dougal-software/bin/datastore.py

import os
import json
import psycopg2
import configuration
import preplots
import p111

"""
Interface to the PostgreSQL database.
"""

def file_hash(file):
	"""
	Calculate a file hash based on its size, inode, modification and creation times.

	The hash is used to uniquely identify files in the database and detect if they
	have changed.
	"""
	st = os.stat(file)
	return ":".join([str(v) for v in [st.st_size, st.st_mtime, st.st_ctime, st.st_ino]])

class Datastore:
	"""
	The database interface.

	Usage:
		db = Datastore()
	"""
	conn = None
	autocommit = True

	def __init__(self, **opts):
		self.settings = configuration.read()["db"]
		self.options = opts

	def connect(self, **opts):
		"""
		Connect to the database.

		opts: Dictionary of options to pass to psycopg2.connect in addition to the
		connection string found in the system configuration (see configuration.py).

		Does not normally need to be invoked directly, as it is called by the
		set_survey() method.
		"""
		if self.conn is not None:
			self.conn.close()

		self.conn = psycopg2.connect(configuration.read()["db"]["connection_string"], **opts)

	def set_autocommit(value = True):
		"""
		Enable or disable autocommit.

		By default, each one of this class' methods commit their results before returning.
		Sometimes that is not desirable so this methods allows the caller to change that
		behaviour. If autocommit is disabled, the caller should commit / rollback explicitly,
		e.g., by calling Datastore#conn.commit()
		"""
		self.autocommit = value

	def maybe_commit(self):
		if self.autocommit is True:
			self.conn.commit()

	def set_survey(self, schema = None):
		"""
		Set the schema corresponding to the survey to which subsequent operations will apply.
		Note that this will replace the existing connection (if any) with a new one.
		If no schema is given, defaults to 'public'.
		"""

		if schema is None:
			search_path = "public"
		else:
			search_path = ",".join([schema, "public"])

		if self.conn:
			self.conn.close()

		self.connect(options=f"-c search_path={search_path}")


	def file_in_db(self, filepath):
		"""
		Check if the file is already in the database.
		"""
		with self.conn:
			with self.conn.cursor() as cursor:
				qry = "SELECT path, hash FROM files WHERE path = %s;"
				cursor.execute(qry, (filepath,))
				results = cursor.fetchall()
				if len(results):
					return (filepath, file_hash(filepath)) in results


	def add_file(self, path, cursor = None):
		"""
		Add a file to the `files` table of a survey.
		"""
		if cursor is None:
			cur = self.conn.cursor()
		else:
			cur = cursor

		hash = file_hash(path)
		qry = "CALL add_file(%s, %s);"
		cur.execute(qry, (path, hash))
		if cursor is None:
			self.maybe_commit()
			# We do not commit if we've been passed a cursor, instead
			# we assume that we are in the middle of a transaction
		return hash

	def del_file(self, path, cursor = None):
		"""
		Remove a file from a survey's `file` table.
		"""
		if cursor is None:
			cur = self.conn.cursor()
		else:
			cur = cursor

		qry = "DELETE FROM files WHERE path = %s;"
		cur.execute(qry, (path,))
		if cursor is None:
			self.maybe_commit()
			# We do not commit if we've been passed a cursor, instead
			# we assume that we are in the middle of a transaction

	def del_hash(self, hash, cursor = None):
		"""
		Remove a hash from a survey's `file` table.
		"""
		if cursor is None:
			cur = self.conn.cursor()
		else:
			cur = cursor

		qry = "DELETE FROM files WHERE hash = %s;"
		cur.execute(qry, (hash,))
		if cursor is None:
			self.maybe_commit()
			# We do not commit if we've been passed a cursor, instead
			# we assume that we are in the middle of a transaction

	def list_files(self, cursor = None):
		"""
		List all files known to a survey.
		"""
		if cursor is None:
			cur = self.conn.cursor()
		else:
			cur = cursor

