database_tools.py 72.4 KB
Newer Older
1
import collections
2
import glob
3
import itertools
4
5
import os
import re
6
import shutil
7
import sys
8
import traceback
9
10
import warnings
from datetime import datetime
11
from typing import Union, TYPE_CHECKING  # noqa F401  # flake8 issue
Daniel Scheffler's avatar
GEOP:    
Daniel Scheffler committed
12

13
14
import numpy as np
import pandas as pd
Daniel Scheffler's avatar
Daniel Scheffler committed
15
from pandas.io.sql import pandasSQL_builder, SQLTable
16
import psycopg2
Daniel Scheffler's avatar
Daniel Scheffler committed
17
from shapely.wkb import loads as wkb_loads
18
from geoalchemy2.types import Geometry as GEOMETRY
19
20
21
22
from geopandas import GeoDataFrame, GeoSeries
from shapely.geometry import Polygon, box, MultiPolygon
from sqlalchemy import create_engine
from sqlalchemy.types import to_instance, TypeEngine
23

24
from ..options.config import GMS_config as CFG
25
from . import path_generator as PG
26
from .definition_dicts import proc_chain
27

28
29
30
if TYPE_CHECKING:
    from ..model.gms_object import GMS_object  # noqa F401  # flake8 issue

31
32
# + misc.helper_functions.cornerLonLat_to_postgreSQL_poly: (left out here in order to avoid circular dependencies)

33
34
__author__ = 'Daniel Scheffler'

35

36
def execute_pgSQL_query(cursor, query_command):
37
38
    """Executes a postgreSQL query catches the full error message if there is one.
    """
Daniel Scheffler's avatar
Daniel Scheffler committed
39

Daniel Scheffler's avatar
GEOP:    
Daniel Scheffler committed
40
41
42
43
44
45
    try:
        cursor.execute(query_command)
    except psycopg2.ProgrammingError as e:
        raise psycopg2.ProgrammingError(e.pgerror + 'Query failed. Command was:\n%s' % query_command)


46
def get_scene_and_dataset_infos_from_postgreSQLdb(sceneid):
47
48
    # type: (int) -> collections.OrderedDict
    """Creates an OrderedDict containing further information about a given scene ID by querying the pgSQL database.
49
50
51

    :param sceneid:   <int> the GMS scene ID to get information for
    """
Daniel Scheffler's avatar
Daniel Scheffler committed
52

53
    def query(tablename, vals2return, cond_dict, records2fetch=0):
54
        return get_info_from_postgreSQLdb(CFG.conn_database, tablename, vals2return, cond_dict, records2fetch)
55
    resultset = query('scenes', ['datasetid', 'satelliteid', 'sensorid', 'subsystemid', 'acquisitiondate', 'entityid',
56
57
58
                                 'filename'], {'id': sceneid})
    if len(resultset) == 0:
        sys.stderr.write("Scene with id %s not found. Skipping.." % sceneid)
59
60
61

    scenedata = resultset[0]
    ds = collections.OrderedDict()
62
63
64
65
66
67
68
69
70
71
72
    proc_level_tmp = query('scenes_proc', 'proc_level', {'sceneid': sceneid})
    ds.update({'proc_level': 'L0A' if proc_level_tmp == [] else proc_level_tmp[0][0]})
    ds.update({'scene_ID': sceneid})
    ds.update({'datasetid': scenedata[0]})
    ds.update({'image_type': query('datasets', 'image_type', {'id': scenedata[0]})[0][0]})
    ds.update({'satellite': query('satellites', 'name', {'id': scenedata[1]})[0][0]})
    ds.update({'sensor': query('sensors', 'name', {'id': scenedata[2]})[0][0]})
    ds.update({'subsystem': query('subsystems', 'name', {'id': scenedata[3]})[0][0] if scenedata[3] else None})
    ds.update({'acq_datetime': scenedata[4]})
    ds.update({'entity_ID': scenedata[5]})
    ds.update({'filename': scenedata[6]})
73
74
75
    return ds


76
def get_postgreSQL_value(value):
77
    # type: (any) -> str
78
79
80
    """Converts Python variable to a postgreSQL value respecting postgreSQL type casts.
    The resulting value can be directly inserted into a postgreSQL query."""

81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
    assert type(value) in [int, float, bool, str, Polygon, datetime, list, tuple] or value is None, \
        "Unsupported value type within postgreSQL matching expression. Got %s." % type(value)
    if isinstance(value, int):
        pgV = value
    elif isinstance(value, float):
        pgV = value
    elif isinstance(value, bool):
        pgV = value
    elif value is None:
        pgV = 'NULL'
    elif isinstance(value, str):
        pgV = "'%s'" % value.replace("'", "")
    elif isinstance(value, Polygon):
        pgV = "'%s'" % value.wkb_hex
    elif isinstance(value, datetime):
        pgV = "TIMESTAMP '%s'" % str(value)
    else:  # list or tuple in value
        if not value:  # empty list/tuple
99
100
101
            pgV = 'NULL'
        else:
            dTypes_in_value = list(set([type(i) for i in value]))
102
103
            assert len(dTypes_in_value) == 1, \
                'Mixed data types in postgreSQL matching expressions are not supported. Got %s.' % dTypes_in_value
104
            assert dTypes_in_value[0] in [int, str, float, np.int64, bool]
105
106
            pgList = ",".join(["'%s'" % i if isinstance(value[0], str) else "%s" % i for i in value])
            pgV = "'{%s}'" % pgList
107
108
109
    return pgV


110
def get_postgreSQL_matchingExp(key, value):
111
    # type: (str,any) -> str
112
113
114
115
    """Converts a key/value pair to a postgreSQL matching expression in the form "column=value" respecting postgreSQL
    type casts. The resulting string can be directly inserted into a postgreSQL query.
    """
    pgVal = get_postgreSQL_value(value)
116
117
118
119
    if isinstance(pgVal, str) and pgVal.startswith("'{") and pgVal.endswith("}'"):
        return '%s in %s' % (key, pgVal.replace("'{", '(').replace("}'", ')'))  # '{1,2,3}' => (1,2,3)
    elif pgVal == 'NULL':
        return '%s is NULL' % key
120
    else:
121
        return '%s=%s' % (key, pgVal)
122

123

124
def get_info_from_postgreSQLdb(conn_params, tablename, vals2return, cond_dict=None, records2fetch=0, timeout=15000):
Daniel Scheffler's avatar
Daniel Scheffler committed
125
    # type: (str, str, Union[list, str], dict, int, int) -> Union[list, str]
126
    """Queries a postgreSQL database for the given parameters.
127

128
    :param conn_params:     <str> connection parameters as provided by CFG.conn_params
129
130
131
    :param tablename:       <str> name of the table within the database to be queried
    :param vals2return:     <list or str> a list of strings containing the column titles of the values to be returned
    :param cond_dict:       <dict> a dictionary containing the query conditions in the form {'column_name':<value>}
132
133
                            HINT: <value> can also be a list or a tuple of elements to match, BUT note that the order
                                  of the list items is NOT respected!
134
    :param records2fetch:   <int> number of records to be fetched (default=0: fetch unlimited records)
135
136
    :param timeout:         <int> allows to set a custom statement timeout (milliseconds)
    """
Daniel Scheffler's avatar
Daniel Scheffler committed
137

