HR_READ,
+
+ FIELD_WITH_BOOLEAN_VALUE = [intent_parser_constants.PARAMETER_MEASUREMENT_INFO_36_HR_READ,
intent_parser_constants.PARAMETER_RUN_INFO_READ_EACH_RECOVER,
intent_parser_constants.PARAMETER_RUN_INFO_READ_EACH_INDUCTION,
- intent_parser_constants.PARAMETER_RUN_INFO_SAVE_FOR_RNASEQ,
- intent_parser_constants.PARAMETER_RUN_INFO_SKIP_FIRST_FLOW,
- intent_parser_constants.PARAMETER_RUN_INFO_ONLY_ENDPOINT_FLOW,
+ intent_parser_constants.PARAMETER_RUN_INFO_SAVE_FOR_RNASEQ,
+ intent_parser_constants.PARAMETER_RUN_INFO_SKIP_FIRST_FLOW,
+ intent_parser_constants.PARAMETER_RUN_INFO_ONLY_ENDPOINT_FLOW,
intent_parser_constants.PARAMETER_VALIDATE_SAMPLES]
-
+
FIELD_WITH_FLOAT_VALUE = [intent_parser_constants.PARAMETER_PLATE_READER_INFO_GAIN]
-
- FIELD_WITH_NESTED_STRUCTURE = [intent_parser_constants.PARAMETER_INDUCTION_INFO_REAGENTS_INDUCER,
+
+ FIELD_WITH_NESTED_STRUCTURE = [intent_parser_constants.PARAMETER_INDUCTION_INFO_REAGENTS,
+ intent_parser_constants.PARAMETER_INDUCTION_INFO_REAGENTS_INDUCER,
+ intent_parser_constants.PARAMETER_INDUCTION_INFO_SAMPLING_INFO,
intent_parser_constants.PARAMETER_MEASUREMENT_INFO_FLOW_INFO,
- intent_parser_constants.PARAMETER_MEASUREMENT_INFO_PLATE_READER_INFO,
- intent_parser_constants.PARAMETER_REAGENT_INFO_INDUCER_INFO,
+ intent_parser_constants.PARAMETER_MEASUREMENT_INFO_PLATE_READER_INFO,
+ intent_parser_constants.PARAMETER_REAGENT_INFO_INDUCER_INFO,
intent_parser_constants.PARAMETER_REAGENT_INFO_KILL_SWITCH,
intent_parser_constants.PARAMETER_RECOVERY_INFO]
@@ -39,7 +44,8 @@ class ParameterTable(object):
intent_parser_constants.PARAMETER_PROTOCOL,
intent_parser_constants.PARAMETER_STRAIN_PROPERTY,
intent_parser_constants.PARAMETER_XPLAN_PATH,
- intent_parser_constants.PARAMETER_PROTOCOL_ID]
+ intent_parser_constants.PARAMETER_PROTOCOL_ID,
+ intent_parser_constants.PARAMETER_EXPERIMENT_REFERENCE_URL_FOR_XPLAN]
FIELD_WITH_INT_VALUES = [intent_parser_constants.PARAMETER_PLATE_SIZE,
intent_parser_constants.PARAMETER_PLATE_NUMBER]
@@ -51,22 +57,33 @@ def __init__(self, intent_parser_table, parameter_fields={}):
self._parameter_fields = parameter_fields
self._validation_errors = []
self._validation_warnings = []
- self._intent_parser_table = intent_parser_table
+ self._intent_parser_table = intent_parser_table
self._table_caption = None
def process_table(self):
self._table_caption = self._intent_parser_table.caption()
- for row_index in range(self._intent_parser_table.data_row_start_index(), self._intent_parser_table.number_of_rows()):
+ for row_index in range(self._intent_parser_table.data_row_start_index(),
+ self._intent_parser_table.number_of_rows()):
self._process_row(row_index)
def get_experiment(self):
- return self.param_intent.to_experiment()
+ experiment_result = self.param_intent.to_experiment()
+ for key, value in experiment_result.items():
+ if key == intent_parser_constants.PARAMETER_CONTAINER_SEARCH_STRING and value is None:
+ self.param_intent.set_field(intent_parser_constants.PARAMETER_CONTAINER_SEARCH_STRING,
+ dc_constants.GENERATE)
+ if key == intent_parser_constants.DEFAULT_PARAMETERS and value is None:
+ self._validation_warnings.append('%s is emtpy' % intent_parser_constants.DEFAULT_PARAMETERS)
+ if key is not intent_parser_constants.PARAMETER_BASE_DIR and value is None:
+ self._validation_warnings.append('Parameter Table is missing a value for %s.' % (key))
+ return experiment_result
def get_structured_request(self):
return self.param_intent.to_structured_request()
def set_experiment_ref(self, experiment_ref_url):
- self.param_intent.set_field(intent_parser_constants.PARAMETER_EXPERIMENT_REFERENCE_URL_FOR_XPLAN, experiment_ref_url)
+ self.param_intent.set_field(intent_parser_constants.PARAMETER_EXPERIMENT_REFERENCE_URL_FOR_XPLAN,
+ experiment_ref_url)
def _flatten_parameter_values(self, param_field, param_value_list):
if len(param_value_list) == 0:
@@ -75,7 +92,11 @@ def _flatten_parameter_values(self, param_field, param_value_list):
self.param_intent.set_field(param_field, param_value_list[0])
return
elif param_field in self.EXPERIMENT_FIELDS_WITH_LIST:
- self.param_intent.set_field(param_field, param_value_list)
+ if len(param_value_list) == 1 and param_value_list[0] == dc_constants.GENERATE:
+ self.param_intent.set_field(param_field, param_value_list[0])
+ else:
+ self.param_intent.set_field(param_field, param_value_list)
+
return
elif len(param_value_list) == 1:
self.param_intent.add_default_parameter(param_field, param_value_list[0])
@@ -94,43 +115,65 @@ def _process_row(self, row_index):
header_row_index = self._intent_parser_table.header_row_index()
header_cell = self._intent_parser_table.get_cell(header_row_index, cell_index)
cell_type = cell_parser.PARSER.get_header_type(header_cell.get_text())
+
if intent_parser_constants.HEADER_PARAMETER_TYPE == cell_type:
cell_param_field = cell
elif intent_parser_constants.HEADER_PARAMETER_VALUE_TYPE == cell_type:
cell_param_value = cell
- if cell_param_field is None and cell_param_value:
- self._validation_errors.append('Parameter table cannot assign %s as a parameter value to an empty parameter.' % cell_param_value.get_text())
+ if ((cell_param_field is None) or (not cell_param_field.get_text().strip())) and cell_param_value:
+ self._validation_errors.append(
+ 'Parameter table cannot assign %s as a parameter value to an empty parameter.' % cell_param_value.get_text())
return
if cell_param_field:
- if (cell_param_value is None) or (not cell_param_value.get_text()):
+ if cell_param_value is None:
+ self._logger.error(
+ 'Unable to detect a table cell for a parameter value assigned to %s' % cell_param_field.get_text())
return
- self._parse_parameter_field_value(self._get_parameter_field(cell_param_field), cell_param_value.get_text())
-
+ self._parse_parameter_field_value(self._get_parameter_field(cell_param_field),
+ cell_param_value.get_text().strip())
+
def _parse_parameter_field_value(self, parameter_field, parameter_value):
- computed_value = None
- if parameter_field in self.FIELD_WITH_FLOAT_VALUE:
+ if parameter_field in self.FIELD_WITH_FLOAT_VALUE and parameter_value:
self.process_numbered_parameter(parameter_field, parameter_value, float)
- elif parameter_field in self.FIELD_WITH_BOOLEAN_VALUE:
+ elif parameter_field in self.FIELD_WITH_BOOLEAN_VALUE and parameter_value:
self.process_boolean_parameter(parameter_field, parameter_value)
+ elif parameter_field == intent_parser_constants.PARAMETER_PROTOCOL:
+ self._flatten_parameter_values(parameter_field, [parameter_value])
elif parameter_field in self.FIELD_WITH_STRING_COMMAS:
self._flatten_parameter_values(parameter_field, [parameter_value])