		qry = "SELECT * FROM files WHERE hash NOT LIKE '*%';"
		cur.execute(qry)
		res = cur.fetchall()

		if cursor is None:
			self.maybe_commit()
			# We do not commit if we've been passed a cursor, instead
			# we assume that we are in the middle of a transaction
		return res

	def set_ntbp(self, path, ntbp, cursor = None):
		"""
		Set or remove a sequence's NTBP flag
		"""
		if cursor is None:
			cur = self.conn.cursor()
		else:
			cur = cursor

		hash = file_hash(path)
		qry = """
			UPDATE raw_lines rl
			SET ntbp = %s
			FROM raw_shots rs, files f
			WHERE rs.hash = f.hash AND rs.sequence = rl.sequence AND f.hash = %s;
		"""
		cur.execute(qry, (ntbp, hash))

		if cursor is None:
			self.maybe_commit()
			# We do not commit if we've been passed a cursor, instead
			# we assume that we are in the middle of a transaction

	def save_preplots(self, lines, filepath, preplot_class, epsg = 0, filedata = None):
		"""
		Save preplot data.

		Arguments:

		lines (iterable): should be a collection of lines returned from
		one of the preplot-reading functions (see preplots.py).

		filepath (string): the full path to the preplot file from where the lines
		have been read. It will be added to the survey's `file` table so that
		it can be monitored for changes.

		preplot_class (string): a valid preplot class code (`V` for saillines,
		`S` for sources).

		epsg (number): the EPSG code that identifies the preplot's CRS. Defaults
		to unknown.
		"""

		with self.conn.cursor() as cursor:
			cursor.execute("BEGIN;")

			hash = self.add_file(filepath, cursor)
			count=0
			for line in lines:
				count += 1
				print(f"\u001b[2KSaving line {count} / {len(lines)} ({len(line['points'])} points)", end="\r", flush=True)

				p0 = line["points"][0]
				p1 = line["points"][-1]
				incr = p0["point_number"] <= p1["point_number"]
				geom = f'LINESTRING({p0["easting"]} {p0["northing"]}, {p1["easting"]} {p1["northing"]})'

				qry = """
					INSERT INTO preplot_lines AS pl
						(line, incr, class, remarks, geometry, hash)
					VALUES
						(%s, %s, %s, '', ST_GeomFromText(%s, %s), %s)
					ON CONFLICT (line, class) DO UPDATE
						SET incr = EXCLUDED.incr, geometry = EXCLUDED.geometry, hash = EXCLUDED.hash
						WHERE pl.hash <> EXCLUDED.hash;
						-- Note that remarks are *not* overwritten
				"""

				cursor.execute(qry, (line["line_name"], incr, preplot_class, geom, epsg, hash))

				points = [ (line["line_name"], p["point_number"], preplot_class, p["easting"], p["northing"], epsg) for p in line["points"] ]

				qry = """
					INSERT INTO preplot_points
						(line, point, class, geometry)
					VALUES
						(%s, %s, %s, ST_SetSRID(ST_MakePoint(%s, %s), %s))
					ON CONFLICT (line, point, class) DO UPDATE
						SET geometry = EXCLUDED.geometry;
				"""

				cursor.executemany(qry, points)

			if filedata is not None:
				self.save_file_data(filepath, json.dumps(filedata), cursor)

		self.maybe_commit()

	def save_raw_p190(self, records, fileinfo, filepath, epsg = 0, filedata = None, ntbp = False):
		"""
		Save raw P1 data.

		Note that despite its name, this function does not care whether the data
		comes from a P1/90 or a P1/11 or something else altogether.