138
139
    if not isinstance(vals2return, list):
        vals2return = [vals2return]
140
141
    assert isinstance(records2fetch, int), "get_info_from_postgreSQLdb: Expected an integer for the argument " \
                                           "'records2return'. Got %s" % type(records2fetch)
142
    cond_dict = cond_dict if cond_dict else {}
143
    conn_params = "%s options = '-c statement_timeout=%s'" % (conn_params, timeout)
144
    connection = psycopg2.connect(conn_params)
145
146
147
    if connection is None:
        warnings.warn('database connection fault')
        return 'database connection fault'
148
149
150
151
152
    cursor = connection.cursor()
    condition = "WHERE " + " AND ".join([get_postgreSQL_matchingExp(k, v) for k, v in cond_dict.items()]) \
        if cond_dict else ""
    cmd = "SELECT " + ','.join(vals2return) + " FROM " + tablename + " " + condition
    execute_pgSQL_query(cursor, cmd)
153

154
    records2return = cursor.fetchall() if records2fetch == 0 else [cursor.fetchone()] if records2fetch == 1 else \
155
        cursor.fetchmany(size=records2fetch)  # e.g. [('LE71950282003121EDC00',), ('LE71950282003105ASN00',)]
156
157
158
159
    cursor.close()
    connection.close()
    return records2return

160

161
def update_records_in_postgreSQLdb(conn_params, tablename, vals2update_dict, cond_dict=None, timeout=15000):
162
    # type: (str, str, dict, dict, int) -> Union[None, str]
163
    """Queries a postgreSQL database for the given parameters and updates the given columns of the query result.
164

165
    :param conn_params:       <str> connection parameters as provided by CFG.conn_params
166
167
168
169
    :param tablename:         <str> name of the table within the database to be updated
    :param vals2update_dict:  <dict> a dictionary containing keys and values to be set in the form {'col_name':<value>}
    :param cond_dict:         <dict> a dictionary containing the query conditions in the form {'column_name':<value>}
                              HINT: <value> can also be a list or a tuple of elements to match
170
171
    :param timeout:           <int> allows to set a custom statement timeout (milliseconds)
    """
Daniel Scheffler's avatar
Daniel Scheffler committed
172

173
    cond_dict = cond_dict if cond_dict else {}
174
    conn_params = "%s options = '-c statement_timeout=%s'" % (conn_params, timeout)
175
    connection = psycopg2.connect(conn_params)
176
177
178
    if connection is None:
        warnings.warn('database connection fault')
        return 'database connection fault'
179
180
181
    cursor = connection.cursor()
    condition = "WHERE " + " AND ".join([get_postgreSQL_matchingExp(k, v) for k, v in cond_dict.items()]) \
        if cond_dict else ""
182
183
    update_cond = "SET " + ', '.join(['%s=%s' % (k, get_postgreSQL_value(vals2update_dict[k]))
                                      for k in vals2update_dict.keys()])
184
    execute_pgSQL_query(cursor, "SELECT EXISTS(SELECT 1 FROM scenes %s);" % condition)
185
    if cursor.fetchone()[0] == 0:
186
        warnings.warn("No record found fulfilling this condition: \n'%s'." % condition)
187
    else:
188
        execute_pgSQL_query(cursor, "UPDATE " + tablename + " " + update_cond + " " + condition)
189

190
191
192
    if 'connection' in locals():
        connection.commit()
        connection.close()
193
194


195
def append_item_to_arrayCol_in_postgreSQLdb(conn_params, tablename, vals2append_dict, cond_dict=None, timeout=15000):
196
    # type: (str, str, dict, dict, int) -> Union[None, str]
197
198
199
    """Queries a postgreSQL database for the given parameters
    and appends the given value to the specified column of the query result.

200
    :param conn_params:       <str> connection parameters as provided by CFG.conn_params
201
202
203
204
205
206
207
    :param tablename:         <str> name of the table within the database to be updated
    :param vals2append_dict:  <dict> a dictionary containing keys and value(s) to be set in the form
                              {'col_name':[<value>,<value>]}
    :param cond_dict:         <dict> a dictionary containing the query conditions in the form {'column_name':<value>}
                              HINT: <value> can also be a list or a tuple of elements to match
    :param timeout:           <int> allows to set a custom statement timeout (milliseconds)
    """
Daniel Scheffler's avatar
Daniel Scheffler committed
208

209
210
    assert len(vals2append_dict) == 1, 'Values can be appended to only one column at once.'
    if type(list(vals2append_dict.values())[0]) in [list, tuple]:
211
        raise NotImplementedError('Appending multiple values to one column at once is not yet supported.')
212
    cond_dict = cond_dict if cond_dict else {}
213
    conn_params = "%s options = '-c statement_timeout=%s'" % (conn_params, timeout)
214
    connection = psycopg2.connect(conn_params)
215
216
217
    if connection is None:
        warnings.warn('database connection fault')
        return 'database connection fault'
218
219
220
221
222
223
224
225
    cursor = connection.cursor()
    condition = "WHERE " + " AND ".join([get_postgreSQL_matchingExp(k, v) for k, v in cond_dict.items()]) \
        if cond_dict else ""
    col2update = list(vals2append_dict.keys())[0]
    pgSQL_val = get_postgreSQL_value(vals2append_dict[col2update])
    pgSQL_val = pgSQL_val if type(vals2append_dict[col2update]) in [list, tuple] else '{%s}' % pgSQL_val
    append_cond = "SET %s = array_cat(%s, '%s')" % (col2update, col2update, pgSQL_val)
    execute_pgSQL_query(cursor, "SELECT EXISTS(SELECT 1 FROM scenes %s);" % condition)
226
    if cursor.fetchone()[0] == 0:
227
        warnings.warn("No record found fulfilling this condition: \n'%s'." % condition)
228
    else:
229
230
231
232
        execute_pgSQL_query(cursor, "UPDATE " + tablename + " " + append_cond + " " + condition + ';')
    if 'connection' in locals():
        connection.commit()
        connection.close()
233
234
235


def remove_item_from_arrayCol_in_postgreSQLdb(conn_params, tablename, vals2remove_dict, cond_dict=None, timeout=15000):
236
    # type: (str, str, dict, dict, int) -> Union[None, str]
237
238
239
    """Queries a postgreSQL database for the given parameters
    and removes the given value from the specified column of the query result.