- elif parameter_field in self.FIELD_WITH_SINGLE_STRING:
+ elif parameter_field in self.FIELD_WITH_SINGLE_STRING and parameter_value:
self.process_name_parameter(parameter_field, parameter_value)
- elif parameter_field in self.FIELD_WITH_INT_VALUES:
+ elif parameter_field in self.FIELD_WITH_INT_VALUES and parameter_value:
self.process_numbered_parameter(parameter_field, parameter_value, int)
elif parameter_field in self.FIELD_WITH_NESTED_STRUCTURE:
- json_parameter_value = json.loads(parameter_value)
- computed_value = [json_parameter_value]
- self._flatten_parameter_values(parameter_field, computed_value)
+ try:
+ if parameter_value:
+ json_parameter_value = json.loads(parameter_value)
+ computed_value = [json_parameter_value]
+ self._flatten_parameter_values(parameter_field, computed_value)
+ except JSONDecodeError as err:
+ errors = [
+ 'Parameter table has invalid Parameter Value: %s is an invalid json format.' % (parameter_value)]
+ self._validation_errors.append(errors)
+ elif parameter_field == intent_parser_constants.PARAMETER_CONTAINER_SEARCH_STRING:
+ if not parameter_value:
+ self._flatten_parameter_values(parameter_field, [dc_constants.GENERATE])
+ else:
+ self.process_name_parameter(parameter_field, parameter_value)
else:
- computed_value = cell_parser.PARSER.transform_strateos_string(parameter_value)
- self._flatten_parameter_values(parameter_field, computed_value)
-
+ if parameter_value:
+ computed_value = cell_parser.PARSER.transform_strateos_string(parameter_value)
+ self._flatten_parameter_values(parameter_field, computed_value)
+
def _get_parameter_field(self, cell):
parameter = cell.get_text().strip()
- if parameter in self._parameter_fields:
- error = 'Parameter table has invalid %s value: %s does not map to a TACC UID in the SBOL dictionary.' % (intent_parser_constants.HEADER_PARAMETER_VALUE, parameter)
-
+ if parameter.lower() == intent_parser_constants.PARAMETER_PROTOCOL:
+ return parameter.lower()
+ if parameter not in self._parameter_fields:
+ error = ['Parameter table has invalid %s value: %s does not map to a TACC UID in the SBOL dictionary.' % (
+ intent_parser_constants.HEADER_PARAMETER_VALUE, parameter)]
+ self._validation_errors.append(error)
+ return ''
return self._parameter_fields[parameter]
def get_validation_errors(self):
@@ -139,19 +182,16 @@ def get_validation_errors(self):
def process_boolean_parameter(self, parameter_field, parameter_value):
boolean_value = cell_parser.PARSER.process_boolean_flag(parameter_value)
if boolean_value is None:
- message = 'Parameter table has invalid %s value: %s should be a boolean value' % (parameter_field, parameter_value)
+ message = 'Parameter table has invalid %s value: %s should be a boolean value' % (
+ parameter_field, parameter_value)
self._validation_errors.append(message)
else:
computed_value = [boolean_value]
self._flatten_parameter_values(parameter_field, computed_value)
def process_name_parameter(self, parameter_field, parameter_value):
- if cell_parser.PARSER.is_name(parameter_value):
- computed_value = [value for value, _ in cell_parser.PARSER.process_names_with_uri(parameter_value)]
- self._flatten_parameter_values(parameter_field, computed_value)
- else:
- message = 'Parameter table has invalid %s value: %s should only contain a list of names' % (parameter_field, parameter_value)
- self._validation_errors.append(message)
+ computed_value = [value for value, _ in cell_parser.PARSER.process_names_with_uri(parameter_value)]
+ self._flatten_parameter_values(parameter_field, computed_value)
def process_numbered_parameter(self, parameter_field, parameter_value, number_convert):
try:
@@ -161,10 +201,12 @@ def process_numbered_parameter(self, parameter_field, parameter_value, number_co
message = 'Parameter table has invalid %s value: %s' % (parameter_field, err)
self._validation_errors.append(message)
+
class _ParameterIntent(object):
def __init__(self):
self.intent = {
+ intent_parser_constants.PARAMETER_BASE_DIR: None,
intent_parser_constants.PARAMETER_XPLAN_REACTOR: 'xplan',
intent_parser_constants.PARAMETER_PLATE_SIZE: None,
intent_parser_constants.PARAMETER_PROTOCOL: None,
@@ -184,7 +226,8 @@ def set_field(self, field, value):
raise TableException('Parameter Table cannot identify row of type %s.' % field)
if self.intent[field] is not None:
- raise TableException('Parameter Table has a conflict for %s. Found %s and %s.' % (field, self.intent[field], value))
+ raise TableException(
+ 'Parameter Table has a conflict for %s. Found %s and %s.' % (field, self.intent[field], value))
self.intent[field] = value
@@ -196,12 +239,7 @@ def add_default_parameter(self, field, value):
self.intent[intent_parser_constants.DEFAULT_PARAMETERS][field] = value
def to_experiment(self):
- for key, value in self.intent.items():
- if value is None:
- raise TableException('Parameter Table is missing a %s row.' % key)
-
return self.intent
def to_structured_request(self):
return self.intent[intent_parser_constants.DEFAULT_PARAMETERS]
-
diff --git a/intent_parser/tests/test_cell_parser.py b/intent_parser/tests/test_cell_parser.py
index b447b376..4105ae77 100644
--- a/intent_parser/tests/test_cell_parser.py
+++ b/intent_parser/tests/test_cell_parser.py
@@ -89,7 +89,6 @@ def test_cell_with_strateos_name(self):
def test_cell_with_unit_containing_multiple_abbreviations(self):
cell_str = '1 h, 2 hr, 3 hours'
- expected_values = ['1', '2', '3']
result = self.parser.process_values_unit(cell_str, units={'hour'}, unit_type='timepoints')
self.assertEqual(3, len(result))
self.assertEqual({'value': '1', 'unit': 'hour'}, result[0])
@@ -149,7 +148,7 @@ def test_parse_content_item_with_name_value_unit_timepoint(self):
def test_parse_content_item_with_name_uri_value_unit(self):
cell = IntentParserCell()
cell.add_paragraph('name1', link='https://hub.sd2e.org/user/sd2e/design/beta_estradiol/1')
- cell.add_paragraph('123 unit')
+ cell.add_paragraph(' 123 unit')
results = self.parser.parse_content_item(cell.get_text(),
cell.get_text_with_url(),
timepoint_units={'unit', 'timeunit'})
diff --git a/intent_parser/tests/test_google_accessor.py b/intent_parser/tests/test_google_accessor.py
index 4f1bc959..a02cfe4e 100644
--- a/intent_parser/tests/test_google_accessor.py
+++ b/intent_parser/tests/test_google_accessor.py
@@ -1,4 +1,5 @@
from intent_parser.accessor.google_accessor import GoogleAccessor
+import traceback
import unittest
class GoogleAccessorTest(unittest.TestCase):
@@ -24,9 +25,13 @@ def test_create_spreadsheet_from_given_folder(self):
self.assertTrue(spreadsheet_id)
self.assertTrue(self.drive_accessor.delete_file(spreadsheet_id))
- def test_app_script(self):
- pass
-
+ def test_get_doc_from_google_drive(self):