		Arguments:

		records (iterable): a collection of P1 records as produced for instance by
		the from_file() function from p190.py.

		fileinfo (dictionary): information about the source file. It must have at
		least "line" and "sequence" elements.

		filepath (string): the full path to the file from where the lines have been
		read.

		epsg (number): the EPSG code identifying this dataset's CRS. Defaults to unknown.

		filedata (dictionary): Arbitrary data associated with this file and saved in the
		`file_data` table.
		"""

		with self.conn.cursor() as cursor:
			cursor.execute("BEGIN;")

			hash = self.add_file(filepath, cursor)
			incr = records[0]["point_number"] <= records[-1]["point_number"]

			# Start by deleting any online data we may have for this sequence
			self.del_hash("*online*", cursor)

			qry = """
				INSERT INTO raw_lines (sequence, line, remarks, ntbp, incr)
				VALUES (%s, %s, '', %s, %s)
				ON CONFLICT DO NOTHING;
			"""

			cursor.execute(qry, (fileinfo["sequence"], fileinfo["line"], ntbp, incr))

			qry = """
				INSERT INTO raw_lines_files (sequence, hash)
				VALUES (%s, %s)
				ON CONFLICT DO NOTHING;
			"""

			cursor.execute(qry, (fileinfo["sequence"], hash))


			shots = [ (fileinfo["sequence"], r["point_number"], r["record_type"], r["objref"], r["tstamp"], hash, r["easting"], r["northing"], epsg) for r in records ]

			qry = """
				INSERT INTO raw_shots (sequence, point, class, objref, tstamp, hash, geometry)
				VALUES (%s, %s, %s, %s, %s, %s, ST_SetSRID(ST_MakePoint(%s, %s), %s))
				ON CONFLICT (sequence, point, class) DO UPDATE
					SET
						objref = EXCLUDED.objref, tstamp = EXCLUDED.tstamp,
						hash = EXCLUDED.hash, geometry = EXCLUDED.geometry;
			"""

			cursor.executemany(qry, shots)

			if filedata is not None:
				self.save_file_data(filepath, json.dumps(filedata), cursor)

		self.maybe_commit()

	def save_final_p190(self, records, fileinfo, filepath, epsg = 0, filedata = None):
		"""
		Save final P1 data.

		Note that despite its name, this function does not care whether the data
		comes from a P1/90 or a P1/11 or something else altogether.

		Arguments:

		records (iterable): a collection of P1 records as produced for instance by
		the from_file() function from p190.py.

		fileinfo (dictionary): information about the source file. It must have at
		least "line" and "sequence" elements.

		filepath (string): the full path to the file from where the lines have been
		read.

		epsg (number): the EPSG code identifying this dataset's CRS. Defaults to unknown.

		filedata (dictionary): Arbitrary data associated with this file and saved in the
		`file_data` table.
		"""

		with self.conn.cursor() as cursor:
			cursor.execute("BEGIN;")

			hash = self.add_file(filepath, cursor)
			#print(records[0])
			#print(records[-1])
			incr = records[0]["point_number"] <= records[-1]["point_number"]

			qry = """
				INSERT INTO final_lines (sequence, line, remarks)
				VALUES (%s, %s, '')
				ON CONFLICT DO NOTHING;
			"""

			cursor.execute(qry, (fileinfo["sequence"], fileinfo["line"]))

			qry = """
				INSERT INTO final_lines_files (sequence, hash)
				VALUES (%s, %s)
				ON CONFLICT DO NOTHING;
			"""

			cursor.execute(qry, (fileinfo["sequence"], hash))


			shots = [ (fileinfo["sequence"], r["point_number"], r["record_type"], r["objref"], r["tstamp"], hash, r["easting"], r["northing"], epsg) for r in records ]

			qry = """
				INSERT INTO final_shots (sequence, point, class, objref, tstamp, hash, geometry)
				VALUES (%s, %s, %s, %s, %s, %s, ST_SetSRID(ST_MakePoint(%s, %s), %s))
				ON CONFLICT (sequence, point, class) DO UPDATE
					SET
						objref = EXCLUDED.objref, tstamp = EXCLUDED.tstamp,
						hash = EXCLUDED.hash, geometry = EXCLUDED.geometry;
			"""

			cursor.executemany(qry, shots)

			if filedata is not None:
				self.save_file_data(filepath, json.dumps(filedata), cursor)

		self.maybe_commit()

	def save_raw_p111 (self, records, fileinfo, filepath, epsg = 0, filedata = None, ntbp = False):

		with self.conn.cursor() as cursor:
			cursor.execute("BEGIN;")
			
			hash = self.add_file(filepath, cursor)
			incr = p111.point_number(records[0]) <= p111.point_number(records[-1])