240
    :param conn_params:       <str> connection parameters as provided by CFG.conn_params
241
242
243
244
245
246
247
    :param tablename:         <str> name of the table within the database to be updated
    :param vals2remove_dict:  <dict> a dictionary containing keys and value(s) to be set in the form
                              {'col_name':[<value>,<value>]}
    :param cond_dict:         <dict> a dictionary containing the query conditions in the form {'column_name':<value>}
                              HINT: <value> can also be a list or a tuple of elements to match
    :param timeout:           <int> allows to set a custom statement timeout (milliseconds)
    """
Daniel Scheffler's avatar
Daniel Scheffler committed
248

249
250
    assert len(vals2remove_dict) == 1, 'Values can be removed from only one column at once.'
    if type(list(vals2remove_dict.values())[0]) in [list, tuple]:
251
        raise NotImplementedError('Removing multiple values from one column at once is not yet supported.')
252
    cond_dict = cond_dict if cond_dict else {}
253
    conn_params = "%s options = '-c statement_timeout=%s'" % (conn_params, timeout)
254
    connection = psycopg2.connect(conn_params)
255
256
257
    if connection is None:
        warnings.warn('database connection fault')
        return 'database connection fault'
258
259
260
261
262
263
264
265
    cursor = connection.cursor()
    condition = "WHERE " + " AND ".join([get_postgreSQL_matchingExp(k, v) for k, v in cond_dict.items()]) \
        if cond_dict else ""
    col2update = list(vals2remove_dict.keys())[0]
    pgSQL_val = get_postgreSQL_value(vals2remove_dict[col2update])
    pgSQL_val = pgSQL_val if type(vals2remove_dict[col2update]) in [list, tuple] else '{%s}' % pgSQL_val
    remove_cond = "SET %s = array_remove(%s, '%s')" % (col2update, col2update, pgSQL_val)
    execute_pgSQL_query(cursor, "SELECT EXISTS(SELECT 1 FROM scenes %s);" % condition)
266
    if cursor.fetchone()[0] == 0:
267
        warnings.warn("No record found fulfilling this condition: \n'%s'." % condition)
268
    else:
269
270
271
272
        execute_pgSQL_query(cursor, "UPDATE " + tablename + " " + remove_cond + " " + condition + ';')
    if 'connection' in locals():
        connection.commit()
        connection.close()
273
274


275
276
def increment_decrement_arrayCol_in_postgreSQLdb(conn_params, tablename, col2update, idx_val2decrement=None,
                                                 idx_val2increment=None, cond_dict=None, timeout=15000):
277
    # type: (str, str, str, int, int, dict, int) -> Union[None, str]
278
    """Updates an array column of a specific postgreSQL table in the form that it increments or decrements the elements
279
    at a given position. HINT: The column must have values like that: [52,0,27,10,8,0,0,0,0]
280

281
    :param conn_params:         <str> connection parameters as provided by CFG.conn_params
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
    :param tablename:           <str> name of the table within the database to be update
    :param col2update:          <str> column name of the column to be updated
    :param idx_val2decrement:   <int> the index of the array element to be decremented (starts with 1)
    :param idx_val2increment:   <int> the index of the array element to be incremented (starts with 1)
    :param cond_dict:           <dict> a dictionary containing the query conditions in the form {'column_name':<value>}
                                HINT: <value> can also be a list or a tuple of elements to match
    :param timeout:             <int> allows to set a custom statement timeout (milliseconds)
    :return:
    """

    cond_dict = cond_dict if cond_dict else {}
    conn_params = "%s options = '-c statement_timeout=%s'" % (conn_params, timeout)
    connection = psycopg2.connect(conn_params)
    if connection is None:
        warnings.warn('database connection fault')
        return 'database connection fault'
    cursor = connection.cursor()
    condition = "WHERE " + " AND ".join([get_postgreSQL_matchingExp(k, v) for k, v in cond_dict.items()]) \
        if cond_dict else ""

    dec_str = '' if idx_val2decrement is None else \
303
        "%s[%s] = %s[%s]-1" % (col2update, idx_val2decrement, col2update, idx_val2decrement)
304
    inc_str = '' if idx_val2increment is None else \
305
        "%s[%s] = %s[%s]+1" % (col2update, idx_val2increment, col2update, idx_val2increment)
306
307
308

    if dec_str or inc_str:
        dec_inc_str = ','.join([dec_str, inc_str])
309
        execute_pgSQL_query(cursor, "UPDATE %s SET %s %s" % (tablename, dec_inc_str, condition))
310

311
312
313
    if 'connection' in locals():
        connection.commit()
        connection.close()
314
315


316
def create_record_in_postgreSQLdb(conn_params, tablename, vals2write_dict, timeout=15000):
317
    # type: (str, str, dict, dict, int) -> Union[int, str]
318
319
    """Creates a single new record in a postgreSQL database and pupulates its columns with the given values.

320
    :param conn_params:       <str> connection parameters as provided by CFG.conn_params
321
322
323
324
    :param tablename:         <str> name of the table within the database to be updated
    :param vals2write_dict:   <dict> a dictionary containing keys and values to be set in the form {'col_name':<value>}
    :param timeout:           <int> allows to set a custom statement timeout (milliseconds)
    """
Daniel Scheffler's avatar
Daniel Scheffler committed
325

326
    conn_params = "%s options = '-c statement_timeout=%s'" % (conn_params, timeout)
327
    connection = psycopg2.connect(conn_params)
328
329
330
    if connection is None:
        warnings.warn('database connection fault')
        return 'database connection fault'
331
    cursor = connection.cursor()
332
333
334
335

    keys, vals = zip(*[(k, str(get_postgreSQL_value(v))) for k, v in vals2write_dict.items()])

    execute_pgSQL_query(cursor, "INSERT INTO %s (%s) VALUES (%s);" % (tablename, ','.join(keys), ','.join(vals)))
336
    execute_pgSQL_query(cursor, "SELECT id FROM %s ORDER BY id DESC LIMIT 1" % tablename)
337
338
    newID = cursor.fetchone()[0]

339
340
341
    if 'connection' in locals():
        connection.commit()
        connection.close()
342
343
344
345

    return newID


346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
def delete_record_in_postgreSQLdb(conn_params, tablename, record_id, timeout=15000):
    # type: (str, str, dict, dict, int) -> Union[int, str]
    """Delete a single record in a postgreSQL database.

    :param conn_params:       <str> connection parameters as provided by CFG.conn_params
    :param tablename:         <str> name of the table within the database to be updated
    :param record_id:         <dict> ID of the record to be deleted
    :param timeout:           <int> allows to set a custom statement timeout (milliseconds)
    """

    conn_params = "%s options = '-c statement_timeout=%s'" % (conn_params, timeout)
    connection = psycopg2.connect(conn_params)
    if connection is None:
        warnings.warn('database connection fault')
        return 'database connection fault'
    cursor = connection.cursor()

    execute_pgSQL_query(cursor, "DELETE FROM %s WHERE id=%s;" % (tablename, record_id))
    execute_pgSQL_query(cursor, "SELECT id FROM %s WHERE id=%s" % (tablename,  record_id))

    res = cursor.fetchone()

    if 'connection' in locals():
        connection.commit()
        connection.close()

    return 'success' if res is None else 'fail'


375
def get_pgSQL_geospatial_query_cond(conn_params, table2query, geomCol2use='bounds', tgt_corners_lonlat=None,
376
                                    scene_ID=None, queryfunc='ST_Intersects', crossing_dateline_check=True):
377
    assert tgt_corners_lonlat if scene_ID is None else scene_ID, "Provide eihter scene_ID or tgt_corners_lonlat!"
Daniel Scheffler's avatar
GEOP:    
Daniel Scheffler committed
378