+ document_id = '1zf9l0K4rj7I08ZRpxV2ZY54RMMQc15Rlg7ULviJ7SBQ'
+ try:
+ response = self.doc_accessor.get_document(document_id=document_id)
+ except Exception as ex:
+ err = ''.join(traceback.format_exception(etype=type(ex), value=ex, tb=ex.__traceback__))
+ print(err)
if __name__ == "__main__":
unittest.main()
\ No newline at end of file
diff --git a/intent_parser/tests/test_intent_parser_server.py b/intent_parser/tests/test_intent_parser_server.py
index c1935940..cc00917a 100644
--- a/intent_parser/tests/test_intent_parser_server.py
+++ b/intent_parser/tests/test_intent_parser_server.py
@@ -2,6 +2,7 @@
from intent_parser.server.http_message import HttpMessage
from intent_parser.server.intent_parser_server import IntentParserServer
from unittest.mock import Mock, patch
+import intent_parser.constants.ip_app_script_constants as addon_constants
import intent_parser.constants.intent_parser_constants as ip_constants
import intent_parser.utils.intent_parser_view as intent_parser_view
import json
@@ -191,6 +192,405 @@ def test_process_analyze_document(self):
self._verify_response_status(response, HTTPStatus.OK)
self._verify_response_body(response, expected_actions)
+ def test_process_analyze_yes_for_search_results_size_1(self):
+ text_paragraph_index = 13
+ text_start_offset = 183
+ text_end_offset = 185
+ document_term = 'DNA'
+ dictionary_matched_term = 'DNA'
+ desired_sbh_link = 'https://hub.sd2e.org/user/sd2e/design/DNA/1'
+ self.mock_sbol_dictionary_accessor.get_common_names_to_uri.return_value = {dictionary_matched_term: desired_sbh_link}
+ json_body = {addon_constants.DATA: {addon_constants.BUTTON_ID: {addon_constants.ANALYZE_PARAGRAPH_INDEX: text_paragraph_index,
+ addon_constants.ANALYZE_END_OFFSET: text_end_offset,
+ addon_constants.ANALYZE_TERM: dictionary_matched_term,
+ addon_constants.ANALYZE_CONTENT_TERM: document_term,
+ addon_constants.DOCUMENT_ID: 'foo',
+ addon_constants.ANALYZE_LINK: desired_sbh_link,
+ addon_constants.ANALYZE_OFFSET: text_start_offset}}}
+ client_state = {addon_constants.ANALYZE_SEARCH_RESULTS: [{addon_constants.ANALYZE_PARAGRAPH_INDEX: text_paragraph_index,
+ addon_constants.ANALYZE_OFFSET: text_start_offset,
+ addon_constants.ANALYZE_END_OFFSET: text_end_offset,
+ addon_constants.ANALYZE_TERM: dictionary_matched_term,
+ 'uri': desired_sbh_link,
+ addon_constants.ANALYZE_LINK: None,
+ 'text': document_term}],
+ addon_constants.ANALYZE_SEARCH_RESULT_INDEX: 0}
+ response = self.ip_server.process_analyze_yes(json_body=json_body, client_state=client_state)
+ expected_actions = [intent_parser_view.simple_sidebar_dialog('Finished Analyzing Document.', [])]
+ self.assertEqual(response, expected_actions)
+
+ def test_process_analyze_yes_for_search_results_size_2(self):
+ text_paragraph_index = 13
+ text_start_offset = 183
+ text_end_offset = 185
+ document_term = 'DNA'
+ dictionary_matched_term = 'DNA'
+ desired_sbh_link = 'https://hub.sd2e.org/user/sd2e/design/DNA/1'
+ self.mock_sbol_dictionary_accessor.get_common_names_to_uri.return_value = {dictionary_matched_term: desired_sbh_link,
+ 'protein': 'https://hub.sd2e.org/user/sd2e/design/protein/1'}
+ json_body = {addon_constants.DATA: {addon_constants.BUTTON_ID: {addon_constants.ANALYZE_PARAGRAPH_INDEX: text_paragraph_index,
+ addon_constants.ANALYZE_END_OFFSET: text_end_offset,
+ addon_constants.ANALYZE_TERM: dictionary_matched_term,
+ addon_constants.ANALYZE_CONTENT_TERM: document_term,
+ addon_constants.DOCUMENT_ID: 'foo',
+ addon_constants.ANALYZE_LINK: desired_sbh_link,
+ addon_constants.ANALYZE_OFFSET: text_start_offset}}}
+ client_state = {addon_constants.ANALYZE_SEARCH_RESULTS: [{addon_constants.ANALYZE_PARAGRAPH_INDEX: text_paragraph_index,
+ addon_constants.ANALYZE_OFFSET: text_start_offset,
+ addon_constants.ANALYZE_END_OFFSET: text_end_offset,
+ addon_constants.ANALYZE_TERM: dictionary_matched_term,
+ 'uri': desired_sbh_link,
+ addon_constants.ANALYZE_LINK: None,
+ 'text': document_term},
+ {addon_constants.ANALYZE_PARAGRAPH_INDEX: 20,
+ addon_constants.ANALYZE_OFFSET: 15,
+ addon_constants.ANALYZE_END_OFFSET: 23,
+ addon_constants.ANALYZE_TERM: 'protein',
+ 'uri': 'https://hub.sd2e.org/user/sd2e/design/protein/1',
+ addon_constants.ANALYZE_LINK: None,
+ 'text': 'protein'}
+ ],
+ addon_constants.ANALYZE_SEARCH_RESULT_INDEX: 0,
+ 'document_id': 'document_foo'}
+ response = self.ip_server.process_analyze_yes(json_body=json_body, client_state=client_state)
+ expected_actions = [intent_parser_view.link_text(text_paragraph_index, text_start_offset, text_end_offset, desired_sbh_link)]
+ expected_actions.extend(intent_parser_view.create_search_result_dialog('protein', 'https://hub.sd2e.org/user/sd2e/design/protein/1', 'protein', 'document_foo', 20, 15, 23))
+ self.assertEqual(response, expected_actions)
+
+ def test_process_analyze_no_for_search_results_size_1(self):
+ text_paragraph_index = 13
+ text_start_offset = 183
+ text_end_offset = 185
+ document_term = 'DNA'
+ dictionary_matched_term = 'DNA'
+ desired_sbh_link = 'https://hub.sd2e.org/user/sd2e/design/DNA/1'
+ self.mock_sbol_dictionary_accessor.get_common_names_to_uri.return_value = {dictionary_matched_term: desired_sbh_link}
+ json_body = {addon_constants.DATA: {
+ addon_constants.BUTTON_ID: {addon_constants.ANALYZE_PARAGRAPH_INDEX: text_paragraph_index,
+ addon_constants.ANALYZE_END_OFFSET: text_end_offset,
+ addon_constants.ANALYZE_TERM: dictionary_matched_term,
+ addon_constants.ANALYZE_CONTENT_TERM: document_term,
+ addon_constants.DOCUMENT_ID: 'foo',
+ addon_constants.ANALYZE_LINK: desired_sbh_link,
+ addon_constants.ANALYZE_OFFSET: text_start_offset}}}
+ client_state = {
+ addon_constants.ANALYZE_SEARCH_RESULTS: [{addon_constants.ANALYZE_PARAGRAPH_INDEX: text_paragraph_index,
+ addon_constants.ANALYZE_OFFSET: text_start_offset,
+ addon_constants.ANALYZE_END_OFFSET: text_end_offset,
+ addon_constants.ANALYZE_TERM: dictionary_matched_term,
+ 'uri': desired_sbh_link,
+ addon_constants.ANALYZE_LINK: None,
+ 'text': document_term}],
+ addon_constants.ANALYZE_SEARCH_RESULT_INDEX: 0}
+ response = self.ip_server.process_analyze_no(json_body=json_body, client_state=client_state)
+ expected_actions = [intent_parser_view.simple_sidebar_dialog('Finished Analyzing Document.', [])]
+ self.assertEqual(response, expected_actions)
+
+ def test_process_analyze_no_for_search_results_size_2(self):
+ text_paragraph_index = 13
+ text_start_offset = 183
+ text_end_offset = 185
+ document_term = 'DNA'
+ dictionary_matched_term = 'DNA'
+ desired_sbh_link = 'https://hub.sd2e.org/user/sd2e/design/DNA/1'
+ self.mock_sbol_dictionary_accessor.get_common_names_to_uri.return_value = {dictionary_matched_term: desired_sbh_link,