			# Start by deleting any online data we may have for this sequence
			self.del_hash("*online*", cursor)

			qry = """
				INSERT INTO raw_lines (sequence, line, remarks, ntbp, incr)
				VALUES (%s, %s, '', %s, %s)
				ON CONFLICT DO NOTHING;
			"""

			cursor.execute(qry, (fileinfo["sequence"], fileinfo["line"], ntbp, incr))

			qry = """
				INSERT INTO raw_lines_files (sequence, hash)
				VALUES (%s, %s)
				ON CONFLICT DO NOTHING;
			"""

			cursor.execute(qry, (fileinfo["sequence"], hash))


			shots = [ (fileinfo["sequence"], p111.line(r), p111.point_number(r), r["Object Ref. Number"], r["tstamp"], hash, p111.easting(r), p111.northing(r), epsg) for r in records ]

			qry = """
				INSERT INTO raw_shots (sequence, line, point, objref, tstamp, hash, geometry)
				VALUES (%s, %s, %s, %s, %s, %s, ST_SetSRID(ST_MakePoint(%s, %s), %s))
				ON CONFLICT (sequence, point) DO UPDATE
					SET
						objref = EXCLUDED.objref, tstamp = EXCLUDED.tstamp,
						hash = EXCLUDED.hash, geometry = EXCLUDED.geometry;
			"""

			cursor.executemany(qry, shots)

			if filedata is not None:
				self.save_file_data(filepath, json.dumps(filedata), cursor)

		self.maybe_commit()

	def save_final_p111 (self, records, fileinfo, filepath, epsg = 0, filedata = None):

		with self.conn.cursor() as cursor:
			cursor.execute("BEGIN;")
			
			hash = self.add_file(filepath, cursor)

			qry = """
				INSERT INTO final_lines (sequence, line, remarks)
				VALUES (%s, %s, '')
				ON CONFLICT DO NOTHING;
			"""

			cursor.execute(qry, (fileinfo["sequence"], fileinfo["line"]))

			qry = """
				INSERT INTO final_lines_files (sequence, hash)
				VALUES (%s, %s)
				ON CONFLICT DO NOTHING;
			"""

			cursor.execute(qry, (fileinfo["sequence"], hash))


			shots = [ (fileinfo["sequence"], p111.line(r), p111.point_number(r), r["Object Ref. Number"], r["tstamp"], hash, p111.easting(r), p111.northing(r), epsg) for r in records ]

			qry = """
				INSERT INTO final_shots (sequence, line, point, objref, tstamp, hash, geometry)
				VALUES (%s, %s, %s, %s, %s, %s, ST_SetSRID(ST_MakePoint(%s, %s), %s))
				ON CONFLICT (sequence, point) DO UPDATE
					SET
						objref = EXCLUDED.objref, tstamp = EXCLUDED.tstamp,
						hash = EXCLUDED.hash, geometry = EXCLUDED.geometry;
			"""

			cursor.executemany(qry, shots)

			if filedata is not None:
				self.save_file_data(filepath, json.dumps(filedata), cursor)

		self.maybe_commit()

	def save_raw_smsrc (self, records, fileinfo, filepath, filedata = None):

		with self.conn.cursor() as cursor:
			cursor.execute("BEGIN;")

			hash = self.add_file(filepath, cursor)

			# Start by deleting any online data we may have for this sequence
			# NOTE: Do I need to do this?
			#self.del_hash("*online*", cursor)

