pymodis script added

.renku/refs/datasets/how_spr

+../../../pymodis/.renku/datasets/ad3d2f9a-2a89-4ac6-8286-86104be9e0c0/metadata.yml
\ No newline at end of file

pymodis/.renku/datasets/ad3d2f9a-2a89-4ac6-8286-86104be9e0c0/metadata.yml

+'@context':
+  '@version': 1.1
+  _id: '@id'
+  _project:
+    '@context':
+      '@version': 1.1
+      _id: '@id'
+      created: schema:dateCreated
+      creator:
+        '@context':
+          '@version': 1.1
+          _id: '@id'
+          affiliation: schema:affiliation
+          alternate_name: schema:alternateName
+          email: schema:email
+          label: rdfs:label
+          name: schema:name
+          prov: http://www.w3.org/ns/prov#
+          rdfs: http://www.w3.org/2000/01/rdf-schema#
+          schema: http://schema.org/
+        '@id': schema:creator
+      name: schema:name
+      prov: http://www.w3.org/ns/prov#
+      schema: http://schema.org/
+      updated: schema:dateUpdated
+      version: schema:schemaVersion
+    '@id': schema:isPartOf
+  created: schema:dateCreated
+  creator:
+    '@context':
+      '@version': 1.1
+      _id: '@id'
+      affiliation: schema:affiliation
+      alternate_name: schema:alternateName
+      email: schema:email
+      label: rdfs:label
+      name: schema:name
+      prov: http://www.w3.org/ns/prov#
+      rdfs: http://www.w3.org/2000/01/rdf-schema#
+      schema: http://schema.org/
+    '@id': schema:creator
+  date_published: schema:datePublished
+  description: schema:description
+  files:
+    '@context':
+      '@version': 1.1
+      _id: '@id'
+      _project:
+        '@context':
+          '@version': 1.1
+          _id: '@id'
+          created: schema:dateCreated
+          creator:
+            '@context':
+              '@version': 1.1
+              _id: '@id'
+              affiliation: schema:affiliation
+              alternate_name: schema:alternateName
+              email: schema:email
+              label: rdfs:label
+              name: schema:name
+              prov: http://www.w3.org/ns/prov#
+              rdfs: http://www.w3.org/2000/01/rdf-schema#
+              schema: http://schema.org/
+            '@id': schema:creator
+          name: schema:name
+          prov: http://www.w3.org/ns/prov#
+          schema: http://schema.org/
+          updated: schema:dateUpdated
+          version: schema:schemaVersion
+        '@id': schema:isPartOf
+      added: schema:dateCreated
+      based_on: schema:isBasedOn
+      creator:
+        '@context':
+          '@version': 1.1
+          _id: '@id'
+          affiliation: schema:affiliation
+          alternate_name: schema:alternateName
+          email: schema:email
+          label: rdfs:label