379
    if tgt_corners_lonlat:
380
381
382
383
384
385
386
        # handle coordinates crossing the 180 degress meridian (dateline)
        # FIXME in that case the polygone has to be split at the dateline. otherwise pgSQL may yield wrong results
        if crossing_dateline_check:
            xvals = [x for x, y in tgt_corners_lonlat]
            if max(xvals) - min(xvals) > 180:
                tgt_corners_lonlat = [(x, y) if x > 0 else (x + 360, y) for x, y in tgt_corners_lonlat]

387
        from .helper_functions import cornerLonLat_to_postgreSQL_poly
388
        pGSQL_poly = cornerLonLat_to_postgreSQL_poly(tgt_corners_lonlat)
389
390
391
392
393
        src_geom = "'SRID=4326;%s'::geometry" % pGSQL_poly  # source geometry is given
        # FIXME scenes tabelle hat "geography" geoinfos -> eigener Index wird bei "geometry" nicht genutzt:
        tgt_geom = "%s.%s::geometry" % (table2query, geomCol2use)
        geocond = "%s(%s, %s)" % (queryfunc, src_geom, tgt_geom)
    else:  # scene_ID is not None:
Daniel Scheffler's avatar
GEOP:    
Daniel Scheffler committed
394
        connection = psycopg2.connect(conn_params)
395
396
        if connection is None:
            return 'database connection fault'
Daniel Scheffler's avatar
GEOP:    
Daniel Scheffler committed
397
        cursor = connection.cursor()
398
399
400
        cmd = "SELECT ST_AsText(bounds) FROM scenes WHERE scenes.id = %s" % scene_ID
        execute_pgSQL_query(cursor, cmd)
        res = cursor.fetchone()
Daniel Scheffler's avatar
GEOP:    
Daniel Scheffler committed
401
402
403
        cursor.close()
        connection.close()
        if len(res):
404
            src_geom = "'SRID=4326;%s'::geometry" % res
Daniel Scheffler's avatar
GEOP:    
Daniel Scheffler committed
405
406
407
        else:
            print('The scene with the ID %s does not exist in the scenes table.')
            return []
408
        geocond = "%s(%s, %s.%s::geometry)" % (queryfunc, src_geom, table2query, geomCol2use)
Daniel Scheffler's avatar
GEOP:    
Daniel Scheffler committed
409
410
411
    return geocond


412
def get_overlapping_scenes_from_postgreSQLdb(conn_params, table='scenes_proc', scene_ID=None,
413
                                             tgt_corners_lonlat=None, conditions=None, add_cmds='', timeout=15000):
414
    # type: (str, str, int, list, Union[list, str], str, int) -> Union[list, str]
Daniel Scheffler's avatar
Daniel Scheffler committed
415

416
417
    """Queries the postgreSQL database in order to find those scenes of a specified reference satellite (Landsat-8 or
    Sentinel-2) that have an overlap to the given corner coordinates AND that fulfill the given conditions.
418

419
    :param conn_params:             <str> connection parameters as provided by CFG.conn_params
420
421
    :param table:                   <str> name of the table within the database to be updated
    :param scene_ID:                <int> a sceneID to get the target geographical extent from
422
423
424
                                        (needed if tgt_corners_lonlat is not provided)
    :param tgt_corners_lonlat:      <list> a list of coordinates defining the target geographical extent
                                           (needed if scene_ID is not provided)
425
426
427
428
    :param conditions:              <list> a list of additional query conditions
    :param add_cmds:                <str> additional pgSQL commands to be added to the pgSQL query
    :param timeout:                 <int> allows to set a custom statement timeout (milliseconds)
    """
Daniel Scheffler's avatar
Daniel Scheffler committed
429

430
    conditions = [] if conditions is None else conditions if isinstance(conditions, list) else [conditions]
431
    conn_params = "%s options = '-c statement_timeout=%s'" % (conn_params, timeout)
432
    connection = psycopg2.connect(conn_params)
433
434
    if connection is None:
        return 'database connection fault'
435
    datasetids = [int(d.split('=')[1].strip()) for d in conditions if d.startswith('datasetid')]
436
437
438
439
440
441
442
    datasetid = datasetids[0] if datasetids else 104  # Landsat-8
    # FIXME: use Landsat-8 instead of Sentinel-2 as long as S2 L1A_P is not working:
    datasetid = 104 if datasetid == 249 else datasetid

    if table != 'scenes_proc':
        assert datasetid, "filtdsId is needed if table is not 'scenes_proc'"
    if scene_ID is None:
443
        assert tgt_corners_lonlat, "Provide either scene_ID or tgt_corners_lonlat!"
444
    if tgt_corners_lonlat is None:
445
        assert scene_ID, "Provide either scene_ID or tgt_corners_lonlat!"
446
447
448
449
450
451
452
453
454
455

    val2get = "scenes.id" if table == 'scenes' else "%s.sceneid" % table
    # refcond  = ['scenes_proc.georef = True'] if not datasetids else ['scenes.datasetid = %s' %datasetid]
    refcond = ['scenes.datasetid = %s' % datasetid]

    geocond = [get_pgSQL_geospatial_query_cond(conn_params, table, tgt_corners_lonlat=tgt_corners_lonlat,
                                               scene_ID=scene_ID, queryfunc='ST_Intersects',
                                               crossing_dateline_check=True)]

    join = "INNER JOIN scenes ON (%s.sceneid = scenes.id) " % table if table != 'scenes' and datasetids else ''
456
    conditions = [c for c in conditions if not c.startswith('datasetid')]
457
458
459
460
    where = "WHERE %s" % " AND ".join(geocond + refcond + conditions)
    usedtbls = "scenes" if table == 'scenes' else "%s, scenes" % table if 'scenes.' in where and join == '' else table
    query = "SELECT %s FROM %s %s%s %s" % (val2get, usedtbls, join, where, add_cmds)
    cursor = connection.cursor()
461
    execute_pgSQL_query(cursor, query)
462
463
464
465
466
    records2return = cursor.fetchall()
    cursor.close()
    connection.close()
    return records2return

467

468
def get_overlapping_MGRS_tiles(conn_params, scene_ID=None, tgt_corners_lonlat=None, timeout=15000):
Daniel Scheffler's avatar
GEOP:    
Daniel Scheffler committed
469
470
    """In contrast to pgSQL 'Overlapping' here means that both geometries share some spatial area.
    So it combines ST_Overlaps and ST_Contains."""
471
    assert tgt_corners_lonlat if scene_ID is None else scene_ID, "Provide eihter scene_ID or tgt_corners_lonlat!"
Daniel Scheffler's avatar
GEOP:    
Daniel Scheffler committed
472
473
474

    conn_params = "%s options = '-c statement_timeout=%s'" % (conn_params, timeout)
    connection = psycopg2.connect(conn_params)
475
476
    if connection is None:
        return 'database connection fault'
Daniel Scheffler's avatar
GEOP:    
Daniel Scheffler committed
477
478