			# The shots should already exist, e.g., from a P1 import
			# …but what about if the SMSRC file gets read *before* the P1?
			# We need to check
			qry = "SELECT count(*) FROM raw_shots WHERE sequence = %s;"
			values = (fileinfo["sequence"],)
			cursor.execute(qry, values)
			shotcount = cursor.fetchone()[0]
			if shotcount == 0:
				# No shots yet or not all imported, so we do *not*
				# save the gun data. It will eventually get picked
				# up in the next run.
				# Let's remove the file from the file list and bail
				# out.
				print("No raw shots for sequence", fileinfo["sequence"])
				self.conn.rollback()
				return

			values = [ (json.dumps(record), fileinfo["sequence"], record["shot"]) for record in records ]

			qry = """
				UPDATE raw_shots
				SET meta = jsonb_set(meta, '{smsrc}', %s::jsonb, true)
				WHERE sequence = %s AND point = %s;
			"""

			cursor.executemany(qry, values)

			if filedata is not None:
				self.save_file_data(filepath, json.dumps(filedata), cursor)

		self.maybe_commit()


	def save_file_data(self, path, filedata, cursor = None):
		"""
		Save arbitrary data associated with a file.

		Arguments:

		path (string): the full path to the file that the data is to be associated with.

		filedata (object): arbitrary data – will be converted to JSON.

		cursor (DB Cursor): if a cursor is passed by the caller, this function will not
		call conn.commit() even if autocommit is True.
		"""
		if cursor is None:
			cur = self.conn.cursor()
		else:
			cur = cursor

		hash = self.add_file(path, cursor)

		qry = """
			INSERT INTO file_data (hash, data)
			VALUES (%s, %s::json)
			ON CONFLICT (hash) DO UPDATE
				SET data = EXCLUDED.data;
		"""

		cur.execute(qry, (hash, filedata))

		if cursor is None:
			self.maybe_commit()
			# We do not commit if we've been passed a cursor, instead
			# we assume that we are in the middle of a transaction


	def apply_survey_configuration(self, cursor = None):
		if cursor is None:
			cur = self.conn.cursor()
		else:
			cur = cursor

		qry = """
			INSERT INTO labels (name, data)
			SELECT l.key, l.value
			FROM file_data fd,
			jsonb_each(fd.data->'labels') l
			WHERE fd.data::jsonb ? 'labels'
			ON CONFLICT (name) DO UPDATE SET data = excluded.data;
		"""

		cur.execute(qry)

		if cursor is None:
			self.maybe_commit()
			# We do not commit if we've been passed a cursor, instead
			# we assume that we are in the middle of a transaction


	def add_info(self, key, value, cursor = None):
		"""
		Add an item of information to the project
		"""
		if cursor is None:
			cur = self.conn.cursor()
		else:
			cur = cursor

		qry = """
			INSERT INTO info (key, value)
			VALUES(%s, %s)
			ON CONFLICT (key) DO UPDATE
				SET value = EXCLUDED.value;
		"""
		cur.execute(qry, (key, value))
		if cursor is None:
			self.maybe_commit()
			# We do not commit if we've been passed a cursor, instead
			# we assume that we are in the middle of a transaction

	def get_info(self, key, cursor = None):
		"""
		Retrieve an item of information from the project
		"""
		if cursor is None:
			cur = self.conn.cursor()
		else:
			cur = cursor

		qry = "SELECT value FROM info WHERE key = %s;"
		cur.execute(qry, (key,))
		res = cur.fetchone()
		if cursor is None:
			self.maybe_commit()
			# We do not commit if we've been passed a cursor, instead
			# we assume that we are in the middle of a transaction

		return res

	def del_info(self, key, cursor = None):
		"""
		Remove a an item of information from the project
		"""
		if cursor is None:
			cur = self.conn.cursor()
		else:
			cur = cursor

		qry = "DELETE FROM info WHERE key = %s;"
		cur.execute(qry, (key,))
		if cursor is None:
			self.maybe_commit()
			# We do not commit if we've been passed a cursor, instead
			# we assume that we are in the middle of a transaction