Merge pull request #46 from CBIIT/CRDCDH-2168-001-pgu

CRDCDH 2168

README-technical.md

@@ -57,11 +57,6 @@ Usage of the CLI tool:
     Following arguments are needed to read important data from manifest, conditional required when type = “data file”
 
     -m --manifest, path to manifest file, conditional required when type = “data file”
-    -n --name-field
-    -s --size-field
-    -m --md5-field
-    -i --id-field
-    -o --omit-DCF-prefix
 
     CLI configuration module will validate and combine parameters from CLI and/or config file
     If config_file is given, then everything else is potentially optional (if it’s included in config file)

README.md

@@ -90,12 +90,6 @@ You can put a manifest in the same folder with the data files, or you can put it
 - data: local path to the folder that contains the data files to be uploaded
 - manifest: local path to the manifest file
 - id-field: column name in the manifest file that contains file IDs(Keys). Please refer to the data model to determine which property is the ID/Key property.
-- omit-DCF-prefix: for most data commons, this should be set to “false”. One exception is ICDC, which should be set to “true”.
-- name-field: column name in the manifest file that contains data file names
-- size-field: column name in the manifest file that contains data file sizes
-- md5-field: column name in the manifest file that contains data file MD5 checksums
-- id-field: column name in the manifest file that contains data file ID
-- omit-DCF-prefix: boolean to define if need DCF prefix "dg.4DFC"
 - retries: number of retries the CLI tool will perform after a failed upload 
 - overwrite: if set to “true”, CLI will upload a data file to overwrite the data file with same name that already exists in the Data Hub target storage. If set to “false”, CLI will not upload a data file if a data file with the same name exists in the Data Hub target storage.
 - dryrun: if set to “true”, CLI will not upload any data files to the Data Hub target storage. If set to “false”, CLI will upload data files to the Data Hub target storage.

configs/uploader-file-config.example.yml

@@ -17,21 +17,6 @@ Config:
     # path to manifest file, conditional required when type = data file
     manifest: /path_to_the_manifest_file
 
-    # Property name for Key/ID property of file node. For example, "file_id" is the Key/ID property of file node in CDS.
-    id-field: file_id
-
-    # Whether to omit DCF prefix when generating file IDs. For example, false means include DCF prefix when generating file IDs.
-    omit-DCF-prefix: false
-
-    # file name header name in the manifest file. For example, "file_name" is the header name for CDS.
-    name-field: file_name
-
-    # file size header name in the manifest file. For example, "file_size" is the header name for CDS.
-    size-field: file_size
-
-    # file md5 header name in the manifest file. For example, "md5sum" is the header name for CDS.
-    md5-field: md5sum
-
     # file uploading retries
     retries: 3
 

src/common/graphql_client.py

@@ -145,6 +145,43 @@ def update_batch(self, batchID, uploaded_files):
             self.log.debug(e)
             self.log.exception(f'Update batch failed - internal error. Please try again and contact the helpdesk if this error persists.')
             return False
+
+    # 4) get_data_file_config()
+    def get_data_file_config(self, submissionID):
+        body = f"""
+        query {{
+            retrieveFileNodeConfig (submissionID: \"{submissionID}\") {{
+                id_field,
+                name_field,
+                size_field,
+                md5_field,
+                omit_DCF_prefix
+            }}
+        }}
+        """
+        try:
+            response = requests.post(url=self.url, headers=self.headers, json={"query": body})
+            status = response.status_code
+            self.log.info(f"get_data_file_config response status code: {status}.")
+            if status == 200:
+                results = response.json()
+                if results.get("errors"):
+                    self.log.error(f'Get data file config failed: {results.get("errors")[0].get("message")}.')
+                else:
+                    data_file_config = results.get("data").get("retrieveFileNodeConfig")
+                    if data_file_config:
+                        return True, data_file_config
+                    else:
+                        self.log.error('Get data file config failed!')
+                        return False, None
+            else:
+                self.log.error(f'Get data file config failed (code: {status}) - internal error. Please try again and contact the helpdesk if this error persists.')
+                return False, None
+
+        except Exception as e:
+            self.log.debug(e)
+            self.log.exception(f'Get data file config failed - internal error. Please try again and contact the helpdesk if this error persists.')
+            return False, None
 
 
 

src/upload_config.py

@@ -21,11 +21,6 @@ def __init__(self):
         parser.add_argument('--dryrun', default=False, type=bool, help='Only check original file, won\'t copy any files, optional, default is false')
         #args for data file type
         parser.add_argument('-f', '--manifest', help='path to manifest file, conditional required when type = “data file"')
-        parser.add_argument('-n', '--name-field', help='header file name in manifest, optional, default value is "file_name"')
-        parser.add_argument('-s', '--size-field', help='header file size in manifest, optional, default value is "file_size"')
-        parser.add_argument('-m', '--md5-field', help='header md5 name in manifest, optional, default value is "md5sum"')
-        parser.add_argument('-i', '--id-field', help='header file ID name in manifest, optional, default value is "file_id"')
-        parser.add_argument('-o', '--omit-DCF-prefix', help='boolean to define if need DCF prefix "dg.4DFC"')
 
         parser.add_argument('-r', '--retries', default=3, type=int, help='file uploading retries, optional, default value is 3')
 