+ 'protein': 'https://hub.sd2e.org/user/sd2e/design/protein/1'}
+ json_body = {addon_constants.DATA: {addon_constants.BUTTON_ID: {addon_constants.ANALYZE_PARAGRAPH_INDEX: text_paragraph_index,
+ addon_constants.ANALYZE_END_OFFSET: text_end_offset,
+ addon_constants.ANALYZE_TERM: dictionary_matched_term,
+ addon_constants.ANALYZE_CONTENT_TERM: document_term,
+ addon_constants.DOCUMENT_ID: 'foo',
+ addon_constants.ANALYZE_LINK: desired_sbh_link,
+ addon_constants.ANALYZE_OFFSET: text_start_offset}}}
+ client_state = {addon_constants.ANALYZE_SEARCH_RESULTS: [{addon_constants.ANALYZE_PARAGRAPH_INDEX: text_paragraph_index,
+ addon_constants.ANALYZE_OFFSET: text_start_offset,
+ addon_constants.ANALYZE_END_OFFSET: text_end_offset,
+ addon_constants.ANALYZE_TERM: dictionary_matched_term,
+ 'uri': desired_sbh_link,
+ addon_constants.ANALYZE_LINK: None,
+ 'text': document_term},
+ {addon_constants.ANALYZE_PARAGRAPH_INDEX: 20,
+ addon_constants.ANALYZE_OFFSET: 15,
+ addon_constants.ANALYZE_END_OFFSET: 23,
+ addon_constants.ANALYZE_TERM: 'protein',
+ 'uri': 'https://hub.sd2e.org/user/sd2e/design/protein/1',
+ addon_constants.ANALYZE_LINK: None,
+ 'text': 'protein'}
+ ],
+ addon_constants.ANALYZE_SEARCH_RESULT_INDEX: 0,
+ 'document_id': 'document_foo'}
+ response = self.ip_server.process_analyze_no(json_body=json_body, client_state=client_state)
+ expected_actions = intent_parser_view.create_search_result_dialog('protein', 'https://hub.sd2e.org/user/sd2e/design/protein/1', 'protein', 'document_foo', 20, 15, 23)
+ self.assertEqual(response, expected_actions)
+
+ def test_process_analyze_no_to_all_for_1_term_occurrence_with_search_results_size_1(self):
+ text_paragraph_index = 13
+ text_start_offset = 183
+ text_end_offset = 185
+ document_term = 'DNA'
+ dictionary_matched_term = 'DNA'
+ desired_sbh_link = 'https://hub.sd2e.org/user/sd2e/design/DNA/1'
+ self.mock_sbol_dictionary_accessor.get_common_names_to_uri.return_value = {
+ dictionary_matched_term: desired_sbh_link}
+ json_body = {addon_constants.DATA: {
+ addon_constants.BUTTON_ID: {addon_constants.ANALYZE_PARAGRAPH_INDEX: text_paragraph_index,
+ addon_constants.ANALYZE_END_OFFSET: text_end_offset,
+ addon_constants.ANALYZE_TERM: dictionary_matched_term,
+ addon_constants.ANALYZE_CONTENT_TERM: document_term,
+ addon_constants.DOCUMENT_ID: 'foo',
+ addon_constants.ANALYZE_LINK: desired_sbh_link,
+ addon_constants.ANALYZE_OFFSET: text_start_offset}}}
+ client_state = {
+ addon_constants.ANALYZE_SEARCH_RESULTS: [{addon_constants.ANALYZE_PARAGRAPH_INDEX: text_paragraph_index,
+ addon_constants.ANALYZE_OFFSET: text_start_offset,
+ addon_constants.ANALYZE_END_OFFSET: text_end_offset,
+ addon_constants.ANALYZE_TERM: dictionary_matched_term,
+ 'uri': desired_sbh_link,
+ addon_constants.ANALYZE_LINK: None,
+ 'text': document_term}
+ ],
+ addon_constants.ANALYZE_SEARCH_RESULT_INDEX: 0}
+ response = self.ip_server.process_no_to_all(json_body=json_body, client_state=client_state)
+ expected_actions = [intent_parser_view.simple_sidebar_dialog('Finished Analyzing Document.', [])]
+ self.assertEqual(response, expected_actions)
+
+ def test_process_analyze_no_to_all_for_2_term_occurrences_with_search_results_size_2(self):
+ text_paragraph_index = 13
+ text_start_offset = 183
+ text_end_offset = 185
+ document_term = 'DNA'
+ dictionary_matched_term = 'DNA'
+ desired_sbh_link = 'https://hub.sd2e.org/user/sd2e/design/DNA/1'
+ self.mock_sbol_dictionary_accessor.get_common_names_to_uri.return_value = {
+ dictionary_matched_term: desired_sbh_link}
+ json_body = {addon_constants.DATA: {
+ addon_constants.BUTTON_ID: {addon_constants.ANALYZE_PARAGRAPH_INDEX: text_paragraph_index,
+ addon_constants.ANALYZE_END_OFFSET: text_end_offset,
+ addon_constants.ANALYZE_TERM: dictionary_matched_term,
+ addon_constants.ANALYZE_CONTENT_TERM: document_term,
+ addon_constants.DOCUMENT_ID: 'foo',
+ addon_constants.ANALYZE_LINK: desired_sbh_link,
+ addon_constants.ANALYZE_OFFSET: text_start_offset}}}
+ client_state = {
+ addon_constants.ANALYZE_SEARCH_RESULTS: [{addon_constants.ANALYZE_PARAGRAPH_INDEX: text_paragraph_index,
+ addon_constants.ANALYZE_OFFSET: text_start_offset,
+ addon_constants.ANALYZE_END_OFFSET: text_end_offset,
+ addon_constants.ANALYZE_TERM: dictionary_matched_term,
+ 'uri': desired_sbh_link,
+ addon_constants.ANALYZE_LINK: None,
+ 'text': document_term},
+ {addon_constants.ANALYZE_PARAGRAPH_INDEX: 20,
+ addon_constants.ANALYZE_OFFSET: 200,
+ addon_constants.ANALYZE_END_OFFSET: 210,
+ addon_constants.ANALYZE_TERM: dictionary_matched_term,
+ 'uri': desired_sbh_link,
+ addon_constants.ANALYZE_LINK: None,
+ 'text': document_term}
+ ],
+ addon_constants.ANALYZE_SEARCH_RESULT_INDEX: 0}
+ response = self.ip_server.process_no_to_all(json_body=json_body, client_state=client_state)
+ expected_actions = [intent_parser_view.simple_sidebar_dialog('Finished Analyzing Document.', [])]
+ self.assertEqual(response, expected_actions)
+
+ def test_process_analyze_yes_to_all_for_1_term_occurrence(self):
+ text_paragraph_index = 13
+ text_start_offset = 183
+ text_end_offset = 185
+ document_term = 'DNA'
+ dictionary_matched_term = 'DNA'
+ desired_sbh_link = 'https://hub.sd2e.org/user/sd2e/design/DNA/1'
+ self.mock_sbol_dictionary_accessor.get_common_names_to_uri.return_value = {
+ dictionary_matched_term: desired_sbh_link}
+ json_body = {addon_constants.DATA: {
+ addon_constants.BUTTON_ID: {addon_constants.ANALYZE_PARAGRAPH_INDEX: text_paragraph_index,
+ addon_constants.ANALYZE_END_OFFSET: text_end_offset,
+ addon_constants.ANALYZE_TERM: dictionary_matched_term,
+ addon_constants.ANALYZE_CONTENT_TERM: document_term,
+ addon_constants.DOCUMENT_ID: 'foo',
+ addon_constants.ANALYZE_LINK: desired_sbh_link,
+ addon_constants.ANALYZE_OFFSET: text_start_offset}}}
+ client_state = {
+ addon_constants.ANALYZE_SEARCH_RESULTS: [{addon_constants.ANALYZE_PARAGRAPH_INDEX: text_paragraph_index,
+ addon_constants.ANALYZE_OFFSET: text_start_offset,
+ addon_constants.ANALYZE_END_OFFSET: text_end_offset,
+ addon_constants.ANALYZE_TERM: dictionary_matched_term,
+ 'uri': desired_sbh_link,
+ addon_constants.ANALYZE_LINK: None,
+ 'text': document_term}
+ ],
+ addon_constants.ANALYZE_SEARCH_RESULT_INDEX: 0}
+ response = self.ip_server.process_link_all(json_body=json_body, client_state=client_state)
+ expected_actions = [intent_parser_view.link_text(text_paragraph_index, text_start_offset, text_end_offset, desired_sbh_link),
+ intent_parser_view.simple_sidebar_dialog('Finished Analyzing Document.', [])]
+ self.assertEqual(response, expected_actions)
+
+ def test_process_analyze_yes_to_all_for_2_term_occurrences_with_search_results_size_2(self):