    vals2get = ['grid100k', 'grid1mil', 'geom']
479
    # FIXME this is covered by ST_Intersects:
Daniel Scheffler's avatar
Daniel Scheffler committed
480
    # geocond1 = get_pgSQL_geospatial_query_cond(conn_params, 'mgrs_tiles', geomCol2use='geom', queryfunc='ST_Overlaps',
481
    #                                            tgt_corners_lonlat=tgt_corners_lonlat, scene_ID=scene_ID)
Daniel Scheffler's avatar
Daniel Scheffler committed
482
483
484
485
486
    # geocond2 = get_pgSQL_geospatial_query_cond(conn_params, 'mgrs_tiles', geomCol2use='geom', queryfunc='ST_Contains',
    #                                            tgt_corners_lonlat=tgt_corners_lonlat, scene_ID=scene_ID)
    # geocond3 = get_pgSQL_geospatial_query_cond(conn_params, 'mgrs_tiles', geomCol2use='geom', queryfunc='ST_Within',
    #                                            tgt_corners_lonlat=tgt_corners_lonlat, scene_ID=scene_ID)
    geocond = get_pgSQL_geospatial_query_cond(conn_params, 'mgrs_tiles', geomCol2use='geom', queryfunc='ST_Intersects',
487
488
                                              tgt_corners_lonlat=tgt_corners_lonlat, scene_ID=scene_ID,
                                              crossing_dateline_check=True)
489
490
    # query = "SELECT %s FROM %s WHERE %s OR %s OR %s"
    #     % (', '.join(vals2get), 'mgrs_tiles', geocond1, geocond2, geocond3)
Daniel Scheffler's avatar
Daniel Scheffler committed
491
    query = "SELECT %s FROM %s WHERE %s" % (', '.join(vals2get), 'mgrs_tiles', geocond)
Daniel Scheffler's avatar
GEOP:    
Daniel Scheffler committed
492
493
494
495
496
497
498
499
    cursor = connection.cursor()
    execute_pgSQL_query(cursor, query)
    records = cursor.fetchall()
    cursor.close()
    connection.close()

    GDF = GeoDataFrame(records, columns=['grid100k', 'grid1mil', 'wkb_hex'])

Daniel Scheffler's avatar
Daniel Scheffler committed
500
    GDF['shapelyPoly_LonLat'] = list(GDF['wkb_hex'].map(lambda wkb_hex: wkb_loads(wkb_hex, hex=True)))
501
502
    GDF['granuleid'] = GDF['grid1mil'].str.cat(GDF['grid100k'])
    return GDF[['granuleid', 'shapelyPoly_LonLat']]
Daniel Scheffler's avatar
GEOP:    
Daniel Scheffler committed
503
504


505
506
def get_overlapping_MGRS_tiles2(conn_params, scene_ID=None, tgt_corners_lonlat=None, timeout=15000):
    assert tgt_corners_lonlat if scene_ID is None else scene_ID, "Provide eihter scene_ID or tgt_corners_lonlat!"
Daniel Scheffler's avatar
GEOP:    
Daniel Scheffler committed
507
508
509

    conn_params = "%s options = '-c statement_timeout=%s'" % (conn_params, timeout)
    connection = psycopg2.connect(conn_params)
510
511
    if connection is None:
        return 'database connection fault'
Daniel Scheffler's avatar
GEOP:    
Daniel Scheffler committed
512
513

    vals2get = ['granuleid', 'footprint_wgs84']
514
515
    geocond = get_pgSQL_geospatial_query_cond(conn_params, 'footprints_sentinel2_granules',
                                              geomCol2use='footprint_wgs84',
516
                                              tgt_corners_lonlat=tgt_corners_lonlat, scene_ID=scene_ID)
Daniel Scheffler's avatar
GEOP:    
Daniel Scheffler committed
517
518
519
520
521
522
523
524
525
526
    query = "SELECT %s FROM %s WHERE %s" % (', '.join(vals2get), 'footprints_sentinel2_granules', geocond)

    cursor = connection.cursor()
    execute_pgSQL_query(cursor, query)
    records = cursor.fetchall()
    cursor.close()
    connection.close()

    GDF = GeoDataFrame(records, columns=['granuleid', 'wkb_hex'])

Daniel Scheffler's avatar
Daniel Scheffler committed
527
    GDF['shapelyPoly_LonLat'] = list(GDF['wkb_hex'].map(lambda wkb_hex: wkb_loads(wkb_hex, hex=True)))
Daniel Scheffler's avatar
GEOP:    
Daniel Scheffler committed
528
529
530
531

    return GDF[['granuleid', 'shapelyPoly_LonLat']]


532
533
534
def get_dict_satellite_name_id(conn_params):
    # type: (str) -> dict
    """Returns a dictionary with satellite names as keys and satellite IDs as values as read from pgSQL database.
535
536
537

    :param conn_params:     <str> pgSQL database connection parameters
    """
Daniel Scheffler's avatar
Daniel Scheffler committed
538

539
540
    res = get_info_from_postgreSQLdb(conn_params, 'satellites', ['name', 'id'])
    assert len(res) > 0, 'Error getting satellite names from postgreSQL database.'
541
    arr = np.array(res)
542
    return dict(zip(list(arr[:, 0]), list(arr[:, 1])))
543
544
545
546
547
548


def get_dict_sensor_name_id(conn_params):
    # type: (str) -> dict
    """Returns a dictionary with sensor names as keys and sensor IDs as values as read from pgSQL database.
    :param conn_params:     <str> pgSQL database connection parameters """
Daniel Scheffler's avatar
Daniel Scheffler committed
549

550
551
    res = get_info_from_postgreSQLdb(conn_params, 'sensors', ['name', 'id'])
    assert len(res) > 0, 'Error getting sensor names from postgreSQL database.'
552
    arr = np.array(res)
553
    return dict(zip(list(arr[:, 0]), list(arr[:, 1])))
554
555


556
def get_entityIDs_from_filename(conn_DB, filename):
557
558
559
    # type: (str, str) -> list
    """Returns entityID(s) for the given filename. In case of Sentinel-2 there can be more multiple entity IDs if
    multiple granules are saved in one .zip file.
560

561
562
563
    :param conn_DB:     <str> pgSQL database connection parameters
    :param filename:    <str> the filename to get the corresponding entity ID(s) for
    """
Daniel Scheffler's avatar
Daniel Scheffler committed
564

565
    if filename[:2] in ['LE', 'LC', 'LO'] and filename.endswith('.tar.gz'):  # Landsat
566
567
        entityIDs = [filename.split('.tar.gz')[0]]
    else:
568
569
570
        print('Querying database in order to get entityIDs for %s...' % filename)
        res = get_info_from_postgreSQLdb(conn_DB, 'scenes', ['entityid'], {'filename': filename}, timeout=40000)
        entityIDs = [subres[0] for subres in res] if len(res) > 0 else []
571
572
573
574
575
576
    return entityIDs


def get_filename_by_entityID(conn_DB, entityid, satellite):
    # type: (str,str,str) -> str
    """Returns the filename for the given entity ID.
577

578
579
580
581
    :param conn_DB:     <str> pgSQL database connection parameters
    :param entityid:    <str> entity ID
    :param satellite:   <str> satellite name to which the entity ID is belonging
    """
Daniel Scheffler's avatar
Daniel Scheffler committed
582

