Merge pull request #300 from NASA-PDS/299_group_write_permissions

Group Write Permission Fix

src/pds_doi_service/core/actions/release.py

@@ -267,33 +267,40 @@ def run(self, **kwargs):
             dois = self._complete_dois(dois)
             dois = self._validate_dois(dois)
 
-            for doi in dois:
+            for input_doi in dois:
                 # Create a JSON format label to send to the service provider
-                io_doi_label = self._record_service.create_doi_record(doi, content_type=CONTENT_TYPE_JSON)
+                io_doi_label = self._record_service.create_doi_record(input_doi, content_type=CONTENT_TYPE_JSON)
 
                 # If the next step is to release, submit to the service provider and
                 # use the response label for the local transaction database entry
                 if not self._review:
                     # Determine the correct HTTP verb and URL for submission of this DOI
-                    method, url = self._web_client.endpoint_for_doi(doi, self._name)
+                    method, url = self._web_client.endpoint_for_doi(input_doi, self._name)
 
-                    doi, o_doi_label = self._web_client.submit_content(
+                    output_doi, o_doi_label = self._web_client.submit_content(
                         url=url, method=method, payload=io_doi_label, content_type=CONTENT_TYPE_JSON
                     )
+                # Otherwise, DOI object is ready to be logged
+                else:
+                    output_doi = input_doi
 
                 # Otherwise, if the next step is review, the label we've already
                 # created has marked all the Doi's as being the "review" step
                 # so its ready to be submitted to the local transaction history
                 transaction = self.m_transaction_builder.prepare_transaction(
-                    self._node, self._submitter, doi, input_path=self._input, output_content_type=CONTENT_TYPE_JSON
+                    self._node,
+                    self._submitter,
+                    output_doi,
+                    input_path=input_doi.input_source,
+                    output_content_type=CONTENT_TYPE_JSON,
                 )
 
                 # Commit the transaction to the local database
                 transaction.log()
 
                 # Append the latest version of the Doi object to return
                 # as a label
-                output_dois.append(doi)
+                output_dois.append(output_doi)
         # Propagate input format exceptions, force flag should not affect
         # these being raised and certain callers (such as the API) look
         # for this exception specifically

src/pds_doi_service/core/actions/reserve.py

@@ -245,29 +245,32 @@ def run(self, **kwargs):
             dois = self._complete_dois(dois)
             dois = self._validate_dois(dois)
 
-            for doi in dois:
+            for input_doi in dois:
                 # Create the JSON request label to send
-                io_doi_label = self._record_service.create_doi_record(doi, content_type=CONTENT_TYPE_JSON)
+                io_doi_label = self._record_service.create_doi_record(input_doi, content_type=CONTENT_TYPE_JSON)
 
                 # Submit the Reserve request
                 # Determine the correct HTTP verb and URL for submission of this DOI
-                method, url = self._web_client.endpoint_for_doi(doi, self._name)
+                method, url = self._web_client.endpoint_for_doi(input_doi, self._name)
 
-                doi, o_doi_label = self._web_client.submit_content(
+                output_doi, o_doi_label = self._web_client.submit_content(
                     method=method, url=url, payload=io_doi_label, content_type=CONTENT_TYPE_JSON
                 )
 
                 # Log the inputs and outputs of this transaction
                 transaction = self.m_transaction_builder.prepare_transaction(
-                    self._node, self._submitter, doi, input_path=self._input, output_content_type=CONTENT_TYPE_JSON
+                    self._node,
+                    self._submitter,
+                    output_doi,
+                    input_path=input_doi.input_source,
+                    output_content_type=CONTENT_TYPE_JSON,
                 )
 
                 # Commit the transaction to the local database
                 transaction.log()
 
-                # Append the latest version of the Doi object to return
-                # as a label
-                output_dois.append(doi)
+                # Append the latest version of the Doi object to return as a label
+                output_dois.append(output_doi)
 