+ text_paragraph_index = 13
+ text_start_offset = 183
+ text_end_offset = 185
+ document_term = 'DNA'
+ dictionary_matched_term = 'DNA'
+ desired_sbh_link = 'https://hub.sd2e.org/user/sd2e/design/DNA/1'
+ self.mock_sbol_dictionary_accessor.get_common_names_to_uri.return_value = {
+ dictionary_matched_term: desired_sbh_link}
+ json_body = {addon_constants.DATA: {
+ addon_constants.BUTTON_ID: {addon_constants.ANALYZE_PARAGRAPH_INDEX: text_paragraph_index,
+ addon_constants.ANALYZE_END_OFFSET: text_end_offset,
+ addon_constants.ANALYZE_TERM: dictionary_matched_term,
+ addon_constants.ANALYZE_CONTENT_TERM: document_term,
+ addon_constants.DOCUMENT_ID: 'foo',
+ addon_constants.ANALYZE_LINK: desired_sbh_link,
+ addon_constants.ANALYZE_OFFSET: text_start_offset}}}
+ client_state = {
+ addon_constants.ANALYZE_SEARCH_RESULTS: [{addon_constants.ANALYZE_PARAGRAPH_INDEX: text_paragraph_index,
+ addon_constants.ANALYZE_OFFSET: text_start_offset,
+ addon_constants.ANALYZE_END_OFFSET: text_end_offset,
+ addon_constants.ANALYZE_TERM: dictionary_matched_term,
+ 'uri': desired_sbh_link,
+ addon_constants.ANALYZE_LINK: None,
+ 'text': document_term},
+ {addon_constants.ANALYZE_PARAGRAPH_INDEX: 20,
+ addon_constants.ANALYZE_OFFSET: 200,
+ addon_constants.ANALYZE_END_OFFSET: 210,
+ addon_constants.ANALYZE_TERM: dictionary_matched_term,
+ 'uri': desired_sbh_link,
+ addon_constants.ANALYZE_LINK: None,
+ 'text': document_term}
+ ],
+ addon_constants.ANALYZE_SEARCH_RESULT_INDEX: 0}
+ response = self.ip_server.process_link_all(json_body=json_body, client_state=client_state)
+ expected_actions = [intent_parser_view.link_text(text_paragraph_index, text_start_offset, text_end_offset, desired_sbh_link),
+ intent_parser_view.link_text(20, 200, 210, desired_sbh_link),
+ intent_parser_view.simple_sidebar_dialog('Finished Analyzing Document.', [])]
+ self.assertEqual(response, expected_actions)
+
+ def test_process_analyze_yes_to_all_for_2_term_occurrences_with_search_results_size_3(self):
+ text_paragraph_index = 13
+ text_start_offset = 183
+ text_end_offset = 185
+ document_term = 'DNA'
+ dictionary_matched_term = 'DNA'
+ desired_sbh_link = 'https://hub.sd2e.org/user/sd2e/design/DNA/1'
+ self.mock_sbol_dictionary_accessor.get_common_names_to_uri.return_value = {
+ dictionary_matched_term: desired_sbh_link,
+ 'protein': 'https://hub.sd2e.org/user/sd2e/design/protein/1'}
+ json_body = {addon_constants.DATA: {
+ addon_constants.BUTTON_ID: {addon_constants.ANALYZE_PARAGRAPH_INDEX: text_paragraph_index,
+ addon_constants.ANALYZE_END_OFFSET: text_end_offset,
+ addon_constants.ANALYZE_TERM: dictionary_matched_term,
+ addon_constants.ANALYZE_CONTENT_TERM: document_term,
+ addon_constants.DOCUMENT_ID: 'foo',
+ addon_constants.ANALYZE_LINK: desired_sbh_link,
+ addon_constants.ANALYZE_OFFSET: text_start_offset}}}
+ client_state = {
+ addon_constants.ANALYZE_SEARCH_RESULTS: [{addon_constants.ANALYZE_PARAGRAPH_INDEX: text_paragraph_index,
+ addon_constants.ANALYZE_OFFSET: text_start_offset,
+ addon_constants.ANALYZE_END_OFFSET: text_end_offset,
+ addon_constants.ANALYZE_TERM: dictionary_matched_term,
+ 'uri': desired_sbh_link,
+ addon_constants.ANALYZE_LINK: None,
+ 'text': document_term},
+ {addon_constants.ANALYZE_PARAGRAPH_INDEX: 20,
+ addon_constants.ANALYZE_OFFSET: 200,
+ addon_constants.ANALYZE_END_OFFSET: 210,
+ addon_constants.ANALYZE_TERM: dictionary_matched_term,
+ 'uri': desired_sbh_link,
+ addon_constants.ANALYZE_LINK: None,
+ 'text': document_term},
+ {addon_constants.ANALYZE_PARAGRAPH_INDEX: 20,
+ addon_constants.ANALYZE_OFFSET: 15,
+ addon_constants.ANALYZE_END_OFFSET: 23,
+ addon_constants.ANALYZE_TERM: 'protein',
+ 'uri': 'https://hub.sd2e.org/user/sd2e/design/protein/1',
+ addon_constants.ANALYZE_LINK: None,
+ 'text': 'protein'}
+ ],
+ addon_constants.ANALYZE_SEARCH_RESULT_INDEX: 0,
+ 'document_id': 'document_foo'}
+ response = self.ip_server.process_link_all(json_body=json_body, client_state=client_state)
+ expected_actions = [intent_parser_view.link_text(text_paragraph_index, text_start_offset, text_end_offset, desired_sbh_link),
+ intent_parser_view.link_text(20, 200, 210, desired_sbh_link)]
+ expected_actions.extend(intent_parser_view.create_search_result_dialog('protein', 'https://hub.sd2e.org/user/sd2e/design/protein/1', 'protein', 'document_foo', 20, 15, 23))
+ self.assertEqual(response, expected_actions)
+
+ def test_process_analyze_never_link_terms_for_1_occurrence_with_search_results_size_1(self):
+ text_paragraph_index = 13
+ text_start_offset = 183
+ text_end_offset = 185
+ document_term = 'foo'
+ dictionary_matched_term = 'foo'
+ desired_sbh_link = 'https://hub.sd2e.org/user/sd2e/design/DNA/1'
+
+ json_body = {addon_constants.DATA: {
+ addon_constants.BUTTON_ID: {addon_constants.ANALYZE_PARAGRAPH_INDEX: text_paragraph_index,
+ addon_constants.ANALYZE_END_OFFSET: text_end_offset,
+ addon_constants.ANALYZE_TERM: dictionary_matched_term,
+ addon_constants.ANALYZE_CONTENT_TERM: document_term,
+ addon_constants.DOCUMENT_ID: 'foo',
+ addon_constants.ANALYZE_LINK: desired_sbh_link,
+ addon_constants.ANALYZE_OFFSET: text_start_offset}}}
+ client_state = {
+ addon_constants.ANALYZE_SEARCH_RESULTS: [{addon_constants.ANALYZE_PARAGRAPH_INDEX: text_paragraph_index,
+ addon_constants.ANALYZE_OFFSET: text_start_offset,
+ addon_constants.ANALYZE_END_OFFSET: text_end_offset,
+ addon_constants.ANALYZE_TERM: dictionary_matched_term,
+ 'uri': desired_sbh_link,
+ addon_constants.ANALYZE_LINK: None,
+ 'text': document_term}
+ ],
+ addon_constants.ANALYZE_SEARCH_RESULT_INDEX: 0,
+ addon_constants.USER_ID: 'admin',
+ 'document_id': 'document_foo'}
+ response = self.ip_server.process_never_link(json_body=json_body, client_state=client_state)
+ expected_actions = [intent_parser_view.simple_sidebar_dialog('Finished Analyzing Document.', [])]
+ self.assertEqual(response, expected_actions)
+
+ def test_process_analyze_never_link_terms_for_1_occurrence_with_search_results_size_3(self):
+ text_paragraph_index = 13
+ text_start_offset = 183
+ text_end_offset = 185
+ document_term = 'foo'
+ dictionary_matched_term = 'foo'
+ desired_sbh_link = 'https://hub.sd2e.org/user/sd2e/design/DNA/1'
+
+ json_body = {addon_constants.DATA: {
+ addon_constants.BUTTON_ID: {addon_constants.ANALYZE_PARAGRAPH_INDEX: text_paragraph_index,
+ addon_constants.ANALYZE_END_OFFSET: text_end_offset,
+ addon_constants.ANALYZE_TERM: dictionary_matched_term,
+ addon_constants.ANALYZE_CONTENT_TERM: document_term,
+ addon_constants.DOCUMENT_ID: 'foo',
+ addon_constants.ANALYZE_LINK: desired_sbh_link,
+ addon_constants.ANALYZE_OFFSET: text_start_offset}}}
+ client_state = {