+          name: schema:name
+          prov: http://www.w3.org/ns/prov#
+          rdfs: http://www.w3.org/2000/01/rdf-schema#
+          schema: http://schema.org/
+        '@id': schema:creator
+      name: schema:name
+      path: prov:atLocation
+      prov: http://www.w3.org/ns/prov#
+      schema: http://schema.org/
+      url: schema:url
+      wfprov: http://purl.org/wf4ever/wfprov#
+    '@id': schema:hasPart
+  identifier: schema:identifier
+  in_language:
+    '@context':
+      '@version': 1.1
+      alternate_name: schema:alternateName
+      name: schema:name
+      schema: http://schema.org/
+    '@id': schema:inLanguage
+  keywords: schema:keywords
+  license: schema:license
+  name: schema:name
+  path: prov:atLocation
+  prov: http://www.w3.org/ns/prov#
+  same_as:
+    '@context':
+      '@version': 1.1
+      _id: '@id'
+      schema: http://schema.org/
+      url: schema:url
+    '@id': schema:sameAs
+  schema: http://schema.org/
+  short_name: schema:alternateName
+  tags:
+    '@context':
+      '@version': 1.1
+      _id: '@id'
+      commit: schema:location
+      created: schema:startDate
+      dataset: schema:about
+      description: schema:description
+      name: schema:name
+      schema: http://schema.org/
+    '@id': schema:subjectOf
+  url: schema:url
+  version: schema:version
+  wfprov: http://purl.org/wf4ever/wfprov#
+'@type':
+- prov:Entity
+- schema:Dataset
+- wfprov:Artifact
+_id: https://renkulab.io/datasets/ad3d2f9a-2a89-4ac6-8286-86104be9e0c0
+_label: ad3d2f9a-2a89-4ac6-8286-86104be9e0c0
+_project:
+  '@type':
+  - prov:Location
+  - schema:Project
+  _id: https://renkulab.io/projects/gitanjali.thakur/fpar-data
+  created: '2020-04-19T09:47:45.966000+00:00'
+  creator:
+    '@type':
+    - prov:Person
+    - schema:Person
+    _id: mailto:gitanjali.thakur@list.lu
+    affiliation: null
+    alternate_name: null
+    email: gitanjali.thakur@list.lu
+    label: gitanjali Thakur
+    name: gitanjali Thakur
+  name: Fpar DATA
+  updated: '2020-04-19T09:47:45.966000+00:00'
+  version: '3'
+created: '2020-05-13T12:03:35.887717+00:00'
+creator:
+- '@type':
+  - prov:Person
+  - schema:Person
+  _id: mailto:gitanjali.thakur@list.lu
+  affiliation: null
+  alternate_name: null
+  email: gitanjali.thakur@list.lu
+  label: gitanjali Thakur
+  name: gitanjali Thakur
+date_published: null
+description: null
+files: []
+identifier: ad3d2f9a-2a89-4ac6-8286-86104be9e0c0
+in_language: null
+keywords: []
+license: null
+name: how_spr
+path: .renku/datasets/ad3d2f9a-2a89-4ac6-8286-86104be9e0c0
+same_as: null
+short_name: how_spr
+tags: []
+url: https://renkulab.io/datasets/ad3d2f9a-2a89-4ac6-8286-86104be9e0c0
+version: null