         # Propagate input format exceptions, force flag should not affect
         # these being raised and certain callers (such as the API) look

src/pds_doi_service/core/actions/update.py

@@ -325,7 +325,7 @@ def run(self, **kwargs):
 
             for doi in dois:
                 transaction = self.m_transaction_builder.prepare_transaction(
-                    self._node, self._submitter, doi, input_path=self._input, output_content_type=CONTENT_TYPE_JSON
+                    self._node, self._submitter, doi, input_path=doi.input_source, output_content_type=CONTENT_TYPE_JSON
                 )
 
                 transaction.log()

src/pds_doi_service/core/db/doi_database.py

@@ -12,7 +12,9 @@
 Contains classes and functions for interfacing with the local transaction
 database (SQLite3).
 """
+import os
 import sqlite3
+import stat
 from collections import OrderedDict
 from datetime import datetime
 from datetime import timedelta
@@ -94,6 +96,14 @@ def create_connection(self):
         except Error as my_error:
             logger.error("Failed to connect to database, reason: %s", my_error)
 
+        # Make sure Database has proper group permissions set
+        st = os.stat(self.m_database_name)
+        has_group_rw = bool(st.st_mode & stat.S_IRGRP & stat.S_IWGRP)
+
+        if not has_group_rw:
+            logger.debug("Setting group read/write bits on database %s", self.m_database_name)
+            os.chmod(self.m_database_name, st.st_mode | stat.S_IRGRP | stat.S_IWGRP)
+
     def get_connection(self, table_name=None):
         """
         Returns a connection to the SQLite database. If a connection does

src/pds_doi_service/core/entities/doi.py

@@ -43,9 +43,6 @@ class DoiStatus(str, Enum):
             An error has occurred with the DOI submission.
         Unknown -
             Default starting state for DOI transactions.
-        Reserve_not_submitted -
-            DOI reserve request in local database, but not published/released.
-            Used for testing of the reserve action.
         Reserved -
             DOI reserve request submitted, but not yet published/released.
         Draft -
@@ -127,3 +124,4 @@ class Doi:
     date_record_added: Optional[datetime] = None
     date_record_updated: Optional[datetime] = None
     event: Optional[DoiEvent] = None
+    input_source: Optional[str] = None

src/pds_doi_service/core/input/input_util.py

@@ -504,6 +504,11 @@ def _read_from_path(self, path):
 
         Returns
         -------
+        dois : list[doi]
+            The list of Doi objects parsed from the provided path.
+
+        Raises
+        -------
         InputFormatException
             If an error is encountered while reading a local file.
 
@@ -526,6 +531,12 @@ def _read_from_path(self, path):
 
                     logger.error(msg)
                     raise InputFormatException(msg)
+
+                # Make a note of where we can find the original input file that
+                # resulted in these DOI's so we can save it to the transaction
+                # history later on
+                for doi in dois:
+                    doi.input_source = path
             else:
                 logger.info("File %s has unsupported extension, ignoring", path)
         else:
@@ -580,7 +591,14 @@ def _read_from_remote(self, input_url):
             temp_file.write(response.content)
             temp_file.seek(0)
 
-            return self._read_from_path(temp_file.name)
+            dois = self._read_from_path(temp_file.name)
+
+        # Update input source to point to original URL, as the temp file paths
+        # assigned by _read_from_path no longer exist
+        for doi in dois:
+            doi.input_source = input_url
+
+        return dois
 
     def parse_dois_from_input_file(self, input_file):
         """

src/pds_doi_service/core/outputs/test/__init__.py

@@ -7,11 +7,13 @@
 from . import datacite_test
 from . import doi_validator_test
 from . import osti_test
+from . import transaction_test
 
 
 def suite():
     suite = unittest.TestSuite()
     suite.addTests(unittest.defaultTestLoader.loadTestsFromModule(datacite_test))
     suite.addTests(unittest.defaultTestLoader.loadTestsFromModule(doi_validator_test))
     suite.addTests(unittest.defaultTestLoader.loadTestsFromModule(osti_test))
+    suite.addTests(unittest.defaultTestLoader.loadTestsFromModule(transaction_test))
     return suite

src/pds_doi_service/core/outputs/test/data/pds4_bundle.xml

@@ -0,0 +1 @@
+../../../actions/test/data/pds4_bundle.xml