583
584
585
586
587
588
589
590
591
592
    if re.search('Landsat', satellite, re.I):
        filename = '%s.tar.gz' % entityid
    elif re.search('Sentinel-2', satellite, re.I):
        filename = get_info_from_postgreSQLdb(conn_DB, 'scenes', ['filename'],
                                              {'entityid': entityid}, records2fetch=1)[0][0]
    else:
        raise NotImplementedError
    return filename


593
def get_notDownloadedsceneIDs(conn_DB, entityIDs, satellite, sensor, src_folder):
594
595
596
597
    # type: (str,list,str,str,str) -> np.ndarray
    """Takes a list of entity IDs and extracts those records that have the corresponding archive file in the given
    source folder and that have the processing level 'METADATA' in the pgSQL database. Based on this subset a numpy
    array containing the corresponding scene IDs and the target filenames for the fileserver is returned.
598

599
600
601
602
603
604
    :param conn_DB:     <str> pgSQL database connection parameters
    :param entityIDs:   <list> a list of entity IDs
    :param satellite:   <str> the name of the satellite to restrict the query on
    :param sensor:      <str> the name of the sensor to restrict the query on
    :param src_folder:  <str> the source directory where archive files are saved
    """
Daniel Scheffler's avatar
Daniel Scheffler committed
605

606
607
608
    columns = ['id', 'entityid', 'satelliteid', 'sensorid', 'filename', 'proc_level']
    result = get_info_from_postgreSQLdb(conn_DB, 'scenes', columns, {'entityid': entityIDs})
    df = pd.DataFrame(result, columns=columns)
609
610

    satNameID_dic = get_dict_satellite_name_id(conn_DB)
611
    satID = satNameID_dic[satellite]
612
    target_folder = os.path.join(CFG.path_archive, satellite, sensor)
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632

    def get_fName(entityid): return get_filename_by_entityID(conn_DB, entityid, satellite)

    def tgt_exists(fileName): return os.path.exists(os.path.join(target_folder, fileName))

    def src_exists(entityid):
        return os.path.exists(os.path.join(src_folder, get_filename_by_entityID(conn_DB, entityid, satellite)))
    df['tgt_fileName'] = list(df['entityid'].map(get_fName))
    df['tgtFile_exists'] = list(df['tgt_fileName'].map(tgt_exists))
    df['srcFile_exists'] = list(df['entityid'].map(src_exists))
    tgt_satID = (df.satelliteid == float(satID))
    # isDL = (df.proc_level == 'DOWNLOADED')
    isMET = (df.proc_level == 'METADATA')
    # tgtE = (df.tgtFile_exists == True)
    srcE = df.srcFile_exists  # (df.srcFile_exists == True)
    # sceneIDs_notDL_tgtE = df[tgt_satID & (isDL == 0) & tgtE]  # maybe needed later
    # sceneIDs_DL_tgtNE = df[tgt_satID & isDL & (tgtE == 0)]  # maybe needed later
    # sceneIDs_DL_tgtE = df[tgt_satID & isDL & tgtE]  # maybe needed later
    sceneIDs_isMET_srcE = df[tgt_satID & isMET & srcE]
    return sceneIDs_isMET_srcE[['id', 'tgt_fileName']].values
633
634


635
class GMS_JOB(object):
636
    """gms_preprocessing job manager"""
637

638
    def __init__(self, conn_db):
639
        # type: (str) -> None
640
        """
641
        :param conn_db: <str> the database connection parameters as given by CFG.conn_params
642
        """
643
644
        # privates
        self._virtualsensorid = None
Daniel Scheffler's avatar
Daniel Scheffler committed
645

646
        # defaults
647
648
649
        self.conn = conn_db
        self.dataframe = GeoDataFrame()
        self.scene_counts = {}  # set by self.create()
650

651
652
        self.exists_in_db = False
        self.id = None  #: int
653
        self.creationtime = datetime.now()  # default, needed to create new job
654
655
656
657
        self.finishtime = None
        self.sceneids = []
        self.timerange_start = datetime.min
        self.timerange_end = datetime.max
658
        self.bounds = box(-180, -90, 180, 90)  # default, needed to create new job
659
660
661
662
663
664
        self.distribution_index = None
        self.progress = None
        self.feedback = None
        self.failed_sceneids = []
        self.ref_job_id = None
        self.datacube_mgrs_tiles_proc = []
665
666
667
668
669
        self.non_ref_datasetids = []
        self.max_cloudcover = None
        self.season_code = None  # type: int
        self.path_analysis_script = ''  # TODO
        self.job_mode = 'processing_only'  # FIXME download/processing/...
670
671
672
673
        self.jobs_table_columns = ['id', 'creationtime', 'finishtime', 'sceneids', 'timerange_start',
                                   'timerange_end', 'bounds', 'distribution_index', 'progress', 'feedback',
                                   'failed_sceneids', 'datasetid_spatial_ref',
                                   'virtualsensorid', 'ref_job_id', 'datacube_mgrs_tiles_proc', 'comment',
674
675
676
677
                                   'non_ref_datasetids', 'max_cloudcover', 'season_code', 'status',
                                   'path_analysis_script', 'analysis_parameter', 'statistics', 'job_mode']
        self.datasetid_spatial_ref = 249  # this is overwritten if existing job is read from DB but needed to create new
        self.datasetname_spatial_ref = 'SENTINEL-2A'  # same here
678
679
680
681
682
        self.status = None
        self.statistics = []
        self.comment = None
        self.epsg = None  # set by self._set_target_sensor_specs()
        self.ground_spatial_sampling = None  # set by self._set_target_sensor_specs()
683
        self.analysis_parameter = None
684

685
686
687
    def __repr__(self):
        return 'GMS job:\n\n' + GeoSeries(self.db_entry).to_string()

688
689
690
691
692
693
694
695
696
697
698
    @property
    def virtualsensorid(self):
        return self._virtualsensorid

    @virtualsensorid.setter
    def virtualsensorid(self, value):
        """Set virtual sensor ID but continue if no data value is received
        NOTE:  set by self._set_target_sensor_specs() and self.from_ID()"""
        if value != -1:  # no data value
            self._virtualsensorid = value

699
    def _set_target_sensor_specs(self, virtual_sensor_id, datasetid_spatial_ref):
700
        self.virtualsensorid = virtual_sensor_id
701
702
703
704

        if not isinstance(datasetid_spatial_ref, int):
            raise ValueError(datasetid_spatial_ref)

705
706
707
708
709
710
711
712
713
714
715
716
        res = get_info_from_postgreSQLdb(self.conn, 'virtual_sensors', ['spatial_resolution',
                                                                        "projection_epsg"], {'id': virtual_sensor_id})
        assert res, \
            "'virtual_sensor_id'=%s does not exist in the table 'virtual_sensors' of the database." % virtual_sensor_id
        target_gsd = res[0][0]
        self.ground_spatial_sampling = [target_gsd, target_gsd] if type(target_gsd) in [int, float] else target_gsd
        self.epsg = int(res[0][1])

        self.datasetid_spatial_ref = datasetid_spatial_ref
        res = get_info_from_postgreSQLdb(self.conn, 'datasets', ['name'], {'id': datasetid_spatial_ref})
        assert res, \
            "'datasetid_spatial_ref'=%s does not exist in the table 'datasets' of the database." % datasetid_spatial_ref
717
718
719
720
        self.datasetname_spatial_ref = res