pymodis/modis_download.py

+#!/usr/bin/env python
+# script to download massive MODIS data from ftp
+#
+#  (c) Copyright Luca Delucchi 2010
+#  Authors: Luca Delucchi
+#  Email: luca dot delucchi at iasma dot it
+#
+##################################################################
+#
+#  This MODIS Python script is licensed under the terms of GNU GPL 2.
+#  This program is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU General Public License as
+#  published by the Free Software Foundation; either version 2 of
+#  the License, or (at your option) any later version.
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+#  See the GNU General Public License for more details.
+#
+##################################################################
+"""Script to download massive MODIS data"""
+import sys
+import os
+import getpass
+try:
+    from pymodis import optparse_gui
+    WXPYTHON = True
+except:
+    WXPYTHON = False
+from pymodis import optparse_required
+from pymodis import downmodis
+
+
+def main():
+    """Main function"""
+    # usage
+    usage = "usage: %prog [options] destination_folder"
+    if 1 == len(sys.argv) and WXPYTHON:
+        option_parser_class = optparse_gui.OptionParser
+    else:
+        option_parser_class = optparse_required.OptionParser
+    parser = option_parser_class(usage=usage, description='modis_download')
+    # url
+    parser.add_option("-u", "--url", default="https://e4ftl01.cr.usgs.gov",
+                      help="http/ftp server url [default=%default]",
+                      dest="url")
+    # username and password from stdin
+    parser.add_option("-I", "--input", dest="input", action="store_true",
+                      help="insert user and password from standard input")
+    # password
+    parser.add_option("-P", "--password", dest="password",
+                      help="password to connect to the server")
+    # username
+    parser.add_option("-U", "--username", dest="user",
+                      help="username to connect to the server")
+    # tiles
+    parser.add_option("-t", "--tiles", dest="tiles", default=None,
+                      help="string of tiles separated with comma "
+                      "[default=%default for all tiles]")
+    # path to add the path in the server
+    parser.add_option("-s", "--source", dest="path", default="MOLT",
+                      help="directory on the http/ftp server "
+                      "[default=%default]")
+    # path to add the url
+    parser.add_option("-p", "--product", dest="prod", default="MOD11A1.005",
+                      help="product name as on the http/ftp server "
+                      "[default=%default]")
+    # delta
+    parser.add_option("-D", "--delta", dest="delta", default=10,
+                      help="delta of day from the first day "
+                      "[default=%default]")
+    # first day
+    parser.add_option("-f", "--firstday", dest="today", default=None,
+                      help="the day to start download [default=%default is for"
+                      " today]; if you want change data you must use "
+                      "this format YYYY-MM-DD", metavar="FIRST_DAY")
+    # last day
+    parser.add_option("-e", "--endday", dest="enday", default=None,
+                      metavar="LAST_DAY", help="the day to stop download "
+                      "[default=%default]; if you want change"
+                      " data you must use this format YYYY-MM-DD")
+    # debug
+    parser.add_option("-x", action="store_true", dest="debug", default=False,
+                      help="this is useful for debugging the "
+                      "download [default=%default]")
+    # jpg
+    parser.add_option("-j", action="store_true", dest="jpg", default=False,
+                      help="download also the jpeg files [default=%default]")
+    # only one day
+    parser.add_option("-O", dest="oneday", action="store_true", default=False,
+                      help="download only one day, it set "
+                      "delta=1 [default=%default]")
+    # all days
+    parser.add_option("-A", dest="alldays", action="store_true", default=False,
+                      help="download all days, it useful for initial download"
+                      " of a product. It overwrite the 'firstday' and "
+                      "'endday' options [default=%default]")
+    # remove file with size = 0
+    parser.add_option("-r", dest="empty", action="store_true", default=False,
+                      help="remove empty files (size equal to zero) from "
+                      "'destination_folder'  [default=%default]")
+    #parser.add_option("-A", dest="alldays", action="store_true", default=True,
+                      #help="download all days from the first")
+
+    # set false several options
+    parser.set_defaults(oneday=False)
+    parser.set_defaults(debug=False)
+    parser.set_defaults(jpg=False)
+
+    # return options and argument
+    (options, args) = parser.parse_args()
+    # test if args[0] it is set
+    if len(args) == 0 and not WXPYTHON:
+        parser.print_help()
+        sys.exit(1)
+    if len(args) == 0:
+        parser.error("You have to define the destination folder for HDF file")
+    if not os.path.isdir(args[0]):
+        parser.error("The destination folder is not a dir or not exists")
+
+    # check if oneday option it is set
+    if options.oneday:
+        options.delta = 1
+    if options.input:
+        if sys.version_info.major == 3:
+            user = input("Username: ")
+        else:
+            user = raw_input("Username: ")
+        password = getpass.getpass()
+    else:
+        user = options.user
+        password = options.password
+
+    # set modis object
+    modisOgg = downmodis.downModis(url=options.url, user=user,
+                                   password=password,
+                                   destinationFolder=args[0],
+                                   tiles=options.tiles, path=options.path,
+                                   product=options.prod, today=options.today,
+                                   enddate=options.enday, jpg=options.jpg,
+                                   delta=int(options.delta),
+                                   debug=options.debug)
+    # connect to ftp
+    modisOgg.connect()
+    if modisOgg.nconnection <= 20:
+        # download data
+        modisOgg.downloadsAllDay(clean=options.empty, allDays=options.alldays)
+    else:
+        parser.error("A problem with the connection occured")
+
+#add options
+if __name__ == "__main__":
+    main()