@@ -103,7 +98,7 @@ def validate(self):
             return False
         elif type not in UPLOAD_TYPES:
             self.log.critical(f'Configuration error in "type": “{type}” is not valid. Valid “type” value can be one of [“data file”, “metadata”]')
-            return False
+            return False  
         else:
             if type == TYPE_FILE: #data file
                 #check manifest
@@ -117,27 +112,6 @@ def validate(self):
                         return False
 
                 self.data[PRE_MANIFEST]  = manifest
-                #check header names in manifest file
-                file_name_header= self.data.get(FILE_NAME_FIELD)
-                if file_name_header is None:
-                    self.data[FILE_NAME_FIELD] = FILE_NAME_DEFAULT
-
-                file_size_header = self.data.get(FILE_SIZE_FIELD)
-                if file_size_header is None:
-                    self.data[FILE_SIZE_FIELD] = FILE_SIZE_DEFAULT
-
-                md5_header = self.data.get(FILE_MD5_FIELD)
-                if  md5_header is None:
-                    self.data[FILE_MD5_FIELD] = MD5_DEFAULT
-
-                file_id_header= self.data.get(FILE_ID_FIELD)
-                if file_id_header is None:
-                    self.log.critical(f'file id field is required.')
-                    return False
-
-                omit_dcf_prefix = self.data.get(OMIT_DCF_PREFIX)
-                if omit_dcf_prefix is None:
-                    self.data[OMIT_DCF_PREFIX] = False
 
         filepath = self.data.get(FILE_DIR)
         if filepath is None:
@@ -154,4 +128,29 @@ def validate(self):
                 self.data[FROM_S3] = True
 
         return True
+
+    def validate_file_config(self, data_file_config):
+        #check header names in manifest file
+        file_name_header= data_file_config.get(FILE_NAME_FIELD.replace("-", "_"))
+        self.data[FILE_NAME_FIELD] = file_name_header if file_name_header else FILE_NAME_DEFAULT
+
+        file_size_header = data_file_config.get(FILE_SIZE_FIELD.replace("-", "_"))
+        self.data[FILE_SIZE_FIELD] = file_size_header if file_size_header else FILE_SIZE_DEFAULT
+
+        md5_header = data_file_config.get(FILE_MD5_FIELD.replace("-", "_"))
+        self.data[FILE_MD5_FIELD] = md5_header if md5_header else MD5_DEFAULT
+
+        file_id_header= data_file_config.get(FILE_ID_FIELD.replace("-", "_"))
+        if file_id_header is None:
+            self.log.critical(f'file id field is required.')
+            return False
+
+        self.data[FILE_ID_FIELD] = file_id_header
+
+        omit_dcf_prefix = data_file_config.get(OMIT_DCF_PREFIX.replace("-", "_"))
+        self.data[OMIT_DCF_PREFIX] = False if omit_dcf_prefix is None else omit_dcf_prefix
+
+        return True
+
+
 

src/uploader.py

@@ -28,9 +28,24 @@ def controller():
         log.error("Failed to upload files: missing required valid parameter(s)!")
         print("Failed to upload files: invalid parameter(s)!  Please check log file in tmp folder for details.")
         return 1
-
+    
     #step 2: validate file or metadata
     configs = config.data
+    apiInvoker = APIInvoker(configs)
+    # get data file config
+    if configs[UPLOAD_TYPE] == TYPE_FILE:
+        # retrieve data file configuration
+        result, data_file_config = apiInvoker.get_data_file_config(configs["submission"])
+        if not result or not data_file_config:
+            log.error("Failed to upload files: can't get data file config!")
+            print("Failed to upload files: can't get data file config! Please check log file in tmp folder for details.")
+            return 1
+
+        if not config.validate_file_config(data_file_config):
+            log.error("Failed to upload files: invalid file config!")
+            print("Failed to upload files: invalid file config! Please check log file in tmp folder for details.")
+            return 1
+
     validator = FileValidator(configs)
     if not validator.validate():
         log.error("Failed to upload files: found invalid file(s)!")
@@ -40,7 +55,6 @@ def controller():
 
     if validator.invalid_count == 0:
         #step 3: create a batch
-        apiInvoker = APIInvoker(configs)
         # file_array = [{"fileName": item[FILE_NAME_DEFAULT], "size": item[FILE_SIZE_DEFAULT]} for item in file_list]
         file_array = [ item[FILE_NAME_DEFAULT] for item in file_list]
         newBatch = None