Merge branch 'master' of https://github.com/SD2E/experimental-intent-…

…parser

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:
     
         ```

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()

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.

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

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 = '<h2> Controls Table </h2>\n' +
+		'<p><b>Description</b>: control definition based on time, strain, contents, etc.</p>\n' +
+		'<b>Required fields:</b>\n' +
+		'<ul>\n' +
+		'\t<li><a href="https://schema.catalog.sd2e.org/schemas/control_type.json"> <b>Type</b></a>: an expected type for this control. <i>Example:</i> HIGH_FITC</li>\n' +
+		'\t<li><b>Strains</b>: a list of one or more string values representing a strain listed in the SBOL Dictionary lab name. <i>Example:</i> B_subtilis_comKS_mCherry_1x</li>\n' +
+		'</ul>\n' +
+		'<b>Optional fields:</b>\n' +
+		'<ul>\n' +
+		'\t<li><b>Channel</b>: a string value representing FCS channel. <i>Example:</i> BL1-A</li>\n' +
+		'\t<li><b>Contents</b>: 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. <i>Example:</i> beta_estradiol or beta_estradiol 0.05 micromole</li>\n' +
+		'\t<li><b><a href="https://schema.catalog.sd2e.org/schemas/time_unit.json">Timepoints</a></b>: a list of one or more string values representing point in a time series. <i>Example:</i> 2, 4 hours</li>\n' +
+		'</ul>';
+	showSidebar(html_content);
+}
+
+function reportLabInfo(){
+	html_content = '<h2> Lab Table </h2>\n' +
+		'<p><b>Description</b>: information linked to a lab.</p>\n' +
+		'<b>Required fields:</b>\n' +
+		'<ul>\n' +
+		'\t<li><a href="https://schema.catalog.sd2e.org/schemas/lab.json"> <b>Lab</b></a>: a string value representing the lab that performed this experiment. <i>Example:</i> TACC</li>\n' +
+		'</ul>\n' +
+		'<b>Optionalfields:</b>\n' +
+		'<ul>\n' +
+		'\t<li><b>Experiment_id</b>: a string identifier, namespaced performer, for the experiment. <i>Example:</i> 123</li>\n' +
+		'</ul>';
+	showSidebar(html_content);
+}
+
+function reportMeasurementsInfo(){
+	html_content = '<h2> Measurements Table </h2>\n' +
+		'<p><b>Description</b>: measurements expected to be produced for a run, broken down by measurement type and sample conditions.</p>\n' +
+		'<b>Required fields:</b>\n' +
+		'<ul>\n' +
+		'\t<li><a href="https://schema.catalog.sd2e.org/schemas/measurement_type.json"> <b>Measurement Type</b></a>: an expected file type for this measurement. <i>Example:</i> RNA_SEQ</li>\n' +
+		'\t<li><a href="https://schema.catalog.sd2e.org/schemas/filetype_label.json"> <b>File Type</b></a>: a list of one or more expected file type for this measurement. <i>Example:</i> MSWORD, SPREADSHEET</li>\n' +
+		'</ul>\n' +
+		'<b>Optional fields:</b>\n' +
+		'<ul>\n' +
+		'\t<li><b>Batch</b>: a list of one or more numerical values representing the batches a measurement belongs to. <i>Example:</i> 1, 2, 3</li>\n' +
+		'\t<li><b>Controls</b>: a list of Control Table captions for representing expected control elements for this run. <i>Example:</i> Table 1, Table 2</li>\n' +
+		'\t<li><b>Ods</b>: a list of one or more numerical values representing expected optical densities for this measurement. <i>Example:</i> 5</li>\n' +
+		'\t<li><b>Replicates</b>: a list of one or more numerical values representing expected number of replicates. <i>Example:</i> 6</li>\n' +
+		'\t<li><b>Strains</b>: 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. <i>Example:</i> UWBF_6390</li>\n' +
+		'\t<li><a href="https://schema.catalog.sd2e.org/schemas/temperature.json"><b>Temperatures</b></a>: a list of one or more numerical values followed by a temperature unit representing expected temperatures for this measurement. <i>Example</i>: 30 celsius</li>\n' +
+		'\t<li><a href="https://schema.catalog.sd2e.org/schemas/time_unit.json"><b>Timepoints</b></a>: a list of one or more numerical values followed by a timepoint unit representing expected timepoints for this run. <i>Example:</i> 0, 4, 8, 12, 16 hour</li>\n' +
+		'</ul>';
+	showSidebar(html_content);
+}
+
 function showHelp() {
 	var helpHTML = '\
 		<p>\

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 = '*'

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'