+ addon_constants.ANALYZE_SEARCH_RESULTS: [{addon_constants.ANALYZE_PARAGRAPH_INDEX: text_paragraph_index,
+ addon_constants.ANALYZE_OFFSET: text_start_offset,
+ addon_constants.ANALYZE_END_OFFSET: text_end_offset,
+ addon_constants.ANALYZE_TERM: dictionary_matched_term,
+ 'uri': desired_sbh_link,
+ addon_constants.ANALYZE_LINK: None,
+ 'text': document_term},
+ {addon_constants.ANALYZE_PARAGRAPH_INDEX: 20,
+ addon_constants.ANALYZE_OFFSET: 200,
+ addon_constants.ANALYZE_END_OFFSET: 210,
+ addon_constants.ANALYZE_TERM: dictionary_matched_term,
+ 'uri': desired_sbh_link,
+ addon_constants.ANALYZE_LINK: None,
+ 'text': document_term},
+ {addon_constants.ANALYZE_PARAGRAPH_INDEX: 20,
+ addon_constants.ANALYZE_OFFSET: 15,
+ addon_constants.ANALYZE_END_OFFSET: 23,
+ addon_constants.ANALYZE_TERM: 'protein',
+ 'uri': 'https://hub.sd2e.org/user/sd2e/design/protein/1',
+ addon_constants.ANALYZE_LINK: None,
+ 'text': 'protein'}
+ ],
+ addon_constants.ANALYZE_SEARCH_RESULT_INDEX: 0,
+ addon_constants.USER_ID: 'admin',
+ 'document_id': 'document_foo'}
+ response = self.ip_server.process_never_link(json_body=json_body, client_state=client_state)
+ expected_actions = intent_parser_view.create_search_result_dialog('protein', 'https://hub.sd2e.org/user/sd2e/design/protein/1', 'protein', 'document_foo', 20, 15, 23)
+ self.assertEqual(response, expected_actions)
+
def _verify_response_status(self, response, expected_status):
header_from_status = 'HTTP/1.1 %s %s' % (expected_status.value, expected_status.name)
assert response.requestLine == header_from_status
diff --git a/intent_parser/tests/test_measurement_table.py b/intent_parser/tests/test_measurement_table.py
index 19213c46..6e37d7cc 100644
--- a/intent_parser/tests/test_measurement_table.py
+++ b/intent_parser/tests/test_measurement_table.py
@@ -2,7 +2,7 @@
from intent_parser.table.measurement_table import MeasurementTable
from intent_parser.table.intent_parser_cell import IntentParserCell
from intent_parser.table.intent_parser_table_factory import IntentParserTableFactory
-from intent_parser.accessor.sbol_dictionary_accessor import StrainMapping
+from intent_parser.experiment_variables.experiment_variables import ExperimentVariable
import intent_parser.constants.sd2_datacatalog_constants as dc_constants
import intent_parser.tests.test_util as test_utils
import unittest
@@ -89,7 +89,7 @@ def test_table_with_1_strain(self):
data_row = test_utils.create_measurement_table_row(strain_cell=strains)
ip_table.add_row(data_row)
- strain_obj = StrainMapping('https://foo.com', 'myLab', 'AND_00', lab_names={'test_strain', 'foo-strain'})
+ strain_obj = ExperimentVariable('https://foo.com', 'myLab', 'AND_00', lab_names={'test_strain', 'foo-strain'})
strain_mapping = {'https://foo.com': strain_obj}
meas_table = MeasurementTable(ip_table, strain_mapping=strain_mapping)
@@ -109,7 +109,7 @@ def test_strain_with_unknown_links(self):
data_row = test_utils.create_measurement_table_row(strain_cell=strains)
ip_table.add_row(data_row)
- strain_obj = StrainMapping('https://hub.sd2e.org/user/sd2e/design/UWBF_7376/1', 'myLab', 'AND_00', lab_names={'test_strain', 'foo-strain'})
+ strain_obj = ExperimentVariable('https://hub.sd2e.org/user/sd2e/design/UWBF_7376/1', 'myLab', 'AND_00', lab_names={'test_strain', 'foo-strain'})
strain_mapping = {'https://hub.sd2e.org/user/sd2e/design/UWBF_7376/1': strain_obj}
meas_table = MeasurementTable(ip_table, strain_mapping=strain_mapping)
@@ -124,7 +124,7 @@ def test_strain_not_supported_in_lab_name(self):
data_row = test_utils.create_measurement_table_row(strain_cell=strains)
ip_table.add_row(data_row)
- strain_obj = StrainMapping('https://foo.com', dc_constants.LAB_TACC, 'AND_00', lab_names={'UWBF_7376'})
+ strain_obj = ExperimentVariable('https://foo.com', dc_constants.LAB_TACC, 'AND_00', lab_names={'UWBF_7376'})
strain_mapping = {'https://foo.com': strain_obj}
meas_table = MeasurementTable(ip_table, strain_mapping=strain_mapping)
@@ -145,8 +145,8 @@ def test_strains_with_inconsistent_links(self):
data_row = test_utils.create_measurement_table_row(strain_cell=strains)
ip_table.add_row(data_row)
- strain1_obj = StrainMapping(strain_link1, 'myLab', 'AND_00', lab_names={lab_strain1})
- strain2_obj = StrainMapping(strain_link2, 'myLab', 'AND_01', lab_names={lab_strain2})
+ strain1_obj = ExperimentVariable(strain_link1, 'myLab', 'AND_00', lab_names={lab_strain1})
+ strain2_obj = ExperimentVariable(strain_link2, 'myLab', 'AND_01', lab_names={lab_strain2})
strain_mapping = {strain_link1: strain1_obj,
strain_link2: strain2_obj}
diff --git a/intent_parser/tests/test_parameter_table.py b/intent_parser/tests/test_parameter_table.py
index 766fffb0..4a717dab 100644
--- a/intent_parser/tests/test_parameter_table.py
+++ b/intent_parser/tests/test_parameter_table.py
@@ -2,6 +2,7 @@
from intent_parser.table.intent_parser_table_factory import IntentParserTableFactory
from intent_parser.table.parameter_table import ParameterTable
import intent_parser.constants.sd2_datacatalog_constants as dc_constants
+import intent_parser.constants.intent_parser_constants as ip_constants
import intent_parser.tests.test_util as test_utils
import unittest
@@ -30,7 +31,14 @@ def setUp(self):
'Kill switch': 'reagent_info.kill_switch',
'Media well ids': 'exp_info.media_well_strings',
'Plate reader gain': 'plate_reader_info.gain',
- 'Sample has sbh_uri as an aliquot property': 'validate_samples'
+ 'Sample has sbh_uri as an aliquot property': 'validate_samples',
+ 'Plate Size': ip_constants.PARAMETER_PLATE_SIZE,
+ 'Plate Number': ip_constants.PARAMETER_PLATE_NUMBER,
+ 'Container Search String': ip_constants.PARAMETER_CONTAINER_SEARCH_STRING,
+ 'Strain Property': ip_constants.PARAMETER_STRAIN_PROPERTY,
+ 'XPlan Path': ip_constants.PARAMETER_XPLAN_PATH,
+ 'Protocol ID': ip_constants.PARAMETER_PROTOCOL_ID,
+ 'Experiment reference url for xplan': ip_constants.PARAMETER_EXPERIMENT_REFERENCE_URL_FOR_XPLAN
}
def tearDown(self):
@@ -253,6 +261,221 @@ def test_parameter_with_three_float_values(self):
'plate_reader_info.gain.2': 0.3}
self.assertEqual(3, len(param_result))
self.assertDictEqual(expected_result, param_result)
-
+
+ def test_process_complete_experiment_data_from_parameter_table(self):
+ ip_table = test_utils.create_fake_parameter()
+ plate_size = IntentParserCell()
+ plate_size.add_paragraph('Plate Size')
+ parameter_value = IntentParserCell()
+ parameter_value.add_paragraph('96')
+ data_row = test_utils.create_parameter_table_row(parameter_cell=plate_size,
+ parameter_value_cell=parameter_value)
+ ip_table.add_row(data_row)
+
+ plate_number = IntentParserCell()
+ plate_number.add_paragraph('Plate Number')
+ parameter_value = IntentParserCell()