    @property
    def db_entry(self):
721
722
        """Returns an OrderedDict containing keys and values of the database entry.
        """
Daniel Scheffler's avatar
Daniel Scheffler committed
723

724
725
        db_entry = collections.OrderedDict()
        for i in self.jobs_table_columns:
726
727
728
729
730
731
732
            val = getattr(self, i)

            if i == 'virtualsensorid' and val is None:
                val = -1  # nodata value

            db_entry[i] = val

733
734
        return db_entry

735
    def from_dictlist(self, dictlist_data2process, virtual_sensor_id, datasetid_spatial_ref=249, comment=None):
736
        # type: (list, int, int, str) -> GMS_JOB
737
        """
738
        :param dictlist_data2process:  <list> a list of dictionaries containing the keys "satellite", "sensor" and
739
740
741
742
743
744
                                        "filenames",
                                        e.g. [{'satellite:'Landsat-8,'sensor':'OLI_TIRS','filenames':file.tar.gz},{...}]
        :param virtual_sensor_id :     <int> a valid ID from the 'virtual_sensors' table of the postgreSQL database
        :param datasetid_spatial_ref:  <int> a valid dataset ID of the dataset to be chosen as spatial reference
                                        (from the 'datasets' table of the postgreSQL database)
                                        (default:249 - Sentinel-2A), 104=Landsat-8
745
        :param comment:                <str> a comment describing the job (e.g. 'Beta job')
746
        """
Daniel Scheffler's avatar
Daniel Scheffler committed
747

748
        self._set_target_sensor_specs(virtual_sensor_id, datasetid_spatial_ref)
749
        self.comment = comment
750
751
752

        dictlist_data2process = dictlist_data2process if dictlist_data2process else []

753
        for idx, datadict in enumerate(dictlist_data2process):
754
            assert isinstance(datadict, dict), "Expected only dictionaries within 'dictlist_data2process'. " \
755
                                               "Got %s in there." % type(datadict)
756
            assert False not in [i in datadict for i in ['satellite', 'sensor', 'filenames']]
757
            assert type(datadict['filenames']) in [list, str]
758

759
            if isinstance(datadict['filenames'], str):
760
761
762
763
764
765
                if datadict['filenames'].endswith('.csv'):
                    assert os.path.exists(datadict['filenames'])
                else:
                    datadict['filenames'] = [datadict['filenames']]

        # find all duplicates in input datadicts and build common geodataframe
766
        all_gdfs = []
767
        for datadict in dictlist_data2process:
768
            assert isinstance(datadict, dict)
769

770
771
            if isinstance(datadict['filenames'], str) and datadict['filenames'].endswith('.csv'):
                datadict['filenames'] = None  # TODO implement csv reader here
772
773
774
775
                raise NotImplementedError
            else:
                temp_gdf = GeoDataFrame(datadict, columns=['satellite', 'sensor', 'filenames'])
                if re.search('Landsat-7', datadict['satellite'], re.I) and re.search('ETM+', datadict['sensor'], re.I):
776
                    from .helper_functions import Landsat_entityID_decrypter as LED
777
778
779

                    def get_L7_sensor(fN): return LED(fN.split('.tar.gz')[0]).sensorIncSLC
                    temp_gdf['sensor'] = list(temp_gdf['filenames'].map(get_L7_sensor))
780
781
782
783
784
785

                all_gdfs.append(temp_gdf)

        gdf = GeoDataFrame(pd.concat(all_gdfs)).drop_duplicates()
        gdf.columns = ['satellite', 'sensor', 'filename']

786
787
788
789
790
791
792
793
794
795
796
        # run self.from_dictlist
        sceneInfoGDF = self._get_validated_sceneInfoGDFs(gdf)

        # populate attributes
        self._populate_jobAttrs_from_sceneInfoGDF(sceneInfoGDF)

        return self

    def from_sceneIDlist(self, list_sceneIDs, virtual_sensor_id, datasetid_spatial_ref=249, comment=None):
        # type: (list, int, int, str) -> object
        """
797
        Create a GMS_JOB instance based on the given list of scene IDs.
Daniel Scheffler's avatar
Bugfix    
Daniel Scheffler committed
798

799
800
801
802
803
804
805
806
        :param list_sceneIDs:          <list> of scene IDs, e.g. [26781907, 26781917, 26542650, 26542451, 26541679]
        :param virtual_sensor_id :     <int> a valid ID from the 'virtual_sensors' table of the postgreSQL database
        :param datasetid_spatial_ref:  <int> a valid dataset ID of the dataset to be chosen as spatial reference
                                        (from the 'datasets' table of the postgreSQL database)
                                        (default:249 - Sentinel-2A), 104=Landsat-8
        :param comment:                <str> a comment describing the job (e.g. 'Beta job')
        """

807
        self._set_target_sensor_specs(virtual_sensor_id, datasetid_spatial_ref)
808
809
810
811
812
        self.comment = comment

        list_sceneIDs = list(list_sceneIDs)

        # query 'satellite', 'sensor', 'filename' from database and summarize in GeoDataFrame
813
        with psycopg2.connect(self.conn) as conn:
814
815
816
817
818
819
820
821
            with conn.cursor() as cursor:
                execute_pgSQL_query(cursor,
                                    """SELECT scenes.id, satellites.name, sensors.name, scenes.filename FROM scenes
                                    LEFT JOIN satellites on scenes.satelliteid=satellites.id
                                    LEFT JOIN sensors on scenes.sensorid=sensors.id
                                    WHERE scenes.id in (%s)""" % ','.join([str(i) for i in list_sceneIDs]))
                gdf = GeoDataFrame(cursor.fetchall(), columns=['sceneid', 'satellite', 'sensor', 'filename'])

822
823
824
        # FIXME overwriting 'ETM+_SLC_OFF' with 'ETM+' causes _get_validated_sceneInfoGDFs() to fail because the
        # FIXME sensorid for ETM+_SLC_OFF cannot be retrieved
        # gdf['sensor'] = gdf['sensor'].apply(lambda senN: senN if senN != 'ETM+_SLC_OFF' else 'ETM+')
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
        gdf = gdf.drop_duplicates()

        if gdf.empty:
            raise ValueError('None of the given scene IDs could be found in the GeoMultiSens database. '
                             'Job creation failed.')
        else:
            missing_IDs = [i for i in list_sceneIDs if i not in gdf['sceneid'].values]
            if missing_IDs:
                warnings.warn('The following scene IDs could not been found in the GeoMultiSens database: \n%s'
                              % '\n'.join([str(i) for i in missing_IDs]))

            # run self.from_dictlist
            sceneInfoGDF = self._get_validated_sceneInfoGDFs(gdf)

            # populate attributes
            self._populate_jobAttrs_from_sceneInfoGDF(sceneInfoGDF)

        return self

844
845
846
847
848
849
850
851
    def from_entityIDlist(self, list_entityids, virtual_sensor_id, datasetid_spatial_ref=249, comment=None):
        """Create a GMS_JOB instance based on the given list of entity IDs.