+ parameter_value.add_paragraph('2')
+ data_row = test_utils.create_parameter_table_row(parameter_cell=plate_number,
+ parameter_value_cell=parameter_value)
+ ip_table.add_row(data_row)
+
+ protocol_name = IntentParserCell()
+ protocol_name.add_paragraph('Protocol')
+ parameter_value = IntentParserCell()
+ parameter_value.add_paragraph('ObstacleCourse')
+ data_row = test_utils.create_parameter_table_row(parameter_cell=protocol_name,
+ parameter_value_cell=parameter_value)
+ ip_table.add_row(data_row)
+
+ container_search_string = IntentParserCell()
+ container_search_string.add_paragraph('Container Search String')
+ parameter_value = IntentParserCell()
+ parameter_value.add_paragraph('Ct1e3qc85mqwbz8, ct1e3qc85jc4gj52')
+ data_row = test_utils.create_parameter_table_row(parameter_cell=container_search_string,
+ parameter_value_cell=parameter_value)
+ ip_table.add_row(data_row)
+
+ strain_property = IntentParserCell()
+ strain_property.add_paragraph('Strain Property')
+ parameter_value = IntentParserCell()
+ parameter_value.add_paragraph('SD2_common_name')
+ data_row = test_utils.create_parameter_table_row(parameter_cell=strain_property,
+ parameter_value_cell=parameter_value)
+ ip_table.add_row(data_row)
+
+ xplan_path = IntentParserCell()
+ xplan_path.add_paragraph('XPlan Path')
+ parameter_value = IntentParserCell()
+ parameter_value.add_paragraph('path/foo/xplan_path')
+ data_row = test_utils.create_parameter_table_row(parameter_cell=xplan_path,
+ parameter_value_cell=parameter_value)
+ ip_table.add_row(data_row)
+
+ experiment_reference_url = IntentParserCell()
+ experiment_reference_url.add_paragraph('Experiment reference url for xplan')
+ parameter_value = IntentParserCell()
+ parameter_value.add_paragraph('path/foo/experiment_reference')
+ data_row = test_utils.create_parameter_table_row(parameter_cell=experiment_reference_url,
+ parameter_value_cell=parameter_value)
+ ip_table.add_row(data_row)
+
+ protocol_id = IntentParserCell()
+ protocol_id.add_paragraph('Protocol ID')
+ parameter_value = IntentParserCell()
+ parameter_value.add_paragraph('pr1e5gw8bdekdxv')
+ data_row = test_utils.create_parameter_table_row(parameter_cell=protocol_id,
+ parameter_value_cell=parameter_value)
+ ip_table.add_row(data_row)
+
+ deafult_params = IntentParserCell()
+ deafult_params.add_paragraph('Inoculation volume')
+ parameter_value = IntentParserCell()
+ parameter_value.add_paragraph('5 microliter')
+ data_row = test_utils.create_parameter_table_row(parameter_cell=deafult_params,
+ parameter_value_cell=parameter_value)
+ ip_table.add_row(data_row)
+
+ param_table = ParameterTable(ip_table, parameter_fields=self.parameter_fields)
+ param_table.process_table()
+ sr_result = param_table.get_structured_request()
+ exp_result = param_table.get_experiment()
+ expected_sr_result = {'inoc_info.inoc_vol': '5:microliter'}
+ expected_experiment_result = {ip_constants.PARAMETER_BASE_DIR: None,
+ ip_constants.PARAMETER_XPLAN_REACTOR: 'xplan',
+ ip_constants.PARAMETER_PLATE_SIZE: 96,
+ ip_constants.PARAMETER_PROTOCOL: 'ObstacleCourse',
+ ip_constants.PARAMETER_PLATE_NUMBER: 2,
+ ip_constants.PARAMETER_CONTAINER_SEARCH_STRING: ['Ct1e3qc85mqwbz8', 'ct1e3qc85jc4gj52'],
+ ip_constants.PARAMETER_STRAIN_PROPERTY: 'SD2_common_name',
+ ip_constants.PARAMETER_XPLAN_PATH: 'path/foo/xplan_path',
+ ip_constants.PARAMETER_SUBMIT: False,
+ ip_constants.PARAMETER_PROTOCOL_ID: 'pr1e5gw8bdekdxv',
+ ip_constants.PARAMETER_TEST_MODE: True,
+ ip_constants.PARAMETER_EXPERIMENT_REFERENCE_URL_FOR_XPLAN: 'path/foo/experiment_reference',
+ ip_constants.DEFAULT_PARAMETERS: {'inoc_info.inoc_vol': '5:microliter'}}
+ self.assertEqual(1, len(expected_sr_result))
+ self.assertDictEqual(expected_sr_result, sr_result)
+
+ self.assertEqual(13, len(expected_experiment_result))
+ self.assertDictEqual(expected_experiment_result, exp_result)
+
+ def test_process_incomplete_experiment_data_from_parameter_table(self):
+ ip_table = test_utils.create_fake_parameter()
+ plate_size = IntentParserCell()
+ plate_size.add_paragraph('Plate Size')
+ parameter_value = IntentParserCell()
+ parameter_value.add_paragraph('96')
+ data_row = test_utils.create_parameter_table_row(parameter_cell=plate_size,
+ parameter_value_cell=parameter_value)
+ ip_table.add_row(data_row)
+
+ param_table = ParameterTable(ip_table, parameter_fields=self.parameter_fields)
+ param_table.process_table()
+ expected_experiment_result = {ip_constants.PARAMETER_BASE_DIR: None,
+ ip_constants.PARAMETER_XPLAN_REACTOR: 'xplan',
+ ip_constants.PARAMETER_PLATE_SIZE: 96,
+ ip_constants.PARAMETER_PROTOCOL: None,
+ ip_constants.PARAMETER_PLATE_NUMBER: None,
+ ip_constants.PARAMETER_CONTAINER_SEARCH_STRING: dc_constants.GENERATE,
+ ip_constants.PARAMETER_STRAIN_PROPERTY: None,
+ ip_constants.PARAMETER_XPLAN_PATH: None,
+ ip_constants.PARAMETER_SUBMIT: False,
+ ip_constants.PARAMETER_PROTOCOL_ID: None,
+ ip_constants.PARAMETER_TEST_MODE: True,
+ ip_constants.PARAMETER_EXPERIMENT_REFERENCE_URL_FOR_XPLAN: None,
+ ip_constants.DEFAULT_PARAMETERS: {}}
+ self.assertEqual(13, len(param_table.get_experiment()))
+ self.assertDictEqual(expected_experiment_result, param_table.get_experiment())
+
+ def test_container_search_string_with_list(self):
+ ip_table = test_utils.create_fake_parameter()
+ container_search_string = IntentParserCell()
+ container_search_string.add_paragraph('Container Search String')
+ parameter_value = IntentParserCell()
+ parameter_value.add_paragraph('ct1et97fsbvt84h, ct1et97fs59aejp, ct1et97frwr78dx, ct1et97frq988d8, ct1et97frgr528g')
+ data_row = test_utils.create_parameter_table_row(parameter_cell=container_search_string,
+ parameter_value_cell=parameter_value)
+ ip_table.add_row(data_row)
+
+ param_table = ParameterTable(ip_table, parameter_fields=self.parameter_fields)
+ param_table.process_table()
+ expected_experiment_result = {ip_constants.PARAMETER_BASE_DIR: None,
+ ip_constants.PARAMETER_XPLAN_REACTOR: 'xplan',
+ ip_constants.PARAMETER_PLATE_SIZE: None,
+ ip_constants.PARAMETER_PROTOCOL: None,
+ ip_constants.PARAMETER_PLATE_NUMBER: None,
+ ip_constants.PARAMETER_CONTAINER_SEARCH_STRING: ['ct1et97fsbvt84h',
+ 'ct1et97fs59aejp',
+ 'ct1et97frwr78dx',
+ 'ct1et97frq988d8',
+ 'ct1et97frgr528g'],
+ ip_constants.PARAMETER_STRAIN_PROPERTY: None,
+ ip_constants.PARAMETER_XPLAN_PATH: None,
+ ip_constants.PARAMETER_SUBMIT: False,
+ ip_constants.PARAMETER_PROTOCOL_ID: None,
+ ip_constants.PARAMETER_TEST_MODE: True,
+ ip_constants.PARAMETER_EXPERIMENT_REFERENCE_URL_FOR_XPLAN: None,
+ ip_constants.DEFAULT_PARAMETERS: {}}
+ self.assertEqual(13, len(param_table.get_experiment()))
+ self.assertDictEqual(expected_experiment_result, param_table.get_experiment())
+
+ def test_container_search_string_with_single_string(self):
+ ip_table = test_utils.create_fake_parameter()
+ container_search_string = IntentParserCell()
+ container_search_string.add_paragraph('Container Search String')
+ parameter_value = IntentParserCell()
+ parameter_value.add_paragraph('ct1et97fsbvt84h')
+ data_row = test_utils.create_parameter_table_row(parameter_cell=container_search_string,
+ parameter_value_cell=parameter_value)
+ ip_table.add_row(data_row)
+
+ param_table = ParameterTable(ip_table, parameter_fields=self.parameter_fields)
+ param_table.process_table()
+ expected_experiment_result = {ip_constants.PARAMETER_BASE_DIR: None,
+ ip_constants.PARAMETER_XPLAN_REACTOR: 'xplan',
+ ip_constants.PARAMETER_PLATE_SIZE: None,
+ ip_constants.PARAMETER_PROTOCOL: None,
+ ip_constants.PARAMETER_PLATE_NUMBER: None,
+ ip_constants.PARAMETER_CONTAINER_SEARCH_STRING: ['ct1et97fsbvt84h'],
+ ip_constants.PARAMETER_STRAIN_PROPERTY: None,
+ ip_constants.PARAMETER_XPLAN_PATH: None,
+ ip_constants.PARAMETER_SUBMIT: False,
+ ip_constants.PARAMETER_PROTOCOL_ID: None,
+ ip_constants.PARAMETER_TEST_MODE: True,
+ ip_constants.PARAMETER_EXPERIMENT_REFERENCE_URL_FOR_XPLAN: None,
+ ip_constants.DEFAULT_PARAMETERS: {}}
+ self.assertEqual(13, len(param_table.get_experiment()))
+ self.assertDictEqual(expected_experiment_result, param_table.get_experiment())
+
+ def test_container_search_string_with_default_value(self):
+ ip_table = test_utils.create_fake_parameter()
+ container_search_string = IntentParserCell()
+ container_search_string.add_paragraph('Container Search String')
+ parameter_value = IntentParserCell()
+ parameter_value.add_paragraph('\n')
+ data_row = test_utils.create_parameter_table_row(parameter_cell=container_search_string,
+ parameter_value_cell=parameter_value)
+ ip_table.add_row(data_row)
+
+ param_table = ParameterTable(ip_table, parameter_fields=self.parameter_fields)
+ param_table.process_table()
+ expected_experiment_result = {ip_constants.PARAMETER_BASE_DIR: None,
+ ip_constants.PARAMETER_XPLAN_REACTOR: 'xplan',
+ ip_constants.PARAMETER_PLATE_SIZE: None,
+ ip_constants.PARAMETER_PROTOCOL: None,
+ ip_constants.PARAMETER_PLATE_NUMBER: None,
+ ip_constants.PARAMETER_CONTAINER_SEARCH_STRING: dc_constants.GENERATE,
+ ip_constants.PARAMETER_STRAIN_PROPERTY: None,
+ ip_constants.PARAMETER_XPLAN_PATH: None,
+ ip_constants.PARAMETER_SUBMIT: False,
+ ip_constants.PARAMETER_PROTOCOL_ID: None,
+ ip_constants.PARAMETER_TEST_MODE: True,
+ ip_constants.PARAMETER_EXPERIMENT_REFERENCE_URL_FOR_XPLAN: None,
+ ip_constants.DEFAULT_PARAMETERS: {}}
+ self.assertEqual(13, len(param_table.get_experiment()))
+ self.assertDictEqual(expected_experiment_result, param_table.get_experiment())
+
+
if __name__ == "__main__":
unittest.main()
diff --git a/intent_parser/tests/test_structured_request.py b/intent_parser/tests/test_structured_request.py
index bec49541..82ad3e3a 100644
--- a/intent_parser/tests/test_structured_request.py
+++ b/intent_parser/tests/test_structured_request.py
@@ -1,5 +1,5 @@
from intent_parser.intent_parser import IntentParser
-from unittest.mock import Mock, patch
+from unittest.mock import patch
import intent_parser.constants.sd2_datacatalog_constants as dc_constants
import json
import os
diff --git a/intent_parser/utils/analyze_sidebar.html b/intent_parser/utils/analyze_sidebar.html
index 0144f2f2..3a7ac4f7 100644
--- a/intent_parser/utils/analyze_sidebar.html
+++ b/intent_parser/utils/analyze_sidebar.html
@@ -91,12 +91,13 @@
function linkItem(theForm, link) {
var data = {'buttonId' : 'process_analyze_yes',
'link' : link}
- busy('Linking to exsiting SynBioHub entry')
+ busy('Linking to existing SynBioHub entry')
google.script.run.withSuccessHandler(onSuccess).
buttonClick(data)
}
+
function linkAll(theForm, link) {
var data = {'buttonId' : 'process_link_all',
'link' : link}
diff --git a/intent_parser/utils/intent_parser_view.py b/intent_parser/utils/intent_parser_view.py
index 6f35647a..cc16d085 100644
--- a/intent_parser/utils/intent_parser_view.py
+++ b/intent_parser/utils/intent_parser_view.py
@@ -234,27 +234,50 @@ def progress_sidebar_dialog():
return action
def create_search_result_dialog(term, uri, content_term, document_id, paragraph_index, offset, end_offset):
+ """
+ Args:
+ term: term in document represented as a string
+ uri: a SBH uri that the hyperlink text will reference to
+ content_term: matched keyword found in sbol dictionary
+ document_id: id of a document
+ paragraph_index: an integer value to represent the paragraph where the term is found in the document
+ offset: an integer value to mark the starting position where the terms appears in the document paragraph
+ end_offset: an integer value to mark the ending position where the terms appears in the document paragraph
+ """
actions = [highlight_text(paragraph_index, offset, end_offset)]
- buttons = [('Yes', 'process_analyze_yes', 'Creates a hyperlink for the highlighted text, using the suggested URL.'),
- ('No', 'process_analyze_no', 'Skips this term without creating a link.'),
- ('Yes to All', 'process_link_all', 'Creates a hyperlink for the highilghted text and every instance of it in the document, using the suggested URL.'),
- ('No to All', 'process_no_to_all', 'Skips this term and every other instance of it in the document.'),
- ('Never Link', 'process_never_link', 'Never suggest links to this term, in this document or any other.')]
+ yes_button = ('Yes', addon_constants.ANALYZE_YES, 'Creates a hyperlink for the highlighted text, using the suggested URL.')
+ no_button = ('No', addon_constants.ANALYZE_NO, 'Skips this term without creating a link.')
+ yes_to_all_button = ('Yes to All', addon_constants.ANALYZE_YES_TO_ALL, 'Creates a hyperlink for the highilghted text and every instance of it in the document, using the suggested URL.')
+ no_to_all_button = ('No to All', addon_constants.ANALYZE_NO_TO_ALL, 'Skips this term and every other instance of it in the document.')
+ never_link_button = ('Never Link', addon_constants.ANALYZE_NEVER_LINK, 'Never suggest links to this term, in this document or any other.')
+ buttons = [yes_button, no_button, yes_to_all_button, no_to_all_button, never_link_button]
button_HTML = ''
button_script = ''
+
+ data = {addon_constants.DOCUMENT_ID: document_id,
+ addon_constants.ANALYZE_LINK: uri,
+ addon_constants.ANALYZE_PARAGRAPH_INDEX: paragraph_index,
+ addon_constants.ANALYZE_OFFSET: offset,
+ addon_constants.ANALYZE_END_OFFSET: end_offset,
+ addon_constants.ANALYZE_CONTENT_TERM: content_term,
+ addon_constants.ANALYZE_TERM: term}
for button in buttons:
button_HTML += '