        :param list_entityids:
        :param virtual_sensor_id:
        :param datasetid_spatial_ref:
        :param comment:
        :return:
852
        """
Daniel Scheffler's avatar
Bugfix    
Daniel Scheffler committed
853

854
        res_sceneIDs = get_info_from_postgreSQLdb(self.conn, 'scenes', ['id', ], {'entityid': list_entityids})
855
856
857
        if not res_sceneIDs:
            raise ValueError('No matching database entries found for the given entity IDs.')

858
        list_sceneIDs = np.array(res_sceneIDs)[:, 0].tolist()
859
860
861
        count_no_match = len(list_entityids) - len(list_sceneIDs)

        if count_no_match:
862
            warnings.warn('%s datasets could not be found the database. They cannot be processed.' % count_no_match)
863
864
865
866
867
868
869
870
871
872
873
874

        return self.from_sceneIDlist(list_sceneIDs, virtual_sensor_id,
                                     datasetid_spatial_ref=datasetid_spatial_ref, comment=comment)

    def from_filenames(self, list_filenames, virtual_sensor_id, datasetid_spatial_ref=249, comment=None):
        """Create a GMS_JOB instance based on the given list of provider archive filenames.

        :param list_filenames:
        :param virtual_sensor_id:
        :param datasetid_spatial_ref:
        :param comment:
        :return:
875
876
        """

877
        res_sceneIDs = get_info_from_postgreSQLdb(self.conn, 'scenes', ['id', ], {'filename': list_filenames})
878
879
880
        if not res_sceneIDs:
            raise ValueError('No matching database entries found for the given filenames.')

881
        list_sceneIDs = np.array(res_sceneIDs)[:, 0].tolist()
882
883
884
885
886
887
888
        count_no_match = len(list_filenames) - len(list_sceneIDs)

        if count_no_match:
            warnings.warn('%s datasets could not be found the database. They cannot be processed.')

        return self.from_sceneIDlist(list_sceneIDs, virtual_sensor_id,
                                     datasetid_spatial_ref=datasetid_spatial_ref, comment=comment)
889

890
891
892
893
894
895
896
897
898
899
    def _get_validated_sceneInfoGDFs(self, GDF_SatSenFname):
        # type: (GeoDataFrame) -> GeoDataFrame
        """

        :param GDF_SatSenFname:
        :return:
        """

        gdf = GDF_SatSenFname

900
        # loop through all satellite-sensor combinations and get scene information from database
901
902
903
        all_gdf_recs, all_gdf_miss = [], []
        all_satellites, all_sensors = zip(
            *[i.split('__') for i in (np.unique(gdf['satellite'] + '__' + gdf['sensor']))])
904

905
906
        for satellite, sensor in zip(all_satellites, all_sensors):
            cur_gdf = gdf.loc[(gdf['satellite'] == satellite) & (gdf['sensor'] == sensor)]
907
908
909
            filenames = list(cur_gdf['filename'])

            satID_res = get_info_from_postgreSQLdb(self.conn, 'satellites', ['id'], {'name': satellite})
910
            senID_res = get_info_from_postgreSQLdb(self.conn, 'sensors', ['id'], {'name': sensor})
911
            assert len(satID_res), "No satellite named '%s' found in database." % satellite
912
            assert len(senID_res), "No sensor named '%s' found in database." % sensor
913
914

            # append sceneid and wkb_hex bounds
915
916
917
918
919
920
921
922
923
924
925
926
927
            if 'sceneid' in gdf.columns:
                sceneIDs = list(cur_gdf['sceneid'])
                conddict = dict(id=sceneIDs, satelliteid=satID_res[0][0], sensorid=senID_res[0][0])
            else:
                conddict = dict(filename=filenames, satelliteid=satID_res[0][0], sensorid=senID_res[0][0])

            records = get_info_from_postgreSQLdb(
                self.conn, 'scenes', ['filename', 'id', 'acquisitiondate', 'bounds'], conddict)
            records = GeoDataFrame(records, columns=['filename', 'sceneid', 'acquisitiondate', 'geom'])
            if 'sceneid' in gdf.columns:
                del records['sceneid']

            cur_gdf = cur_gdf.merge(records, on='filename', how="outer", copy=False)
928
929

            # separate records with valid matches in database from invalid matches (filename not found in database)
930
931
            gdf_recs = cur_gdf[
                cur_gdf.sceneid.notnull()].copy()  # creates a copy (needed to be able to apply maps later)
932
933
934
            gdf_miss = cur_gdf[cur_gdf.sceneid.isnull()]  # creates a view

            # convert scene ids from floats to integers
935
            gdf_recs['sceneid'] = list(gdf_recs.sceneid.map(lambda sceneid: int(sceneid)))
936
937

            # wkb_hex bounds to shapely polygons
Daniel Scheffler's avatar
Daniel Scheffler committed
938
            gdf_recs['polygons'] = list(gdf_recs.geom.map(lambda wkb_hex: wkb_loads(wkb_hex, hex=True)))
939
940
941
942
943
944
945
946
947
948
949
950
951

            all_gdf_recs.append(gdf_recs)
            all_gdf_miss.append(gdf_miss)

        # merge all dataframes of all satellite-sensor combinations
        gdf_recs_compl = GeoDataFrame(pd.concat(all_gdf_recs))
        gdf_miss_compl = GeoDataFrame(pd.concat(all_gdf_miss))

        # populate attributes
        if not gdf_miss_compl.empty:
            warnings.warn('The following scene filenames could not been found in the GeoMultiSens database: \n%s'
                          % '\n'.join(list(gdf_miss_compl['filename'])))

952
953
954
955
956
957
958
959
960
961
962
        return gdf_recs_compl

    def _populate_jobAttrs_from_sceneInfoGDF(self, sceneInfoGDF):
        # type: (GeoDataFrame) -> None
        """

        :param sceneInfoGDF:
        :return:
        """

        if not sceneInfoGDF.empty:
963
964
965
966
            self.dataframe = sceneInfoGDF
            self.sceneids = list(self.dataframe['sceneid'])
            self.statistics = [len(self.sceneids)] + [0] * 8
            self.bounds = box(*MultiPolygon(list(self.dataframe['polygons'])).bounds)
967
968
            self.timerange_start = self.dataframe.acquisitiondate.min().to_pydatetime()
            self.timerange_end = self.dataframe.acquisitiondate.max().to_pydatetime()
969

970
    def from_job_ID(self, job_ID):
971
        # type: (int) -> GMS_JOB
972
        """
973
        Create a GMS_JOB instance by querying the database for a specific job ID.
974
975
        :param job_ID:  <int> a valid id from the database table 'jobs'
        """
Daniel Scheffler's avatar
Daniel Scheffler committed
976

977
        res = get_info_from_postgreSQLdb(self.conn, 'jobs', self.jobs_table_columns, {'id': job_ID})
978
        if not res:
979
            raise ValueError("No job with ID %s found in 'jobs' table of the database." % job_ID)
980

981
        self.exists_in_db = True
982
        [setattr(self, attrName, res[0][i]) for i, attrName in enumerate(self.jobs_table_columns)]
Daniel Scheffler's avatar
Daniel Scheffler committed
983
        self.bounds = wkb_loads(self.bounds, hex=True)
984